================================================================================ ================================================================================ Starting configure run at Fri, 17 Apr 2020 16:11:32 -0300 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc=mpicc --with-fc=mpif90 -with-cxx=mpicxx --prefix=/home/santiago/usr/local --with-make-np=10 --with-shared-libraries --download-fblaslapack=/home/santiago/Documents/installers/petsc/fblaslapack-3.4.2.tar.gz --download-mumps=/home/santiago/Documents/installers/petsc/v5.1.2-p2.tar.gz --download-scalapack=/home/santiago/Documents/installers/petsc/scalapack-2.0.2.tgz --with-debugging=0 COPTFLAGS="-O -O3 -march=native -mtune=native" FOPTFLAGS="-O -O3 -march=native -mtune=native" CXXOPTFLAGS="-O -O3 -march=native -mtune=native" Working directory: /home/santiago/Documents/installers/petsc/petsc-3.13.0 Machine platform: ('Linux', 'isaiasPrecision-7820', '4.15.0-29-generic', '#31-Ubuntu SMP Tue Jul 17 15:39:52 UTC 2018', 'x86_64', 'x86_64') Python version: 2.7.17 (default, Nov 7 2019, 10:07:09) [GCC 7.4.0] ================================================================================ ================================================================================ TEST configureExternalPackagesDir from config.framework(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/framework.py:911) TESTING: configureExternalPackagesDir from config.framework(config/BuildSystem/config/framework.py:911) ================================================================================ TEST configureDebuggers from config.utilities.debuggers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/debuggers.py:21) TESTING: configureDebuggers from config.utilities.debuggers(config/BuildSystem/config/utilities/debuggers.py:21) Find a default debugger and determine its arguments Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Checking for program /home/santiago/usr/local/bin/gdb...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/gdb...not found Checking for program /usr/local/sbin/gdb...not found Checking for program /usr/local/bin/gdb...not found Checking for program /usr/sbin/gdb...not found Checking for program /usr/bin/gdb...found Defined make macro "GDB" to "/usr/bin/gdb" Defined "USE_DEBUGGER" to ""gdb"" Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Defined make macro "DSYMUTIL" to "true" child config.utilities.debuggers 0.014270 ================================================================================ TEST configureDirectories from PETSc.options.petscdir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/petscdir.py:23) TESTING: configureDirectories from PETSc.options.petscdir(config/PETSc/options/petscdir.py:23) Checks PETSC_DIR and sets if not set Version Information: #define PETSC_VERSION_RELEASE 1 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 13 #define PETSC_VERSION_SUBMINOR 0 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "Mar 29, 2020" #define PETSC_VERSION_GIT "v3.13" #define PETSC_VERSION_DATE_GIT "2020-03-29 21:59:40 -0500" #define PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_ PETSC_VERSION_EQ #define PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ child PETSc.options.petscdir 0.003840 ================================================================================ TEST getDatafilespath from PETSc.options.dataFilesPath(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/dataFilesPath.py:29) TESTING: getDatafilespath from PETSc.options.dataFilesPath(config/PETSc/options/dataFilesPath.py:29) Checks what DATAFILESPATH should be child PETSc.options.dataFilesPath 0.000580 ================================================================================ TEST configureGit from config.sourceControl(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/sourceControl.py:24) TESTING: configureGit from config.sourceControl(config/BuildSystem/config/sourceControl.py:24) Find the Git executable Checking for program /home/santiago/usr/local/bin/git...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/git...not found Checking for program /usr/local/sbin/git...not found Checking for program /usr/local/bin/git...not found Checking for program /usr/sbin/git...not found Checking for program /usr/bin/git...not found Checking for program /sbin/git...not found Checking for program /bin/git...not found Checking for program /usr/games/git...not found Checking for program /usr/local/games/git...not found Checking for program /snap/bin/git...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/git...not found Unable to find programs ['git'] providing listing of each search directory to help debug Path provided in Python program Path provided by default path ['adiforfix.py', 'petsc_conf.py', 'petscnagupgrade.py', 'win32fe', 'petscdiff', 'petsc-mpiexec.uni', 'configVars.py', 'PetscBinaryIO.py', 'petsclogformat.py', 'PetscBinaryIOTrajectory.py', 'FASTMathInstaller.py', 'parseargs.py', 'petsc_gen_xdmf.py', 'PetscBinaryIO_tests.py', 'update.py', 'petscnagupgrade.pyc', 'popup', 'petscmpiexec', 'TOPSGenerator.py', 'saws', 'sendToJenkins', 'portabilitycheck.py', 'uncrustify.cfg', 'taucc.py'] ['cat_range_funcs.sh~', 'zip_postproc_yfrac.sh', 'nano', 'rsync_sh.zip', 'utils', 'test_diff.sh', 'set_file_datetime.sh', 'rsync_yfracrun_filelist_base.dat', 'nproc-alt.sh', 'linux_signing_key.pub', 'rsync_yfraccode_filelist_base.dat', 'homedir_generic', 'rsync_bkp_all_msys.sh', 'remove_odd_steps_explicit.sh', 'ubuntu-rdp', 'automated_email', 'rsync_yfracrun_funcs.sh', 'ncpus.sh', 'diffmult.sh', 'unset_proxy.sh', 'ls_dirs.sh', 'rsync_bkp_all.sh', 'au_946492_backspace-doesnt-work-inside-running-bash-script.sh', 'cat_range_funcs.sh', 'img_resize_batch.sh', 'kdeui_shortcuts_print_example.pdf', 'manage_path.sh', 'useful_commands.txt', 'gcc', 'remove_odd_steps.sh', 'zip_yfraccode.sh', 'du1sort.sh', 'split_string_funcs.sh', 'zip_run.sh', 'rsync_utils_msys.sh', 'zip_gmsh_yfrac.sh', 'xlsfonts.dat', 'rsync_delete.sh~', 'double_boot_grub', 'sensors.sh', 'bash_completion.txt', 'rsync_yfracrun.sh', 'echo_command.sh', 'll_dirs.sh', 'rsync_delete.sh', 'rsync_utils.sh', 'utils2017-12.zip', 'apt-get.txt', 'set_proxy.sh', 'rt.bashrc', 'gzip_run.sh', 'rsync_yfraccode_funcs.sh', 'rsync_yfraccode.sh', 'zip_utils.sh', 'inputrc', 'os_distro_funcs.sh', '.directory', 'rm_fast.sh'] [] [] ['apparmor_status', 'pppoe-discovery', 'irqbalance', 'update-default-aspell', 'newusers', 'filefrag', 'update-texmf', 'nfnl_osf', 'ufw', 'add-shell', 'ownership', 'usbmuxd', 'update-passwd', 'chroot', 'rtcwake', 'rtkitctl', 'aptd', 'ippserver', 'biosdecode', 'cups-browsed', 'popcon-largest-unused', 'NetworkManager', 'userdel', 'reject', 'lpc', 'update-dictcommon-hunspell', 'pptp', 'invoke-rc.d', 'genl', 'service', 'grpconv', 'gensprep', 'select-default-wordlist', 'chpasswd', 'avahi-daemon', 'update-dictcommon-aspell', 'grub-set-default', 'update-language-lua', 'update-info-dir', 'update-fmtutil', 'iucode_tool', 'grub-mkdevicemap', 'grpck', 'cppw', 'mklost+found', 'grpunconv', 'lpadmin', 'iio-sensor-proxy', 'create-cracklib-dict', 'groupmems', 'tzconfig', 'spice-vdagentd', 'getweb', 'delgroup', 'usb_modeswitch_dispatcher', 'update-texmf-config', 'aa-remove-unknown', 'iucode-tool', 'update-mime', 'genccode', 'e2freefrag', 'addgroup', 'upgrade-from-grub-legacy', 'update-tl-stacked-conffile', 'lpmove', 'rmt-tar', 'gdm3', 'select-default-ispell', 'escapesrc', 'gencmn', 'grub-bios-setup', 'e4crypt', 'cracklib-packer', 'pwconv', 'lpinfo', 'chat', 'arpd', 'chmem', 'pppoeconf', 'popularity-contest', 'alsa-info', 'make-ssl-cert', 'update-updmap', 'uuidd', 'irqbalance-ui', 'ippusbxd', 'cupsd', 'ispell-autobuildhash', 'alsabat-test', 'dmidecode', 'locale-gen', 'sshd', 'update-java-alternatives', 'pam_timestamp_check', 'cpgr', 'applygnupgdefaults', 'cupsreject', 'cron', 'gconf-schemas', 'update-icon-caches', 'pppstats', 'cupsenable', 'pam_getenv', 'remove-shell', 'vigr', 'usb_modeswitch', 'dpkg-preconfigure', 'cupsaddsmb', 'vpddecode', 'alsactl', 'rmt', 'update-fonts-scale', 'update-pciids', 'pppconfig', 'ModemManager', 'visudo', 'fdformat', 'cupsaccept', 'update-language-def', 'remove-default-ispell', 'rsyslogd', 'e4defrag', 'adduser', 'rfkill', 'update-fonts-alias', 'update-ca-certificates', 'netplan', 'update-default-ispell', 'grub-macbless', 'xrdp', 'cracklib-format', 'acpid', 'bluetoothd', 'nologin', 'cupsctl', 'chgpasswd', 'thermald', 'update-locale', 'readprofile', 'groupdel', 'update-initramfs', 'avahi-autoipd', 'groupadd', 'zic', 'groupmod', 'gennorm2', 'tarcat', 'cracklib-check', 'remove-default-wordlist', 'dpkg-reconfigure', 'logrotate', 'libgvc6-config-update', 'icupkg', 'grub-install', 'pam-auth-update', 'pppd', 'update-fonts-dir', 'xrdp-chansrv', 'useradd', 'paperconfig', 'arp', 'aa-status', 'pptpsetup', 'kerneloops', 'ldattach', 'pppdump', 'cracklib-unpacker', 'iptables-apply', 'vcstime', 'update-usbids', 'update-inetd', 'update-grub2', 'grub-mkconfig', 'cupsfilter', 'addgnupghome', 'setvesablank', 'grub-probe', 'anacron', 'update-grub', 'update-rc.d', 'xrdp-sesman', 'ip6tables-apply', 'update-cracklib', 'pwunconv', 'accessdb', 'update-default-wordlist', 'deluser', 'validlocale', 'cups-genppdupdate', 'grub-reboot', 'iconvconfig', 'update-language-dat', 'saned', 'tcpdump', 'mkinitramfs', 'accept', 'aspell-autobuildhash', 'dnsmasq', 'update-gsfontmap', 'pwck', 'update-grub-gfxpayload', 'usermod', 'vipw', 'cupsdisable', 'gnome-menus-blacklist', 'update-language'] ['ico', 'glib-genmarshal', 'ppmcolors', 'dvipdf', 'ppmtopi1', 'shred', 'findhyph', 'locate', 'htop', 'compare-im6', 'xdg-email', 'savelog', 'envsubst', 'vtkHashSource-7.1', 'mren', 'nad2bin', 'word-list-compress', 'gpgparsemail', 'avahi-resolve-host-name', 'usb-creator-gtk', 'nm-applet', 'dh_autotools-dev_restoreconfig', 'gnome-keyring', 'pslatex', 'passwd', 'routel', 'ppmtoyuvsplit', 'kpsestat', 'cs2cs', 'xgettext', 'traceroute6', 'pnmalias', 'psnup', 'uniq', 'rstart', 'qmlviewer', 'sha512sum', 'qr', 'lsinitramfs', 'gpmetis', 'python3-config', 'automat-visualize3', 'weave', 'gcov-tool-7', 'eps2eps', 'aconnect', 'dpkg-vendor', 'xrdp-keygen', 'oclock', 'qdbusxml2cpp', 'aplaymidi', 'tangle', 'fi_strerror', 'dviinfox', 'leaftoppm', 'pnmtopng', 'apport-bug', 'luit', 'import-im6', 'pod2html', 'corelist', 'gnome-session', 'dviselect', 'sftp', 'xwud', 'de-macro', 'mesg', 'update-notifier', 'pdfxup', 'mandb', 'opl2ofm', 'mkmanifest', 'kernel-install', 'zipnote', 'pr', 'listings-ext', 'make', 'sessreg', 'elfedit', 'xinit', 'lintian', 'ppmtojpeg', 'laptop-detect', 'gvfs-monitor-file', 'gpg', 'tabs', 'dpkg-query', 'xkbvleds', 'makeconv', 'makedtx', 'ps2txt', 'update-perl-sax-parsers', 'kpsewhere', 'whoopsie-preferences', 'sputoppm', 'ntfsdecrypt', 'fc-query', 'pnmtopalm', 'texosquery', 'ppmtouil', 'vpe', 'lsb_release', 'py3versions', 'autoinst', 'pgmbentley', 'mpiexec.openmpi', 'tie', 'showkey', 'grub-glue-efi', 'ubuntu-core-launcher', 'gnome-software-editor', 'lzma', 'gnome-terminal.wrapper', 'aptdcon', 'pbmtowbmp', 'libtoolize', 'mcomp', 'qmlcachegen', 'ckeygen', 'gst-launch-1.0', 'x86_64-linux-gnu-gprof', 'neqn', 'hp-info', 'otangle', 'gpg-zip', 'ps2frag', 'mkocp', 'eject', 'ltxfileinfo', 'pnmflip', 'x86_64-linux-gnu-gcc-ar', 'foo2xqx-wrapper', 'update-desktop-database', 'mpiCC.openmpi', 'baobab', 'qmljs', 'dh_doxygen', 'trial', 'orca-dm-wrapper', 'pod2usage', 'iecset', 'pnmpsnr', 'gpic', 'httex', 'dvitodvi', 'fixcvsdiff', 'spd-conf', 'assistant', 'sudoreplay', 'x-www-browser', 'dpkg-name', 'toe', 'palmtopnm', 'gio', 'dbus-send', 'gsnd', 'patchwork', 'firefox', 'pgmtolispm', 'recode-sr-latin', 'pdf180', 'ndmetis', 'xfd', 'montage', 'vmstat', 'gcov-tool', 'transmission-gtk', 'free', 'import', 'rtstat', 'logname', 'pbibtex', 'pygettext', 'mbadblocks', 'odbcinst', 'dot_builtins', 'gvfs-open', 'apgbfm', 'cpack', 'lp', 'gdal-config', 'syslinux', 'lzegrep', 'pf2afm', 'pdffonts', 'x86_64-linux-gnu-ranlib', 'ppmtoyuv', 'dh_installtex', 'pnmtotiffcmyk', 'mogrify', 't1mac', 'bluetoothctl', 'pnmmontage', 'mawk', 'pnm2ppa', 'qmlimportscanner', 'cmp', 'x86_64', 'pbmtopsg3', 'cpp-7', 'ybmtopbm', 'mingle', 'mfluajit', 'sotruss', 'pdflatexpicscale', 'updatedb', 'ppmshift', 'wc', 'kpsexpand', 'xeyes', 'rename', 'gemtopnm', 'bsd-write', 'updvitype', 'x86_64-linux-gnu-ld', 'run-mailcap', 'cweave', 'pnmgamma', 'isovfy', 'hp-logcapture', 'proxy', 'pdftotext', 'pbmtoepson', 'mdir', 'pdfdetach', 'localc', 'uuidparse', 'fc-list', 'timeout', 'tsort', 'system-config-printer-applet', 'h5fc', 'tred', 'mapscrn', 'prezip', 'objdump', 'pkfix', 'gettext', 'dpkg-distaddfile', 'fc-cache', 'alsabat', 'ibus-daemon', 'h5pcc', 'teckit_compile', 'tgatoppm', 'xauth', 'mathspic', 'dc', 'pbmtomgr', 'mech-dump', 'ps2pdf', 'soelim', 'gcc-ar', 'odvitype', 'xwd', 'telnet.netkit', 'captoinfo', 'rpdfcrop', 'gcov', 'vtkParseOGLExt-7.1', 'lspci', 'dvipdfm', 'gcov-dump', 'avahi-publish', 'kmodsign', 'dbus-update-activation-environment', 'rename.ul', 'fixwpps', 'x86_64-linux-gnu-python3m-config', 'pnmconvol', 'ipod-time-sync', 'gnome-shell', 'ssh-keyscan', 'debconf', 'file', 'pinky', 'foo2hbpl2-wrapper', 'texmaker', 'tbl', 'xrandr', 'cpp', 'wpa_passphrase', 'broadwayd', 'cachepic', 'namei', 'kdeinit5_wrapper', 'httexi', 'ptex', 'dvilj4l', 'xzcmp', 'xzfgrep', 'pnmsplit', 'gdbus', 'pamcut', 'spellintian', 'ppdi', 'dvips', 'pbmpscale', 'systemd-cgls', 'mgrtopbm', 'shasum', 'deallocvt', 'tpic2pdftex', 'getfacl', 'dumpkeys', 'python3m', 'lessfile', 'ttf2pk', 'delpart', 'pgmnoise', 'x86_64-linux-gnu-ld.gold', 'mpost', 'lsipc', 'resizepart', 'gnome-terminal.real', 'extractbb', 'ssh-import-id-gh', 'cd-it8', 'calendar', 'flock', 'qmlprofiler', 'nmtui-connect', 'fiascotopnm', 'rvim', 'i686-linux-gnu-pkg-config', 'cygdb3', 'dh_python2', 'xkeystone', 'pacmd', 'rdoc2.5', 'python2-config', 'fmt', 'totem', 'systemd-delta', 'rletopnm', 'exceltex', 'composite-im6.q16', 'vtkParseJava-7.1', 'xpmtoppm', 'funzip', 'latex2nemeth', 'paplay', 'tracepath', 'poff', 'logger', 'faked-sysv', 'dirmngr-client', 'mxtar', 'pnmcolormap', 'pngtopnm', 'pi1toppm', 'ctstat', 'h5pcc.openmpi', 'podchecker', 'gdb', 'pbmtoepsi', 'disdvi', 'oshrun', 'oshfort', 'vstp', 'plog', 'aa-enabled', 'dbus-cleanup-sockets', 'upower', 'ppmqvga', 'pvserver', 'qlalr', 'ps2pdfwr', 'fakeroot', 'x86_64-linux-gnu-g++', 'perldoc', 'genbrk', 'mkfifo', 'apport-collect', 'kpackagelauncherqml', 'locale', 'brltty-ctb', 'dpkg-trigger', 'avahi-browse', 'ipod-read-sysinfo-extended', 'xzmore', 'pico', 'arecord', 'pyhtmlizer3', 'vtk6python', 'ppmtopcx', 'kbuildsycoca5', 'gnome-session-custom-session', 'tload', 'ttfread', 'kolourpaint', 'lispmtopgm', 'dvipos', 'vlna', 'gtk-update-icon-cache', 'xstdcmap', 'oakdecode', 'dpkg-genbuildinfo', 'sha384sum', 'python-config', 'mdatopbm', 'rstartd', 'xwdtopnm', 'enchant-lsmod', 'rake', 'splitindex', 'xbrlapi', 'wall', 'pgmenhance', 'xkbevd', 'g++', 'select-editor', 'gjs', 'h5c++', 'gc', 'ionice', 'cupstestdsc', 'linux-boot-prober', 'systemd-cgtop', 'xwininfo', 'spd-say', 'e2pall', 'icontopbm', 'pstops', 'eyuvtoppm', 'fontinst', 'Xorg', 'sbkeysync', 'ccomps', 'ischroot', 'nproc', 'dpkg-statoverride', 'zeisstopnm', 'X', 'xman', 'pnmtotiff', 'kbxutil', 'pnmcat', 'mtrace', 'gmsh', 'spice-vdagent', 'gnome-disks', 'gemtopbm', 'libwacom-list-local-devices', 'mattrib', 'python3-qr', 'systemd-mount', 'kshell5', 'texfot', 'x86_64-linux-gnu-python3-config', 'xrefresh', 'gvfs-mkdir', 'pbmtobbnbg', 'ispell-wrapper', 'uic', 'opldecode', 'mdu', 'pnmscalefixed', 'pyversions', 'gtester', 'xclipboard', 'wofm2opl', 'conch', 'mtvtoppm', 'mdel', 'parsechangelog', 'twistd3', 'acpi_listen', 'apport-unpack', 'texdirflatten', 'scor2prt', 'pythontex3', 'glib-gettextize', 'setkeycodes', 'animate-im6', 'grog', 'xdvi-xaw', 'xvminitoppm', 'dt2dv', 'fc-scan', 'evince', 'kwriteconfig5', 'latex-wordcount', 'convert', 'gsdj500', 'scriptreplay', 'driverless', 'taskset', 'showrgb', 'geqn', 'pdfimages', 'pnmnorm', 'kcachegrind', 'snice', 'lsof', 'sbvarsign', 'filterdiff', 'ktrash5', 'lupdate', 'pgmhist', 'mysql_config', 'xzcat', 'arecordmidi', 'pnminvert', 'flipdiff', 'pstree', 'gtf', 'ppmchange', 'unmkinitramfs', 'sfdp', 'updmap-sys', 'lzgrep', 'pdfnup', 'x86_64-linux-gnu-ld.bfd', 'mkindex', 'luatex', 'mpirun', 'hp-plugin', 'proj', 'apport-cli', 'pnmfile', 'ri', 'setxkbmap', 'lwarpmk', 'sort', 'psbook', 'lastlog', 'lexgrog', 'udisksctl', 'pbmto10x', 'lorder', 'xlsclients', 'kpsewhich', 'uptime', 'clear_console', 'h2ph', 'recountdiff', 'symcryptrun', 'mmcli', 'fc-cat', 'faked-tcp', 'dv2dt', 'gnome-shell-extension-prefs', 'msgmerge', 'dpkg-genchanges', 'lsns', 'gem2.5', 'view', 'gcc-ranlib-7', 'bzr', 'pgmramp', 'msgfmt', 'dvilj6', 'mpicc', 'epspdf', 'dpkg-buildflags', 'gconftool', 'eutp', 'pbmlife', 'listres', 'ex', 'join', 'ppmtopuzz', 'qtconfig', 'foo2lava-wrapper', 'gnome-screenshot', 'lsmem', 'kwrapper5', 'gnome-session-inhibit', 'xclock', 'afm2afm', 'geos-config', 'grub-mkimage', 'rawtoppm', 'ppmtomap', 'from', 'perlbug', 'gvmap', 'xfontsel', 'python3', 'gnome-session-quit', 'dvisvgm', 'msgexec', 'perlivp', 'dfu-tool', 'grops', 'mkisofs', 'dot', 'pfarrei', 'mpiexec', 'pydoc3', 'nice', 'st4topgm', 'ckbcomp', 'cut', 'ipcrm', 'as', 'latexfileversion', 'psjoin', 'pnmnoraw', 'msginit', 'pnmindex', 'm2300w-wrapper', 'gdm-screenshot', 'texhash', 'wish', 'minfo', 'tzselect', 'euptex', 'dbus-daemon', 'bdftopcf', 'id', 'fc-match', 'ogdi-config', 'gsftopk', 'ubuntu-software', 'pdftohtml', 'interdiff', 'hex2hcd', 'x-session-manager', 'gnome-software', 'mf2pt1', 'mpicxx.openmpi', 'mtoolstest', 'dpkg-scansources', 'xzegrep', 'texluac', 'h5pfc', 'hp-doctor', 'pwdx', 'lofromtemplate', 'pnmtofits', 'gcc', 'gpu-manager', 'lzfgrep', 'combinediff', 'bioradtopgm', 'giftopnm', 'isdv4-serial-inputattach', 'dviluatex', 'fc-pattern', 'fixwwps', 'kpsepath', 'pdfetex', 'isodump', 'startx', 'ppmtoneo', 'comm', 'pcre-config', 'yplan', 'mcat', 'latex', 'resizecons', 'orted', 'xload', 'snapfuse', 'mkt1font', 'valgrind-di-server', 'gftopk', 'gnome-shell-extension-tool', 'ttfdump', 'nawk', 'unflatten', 'gvfs-move', 'lpq', 'Xephyr', 'msgcmp', 'linux-update-symlinks', 'ppm3d', 'mzip', 'trial3', 'qpdf', 'speech-dispatcher', 'sg', 'hp-align', 'soffice', 'genrb', 'ximtoppm', 'nvidia-detector', 'lastb', '[', 'gvfs-less', 'gst-discoverer-1.0', 'xlogo', 'ppmtoilbm', 'fmtutil-user', 'sbigtopgm', 'gnome-power-statistics', 'xgamma', 'pdf2ps', 'ps2pdf13', 'latexpand', 'whatis', 'gsdj', 'amidi', 'x86_64-linux-gnu-objdump', 'nstat', 'ssh-import-id', 'depythontex3', 'cc', 'ipcmk', 'unzip', 'xkbwatch', 'ptardiff', 'gregorio', 'splain', 'pydoc2.7', 'kreadconfig5', 'wbmptopbm', 'gamma4scanimage', 'fakeroot-tcp', 'hwe-support-status', 'jpegtopnm', 'mailmail', 'ppmtoacad', 'atobm', 'deja-dup', 'canberra-gtk-play', 'uz', 'x86_64-linux-gnu-python-config', 'lzmainfo', 'rgb3toppm', 'colordiff', 'xargs', 'netkit-ftp', 'irb', 'x86_64-linux-gnu-nm', 'apt-config', 'zipgrep', 'xrdp-sesadmin', 'ppmflash', 'lualatex', '411toppm', 'qhelpconverter', 't1ascii', 'systemd-stdio-bridge', 'dh_perl_openssl', 'lspgpot', 'cg_annotate', 'latex-papersize', 'dwp', 'kbdinfo', 'ompi-clean', 't1disasm', 'allec', 'nsupdate', 'ibus-table-createdb', 'pbmtoybm', 'mtype', 'derb', 'm2300w', 'fallocate', 'pstopnm', 'dpkg-checkbuilddeps', 'unlzma', 'systemd-resolve', 'ipcs', 'asciitopgm', 'shotwell', 'xdvi', 'pdflatex', 'g++-7', 'watch', 'gsettings', 'chsh', 'apt', 'avahi-publish-address', 'cmpfillin', 'hp-clean', 'foo2oak-wrapper', 'gcr-viewer', 'transicc', 'pkill', 'who', 'aspell-import', 'pinentry', 'pbmtonokia', 'pager', 'ot2kpx', 'texdoc', 'printafm', 'x86_64-linux-gnu-ar', 'od', 'python2', 'grub-mkstandalone', 'file2brl', 'ruby2.5', 'lnstat', 'lintian-lab-tool', 'mpif77', 'qdoc', 'vi', 'uic3', 'gvfs-save', 'ompi-ps', 'gnome-calendar', 'aleph', 'sgitopnm', 'pbmtolj', 'getkeycodes', 'calibrate_ppa', 'foo2ddst', 'ebb', 'ssh-add', 'kdebugdialog5', 'xdot', 'dpkg-mergechangelogs', 'head', 'compare-im6.q16', 'jpgicc', 'x86_64-linux-gnu-as', 'cd-iccdump', 'avahi-resolve', 'min12xxw', 'dh_bash-completion', 'appstreamcli', 'catchsegv', 'transform', 'ppdmerge', 'unopkg', 'pkmon', 'top', 'mogrify-im6.q16', 'pnmcut', 'hp-pkservice', 'brltty-ttb', 'pygettext3', 'x86_64-linux-gnu-gcc-7', 'gnome-language-selector', 'ptar', 'gpgconf', 'qdbus', 'ri2.5', 'pdfbook2', 'callgrind_annotate', 'h5cc', 'nautilus-desktop', 'pinentry-curses', 'unlink', 'ppmtompeg', 'dviconcat', 'hp-check', 'dvitype', 'gdb-add-index', 'orte-clean', 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'upmendex', 'htmex', 'systemd-socket-activate', 'install-printerdriver', 'python3.6', 'xdg-icon-resource', 'prune', 'update-manager', 'faillog', 'tac', 'kwalletd5', 'codepage', 'lzcat', 'x86_64-linux-gnu-gcov-tool', 'qmlplugindump', 'users', 'dpkg-parsechangelog', 'libnetcfg', 'renice', 'pnmtosgi', 'touch', 'composite', 'unattended-upgrades', 'apt-sortpkgs', 'ctie', 'gdbtui', 'neato', 'pdb3', 'gtscheck', 'pvrenderserver', 'gmock_gen', 'x86_64-linux-gnu-cpp-7', 'xlsatoms', 'crontab', 'nmtui', 'x11perfcomp', 'pbmtoxbm', 'install-info', 'gvcolor', 'bmtoa', 'f2py3', 'gftodvi', 'expiry', 'gpgsm', 'pmpost', 'ginstall-info', 'newgrp', 'tlmgr', 'iptables-xml', 'esc-m', 'printerbanner', 'vtk7', 'gconftool-2', 'lzmore', 'unity-scope-loader', 'telnet', 'xsubpp', 'bibtex', 'x86_64-linux-gnu-pkg-config', 'systemd-path', 'xmlpatternsvalidator', 'chage', 'dpkg', 'pamdeinterlace', 'mfplain', 'python', 'gstreamer-codec-install', 'lcf', 'xhost', 'partx', 'setterm', 'xconsole', 'makejvf', 'gpgv', 'lpstat', 'hp-levels', 'stream-im6.q16', 'valgrind', 'install', 'valgrind.bin', 'orte-top', 'adhocfilelist', 'arping', 'psmerge', 'doxysearch.cgi', 'rhythmbox', 'dehtmldiff', 'encguess', 'pgmedge', 'ppmpat', 'ncal', 'scp1', 'gtbl', 'pax11publish', 'gnome-thumbnail-font', 'xdg-user-dir', 'tkconch', 'xmag', 'perltex', 'avahi-publish-service', 'keyring', 'ssh-keygen1', 'infotocap', 'isoinfo', 'w', 'match_parens', 'otp2ocp', 'mscompress', 'montage-im6.q16', 'gobject-query', 'a5toa4', 'pgmoil', 'sldtoppm', 'prezip-bin', 'ctest', 'texluajit', 'yuvsplittoppm', 'includeres', 'mendex', 'ppmtoleaf', 'pgmtopbm', 'pnmscale', 'preunzip', 'gts2oogl', 'imagetops', 'qtpaths', 'h5pfc.openmpi', 'openssl', 'mshortname', 'psfxtable', 'tkconch3', 'gdialog', 'yuvtoppm', 'prtstat', 'tftopl', 'ppmcie', 'htxelatex', 'hostid', 'pbmtomda', 'strace-log-merge', 'designer', 'makeglossaries', 'xbmtopbm', 'fmtutil-sys', 'sudoedit', 'gsbj', 'appres', 'unicode_stop', 'jexec', 'gnome-keyring-3', 'curl-config', 'libreoffice', 'icu-config', 'expand', 'genisoimage', 'updvitomp', 'pdfjam-pocketmod', 'foo2hp2600-wrapper', 'f95', 'utmpdump', 'rcp', 'msexpand', 'gftype', 'fmtutil', 'fi_pingpong', 'ps2pk', 'pcxtoppm', 'psfaddtable', 'ktelnetservice5', 'autosp', 'foo2slx-wrapper', 'pythontex', 'getmapdl', 'oshcc', 'ckeygen3', 'zipcloak', 'scp', 'c++', 'pfb2pfa', 'pnmmargin', 'psicc', 'helpztags', 'gtk-builder-tool', 'fonttosfnt', 'pamstack', 'gpg-agent', 'software-properties-gtk', 'python3.6m', 'numfmt', 'orte-ps', 'updmap-user', 'lshw', 'pnmtojpeg', 'cal', 'texdiff', 'pdfatfi', 'ppmmake', 'xsetwacom', 'pamstretch', 'xkill', 'gvfs-tree', 'ppmhist', 'pamon', 't1binary', 'fwupdate', 'pnminterp', 'zipdetails', 't4ht', 'smproxy', 'perli11ndoc', 'iceauth', 'snapctl', 'perl5.26.1', 'pnmnlfilt', 'pon', 'grub-mkpasswd-pbkdf2', 'mcookie', 'check-language-support', 'pdftocairo', 'yes', 'vtkWrapPythonInit-7.1', 'pkcheck', 'pldd', 'lslogins', 'hp-makeuri', 'latexdef', 'gnome-font-viewer', 'mousetweaks', 'pnmpaste', 'm2400w', 'pbmtext', 'printf', 'etex', 'base64', 'gslp', 'totem-video-thumbnailer', 'pgrep', 'showconsolefont', 'kpsetool', 'python2-qr', 'twistd', 'fwupdmgr', 'col', 'l2test', 'rfcomm', 'mkzftree', 'pbmtopi3', 'nroff', 'c89', 'editdiff', 'fixscribeps', 'gcov-dump-7', 'ovp2ovf', 'tee', 'gst-play-1.0', 'pbmtocmuwm', 'rawtopgm', 'keytool', 'anytopnm', 'nohup', 'luajittex', 'gnome-www-browser', 'dbus-uuidgen', 'pybuild', 'mf-nowin', 'linux-version', 'host', 'nm-connection-editor', 'erb', 'mpic++.openmpi', 'diff', 'xsm', 'vtkWrapPython-6.3', 'thunderbird', 'makeindex', 'sha224sum', 'xdg-user-dirs-gtk-update', 'xdpyinfo', 'gts2xyz', 'remmina', 'pacat', 'pbmtog3', 'localectl', 'mktexfmt', 'pnmtosir', 'qmlscene', 'mcd', 'ptx', 'dtxgen', 'x86_64-linux-gnu-gcc', 'psfgettable', 'ddstdecode', 'uconv', 'xdriinfo', 'dotty', 'aa-exec', 'pnmhisteq', 'circo', 'checklistings', 'avahi-browse-domains', 'GET', 'mflua-nowin', 'perl5.26-x86_64-linux-gnu', 'ppmtorgb3', 'gvfs-ls', 'foomatic-rip', 'ppmntsc', 'gpgsplit', 'fi_info', 'qmake', 'acyclic', 'zipinfo', 't1unmac', 'mclasserase', 'mpif90', 'cmake', 'hcitool', 'kactivities-cli', 'pedigree', 'gvfs-cat', 'identify-im6.q16', 'ps2epsi', 'foo2lava', 'tl-paper', 'sirtopnm', 'svn-multi', 'catman', 'dosepsbin', 'dig', 'pdb', 'b2sum', 'diff3', 'texdoctk', 'ld.bfd', 'pnmcrop', 'ptargrep', 'x86_64-linux-gnu-readelf', 'valgrind-listener', 'update-gconf-defaults', 'dap-config', 'apturl', 'brltty-trtxt', 'pygmentex', 'dvipdft'] ['dumpe2fs', 'pam_extrausers_update', 'apm_available', 'mount.ntfs-3g', 'cfdisk', 'setvtrgb', 'mii-tool', 'xtables-multi', 'crda', 'wipefs', 'hdparm', 'ldconfig', 'dosfslabel', 'hwclock', 'halt', 'switch_root', 'blockdev', 'unix_update', 'isosize', 'chcpu', 'e2label', 'modinfo', 'blkid', 'mke2fs', 'ntfsresize', 'ifdown', 'fsck.ext4', 'rtacct', 'fatlabel', 'rtmon', 'sfdisk', 'reboot', 'pccardctl', 'mkfs.ntfs', 'pivot_root', 'fixparts', 'brltty', 'mount.lowntfs-3g', 'ipmaddr', 'shadowconfig', 'zramctl', 'swapon', 'getty', 'modprobe', 'mkfs.bfs', 'iwpriv', 'agetty', 'kbdrate', 'capsh', 'ifquery', 'start-stop-daemon', 'pam_tally', 'findfs', 'losetup', 'debugfs', 'poweroff', 'ntfscp', 'iw', 'getpcaps', 'dhclient', 'regdbdump', 'plipconfig', 'fsfreeze', 'alsa', 'slattach', 'rmmod', 'nameif', 'badblocks', 'sgdisk', 'udevadm', 'mkfs', 'dmsetup', 'sulogin', 'e2undo', 'acpi_available', 'iwconfig', 'u-d-c-print-pci-ids', 'killall5', 'ntfsundelete', 'installkernel', 'mount.ntfs', 'iptables', 'fdisk', 'shutdown', 'mkdosfs', 'runlevel', 'blkdeactivate', 'rarp', 'fsck.msdos', 'pam_extrausers_chkpwd', 'brltty-setup', 'ntfsclone', 'setcap', 'iptunnel', 'parted', 'blkdiscard', 'plymouthd', 'ldconfig.real', 'umount.udisks2', 'fsck.vfat', 'mkfs.msdos', 'partprobe', 'mkfs.cramfs', 'wpa_action', 'ifconfig', 'e2fsck', 'iwlist', 'iptables-restore', 'mkswap', 'ifup', 'devlink', 'mkfs.vfat', 'dosfsck', 'mount.fuse', 'cgdisk', 'unix_chkpwd', 'fstab-decode', 'iptables-save', 'ip6tables-restore', 'ip6tables-save', 'iwspy', 'sysctl', 'wpa_supplicant', 'lspcmcia', 'tipc', 'ureadahead', 'mkfs.ext4', 'telinit', 'swapoff', 'lsmod', 'raw', 'iwgetid', 'fsck.ext2', 'depmod', 'e2image', 'init', 'on_ac_power', 'fsck', 'ip6tables', 'mkfs.ext3', 'mkhomedir_helper', 'getcap', 'logsave', 'fsck.ext3', 'resize2fs', 'tc', 'pam_tally2', 'ctrlaltdel', 'runuser', 'swaplabel', 'ip', 'apparmor_parser', 'fsck.minix', 'ntfslabel', 'gdisk', 'dhclient-script', 'iwevent', 'insmod', 'route', 'tune2fs', 'mkfs.ext2', 'fsck.fat', 'dmstats', 'wpa_cli', 'mkntfs', 'mkfs.fat', 'fsck.cramfs', 'bridge', 'mkfs.minix', 'fstrim'] ['cp', 'more', 'chmod', 'systemd', 'gzexe', 'systemd-hwdb', 'nc.openbsd', 'mknod', 'bzegrep', 'mt-gnu', 'sh', 'zmore', 'setupcon', 'true', 'rm', 'nano', 'false', 'fgconsole', 'ntfsfallocate', 'sed', 'ntfscmp', 'getfacl', 'dumpkeys', 'lessfile', 'zgrep', 'bzdiff', 'tar', 'fgrep', 'wdctl', 'systemd-inhibit', 'bzip2recover', 'ed', 'static-sh', 'rnano', 'open', 'systemd-escape', 'ntfsusermap', 'nc', 'mktemp', 'zfgrep', 'bzgrep', 'whiptail', 'chgrp', 'systemctl', 'sh.distrib', 'brltty', 'red', 'zforce', 'dash', 'lowntfs-3g', 'kmod', 'rbash', 'rmdir', 'chvt', 'tempfile', 'ls', 'ypdomainname', 'zegrep', 'dd', 'ntfsls', 'lessecho', 'ntfscat', 'dnsdomainname', 'ln', 'loadkeys', 'znew', 'chacl', 'cat', 'udevadm', 'ping4', 'run-parts', 'gunzip', 'date', 'efibootmgr', 'lesskey', 'journalctl', 'lesspipe', 'systemd-tty-ask-password-agent', 'zcat', 'mountpoint', 'systemd-tmpfiles', 'echo', 'mount', 'login', 'ntfsinfo', 'ss', 'bzcmp', 'uncompress', 'ntfs-3g.probe', 'mv', 'ntfsrecover', 'netstat', 'bzless', 'dir', 'ntfssecaudit', 'mt', 'bzip2', 'ntfscluster', 'less', 'openvt', 'sync', 'ntfstruncate', 'bzmore', 'which', 'egrep', 'systemd-ask-password', 'ntfsmove', 'bzcat', 'bzfgrep', 'bzexe', 'ping', 'kbd_mode', 'zdiff', 'bash', 'bunzip2', 'findmnt', 'gzip', 'netcat', 'mkdir', 'ping6', 'hciconfig', 'setfont', 'su', 'unicode_start', 'networkctl', 'ntfsfix', 'loginctl', 'setfacl', 'df', 'lsmod', 'grep', 'chown', 'domainname', 'plymouth', 'cpio', 'vdir', 'fusermount', 'systemd-notify', 'pwd', 'nisdomainname', 'umount', 'ntfswipe', 'systemd-machine-id-setup', 'pidof', 'efibootdump', 'touch', 'sleep', 'readlink', 'ip', 'systemd-sysusers', 'ps', 'uname', 'zcmp', 'hostname', 'fuser', 'ntfs-3g', 'stty', 'ulockmgr_server', 'dmesg', 'busybox', 'zless', 'lsblk', 'kill'] ['gnome-mahjongg', 'gnome-sudoku', 'sol', 'gnome-mines', 'espdiff'] [] ['gnome-calculator', 'gnome-system-monitor', 'gnome-logs', 'gnome-characters'] Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] child config.sourceControl 0.007801 ================================================================================ TEST configureInstallationMethod from PETSc.options.petscclone(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/petscclone.py:20) TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:20) This is a tarball installation child PETSc.options.petscclone 0.000396 ================================================================================ TEST setNativeArchitecture from PETSc.options.arch(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/arch.py:31) TESTING: setNativeArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:31) ================================================================================ TEST configureArchitecture from PETSc.options.arch(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/arch.py:43) TESTING: configureArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:43) Checks PETSC_ARCH and sets if not set No previous hashfile found Setting hashfile: arch-linux2-c-opt/lib/petsc/conf/configure-hash Deleting configure hash file: arch-linux2-c-opt/lib/petsc/conf/configure-hash Unable to delete configure hash file: arch-linux2-c-opt/lib/petsc/conf/configure-hash child PETSc.options.arch 0.013345 ================================================================================ TEST setInstallDir from PETSc.options.installDir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/installDir.py:35) TESTING: setInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:35) setup installDir to either prefix or if that is not set to PETSC_DIR/PETSC_ARCH Defined make macro "PREFIXDIR" to "/home/santiago/usr/local" ================================================================================ TEST saveReconfigure from PETSc.options.installDir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/installDir.py:80) TESTING: saveReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:80) ================================================================================ TEST cleanConfDir from PETSc.options.installDir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/installDir.py:73) TESTING: cleanConfDir from PETSc.options.installDir(config/PETSc/options/installDir.py:73) ================================================================================ TEST configureInstallDir from PETSc.options.installDir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/installDir.py:57) TESTING: configureInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:57) Makes installDir subdirectories if it does not exist for both prefix install location and PETSc work install location Changed persistence directory to /home/santiago/Documents/installers/petsc/petsc-3.13.0/arch-linux2-c-opt/lib/petsc/conf ================================================================================ TEST restoreReconfigure from PETSc.options.installDir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/installDir.py:93) TESTING: restoreReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:93) child PETSc.options.installDir 0.001034 ================================================================================ TEST setExternalPackagesDir from PETSc.options.externalpackagesdir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/externalpackagesdir.py:15) TESTING: setExternalPackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:15) ================================================================================ TEST cleanExternalpackagesDir from PETSc.options.externalpackagesdir(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/externalpackagesdir.py:22) TESTING: cleanExternalpackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:22) child PETSc.options.externalpackagesdir 0.000227 ================================================================================ TEST configureCLanguage from PETSc.options.languages(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/languages.py:27) TESTING: configureCLanguage from PETSc.options.languages(config/PETSc/options/languages.py:27) Choose whether to compile the PETSc library using a C or C++ compiler C language is C Defined "CLANGUAGE_C" to "1" Defined make macro "CLANGUAGE" to "C" child PETSc.options.languages 0.000402 ================================================================================ TEST printEnvVariables from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1694) TESTING: printEnvVariables from config.setCompilers(config/BuildSystem/config/setCompilers.py:1694) **** printenv **** HISTTIMEFORMAT=%d/%m/%y %T LC_NUMERIC=es_AR.UTF-8 BASHPROFILEREAD=Yes METIS_LIBDIR=/usr/lib/x86_64-linux-gnu HOSTFILE=/etc/hosts LESSOPEN=| /usr/bin/lesspipe %s METIS_INCDIR=/usr/include SSH_CLIENT=10.8.125.236 53694 22 LOGNAME=santiago USER=santiago PROMPT_COMMAND=echo -ne "\033]0;Terminal - ${PWD}\007" PATH=/home/santiago/usr/local/bin:/home/santiago/Documents/soft-hard-ware/linux-ubuntu:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin LC_PAPER=es_AR.UTF-8 HOME=/home/santiago PS1=\[\033[1;34m\][\[\033[1;32m\]\u\[\033[1;34m\]@\[\033[1;32m\]\h\[\033[1;34m\]:\[\033[1;32m\]\w\[\033[1;34m\]]\[\033[1;31m\]$\[\033[00m\] DISPLAY=localhost:10.0 RED=\[\033[1;31m\] LANG=en_US.UTF-8 TERM=xterm SHELL=/bin/bash LC_MEASUREMENT=es_AR.UTF-8 GREEN=\[\033[1;32m\] PETSC_ARCH=arch-linux2-c-opt LD_LIBRARY_PATH= PETSC_DIR=/home/santiago/Documents/installers/petsc/petsc-3.13.0 EDITOR=nano SHLVL=1 XDG_RUNTIME_DIR=/run/user/1002 LC_ADDRESS=es_AR.UTF-8 PYTHONPATH=/usr/lib/python2.7/dist-packages/paraview SSH_AUTH_SOCK=/tmp/ssh-6IKS7MnE1D/agent.6417 RESET=\[\033[00m\] XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop XDG_SESSION_ID=506 DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1002/bus _=./configure BLUE=\[\033[1;34m\] LC_IDENTIFICATION=es_AR.UTF-8 LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36: LESSCLOSE=/usr/bin/lesspipe %s %s PYTHONSTARTUP=/home/santiago/.pythonrc SSH_TTY=/dev/pts/2 OLDPWD=/home/santiago/Documents/installers/petsc LC_TELEPHONE=es_AR.UTF-8 LC_MONETARY=es_AR.UTF-8 PWD=/home/santiago/Documents/installers/petsc/petsc-3.13.0 LC_NAME=es_AR.UTF-8 MAIL=/var/mail/santiago LC_TIME=es_AR.UTF-8 SSH_CONNECTION=10.8.125.236 53694 10.129.62.17 22 ================================================================================ TEST resetEnvCompilers from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1701) TESTING: resetEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1701) ================================================================================ TEST checkEnvCompilers from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1731) TESTING: checkEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1731) ================================================================================ TEST checkMPICompilerOverride from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1664) TESTING: checkMPICompilerOverride from config.setCompilers(config/BuildSystem/config/setCompilers.py:1664) Check if --with-mpi-dir is used along with CC CXX or FC compiler options. This usually prevents mpi compilers from being used - so issue a warning ================================================================================ TEST requireMpiLdPath from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1685) TESTING: requireMpiLdPath from config.setCompilers(config/BuildSystem/config/setCompilers.py:1685) OpenMPI wrappers require LD_LIBRARY_PATH set ================================================================================ TEST checkInitialFlags from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:434) TESTING: checkInitialFlags from config.setCompilers(config/BuildSystem/config/setCompilers.py:434) Initialize the compiler and linker flags Initialized CFLAGS to Initialized CFLAGS to Initialized LDFLAGS to Initialized CUDAFLAGS to Initialized CUDAFLAGS to Initialized LDFLAGS to Initialized CXXFLAGS to Initialized CXX_CXXFLAGS to Initialized LDFLAGS to Initialized FFLAGS to Initialized FFLAGS to Initialized LDFLAGS to Initialized CPPFLAGS to Initialized FPPFLAGS to Initialized CUDAPPFLAGS to -Wno-deprecated-gpu-targets Initialized CXXPPFLAGS to Initialized CC_LINKER_FLAGS to [] Initialized CXX_LINKER_FLAGS to [] Initialized FC_LINKER_FLAGS to [] Initialized CUDAC_LINKER_FLAGS to [] Initialized sharedLibraryFlags to [] Initialized dynamicLibraryFlags to [] ================================================================================ TEST checkCCompiler from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:604) TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:604) Locate a functional C compiler Checking for program /home/santiago/usr/local/bin/mpicc...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpicc...not found Checking for program /usr/local/sbin/mpicc...not found Checking for program /usr/local/bin/mpicc...not found Checking for program /usr/sbin/mpicc...not found Checking for program /usr/bin/mpicc...found Defined make macro "CC" to "mpicc" All intermediate test results are stored in /tmp/petsc-k0jR75 All intermediate test results are stored in /tmp/petsc-k0jR75/config.setCompilers Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o Testing executable /tmp/petsc-k0jR75/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable WITHOUT threads to time it out Executing: mpicc --version stdout: gcc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Since MPI c compiler starts with mpi, force searches for other compilers to only look for MPI compilers ================================================================================ TEST checkCPreprocessor from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:643) TESTING: checkCPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:643) Locate a functional C preprocessor Checking for program /home/santiago/usr/local/bin/mpicc...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpicc...not found Checking for program /usr/local/sbin/mpicc...not found Checking for program /usr/local/bin/mpicc...not found Checking for program /usr/sbin/mpicc...not found Checking for program /usr/bin/mpicc...found Defined make macro "CPP" to "mpicc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkCUDACompiler from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:679) TESTING: checkCUDACompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:679) Locate a functional CUDA compiler Checking for program /home/santiago/usr/local/bin/nvcc...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/nvcc...not found Checking for program /usr/local/sbin/nvcc...not found Checking for program /usr/local/bin/nvcc...not found Checking for program /usr/sbin/nvcc...not found Checking for program /usr/bin/nvcc...not found Checking for program /sbin/nvcc...not found Checking for program /bin/nvcc...not found Checking for program /usr/games/nvcc...not found Checking for program /usr/local/games/nvcc...not found Checking for program /snap/bin/nvcc...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/nvcc...not found Unable to find programs ['nvcc'] providing listing of each search directory to help debug Path provided in Python program Path provided by default path ['adiforfix.py', 'petsc_conf.py', 'petscnagupgrade.py', 'win32fe', 'petscdiff', 'petsc-mpiexec.uni', 'configVars.py', 'PetscBinaryIO.py', 'petsclogformat.py', 'PetscBinaryIOTrajectory.py', 'FASTMathInstaller.py', 'parseargs.py', 'petsc_gen_xdmf.py', 'PetscBinaryIO_tests.py', 'update.py', 'petscnagupgrade.pyc', 'popup', 'petscmpiexec', 'TOPSGenerator.py', 'saws', 'sendToJenkins', 'portabilitycheck.py', 'uncrustify.cfg', 'taucc.py'] ['cat_range_funcs.sh~', 'zip_postproc_yfrac.sh', 'nano', 'rsync_sh.zip', 'utils', 'test_diff.sh', 'set_file_datetime.sh', 'rsync_yfracrun_filelist_base.dat', 'nproc-alt.sh', 'linux_signing_key.pub', 'rsync_yfraccode_filelist_base.dat', 'homedir_generic', 'rsync_bkp_all_msys.sh', 'remove_odd_steps_explicit.sh', 'ubuntu-rdp', 'automated_email', 'rsync_yfracrun_funcs.sh', 'ncpus.sh', 'diffmult.sh', 'unset_proxy.sh', 'ls_dirs.sh', 'rsync_bkp_all.sh', 'au_946492_backspace-doesnt-work-inside-running-bash-script.sh', 'cat_range_funcs.sh', 'img_resize_batch.sh', 'kdeui_shortcuts_print_example.pdf', 'manage_path.sh', 'useful_commands.txt', 'gcc', 'remove_odd_steps.sh', 'zip_yfraccode.sh', 'du1sort.sh', 'split_string_funcs.sh', 'zip_run.sh', 'rsync_utils_msys.sh', 'zip_gmsh_yfrac.sh', 'xlsfonts.dat', 'rsync_delete.sh~', 'double_boot_grub', 'sensors.sh', 'bash_completion.txt', 'rsync_yfracrun.sh', 'echo_command.sh', 'll_dirs.sh', 'rsync_delete.sh', 'rsync_utils.sh', 'utils2017-12.zip', 'apt-get.txt', 'set_proxy.sh', 'rt.bashrc', 'gzip_run.sh', 'rsync_yfraccode_funcs.sh', 'rsync_yfraccode.sh', 'zip_utils.sh', 'inputrc', 'os_distro_funcs.sh', '.directory', 'rm_fast.sh'] [] [] ['apparmor_status', 'pppoe-discovery', 'irqbalance', 'update-default-aspell', 'newusers', 'filefrag', 'update-texmf', 'nfnl_osf', 'ufw', 'add-shell', 'ownership', 'usbmuxd', 'update-passwd', 'chroot', 'rtcwake', 'rtkitctl', 'aptd', 'ippserver', 'biosdecode', 'cups-browsed', 'popcon-largest-unused', 'NetworkManager', 'userdel', 'reject', 'lpc', 'update-dictcommon-hunspell', 'pptp', 'invoke-rc.d', 'genl', 'service', 'grpconv', 'gensprep', 'select-default-wordlist', 'chpasswd', 'avahi-daemon', 'update-dictcommon-aspell', 'grub-set-default', 'update-language-lua', 'update-info-dir', 'update-fmtutil', 'iucode_tool', 'grub-mkdevicemap', 'grpck', 'cppw', 'mklost+found', 'grpunconv', 'lpadmin', 'iio-sensor-proxy', 'create-cracklib-dict', 'groupmems', 'tzconfig', 'spice-vdagentd', 'getweb', 'delgroup', 'usb_modeswitch_dispatcher', 'update-texmf-config', 'aa-remove-unknown', 'iucode-tool', 'update-mime', 'genccode', 'e2freefrag', 'addgroup', 'upgrade-from-grub-legacy', 'update-tl-stacked-conffile', 'lpmove', 'rmt-tar', 'gdm3', 'select-default-ispell', 'escapesrc', 'gencmn', 'grub-bios-setup', 'e4crypt', 'cracklib-packer', 'pwconv', 'lpinfo', 'chat', 'arpd', 'chmem', 'pppoeconf', 'popularity-contest', 'alsa-info', 'make-ssl-cert', 'update-updmap', 'uuidd', 'irqbalance-ui', 'ippusbxd', 'cupsd', 'ispell-autobuildhash', 'alsabat-test', 'dmidecode', 'locale-gen', 'sshd', 'update-java-alternatives', 'pam_timestamp_check', 'cpgr', 'applygnupgdefaults', 'cupsreject', 'cron', 'gconf-schemas', 'update-icon-caches', 'pppstats', 'cupsenable', 'pam_getenv', 'remove-shell', 'vigr', 'usb_modeswitch', 'dpkg-preconfigure', 'cupsaddsmb', 'vpddecode', 'alsactl', 'rmt', 'update-fonts-scale', 'update-pciids', 'pppconfig', 'ModemManager', 'visudo', 'fdformat', 'cupsaccept', 'update-language-def', 'remove-default-ispell', 'rsyslogd', 'e4defrag', 'adduser', 'rfkill', 'update-fonts-alias', 'update-ca-certificates', 'netplan', 'update-default-ispell', 'grub-macbless', 'xrdp', 'cracklib-format', 'acpid', 'bluetoothd', 'nologin', 'cupsctl', 'chgpasswd', 'thermald', 'update-locale', 'readprofile', 'groupdel', 'update-initramfs', 'avahi-autoipd', 'groupadd', 'zic', 'groupmod', 'gennorm2', 'tarcat', 'cracklib-check', 'remove-default-wordlist', 'dpkg-reconfigure', 'logrotate', 'libgvc6-config-update', 'icupkg', 'grub-install', 'pam-auth-update', 'pppd', 'update-fonts-dir', 'xrdp-chansrv', 'useradd', 'paperconfig', 'arp', 'aa-status', 'pptpsetup', 'kerneloops', 'ldattach', 'pppdump', 'cracklib-unpacker', 'iptables-apply', 'vcstime', 'update-usbids', 'update-inetd', 'update-grub2', 'grub-mkconfig', 'cupsfilter', 'addgnupghome', 'setvesablank', 'grub-probe', 'anacron', 'update-grub', 'update-rc.d', 'xrdp-sesman', 'ip6tables-apply', 'update-cracklib', 'pwunconv', 'accessdb', 'update-default-wordlist', 'deluser', 'validlocale', 'cups-genppdupdate', 'grub-reboot', 'iconvconfig', 'update-language-dat', 'saned', 'tcpdump', 'mkinitramfs', 'accept', 'aspell-autobuildhash', 'dnsmasq', 'update-gsfontmap', 'pwck', 'update-grub-gfxpayload', 'usermod', 'vipw', 'cupsdisable', 'gnome-menus-blacklist', 'update-language'] ['ico', 'glib-genmarshal', 'ppmcolors', 'dvipdf', 'ppmtopi1', 'shred', 'findhyph', 'locate', 'htop', 'compare-im6', 'xdg-email', 'savelog', 'envsubst', 'vtkHashSource-7.1', 'mren', 'nad2bin', 'word-list-compress', 'gpgparsemail', 'avahi-resolve-host-name', 'usb-creator-gtk', 'nm-applet', 'dh_autotools-dev_restoreconfig', 'gnome-keyring', 'pslatex', 'passwd', 'routel', 'ppmtoyuvsplit', 'kpsestat', 'cs2cs', 'xgettext', 'traceroute6', 'pnmalias', 'psnup', 'uniq', 'rstart', 'qmlviewer', 'sha512sum', 'qr', 'lsinitramfs', 'gpmetis', 'python3-config', 'automat-visualize3', 'weave', 'gcov-tool-7', 'eps2eps', 'aconnect', 'dpkg-vendor', 'xrdp-keygen', 'oclock', 'qdbusxml2cpp', 'aplaymidi', 'tangle', 'fi_strerror', 'dviinfox', 'leaftoppm', 'pnmtopng', 'apport-bug', 'luit', 'import-im6', 'pod2html', 'corelist', 'gnome-session', 'dviselect', 'sftp', 'xwud', 'de-macro', 'mesg', 'update-notifier', 'pdfxup', 'mandb', 'opl2ofm', 'mkmanifest', 'kernel-install', 'zipnote', 'pr', 'listings-ext', 'make', 'sessreg', 'elfedit', 'xinit', 'lintian', 'ppmtojpeg', 'laptop-detect', 'gvfs-monitor-file', 'gpg', 'tabs', 'dpkg-query', 'xkbvleds', 'makeconv', 'makedtx', 'ps2txt', 'update-perl-sax-parsers', 'kpsewhere', 'whoopsie-preferences', 'sputoppm', 'ntfsdecrypt', 'fc-query', 'pnmtopalm', 'texosquery', 'ppmtouil', 'vpe', 'lsb_release', 'py3versions', 'autoinst', 'pgmbentley', 'mpiexec.openmpi', 'tie', 'showkey', 'grub-glue-efi', 'ubuntu-core-launcher', 'gnome-software-editor', 'lzma', 'gnome-terminal.wrapper', 'aptdcon', 'pbmtowbmp', 'libtoolize', 'mcomp', 'qmlcachegen', 'ckeygen', 'gst-launch-1.0', 'x86_64-linux-gnu-gprof', 'neqn', 'hp-info', 'otangle', 'gpg-zip', 'ps2frag', 'mkocp', 'eject', 'ltxfileinfo', 'pnmflip', 'x86_64-linux-gnu-gcc-ar', 'foo2xqx-wrapper', 'update-desktop-database', 'mpiCC.openmpi', 'baobab', 'qmljs', 'dh_doxygen', 'trial', 'orca-dm-wrapper', 'pod2usage', 'iecset', 'pnmpsnr', 'gpic', 'httex', 'dvitodvi', 'fixcvsdiff', 'spd-conf', 'assistant', 'sudoreplay', 'x-www-browser', 'dpkg-name', 'toe', 'palmtopnm', 'gio', 'dbus-send', 'gsnd', 'patchwork', 'firefox', 'pgmtolispm', 'recode-sr-latin', 'pdf180', 'ndmetis', 'xfd', 'montage', 'vmstat', 'gcov-tool', 'transmission-gtk', 'free', 'import', 'rtstat', 'logname', 'pbibtex', 'pygettext', 'mbadblocks', 'odbcinst', 'dot_builtins', 'gvfs-open', 'apgbfm', 'cpack', 'lp', 'gdal-config', 'syslinux', 'lzegrep', 'pf2afm', 'pdffonts', 'x86_64-linux-gnu-ranlib', 'ppmtoyuv', 'dh_installtex', 'pnmtotiffcmyk', 'mogrify', 't1mac', 'bluetoothctl', 'pnmmontage', 'mawk', 'pnm2ppa', 'qmlimportscanner', 'cmp', 'x86_64', 'pbmtopsg3', 'cpp-7', 'ybmtopbm', 'mingle', 'mfluajit', 'sotruss', 'pdflatexpicscale', 'updatedb', 'ppmshift', 'wc', 'kpsexpand', 'xeyes', 'rename', 'gemtopnm', 'bsd-write', 'updvitype', 'x86_64-linux-gnu-ld', 'run-mailcap', 'cweave', 'pnmgamma', 'isovfy', 'hp-logcapture', 'proxy', 'pdftotext', 'pbmtoepson', 'mdir', 'pdfdetach', 'localc', 'uuidparse', 'fc-list', 'timeout', 'tsort', 'system-config-printer-applet', 'h5fc', 'tred', 'mapscrn', 'prezip', 'objdump', 'pkfix', 'gettext', 'dpkg-distaddfile', 'fc-cache', 'alsabat', 'ibus-daemon', 'h5pcc', 'teckit_compile', 'tgatoppm', 'xauth', 'mathspic', 'dc', 'pbmtomgr', 'mech-dump', 'ps2pdf', 'soelim', 'gcc-ar', 'odvitype', 'xwd', 'telnet.netkit', 'captoinfo', 'rpdfcrop', 'gcov', 'vtkParseOGLExt-7.1', 'lspci', 'dvipdfm', 'gcov-dump', 'avahi-publish', 'kmodsign', 'dbus-update-activation-environment', 'rename.ul', 'fixwpps', 'x86_64-linux-gnu-python3m-config', 'pnmconvol', 'ipod-time-sync', 'gnome-shell', 'ssh-keyscan', 'debconf', 'file', 'pinky', 'foo2hbpl2-wrapper', 'texmaker', 'tbl', 'xrandr', 'cpp', 'wpa_passphrase', 'broadwayd', 'cachepic', 'namei', 'kdeinit5_wrapper', 'httexi', 'ptex', 'dvilj4l', 'xzcmp', 'xzfgrep', 'pnmsplit', 'gdbus', 'pamcut', 'spellintian', 'ppdi', 'dvips', 'pbmpscale', 'systemd-cgls', 'mgrtopbm', 'shasum', 'deallocvt', 'tpic2pdftex', 'getfacl', 'dumpkeys', 'python3m', 'lessfile', 'ttf2pk', 'delpart', 'pgmnoise', 'x86_64-linux-gnu-ld.gold', 'mpost', 'lsipc', 'resizepart', 'gnome-terminal.real', 'extractbb', 'ssh-import-id-gh', 'cd-it8', 'calendar', 'flock', 'qmlprofiler', 'nmtui-connect', 'fiascotopnm', 'rvim', 'i686-linux-gnu-pkg-config', 'cygdb3', 'dh_python2', 'xkeystone', 'pacmd', 'rdoc2.5', 'python2-config', 'fmt', 'totem', 'systemd-delta', 'rletopnm', 'exceltex', 'composite-im6.q16', 'vtkParseJava-7.1', 'xpmtoppm', 'funzip', 'latex2nemeth', 'paplay', 'tracepath', 'poff', 'logger', 'faked-sysv', 'dirmngr-client', 'mxtar', 'pnmcolormap', 'pngtopnm', 'pi1toppm', 'ctstat', 'h5pcc.openmpi', 'podchecker', 'gdb', 'pbmtoepsi', 'disdvi', 'oshrun', 'oshfort', 'vstp', 'plog', 'aa-enabled', 'dbus-cleanup-sockets', 'upower', 'ppmqvga', 'pvserver', 'qlalr', 'ps2pdfwr', 'fakeroot', 'x86_64-linux-gnu-g++', 'perldoc', 'genbrk', 'mkfifo', 'apport-collect', 'kpackagelauncherqml', 'locale', 'brltty-ctb', 'dpkg-trigger', 'avahi-browse', 'ipod-read-sysinfo-extended', 'xzmore', 'pico', 'arecord', 'pyhtmlizer3', 'vtk6python', 'ppmtopcx', 'kbuildsycoca5', 'gnome-session-custom-session', 'tload', 'ttfread', 'kolourpaint', 'lispmtopgm', 'dvipos', 'vlna', 'gtk-update-icon-cache', 'xstdcmap', 'oakdecode', 'dpkg-genbuildinfo', 'sha384sum', 'python-config', 'mdatopbm', 'rstartd', 'xwdtopnm', 'enchant-lsmod', 'rake', 'splitindex', 'xbrlapi', 'wall', 'pgmenhance', 'xkbevd', 'g++', 'select-editor', 'gjs', 'h5c++', 'gc', 'ionice', 'cupstestdsc', 'linux-boot-prober', 'systemd-cgtop', 'xwininfo', 'spd-say', 'e2pall', 'icontopbm', 'pstops', 'eyuvtoppm', 'fontinst', 'Xorg', 'sbkeysync', 'ccomps', 'ischroot', 'nproc', 'dpkg-statoverride', 'zeisstopnm', 'X', 'xman', 'pnmtotiff', 'kbxutil', 'pnmcat', 'mtrace', 'gmsh', 'spice-vdagent', 'gnome-disks', 'gemtopbm', 'libwacom-list-local-devices', 'mattrib', 'python3-qr', 'systemd-mount', 'kshell5', 'texfot', 'x86_64-linux-gnu-python3-config', 'xrefresh', 'gvfs-mkdir', 'pbmtobbnbg', 'ispell-wrapper', 'uic', 'opldecode', 'mdu', 'pnmscalefixed', 'pyversions', 'gtester', 'xclipboard', 'wofm2opl', 'conch', 'mtvtoppm', 'mdel', 'parsechangelog', 'twistd3', 'acpi_listen', 'apport-unpack', 'texdirflatten', 'scor2prt', 'pythontex3', 'glib-gettextize', 'setkeycodes', 'animate-im6', 'grog', 'xdvi-xaw', 'xvminitoppm', 'dt2dv', 'fc-scan', 'evince', 'kwriteconfig5', 'latex-wordcount', 'convert', 'gsdj500', 'scriptreplay', 'driverless', 'taskset', 'showrgb', 'geqn', 'pdfimages', 'pnmnorm', 'kcachegrind', 'snice', 'lsof', 'sbvarsign', 'filterdiff', 'ktrash5', 'lupdate', 'pgmhist', 'mysql_config', 'xzcat', 'arecordmidi', 'pnminvert', 'flipdiff', 'pstree', 'gtf', 'ppmchange', 'unmkinitramfs', 'sfdp', 'updmap-sys', 'lzgrep', 'pdfnup', 'x86_64-linux-gnu-ld.bfd', 'mkindex', 'luatex', 'mpirun', 'hp-plugin', 'proj', 'apport-cli', 'pnmfile', 'ri', 'setxkbmap', 'lwarpmk', 'sort', 'psbook', 'lastlog', 'lexgrog', 'udisksctl', 'pbmto10x', 'lorder', 'xlsclients', 'kpsewhich', 'uptime', 'clear_console', 'h2ph', 'recountdiff', 'symcryptrun', 'mmcli', 'fc-cat', 'faked-tcp', 'dv2dt', 'gnome-shell-extension-prefs', 'msgmerge', 'dpkg-genchanges', 'lsns', 'gem2.5', 'view', 'gcc-ranlib-7', 'bzr', 'pgmramp', 'msgfmt', 'dvilj6', 'mpicc', 'epspdf', 'dpkg-buildflags', 'gconftool', 'eutp', 'pbmlife', 'listres', 'ex', 'join', 'ppmtopuzz', 'qtconfig', 'foo2lava-wrapper', 'gnome-screenshot', 'lsmem', 'kwrapper5', 'gnome-session-inhibit', 'xclock', 'afm2afm', 'geos-config', 'grub-mkimage', 'rawtoppm', 'ppmtomap', 'from', 'perlbug', 'gvmap', 'xfontsel', 'python3', 'gnome-session-quit', 'dvisvgm', 'msgexec', 'perlivp', 'dfu-tool', 'grops', 'mkisofs', 'dot', 'pfarrei', 'mpiexec', 'pydoc3', 'nice', 'st4topgm', 'ckbcomp', 'cut', 'ipcrm', 'as', 'latexfileversion', 'psjoin', 'pnmnoraw', 'msginit', 'pnmindex', 'm2300w-wrapper', 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'ppmtobmp', 'colormgr', 'pslog', 'tput', 'depythontex', 'pip', 'boltctl', 'gnome-help', 'md5sum', 'cmuwmtopbm', 'pkg-config', 'gipddecode', 'pnmenlarge', 'ppdpo', 'mpicc.openmpi', 'peekfd', 'automat-visualize', 'skill', 'pgmcrater', 'xrdb', 'chcon', 'sane-find-scanner', 'python2.7-config', 'x86_64-linux-gnu-gcc-nm', 'vtkWrapJava-7.1', 'unwrapdiff', 'dh_pypy', 'bmptoppm', 'gml2gv', 'foo2oak', 'gresource', 'msgcat', 'ltximg', 'dvipdfmx', 'ssh-copy-id', 'pjtoppm', 'syslinux-legacy', 'pixeltool', 'whoopsie', 'xdg-open', 'pbmmake', 'rasttopnm', 'ms_print', 'fixtpps', 'convert-im6.q16', 'preconv', 'pdf270', 'ssh-import-id-lp', 'afm2pl', 'ps2eps', 'Xwayland', 'sensible-editor', 'pamstretch-gen', 'gettext.sh', 'srcredact', 'pnmtorle', 'setfacl', 'pdfunite', 'gvgen', 'pydoc', 'mcopy', 'dconf', 'oshmem_info', 'whoami', 'infocmp', 'pgmkernel', 'obexctl', 'x86_64-linux-gnu-gold', 'mrd', 'grub-mkrelpath', 'apg', 'printenv', 'pkttyagent', 'pmap', 'ul', 'tex4ht', 'upmpost', 'xdvipdfmx', 'hd', 'uptex', 'fdp', 'sprof', 'mk4ht', 'ccmake', 'pnmtofiasco', 'geteltorito', 'sum', 'stdbuf', 'setlogcons', 'colcrt', 'pyclean', 'rview', 'gst-inspect-1.0', '2to3-2.7', 'msgconv', 'gv2gml', 'scp-dbus-service', 'c99', 'nmtui-hostname', 'invproj', 'pdb3.6', 'xcmsdb', 'debconf-set-selections', 'setleds', 'mmount', 'pooltype', 'ppmquantall', 'du', 'zenity', 'grub-kbdcomp', 'pasuspender', 'psselect', 'notify-send', 'ppmtoicr', 'ruby', 'HEAD', 'pnmtoddif', 'dirmngr', 'dh_autotools-dev_updateconfig', 'apturl-gtk', 'pnmrotate', 'pathchk', 'pbmtoicon', 'gdbus-codegen', 'xcursorgen', 'dvilualatex', 'wish8.6', 'x86_64-linux-gnu-strings', 'thumbpdf', 'linux64', 'run-with-aspell', 'sdiff', 'pnmsmooth', 'gsettings-schema-convert', 'x86_64-linux-gnu-g++-7', 'evince-thumbnailer', 'xedit', 'pcimodules', 'gvfs-mount', 'showchar', 'ssh-keygen', 'hp-setup', 'foo2hbpl2', 'grub-syslinux2cfg', 'mkfontscale', 'pbmupc', 'installfont-tl', 'stream-im6', 'convert-im6', 'volname', 'readelf', 'pftp', 'im-launch', 'hp-firmware', 'gnome-session-properties', 'browse', 'test', 'gvfs-rm', 'mkpic', 'xset', 'gcc-nm', 'sensible-browser', 'lscpu', 'x-terminal-emulator', 'arlatex', 'tex4ebook', 'rediff', 'gencat', 'x86_64-linux-gnu-size', 'lwp-download', 'qdbusviewer', 'pinentry-x11', 'identify-im6', 'pfbtopfa', 'foo2zjs-wrapper', 'xmore', 'gpg-connect-agent', 'freetype-config', 'python3m-config', 'vimdiff', 'on_ac_power', 'kate', 'csplit', 'conjure', 'pkexec', 'pic', 'pbmtoptx', 'twist3', 'pygmentize', 'vim.tiny', 'mpic++', 'pdfpun', 'systemd-detect-virt', 'ppmtopj', 'edit', 'gnome-text-editor', 'msgfilter', 'cheese', 'dvi2tty', 'qvkgen', 'cg_merge', 'l2ping', 'desktop-file-edit', 'mf', 'ppltotf', 'setarch', 'gconf-merge-tree', 'groups', 'pvtkpython', 'bundledoc', 'pycompile', 'eptex', 'hp-query', 'pgmtofs', 'sbverify', 'sccmap', 'tic', 'pbmtoatk', 'identify', 'gcc-ar-7', 'foo2hp', 'repc', 'unxz', 'pvpython', 'qmlmin', 'gvfs-monitor-dir', 'f2py3.6', 'zjsdecode', 'pn2pdf', 'opalc++', 'mflua', 'pkcon', 'debconf-apt-progress', 'icuinfo', 'ttf2tfm', 'pyhtmlizer', 'fixdlsrps', 'grub-mount', 'splitfont', 'realpath', 'ld.gold', 'dpkg-architecture', 'libpng16-config', 'hipercdecode', 'migrate-pubring-from-classic-gpg', 'ua', 'apt-mark', 'nc-config', 'printer-profile', 'hp-testpage', 'deb-systemd-helper', 'hp-colorcal', 'ubuntu-support-status', 'xcutsel', 'libpng-config', 'uuidgen', 'monitor-sensor', 'rhythmbox-client', 'prove', 'lwp-dump', 'makeglossaries-lite', 'rmiregistry', 'systemd-run', 'parec', 'timedatectl', 'ps2ps2', 'erb2.5', 'prepmx', 'cpan5.26-x86_64-linux-gnu', 'ppmrainbow', 'gnome-terminal', 'paste', 'bc', 'editor', 'gtscompare', 'gxl2gv', 'gvfs-set-attribute', 'addr2line', 'unattended-upgrade', 'groff', 'gslj', 'parecord', 'bbox', 'sdptool', 'linguist', 'tr', 'gnome-todo', 'ppmcolormask', 'xdg-desktop-menu', 'simple-scan', 'gcc-7', 'ompi-top', 'mpicxx', 'chardetect3', 'simpdftex', 'vtkWrapPythonInit-6.3', 'repstopdf', 'upbibtex', 'ctanupload', 'msgcomm', 'x86_64-linux-gnu-gcc-ranlib', 'epstopdf', 'bibtex.original', 'pg_config', 'vtkEncodeString-7.1', 'grub-editenv', 'shuf', 'pdfseparate', 'last', 'upmendex', 'htmex', 'systemd-socket-activate', 'install-printerdriver', 'python3.6', 'xdg-icon-resource', 'prune', 'update-manager', 'faillog', 'tac', 'kwalletd5', 'codepage', 'lzcat', 'x86_64-linux-gnu-gcov-tool', 'qmlplugindump', 'users', 'dpkg-parsechangelog', 'libnetcfg', 'renice', 'pnmtosgi', 'touch', 'composite', 'unattended-upgrades', 'apt-sortpkgs', 'ctie', 'gdbtui', 'neato', 'pdb3', 'gtscheck', 'pvrenderserver', 'gmock_gen', 'x86_64-linux-gnu-cpp-7', 'xlsatoms', 'crontab', 'nmtui', 'x11perfcomp', 'pbmtoxbm', 'install-info', 'gvcolor', 'bmtoa', 'f2py3', 'gftodvi', 'expiry', 'gpgsm', 'pmpost', 'ginstall-info', 'newgrp', 'tlmgr', 'iptables-xml', 'esc-m', 'printerbanner', 'vtk7', 'gconftool-2', 'lzmore', 'unity-scope-loader', 'telnet', 'xsubpp', 'bibtex', 'x86_64-linux-gnu-pkg-config', 'systemd-path', 'xmlpatternsvalidator', 'chage', 'dpkg', 'pamdeinterlace', 'mfplain', 'python', 'gstreamer-codec-install', 'lcf', 'xhost', 'partx', 'setterm', 'xconsole', 'makejvf', 'gpgv', 'lpstat', 'hp-levels', 'stream-im6.q16', 'valgrind', 'install', 'valgrind.bin', 'orte-top', 'adhocfilelist', 'arping', 'psmerge', 'doxysearch.cgi', 'rhythmbox', 'dehtmldiff', 'encguess', 'pgmedge', 'ppmpat', 'ncal', 'scp1', 'gtbl', 'pax11publish', 'gnome-thumbnail-font', 'xdg-user-dir', 'tkconch', 'xmag', 'perltex', 'avahi-publish-service', 'keyring', 'ssh-keygen1', 'infotocap', 'isoinfo', 'w', 'match_parens', 'otp2ocp', 'mscompress', 'montage-im6.q16', 'gobject-query', 'a5toa4', 'pgmoil', 'sldtoppm', 'prezip-bin', 'ctest', 'texluajit', 'yuvsplittoppm', 'includeres', 'mendex', 'ppmtoleaf', 'pgmtopbm', 'pnmscale', 'preunzip', 'gts2oogl', 'imagetops', 'qtpaths', 'h5pfc.openmpi', 'openssl', 'mshortname', 'psfxtable', 'tkconch3', 'gdialog', 'yuvtoppm', 'prtstat', 'tftopl', 'ppmcie', 'htxelatex', 'hostid', 'pbmtomda', 'strace-log-merge', 'designer', 'makeglossaries', 'xbmtopbm', 'fmtutil-sys', 'sudoedit', 'gsbj', 'appres', 'unicode_stop', 'jexec', 'gnome-keyring-3', 'curl-config', 'libreoffice', 'icu-config', 'expand', 'genisoimage', 'updvitomp', 'pdfjam-pocketmod', 'foo2hp2600-wrapper', 'f95', 'utmpdump', 'rcp', 'msexpand', 'gftype', 'fmtutil', 'fi_pingpong', 'ps2pk', 'pcxtoppm', 'psfaddtable', 'ktelnetservice5', 'autosp', 'foo2slx-wrapper', 'pythontex', 'getmapdl', 'oshcc', 'ckeygen3', 'zipcloak', 'scp', 'c++', 'pfb2pfa', 'pnmmargin', 'psicc', 'helpztags', 'gtk-builder-tool', 'fonttosfnt', 'pamstack', 'gpg-agent', 'software-properties-gtk', 'python3.6m', 'numfmt', 'orte-ps', 'updmap-user', 'lshw', 'pnmtojpeg', 'cal', 'texdiff', 'pdfatfi', 'ppmmake', 'xsetwacom', 'pamstretch', 'xkill', 'gvfs-tree', 'ppmhist', 'pamon', 't1binary', 'fwupdate', 'pnminterp', 'zipdetails', 't4ht', 'smproxy', 'perli11ndoc', 'iceauth', 'snapctl', 'perl5.26.1', 'pnmnlfilt', 'pon', 'grub-mkpasswd-pbkdf2', 'mcookie', 'check-language-support', 'pdftocairo', 'yes', 'vtkWrapPythonInit-7.1', 'pkcheck', 'pldd', 'lslogins', 'hp-makeuri', 'latexdef', 'gnome-font-viewer', 'mousetweaks', 'pnmpaste', 'm2400w', 'pbmtext', 'printf', 'etex', 'base64', 'gslp', 'totem-video-thumbnailer', 'pgrep', 'showconsolefont', 'kpsetool', 'python2-qr', 'twistd', 'fwupdmgr', 'col', 'l2test', 'rfcomm', 'mkzftree', 'pbmtopi3', 'nroff', 'c89', 'editdiff', 'fixscribeps', 'gcov-dump-7', 'ovp2ovf', 'tee', 'gst-play-1.0', 'pbmtocmuwm', 'rawtopgm', 'keytool', 'anytopnm', 'nohup', 'luajittex', 'gnome-www-browser', 'dbus-uuidgen', 'pybuild', 'mf-nowin', 'linux-version', 'host', 'nm-connection-editor', 'erb', 'mpic++.openmpi', 'diff', 'xsm', 'vtkWrapPython-6.3', 'thunderbird', 'makeindex', 'sha224sum', 'xdg-user-dirs-gtk-update', 'xdpyinfo', 'gts2xyz', 'remmina', 'pacat', 'pbmtog3', 'localectl', 'mktexfmt', 'pnmtosir', 'qmlscene', 'mcd', 'ptx', 'dtxgen', 'x86_64-linux-gnu-gcc', 'psfgettable', 'ddstdecode', 'uconv', 'xdriinfo', 'dotty', 'aa-exec', 'pnmhisteq', 'circo', 'checklistings', 'avahi-browse-domains', 'GET', 'mflua-nowin', 'perl5.26-x86_64-linux-gnu', 'ppmtorgb3', 'gvfs-ls', 'foomatic-rip', 'ppmntsc', 'gpgsplit', 'fi_info', 'qmake', 'acyclic', 'zipinfo', 't1unmac', 'mclasserase', 'mpif90', 'cmake', 'hcitool', 'kactivities-cli', 'pedigree', 'gvfs-cat', 'identify-im6.q16', 'ps2epsi', 'foo2lava', 'tl-paper', 'sirtopnm', 'svn-multi', 'catman', 'dosepsbin', 'dig', 'pdb', 'b2sum', 'diff3', 'texdoctk', 'ld.bfd', 'pnmcrop', 'ptargrep', 'x86_64-linux-gnu-readelf', 'valgrind-listener', 'update-gconf-defaults', 'dap-config', 'apturl', 'brltty-trtxt', 'pygmentex', 'dvipdft'] ['dumpe2fs', 'pam_extrausers_update', 'apm_available', 'mount.ntfs-3g', 'cfdisk', 'setvtrgb', 'mii-tool', 'xtables-multi', 'crda', 'wipefs', 'hdparm', 'ldconfig', 'dosfslabel', 'hwclock', 'halt', 'switch_root', 'blockdev', 'unix_update', 'isosize', 'chcpu', 'e2label', 'modinfo', 'blkid', 'mke2fs', 'ntfsresize', 'ifdown', 'fsck.ext4', 'rtacct', 'fatlabel', 'rtmon', 'sfdisk', 'reboot', 'pccardctl', 'mkfs.ntfs', 'pivot_root', 'fixparts', 'brltty', 'mount.lowntfs-3g', 'ipmaddr', 'shadowconfig', 'zramctl', 'swapon', 'getty', 'modprobe', 'mkfs.bfs', 'iwpriv', 'agetty', 'kbdrate', 'capsh', 'ifquery', 'start-stop-daemon', 'pam_tally', 'findfs', 'losetup', 'debugfs', 'poweroff', 'ntfscp', 'iw', 'getpcaps', 'dhclient', 'regdbdump', 'plipconfig', 'fsfreeze', 'alsa', 'slattach', 'rmmod', 'nameif', 'badblocks', 'sgdisk', 'udevadm', 'mkfs', 'dmsetup', 'sulogin', 'e2undo', 'acpi_available', 'iwconfig', 'u-d-c-print-pci-ids', 'killall5', 'ntfsundelete', 'installkernel', 'mount.ntfs', 'iptables', 'fdisk', 'shutdown', 'mkdosfs', 'runlevel', 'blkdeactivate', 'rarp', 'fsck.msdos', 'pam_extrausers_chkpwd', 'brltty-setup', 'ntfsclone', 'setcap', 'iptunnel', 'parted', 'blkdiscard', 'plymouthd', 'ldconfig.real', 'umount.udisks2', 'fsck.vfat', 'mkfs.msdos', 'partprobe', 'mkfs.cramfs', 'wpa_action', 'ifconfig', 'e2fsck', 'iwlist', 'iptables-restore', 'mkswap', 'ifup', 'devlink', 'mkfs.vfat', 'dosfsck', 'mount.fuse', 'cgdisk', 'unix_chkpwd', 'fstab-decode', 'iptables-save', 'ip6tables-restore', 'ip6tables-save', 'iwspy', 'sysctl', 'wpa_supplicant', 'lspcmcia', 'tipc', 'ureadahead', 'mkfs.ext4', 'telinit', 'swapoff', 'lsmod', 'raw', 'iwgetid', 'fsck.ext2', 'depmod', 'e2image', 'init', 'on_ac_power', 'fsck', 'ip6tables', 'mkfs.ext3', 'mkhomedir_helper', 'getcap', 'logsave', 'fsck.ext3', 'resize2fs', 'tc', 'pam_tally2', 'ctrlaltdel', 'runuser', 'swaplabel', 'ip', 'apparmor_parser', 'fsck.minix', 'ntfslabel', 'gdisk', 'dhclient-script', 'iwevent', 'insmod', 'route', 'tune2fs', 'mkfs.ext2', 'fsck.fat', 'dmstats', 'wpa_cli', 'mkntfs', 'mkfs.fat', 'fsck.cramfs', 'bridge', 'mkfs.minix', 'fstrim'] ['cp', 'more', 'chmod', 'systemd', 'gzexe', 'systemd-hwdb', 'nc.openbsd', 'mknod', 'bzegrep', 'mt-gnu', 'sh', 'zmore', 'setupcon', 'true', 'rm', 'nano', 'false', 'fgconsole', 'ntfsfallocate', 'sed', 'ntfscmp', 'getfacl', 'dumpkeys', 'lessfile', 'zgrep', 'bzdiff', 'tar', 'fgrep', 'wdctl', 'systemd-inhibit', 'bzip2recover', 'ed', 'static-sh', 'rnano', 'open', 'systemd-escape', 'ntfsusermap', 'nc', 'mktemp', 'zfgrep', 'bzgrep', 'whiptail', 'chgrp', 'systemctl', 'sh.distrib', 'brltty', 'red', 'zforce', 'dash', 'lowntfs-3g', 'kmod', 'rbash', 'rmdir', 'chvt', 'tempfile', 'ls', 'ypdomainname', 'zegrep', 'dd', 'ntfsls', 'lessecho', 'ntfscat', 'dnsdomainname', 'ln', 'loadkeys', 'znew', 'chacl', 'cat', 'udevadm', 'ping4', 'run-parts', 'gunzip', 'date', 'efibootmgr', 'lesskey', 'journalctl', 'lesspipe', 'systemd-tty-ask-password-agent', 'zcat', 'mountpoint', 'systemd-tmpfiles', 'echo', 'mount', 'login', 'ntfsinfo', 'ss', 'bzcmp', 'uncompress', 'ntfs-3g.probe', 'mv', 'ntfsrecover', 'netstat', 'bzless', 'dir', 'ntfssecaudit', 'mt', 'bzip2', 'ntfscluster', 'less', 'openvt', 'sync', 'ntfstruncate', 'bzmore', 'which', 'egrep', 'systemd-ask-password', 'ntfsmove', 'bzcat', 'bzfgrep', 'bzexe', 'ping', 'kbd_mode', 'zdiff', 'bash', 'bunzip2', 'findmnt', 'gzip', 'netcat', 'mkdir', 'ping6', 'hciconfig', 'setfont', 'su', 'unicode_start', 'networkctl', 'ntfsfix', 'loginctl', 'setfacl', 'df', 'lsmod', 'grep', 'chown', 'domainname', 'plymouth', 'cpio', 'vdir', 'fusermount', 'systemd-notify', 'pwd', 'nisdomainname', 'umount', 'ntfswipe', 'systemd-machine-id-setup', 'pidof', 'efibootdump', 'touch', 'sleep', 'readlink', 'ip', 'systemd-sysusers', 'ps', 'uname', 'zcmp', 'hostname', 'fuser', 'ntfs-3g', 'stty', 'ulockmgr_server', 'dmesg', 'busybox', 'zless', 'lsblk', 'kill'] ['gnome-mahjongg', 'gnome-sudoku', 'sol', 'gnome-mines', 'espdiff'] [] ['gnome-calculator', 'gnome-system-monitor', 'gnome-logs', 'gnome-characters'] Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] Checking for program /Developer/NVIDIA/CUDA-6.5/bin/nvcc...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/nvcc...not found Unable to find programs ['nvcc'] providing listing of each search directory to help debug Path provided in Python program Warning accessing /Developer/NVIDIA/CUDA-6.5/bin gives errors: [Errno 2] No such file or directory: '/Developer/NVIDIA/CUDA-6.5/bin' Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] Checking for program /usr/local/cuda/bin/nvcc...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/nvcc...not found Unable to find programs ['nvcc'] providing listing of each search directory to help debug Path provided in Python program Warning accessing /usr/local/cuda/bin gives errors: [Errno 2] No such file or directory: '/usr/local/cuda/bin' Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] ================================================================================ TEST checkCUDAPreprocessor from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:719) TESTING: checkCUDAPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:719) Locate a functional CUDA preprocessor ================================================================================ TEST checkCxxCompiler from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:818) TESTING: checkCxxCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:818) Locate a functional Cxx compiler Checking for program /home/santiago/usr/local/bin/mpicxx...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpicxx...not found Checking for program /usr/local/sbin/mpicxx...not found Checking for program /usr/local/bin/mpicxx...not found Checking for program /usr/sbin/mpicxx...not found Checking for program /usr/bin/mpicxx...found Defined make macro "CXX" to "mpicxx" Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o Testing executable /tmp/petsc-k0jR75/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable WITHOUT threads to time it out Executing: mpicxx --version stdout: g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkCxxPreprocessor from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:859) TESTING: checkCxxPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:859) Locate a functional Cxx preprocessor Checking for program /home/santiago/usr/local/bin/mpicxx...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpicxx...not found Checking for program /usr/local/sbin/mpicxx...not found Checking for program /usr/local/bin/mpicxx...not found Checking for program /usr/sbin/mpicxx...not found Checking for program /usr/bin/mpicxx...found Defined make macro "CXXPP" to "mpicxx -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicxx -E -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkFortranCompiler from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:960) TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:960) Locate a functional Fortran compiler Checking for program /home/santiago/usr/local/bin/mpif90...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpif90...not found Checking for program /usr/local/sbin/mpif90...not found Checking for program /usr/local/bin/mpif90...not found Checking for program /usr/sbin/mpif90...not found Checking for program /usr/bin/mpif90...found Defined make macro "FC" to "mpif90" Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o Testing executable /tmp/petsc-k0jR75/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable WITHOUT threads to time it out Executing: mpif90 --version stdout: GNU Fortran (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkFortranPreprocessor from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:997) TESTING: checkFortranPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:997) Locate a functional Fortran preprocessor Checking for program /home/santiago/usr/local/bin/mpif90...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpif90...not found Checking for program /usr/local/sbin/mpif90...not found Checking for program /usr/local/bin/mpif90...not found Checking for program /usr/sbin/mpif90...not found Checking for program /usr/bin/mpif90...found Defined make macro "FPP" to "mpif90 -E" Deleting "FPP" Checking for program /home/santiago/usr/local/bin/mpif90...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpif90...not found Checking for program /usr/local/sbin/mpif90...not found Checking for program /usr/local/bin/mpif90...not found Checking for program /usr/sbin/mpif90...not found Checking for program /usr/bin/mpif90...found Defined make macro "FPP" to "mpif90 --use cpp32" Deleting "FPP" ================================================================================ TEST checkFortranComments from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1019) TESTING: checkFortranComments from config.setCompilers(config/BuildSystem/config/setCompilers.py:1019) Make sure fortran comment "!" works Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main ! comment end Fortran comments can use ! in column 1 ================================================================================ TEST checkLargeFileIO from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1150) TESTING: checkLargeFileIO from config.setCompilers(config/BuildSystem/config/setCompilers.py:1150) ================================================================================ TEST checkArchiver from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1249) TESTING: checkArchiver from config.setCompilers(config/BuildSystem/config/setCompilers.py:1249) Check that the archiver exists and can make a library usable by the compiler Running Executable WITHOUT threads to time it out Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.30 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Running Executable WITHOUT threads to time it out Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.30 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /home/santiago/usr/local/bin/ar...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/ar...not found Checking for program /usr/local/sbin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/sbin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /home/santiago/usr/local/bin/ranlib...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/ranlib...not found Checking for program /usr/local/sbin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/sbin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib -c" Running Executable WITHOUT threads to time it out Executing: /usr/bin/ar cr /tmp/petsc-k0jR75/config.setCompilers/libconf1.a /tmp/petsc-k0jR75/config.setCompilers/conf1.o Running Executable WITHOUT threads to time it out Executing: /usr/bin/ranlib -c /tmp/petsc-k0jR75/config.setCompilers/libconf1.a Possible ERROR while running ranlib: stderr: /usr/bin/ranlib: invalid option -- 'c' Ranlib is not functional with your archiver. Try --with-ranlib=true if ranlib is unnecessary. Running Executable WITHOUT threads to time it out Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.30 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Running Executable WITHOUT threads to time it out Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.30 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /home/santiago/usr/local/bin/ar...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/ar...not found Checking for program /usr/local/sbin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/sbin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /home/santiago/usr/local/bin/ranlib...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/ranlib...not found Checking for program /usr/local/sbin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/sbin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib" Running Executable WITHOUT threads to time it out Executing: /usr/bin/ar cr /tmp/petsc-k0jR75/config.setCompilers/libconf1.a /tmp/petsc-k0jR75/config.setCompilers/conf1.o Running Executable WITHOUT threads to time it out Executing: /usr/bin/ranlib /tmp/petsc-k0jR75/config.setCompilers/libconf1.a Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern int foo(int); int main() { int b = foo(1); if (b); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest /tmp/petsc-k0jR75/config.setCompilers/conftest.o -L/tmp/petsc-k0jR75/config.setCompilers -lconf1 Defined make macro "AR_FLAGS" to "cr" Defined make macro "AR_LIB_SUFFIX" to "a" ================================================================================ TEST checkSharedLinker from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1363) TESTING: checkSharedLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1363) Check that the linker can produce shared libraries Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Checking shared linker mpicc using flags ['-shared'] Checking for program /home/santiago/usr/local/bin/mpicc...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpicc...not found Checking for program /usr/local/sbin/mpicc...not found Checking for program /usr/local/bin/mpicc...not found Checking for program /usr/sbin/mpicc...not found Checking for program /usr/bin/mpicc...found Defined make macro "LD_SHARED" to "mpicc" Trying C compiler flag Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -shared /tmp/petsc-k0jR75/config.setCompilers/conftest.o Valid C linker flag -shared Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared /tmp/petsc-k0jR75/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /tmp/petsc-k0jR75/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `fprintf_ptr' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status Rejected C compiler flag because it was not compatible with shared linker mpicc using flags ['-shared'] Running Executable WITHOUT threads to time it out Executing: mpicc --help | head -n 20 stdout: Usage: gcc [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying C compiler flag -fPIC Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fPIC Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Valid C linker flag -shared Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(void); int main() { int ret = foo(); if (ret) {} ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o -L/tmp/petsc-k0jR75/config.setCompilers -lconftest Using shared linker mpicc with flags ['-shared'] and library extension so Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux ================================================================================ TEST checkPIC from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1097) TESTING: checkPIC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1097) Determine the PIC option for each compiler Trying Cxx for PIC code without any compiler flag Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /tmp/petsc-k0jR75/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `fprintf_ptr' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status Rejected Cxx compiler flag because shared linker cannot handle it Running Executable WITHOUT threads to time it out Executing: mpicxx --help | head -n 20 stdout: Usage: g++ [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying Cxx compiler flag -fPIC for PIC code Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fPIC Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Accepted Cxx compiler flag -fPIC for PIC code Trying FC for PIC code without any compiler flag Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /tmp/petsc-k0jR75/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `xx_' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status Rejected FC compiler flag because shared linker cannot handle it Running Executable WITHOUT threads to time it out Executing: mpif90 --help | head -n 20 stdout: Usage: gfortran [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying FC compiler flag -fPIC for PIC code Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -fPIC Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Accepted FC compiler flag -fPIC for PIC code ================================================================================ TEST checkSharedLinkerPaths from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1475) TESTING: checkSharedLinkerPaths from config.setCompilers(config/BuildSystem/config/setCompilers.py:1475) Determine the shared linker path options - IRIX: -rpath - Linux, OSF: -Wl,-rpath, - Solaris: -R - FreeBSD: -Wl,-R, Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Running Executable WITHOUT threads to time it out Executing: mpicc -V Trying C linker flag -Wl,-rpath, Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -Wl,-rpath,/home/santiago/Documents/installers/petsc/petsc-3.13.0 -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Valid C linker flag -Wl,-rpath,/home/santiago/Documents/installers/petsc/petsc-3.13.0 Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Running Executable WITHOUT threads to time it out Executing: mpicc -V Trying Cxx linker flag -Wl,-rpath, Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.setCompilers/conftest -Wl,-rpath,/home/santiago/Documents/installers/petsc/petsc-3.13.0 /tmp/petsc-k0jR75/config.setCompilers/conftest.o Valid Cxx linker flag -Wl,-rpath,/home/santiago/Documents/installers/petsc/petsc-3.13.0 Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Running Executable WITHOUT threads to time it out Executing: mpicc -V Trying FC linker flag -Wl,-rpath, Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.setCompilers/conftest -Wl,-rpath,/home/santiago/Documents/installers/petsc/petsc-3.13.0 -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Valid FC linker flag -Wl,-rpath,/home/santiago/Documents/installers/petsc/petsc-3.13.0 ================================================================================ TEST checkLibC from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1510) TESTING: checkLibC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1510) Test whether we need to explicitly include libc in shared linking - Mac OSX requires an explicit reference to libc for shared linking Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {void *chunk = malloc(31); free(chunk); return 0;} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o Shared linking does not require an explicit libc reference ================================================================================ TEST checkDynamicLinker from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1556) TESTING: checkDynamicLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1556) Check that the linker can dynamicaly load shared libraries Checking for header: dlfcn.h All intermediate test results are stored in /tmp/petsc-k0jR75/config.headers Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" Checking for functions [dlopen dlsym dlclose] in library ['dl'] [] All intermediate test results are stored in /tmp/petsc-k0jR75/config.libraries Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } char dlsym(); static void _check_dlsym() { dlsym(); } char dlclose(); static void _check_dlclose() { dlclose(); } int main() { _check_dlopen(); _check_dlsym(); _check_dlclose();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC /tmp/petsc-k0jR75/config.libraries/conftest.o -ldl Defined "HAVE_LIBDL" to "1" Adding ['dl'] to LIBS Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Checking dynamic linker mpicc using flags ['-shared'] Checking for program /home/santiago/usr/local/bin/mpicc...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpicc...not found Checking for program /usr/local/sbin/mpicc...not found Checking for program /usr/local/bin/mpicc...not found Checking for program /usr/sbin/mpicc...not found Checking for program /usr/bin/mpicc...found Defined make macro "DYNAMICLINKER" to "mpicc" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o -ldl Valid C linker flag -shared Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {printf("test");return 0;} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o -ldl Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { void *handle = dlopen("/tmp/petsc-k0jR75/config.setCompilers/libconftest.so", 0); int (*foo)(void) = (int (*)(void)) dlsym(handle, "foo"); if (!foo) { printf("Could not load symbol\n"); return -1; } if ((*foo)()) { printf("Invalid return from foo()\n"); return -1; } if (dlclose(handle)) { printf("Could not close library\n"); return -1; } ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.o -ldl Using dynamic linker mpicc with flags ['-shared'] and library extension so ================================================================================ TEST output from config.setCompilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/setCompilers.py:1605) TESTING: output from config.setCompilers(config/BuildSystem/config/setCompilers.py:1605) Output module data as defines and substitutions Substituting "CC" with "mpicc" Substituting "CFLAGS" with " -fPIC" Defined make macro "CC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "CPP" with "mpicc -E" Substituting "CPPFLAGS" with "" Substituting "CXX" with "mpicxx" Substituting "CXX_CXXFLAGS" with " -fPIC" Substituting "CXXFLAGS" with "" Substituting "CXX_LINKER_SLFLAG" with "-Wl,-rpath," Substituting "CXXPP" with "mpicxx -E" Substituting "CXXPPFLAGS" with "" Substituting "FC" with "mpif90" Substituting "FFLAGS" with " -fPIC" Defined make macro "FC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "LDFLAGS" with "" Substituting "LIBS" with "-ldl " Substituting "SHARED_LIBRARY_FLAG" with "-shared" child config.setCompilers 3.843452 ================================================================================ TEST checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/sharedLibraries.py:36) TESTING: checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:36) ================================================================================ TEST configureSharedLibraries from PETSc.options.sharedLibraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/sharedLibraries.py:52) TESTING: configureSharedLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:52) Checks whether shared libraries should be used, for which you must - Specify --with-shared-libraries - Have found a working shared linker Defines PETSC_USE_SHARED_LIBRARIES if they are used Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Defined make rule "shared_arch" with dependencies "shared_linux" and code [] Defined make macro "SONAME_FUNCTION" to "$(1).so.$(2)" Defined make macro "SL_LINKER_FUNCTION" to "-shared -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2))" Defined make macro "BUILDSHAREDLIB" to "yes" Defined "USE_SHARED_LIBRARIES" to "1" ================================================================================ TEST configureDynamicLibraries from PETSc.options.sharedLibraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/sharedLibraries.py:94) TESTING: configureDynamicLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:94) Checks whether dynamic loading is available (with dlfcn.h and libdl) Defined "HAVE_DYNAMIC_LIBRARIES" to "1" ================================================================================ TEST configureSerializedFunctions from PETSc.options.sharedLibraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/sharedLibraries.py:100) TESTING: configureSerializedFunctions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:100) Defines PETSC_SERIALIZE_FUNCTIONS if they are used Requires shared libraries child PETSc.options.sharedLibraries 0.010104 ================================================================================ TEST configureIndexSize from PETSc.options.indexTypes(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/indexTypes.py:39) TESTING: configureIndexSize from PETSc.options.indexTypes(config/PETSc/options/indexTypes.py:39) Defined make macro "PETSC_INDEX_SIZE" to "32" child PETSc.options.indexTypes 0.000970 ================================================================================ TEST configureCompilerFlags from config.compilerFlags(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilerFlags.py:72) TESTING: configureCompilerFlags from config.compilerFlags(config/BuildSystem/config/compilerFlags.py:72) Get the default compiler flags Defined make macro "C_VERSION" to "gcc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0" Defined make macro "MPICC_SHOW" to "gcc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi" Trying C compiler flag -Wall Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wall Trying C compiler flag -Wwrite-strings Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wwrite-strings Trying C compiler flag -Wno-strict-aliasing Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wno-strict-aliasing Trying C compiler flag -Wno-unknown-pragmas Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wno-unknown-pragmas Trying C compiler flag -fstack-protector Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fstack-protector Trying C compiler flag -mfp16-format=ieee Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -mfp16-format=ieee /tmp/petsc-k0jR75/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: gcc: error: unrecognized command line option ‘-mfp16-format=ieee’ Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -mfp16-format=ieee due to nonzero status from link Rejecting compiler flag -mfp16-format=ieee due to gcc: error: unrecognized command line option ‘-mfp16-format=ieee’ PETSc Error: No output file produced Rejected C compiler flag -mfp16-format=ieee Trying C compiler flag -fvisibility=hidden Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fvisibility=hidden Trying C compiler flag -O -O3 -march=native -mtune=native Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -O -O3 -march=native -mtune=native Defined make macro "Cxx_VERSION" to "g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0" Defined make macro "MPICXX_SHOW" to "g++ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_cxx -lmpi" Trying Cxx compiler flag -Wall Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -Wall -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wall Trying Cxx compiler flag -Wwrite-strings Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wwrite-strings Trying Cxx compiler flag -Wno-strict-aliasing Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wno-strict-aliasing Trying Cxx compiler flag -Wno-unknown-pragmas Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wno-unknown-pragmas Trying Cxx compiler flag -fstack-protector Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fstack-protector Trying Cxx compiler flag -fvisibility=hidden Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fvisibility=hidden Trying Cxx compiler flag -O -O3 -march=native -mtune=native Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -O -O3 -march=native -mtune=native Defined make macro "FC_VERSION" to "GNU Fortran (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0" Defined make macro "MPIFC_SHOW" to "gfortran -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi" Trying FC compiler flag -Wall Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wall Trying FC compiler flag -ffree-line-length-0 Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -ffree-line-length-0 Trying FC compiler flag -Wno-unused-dummy-argument Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wno-unused-dummy-argument Trying FC compiler flag -O -O3 -march=native -mtune=native Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -O -O3 -march=native -mtune=native child config.compilerFlags 1.178139 Running Executable WITHOUT threads to time it out Executing: mpicc --help | head -n 20 stdout: Usage: gcc [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and ================================================================================ TEST checkRestrict from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:150) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:150) Check for the C/CXX restrict keyword Running Executable WITHOUT threads to time it out Executing: mpicc -V All intermediate test results are stored in /tmp/petsc-k0jR75/config.compilers Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.compilers/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.compilers/conftest.c:5:20: warning: unused variable ‘x’ [-Wunused-variable] float * __restrict x;; ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set C restrict keyword to __restrict Defined "C_RESTRICT" to "__restrict" ================================================================================ TEST checkCFormatting from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:405) TESTING: checkCFormatting from config.compilers(config/BuildSystem/config/compilers.py:405) Activate format string checking if using the GNU compilers ================================================================================ TEST checkCInline from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:120) TESTING: checkCInline from config.compilers(config/BuildSystem/config/compilers.py:120) Check for C inline keyword Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set C Inline keyword to inline Defined "C_INLINE" to "inline" ================================================================================ TEST checkDynamicLoadFlag from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:416) TESTING: checkDynamicLoadFlag from config.compilers(config/BuildSystem/config/compilers.py:416) Checks that dlopen() takes RTLD_XXX, and defines PETSC_HAVE_RTLD_XXX if it does Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include char *libname; int main() { dlopen(libname, RTLD_LAZY);dlopen(libname, RTLD_NOW);dlopen(libname, RTLD_LOCAL);dlopen(libname, RTLD_GLOBAL); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o -ldl Defined "HAVE_RTLD_LAZY" to "1" Defined "HAVE_RTLD_NOW" to "1" Defined "HAVE_RTLD_LOCAL" to "1" Defined "HAVE_RTLD_GLOBAL" to "1" ================================================================================ TEST checkCLibraries from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:214) TESTING: checkCLibraries from config.compilers(config/BuildSystem/config/compilers.py:214) Determines the libraries needed to link with C compiled code Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -ldl C libraries are not needed when using Fortran linker Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.compilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -ldl C libraries are not needed when using C++ linker ================================================================================ TEST checkDependencyGenerationFlag from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:1363) TESTING: checkDependencyGenerationFlag from config.compilers(config/BuildSystem/config/compilers.py:1363) Check if -MMD works for dependency generation, and add it if it does Trying C compiler flag -MMD -MP Defined make macro "C_DEPFLAGS" to "-MMD -MP" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -MMD -MP /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Trying Cxx compiler flag -MMD -MP Defined make macro "CXX_DEPFLAGS" to "-MMD -MP" Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC -MMD -MP /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ================================================================================ TEST checkC99Flag from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:1408) TESTING: checkC99Flag from config.compilers(config/BuildSystem/config/compilers.py:1408) Check for -std=c99 or equivalent flag Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.setCompilers/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.setCompilers/conftest.c:7:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] float x[2],y; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { float x[2],y; y = FLT_ROUNDS; // c++ comment int j = 2; for (int i=0; i<2; i++){ x[i] = i*j*y; } ; return 0; } Accepted C99 compile flag: Defined "HAVE_C99" to "1" Running Executable WITHOUT threads to time it out Executing: mpicxx --help | head -n 20 stdout: Usage: g++ [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and ================================================================================ TEST checkRestrict from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:150) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:150) Check for the C/CXX restrict keyword Running Executable WITHOUT threads to time it out Executing: mpicc -V Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.compilers/conftest.cc: In function ‘int main()’: /tmp/petsc-k0jR75/config.compilers/conftest.cc:5:20: warning: unused variable ‘x’ [-Wunused-variable] float * __restrict x;; ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set Cxx restrict keyword to __restrict Defined "CXX_RESTRICT" to "__restrict" ================================================================================ TEST checkCxxOptionalExtensions from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:435) TESTING: checkCxxOptionalExtensions from config.compilers(config/BuildSystem/config/compilers.py:435) Check whether the C++ compiler (IBM xlC, OSF5) need special flag for .c files which contain C++ Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { class somename { int i; };; return 0; } ================================================================================ TEST checkCxxInline from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:135) TESTING: checkCxxInline from config.compilers(config/BuildSystem/config/compilers.py:135) Check for C++ inline keyword Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set Cxx Inline keyword to inline Defined "CXX_INLINE" to "inline" ================================================================================ TEST checkCxxLibraries from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:547) TESTING: checkCxxLibraries from config.compilers(config/BuildSystem/config/compilers.py:547) Determines the libraries needed to link with C++ from C and Fortran Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.compilers/confc.o: In function `asub()': conftest.cc:(.text+0x7): undefined reference to `__cxa_allocate_exception' conftest.cc:(.text+0xe): undefined reference to `typeinfo for int' conftest.cc:(.text+0x1e): undefined reference to `__cxa_throw' conftest.cc:(.text+0x37): undefined reference to `__cxa_begin_catch' conftest.cc:(.text+0x3e): undefined reference to `std::cout' conftest.cc:(.text+0x4a): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' conftest.cc:(.text+0x5b): undefined reference to `__cxa_end_catch' conftest.cc:(.text+0x50): undefined reference to `__cxa_end_catch' /tmp/petsc-k0jR75/config.compilers/confc.o: In function `_GLOBAL__sub_I_conftest.cc': conftest.cc:(.text.startup+0xc): undefined reference to `std::ios_base::Init::Init()' conftest.cc:(.text.startup+0x13): undefined reference to `std::ios_base::Init::~Init()' /tmp/petsc-k0jR75/config.compilers/confc.o:(.data.rel.local.DW.ref._ZTIi[DW.ref._ZTIi]+0x0): undefined reference to `typeinfo for int' /tmp/petsc-k0jR75/config.compilers/confc.o:(.data.rel.local.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0' collect2: error: ld returned 1 exit status Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -lstdc++ -ldl compilers: C++ requires -lstdc++ to link with C compiler Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -lstdc++ -ldl C++ libraries are not needed when using FC linker ================================================================================ TEST checkCxxDialect from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:463) TESTING: checkCxxDialect from config.compilers(config/BuildSystem/config/compilers.py:463) Determine the Cxx dialect supported by the compiler [and correspoding compiler option - if any]. -with-cxx-dialect can take options: auto: use highest dialect configure can determine cxx17: [future?] cxx14: gnu++14 or c++14 cxx11: gnu++11 or c++11 0: disable CxxDialect check and use compiler default checkCxxDialect: checking CXX14 with flag: Defined "HAVE_CXX_DIALECT_CXX14" to "1" Defined "HAVE_CXX_DIALECT_CXX11" to "1" Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include template constexpr T Cubed( T x ) { return x*x*x; } int main() { std::random_device rd; std::mt19937 mt(rd()); std::normal_distribution dist(0,1); const double x = dist(mt); std::cout << x; constexpr std::complex I(0.0,1.0); auto lambda = [](auto x, auto y) {return x + y;}; return lambda(3,4); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -V ================================================================================ TEST checkFortranNameMangling from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:854) TESTING: checkFortranNameMangling from config.compilers(config/BuildSystem/config/compilers.py:854) Checks Fortran name mangling, and defines HAVE_FORTRAN_UNDERSCORE, HAVE_FORTRAN_NOUNDERSCORE, HAVE_FORTRAN_CAPS Testing Fortran mangling type underscore with code void d1chk_(void){return;} Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1chk_(void){return;} Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran name mangling is underscore Defined "HAVE_FORTRAN_UNDERSCORE" to "1" Running Executable WITHOUT threads to time it out Executing: mpif90 --version stdout: GNU Fortran (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Defined "FORTRAN_CHARLEN_T" to "int" ================================================================================ TEST checkFortranNameManglingDouble from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:892) TESTING: checkFortranNameManglingDouble from config.compilers(config/BuildSystem/config/compilers.py:892) Checks if symbols containing an underscore append an extra underscore, and defines HAVE_FORTRAN_UNDERSCORE_UNDERSCORE if necessary Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1_chk__(void){return;} Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: program main call d1_chk() end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.compilers/conftest.o: In function `main': conftest.F90:(.text.startup+0x1d): undefined reference to `d1_chk_' collect2: error: ld returned 1 exit status ================================================================================ TEST checkFortranLibraries from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:902) TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:902) Substitutes for FLIBS the libraries needed to link with Fortran This macro is intended to be used in those situations when it is necessary to mix, e.g. C++ and Fortran 77, source code into a single program or shared library. For example, if object files from a C++ and Fortran 77 compiler must be linked together, then the C++ compiler/linker must be used for linking (since special C++-ish things need to happen at link time like calling global constructors, instantiating templates, enabling exception support, etc.). However, the Fortran 77 intrinsic and run-time libraries must be linked in as well, but the C++ compiler/linker does not know how to add these Fortran 77 libraries. This code was translated from the autoconf macro which was packaged in its current form by Matthew D. Langston . However, nearly all of this macro came from the OCTAVE_FLIBS macro in octave-2.0.13/aclocal.m4, and full credit should go to John W. Eaton for writing this extremely useful macro. Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: program main #include call MPI_Allreduce() end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o -lstdc++ -ldl Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: subroutine asub() print*,'testing' call MPI_Allreduce() return end Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern void asub_(void); int main(int argc,char **args) { asub_(); return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.compilers/confc.o: In function `asub_': conftest.F90:(.text+0x31): undefined reference to `_gfortran_st_write' conftest.F90:(.text+0x45): undefined reference to `_gfortran_transfer_character_write' conftest.F90:(.text+0x4d): undefined reference to `_gfortran_st_write_done' conftest.F90:(.text+0x5c): undefined reference to `mpi_allreduce_' collect2: error: ld returned 1 exit status Fortran code cannot directly be linked with C linker, therefore will determine needed Fortran libraries Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: program main end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: Driving: /usr/bin/gfortran -o /tmp/petsc-k0jR75/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o -lstdc++ -ldl -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -l gfortran -l m -shared-libgcc Using built-in specs. COLLECT_GCC=/usr/bin/gfortran COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.4.0-1ubuntu1~18.04.1' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1) Reading specs from /usr/lib/gcc/x86_64-linux-gnu/7/libgfortran.spec rename spec lib to liborig COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-k0jR75/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O' '-O3' '-march=native' '-mtune=native' '-I' '/usr/lib/x86_64-linux-gnu/openmpi/include' '-pthread' '-I' '/usr/lib/x86_64-linux-gnu/openmpi/lib' '-L/usr//lib' '-L/usr/lib/x86_64-linux-gnu/openmpi/lib' '-shared-libgcc' COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-k0jR75/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O' '-O3' '-march=native' '-mtune=native' '-I' '/usr/lib/x86_64-linux-gnu/openmpi/include' '-pthread' '-I' '/usr/lib/x86_64-linux-gnu/openmpi/lib' '-L/usr//lib' '-L/usr/lib/x86_64-linux-gnu/openmpi/lib' '-shared-libgcc' /usr/lib/gcc/x86_64-linux-gnu/7/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/7/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper -plugin-opt=-fresolution=/tmp/ccVlXOZe.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lquadmath -plugin-opt=-pass-through=-lm -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lpthread -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --sysroot=/ --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -z now -z relro -o /tmp/petsc-k0jR75/config.compilers/conftest /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/7/crtbeginS.o -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/7/../../.. /tmp/petsc-k0jR75/config.compilers/conftest.o -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lpthread -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/7/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-k0jR75/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O' '-O3' '-march=native' '-mtune=native' '-I' '/usr/lib/x86_64-linux-gnu/openmpi/include' '-pthread' '-I' '/usr/lib/x86_64-linux-gnu/openmpi/lib' '-L/usr//lib' '-L/usr/lib/x86_64-linux-gnu/openmpi/lib' '-shared-libgcc' compilers: Checking arg Driving: compilers: Unknown arg Driving: compilers: Checking arg /usr/bin/gfortran compilers: Unknown arg /usr/bin/gfortran compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-k0jR75/config.compilers/conftest compilers: Unknown arg /tmp/petsc-k0jR75/config.compilers/conftest compilers: Checking arg -v compilers: Unknown arg -v compilers: Checking arg -fPIC compilers: Unknown arg -fPIC compilers: Checking arg -Wall compilers: Unknown arg -Wall compilers: Checking arg -ffree-line-length-0 compilers: Unknown arg -ffree-line-length-0 compilers: Checking arg -Wno-unused-dummy-argument compilers: Unknown arg -Wno-unused-dummy-argument compilers: Checking arg -O compilers: Unknown arg -O compilers: Checking arg -O3 compilers: Unknown arg -O3 compilers: Checking arg -march=native compilers: Unknown arg -march=native compilers: Checking arg -mtune=native compilers: Unknown arg -mtune=native compilers: Checking arg /tmp/petsc-k0jR75/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-k0jR75/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Found library: -lstdc++ compilers: Checking arg -ldl compilers: Found library: -ldl compilers: Checking arg -I/usr/lib/x86_64-linux-gnu/openmpi/include compilers: Found include directory: /usr/lib/x86_64-linux-gnu/openmpi/include compilers: Checking arg -pthread compilers: Unknown arg -pthread compilers: Checking arg -I/usr/lib/x86_64-linux-gnu/openmpi/lib compilers: Found include directory: /usr/lib/x86_64-linux-gnu/openmpi/lib compilers: Checking arg -L/usr//lib compilers: Checking arg -L/usr/lib/x86_64-linux-gnu/openmpi/lib compilers: Found library directory: -L/usr/lib/x86_64-linux-gnu/openmpi/lib compilers: Checking arg -lmpi_usempif08 compilers: Found library: -lmpi_usempif08 compilers: Checking arg -lmpi_usempi_ignore_tkr compilers: Found library: -lmpi_usempi_ignore_tkr compilers: Checking arg -lmpi_mpifh compilers: Found library: -lmpi_mpifh compilers: Checking arg -lmpi compilers: Found library: -lmpi compilers: Checking arg -l compilers: Found canonical library: -lgfortran compilers: Checking arg -l compilers: Found canonical library: -lm compilers: Checking arg -shared-libgcc compilers: Unknown arg -shared-libgcc compilers: Checking arg Using compilers: Unknown arg Using compilers: Checking arg built-in compilers: Unknown arg built-in compilers: Checking arg specs. compilers: Unknown arg specs. compilers: Checking arg COLLECT_GCC=/usr/bin/gfortran compilers: Unknown arg COLLECT_GCC=/usr/bin/gfortran compilers: Checking arg COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper compilers: Unknown arg COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper compilers: Checking arg OFFLOAD_TARGET_NAMES=nvptx-none compilers: Unknown arg OFFLOAD_TARGET_NAMES=nvptx-none compilers: Checking arg OFFLOAD_TARGET_DEFAULT=1 compilers: Unknown arg OFFLOAD_TARGET_DEFAULT=1 compilers: Checking arg Target: compilers: Unknown arg Target: compilers: Checking arg x86_64-linux-gnu compilers: Unknown arg x86_64-linux-gnu compilers: Checking arg Configured compilers: Unknown arg Configured compilers: Checking arg with: compilers: Unknown arg with: compilers: Checking arg ../src/configure compilers: Unknown arg ../src/configure compilers: Checking arg -v compilers: Unknown arg -v compilers: Checking arg --with-pkgversion= compilers: Unknown arg --with-pkgversion= compilers: Checking arg --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs compilers: Unknown arg --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs compilers: Checking arg --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ compilers: Unknown arg --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ compilers: Checking arg --prefix=/usr compilers: Unknown arg --prefix=/usr compilers: Checking arg --with-gcc-major-version-only compilers: Unknown arg --with-gcc-major-version-only compilers: Checking arg --program-suffix=-7 compilers: Unknown arg --program-suffix=-7 compilers: Checking arg --program-prefix=x86_64-linux-gnu- compilers: Unknown arg --program-prefix=x86_64-linux-gnu- compilers: Checking arg --enable-shared compilers: Unknown arg --enable-shared compilers: Checking arg --enable-linker-build-id compilers: Unknown arg --enable-linker-build-id compilers: Checking arg --libexecdir=/usr/lib compilers: Unknown arg --libexecdir=/usr/lib compilers: Checking arg --without-included-gettext compilers: Unknown arg --without-included-gettext compilers: Checking arg --enable-threads=posix compilers: Unknown arg --enable-threads=posix compilers: Checking arg --libdir=/usr/lib compilers: Unknown arg --libdir=/usr/lib compilers: Checking arg --enable-nls compilers: Unknown arg --enable-nls compilers: Checking arg --with-sysroot=/ compilers: Unknown arg --with-sysroot=/ compilers: Checking arg --enable-clocale=gnu compilers: Unknown arg --enable-clocale=gnu compilers: Checking arg --enable-libstdcxx-debug compilers: Unknown arg --enable-libstdcxx-debug compilers: Checking arg --enable-libstdcxx-time=yes compilers: Unknown arg --enable-libstdcxx-time=yes compilers: Checking arg --with-default-libstdcxx-abi=new compilers: Unknown arg --with-default-libstdcxx-abi=new compilers: Checking arg --enable-gnu-unique-object compilers: Unknown arg --enable-gnu-unique-object compilers: Checking arg --disable-vtable-verify compilers: Unknown arg --disable-vtable-verify compilers: Checking arg --enable-libmpx compilers: Unknown arg --enable-libmpx compilers: Checking arg --enable-plugin compilers: Unknown arg --enable-plugin compilers: Checking arg --enable-default-pie compilers: Unknown arg --enable-default-pie compilers: Checking arg --with-system-zlib compilers: Unknown arg --with-system-zlib compilers: Checking arg --with-target-system-zlib compilers: Unknown arg --with-target-system-zlib compilers: Checking arg --enable-objc-gc=auto compilers: Unknown arg --enable-objc-gc=auto compilers: Checking arg --enable-multiarch compilers: Unknown arg --enable-multiarch compilers: Checking arg --disable-werror compilers: Unknown arg --disable-werror compilers: Checking arg --with-arch-32=i686 compilers: Unknown arg --with-arch-32=i686 compilers: Checking arg --with-abi=m64 compilers: Unknown arg --with-abi=m64 compilers: Checking arg --with-multilib-list=m32,m64,mx32 compilers: Unknown arg --with-multilib-list=m32,m64,mx32 compilers: Checking arg --enable-multilib compilers: Unknown arg --enable-multilib compilers: Checking arg --with-tune=generic compilers: Unknown arg --with-tune=generic compilers: Checking arg --enable-offload-targets=nvptx-none compilers: Unknown arg --enable-offload-targets=nvptx-none compilers: Checking arg --without-cuda-driver compilers: Unknown arg --without-cuda-driver compilers: Checking arg --enable-checking=release compilers: Unknown arg --enable-checking=release compilers: Checking arg --build=x86_64-linux-gnu compilers: Unknown arg --build=x86_64-linux-gnu compilers: Checking arg --host=x86_64-linux-gnu compilers: Unknown arg --host=x86_64-linux-gnu compilers: Checking arg --target=x86_64-linux-gnu compilers: Unknown arg --target=x86_64-linux-gnu compilers: Checking arg Thread compilers: Unknown arg Thread compilers: Checking arg model: compilers: Unknown arg model: compilers: Checking arg posix compilers: Unknown arg posix compilers: Checking arg gcc compilers: Unknown arg gcc compilers: Checking arg version compilers: Unknown arg version compilers: Checking arg 7.4.0 compilers: Unknown arg 7.4.0 compilers: Checking arg (Ubuntu compilers: Unknown arg (Ubuntu compilers: Checking arg 7.4.0-1ubuntu1~18.04.1) compilers: Unknown arg 7.4.0-1ubuntu1~18.04.1) compilers: Checking arg Reading compilers: Unknown arg Reading compilers: Checking arg specs compilers: Unknown arg specs compilers: Checking arg from compilers: Unknown arg from compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/libgfortran.spec compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/libgfortran.spec compilers: Checking arg rename compilers: Unknown arg rename compilers: Checking arg spec compilers: Unknown arg spec compilers: Checking arg lib compilers: Unknown arg lib compilers: Checking arg to compilers: Unknown arg to compilers: Checking arg liborig compilers: Unknown arg liborig compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/ compilers: Skipping arg COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/ compilers: Checking arg LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../:/lib/:/usr/lib/ compilers: Skipping arg LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/7/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/7/../../../:/lib/:/usr/lib/ compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/collect2 compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/collect2 compilers: Checking arg -plugin compilers: Unknown arg -plugin compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/liblto_plugin.so compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/liblto_plugin.so compilers: Checking arg -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper compilers: Unknown arg -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper compilers: Checking arg -plugin-opt=-fresolution=/tmp/ccVlXOZe.res compilers: Unknown arg -plugin-opt=-fresolution=/tmp/ccVlXOZe.res compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg -plugin-opt=-pass-through=-lquadmath compilers: Unknown arg -plugin-opt=-pass-through=-lquadmath compilers: Checking arg -plugin-opt=-pass-through=-lm compilers: Unknown arg -plugin-opt=-pass-through=-lm compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg -plugin-opt=-pass-through=-lpthread compilers: Unknown arg -plugin-opt=-pass-through=-lpthread compilers: Checking arg -plugin-opt=-pass-through=-lc compilers: Unknown arg -plugin-opt=-pass-through=-lc compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg --sysroot=/ compilers: Unknown arg --sysroot=/ compilers: Checking arg --build-id compilers: Unknown arg --build-id compilers: Checking arg --eh-frame-hdr compilers: Unknown arg --eh-frame-hdr compilers: Checking arg -m compilers: Unknown arg -m compilers: Checking arg elf_x86_64 compilers: Unknown arg elf_x86_64 compilers: Checking arg --hash-style=gnu compilers: Unknown arg --hash-style=gnu compilers: Checking arg --as-needed compilers: Unknown arg --as-needed compilers: Checking arg -dynamic-linker compilers: Unknown arg -dynamic-linker compilers: Checking arg /lib64/ld-linux-x86-64.so.2 compilers: Unknown arg /lib64/ld-linux-x86-64.so.2 compilers: Checking arg -pie compilers: Unknown arg -pie compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg now compilers: Unknown arg now compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg relro compilers: Unknown arg relro compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-k0jR75/config.compilers/conftest compilers: Unknown arg /tmp/petsc-k0jR75/config.compilers/conftest compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/Scrt1.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/Scrt1.o compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/crti.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/crti.o compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/crtbeginS.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/crtbeginS.o compilers: Checking arg -L/usr//lib compilers: Checking arg -L/usr/lib/x86_64-linux-gnu/openmpi/lib compilers: Already in lflags so skipping: -L/usr/lib/x86_64-linux-gnu/openmpi/lib compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/7 compilers: Found library directory: -L/usr/lib/gcc/x86_64-linux-gnu/7 compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu compilers: Found library directory: -L/usr/lib/x86_64-linux-gnu compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib compilers: Checking arg -L/lib/x86_64-linux-gnu compilers: Found library directory: -L/lib/x86_64-linux-gnu compilers: Checking arg -L/lib/../lib compilers: Checking arg -L/usr/lib/x86_64-linux-gnu compilers: Already in lflags so skipping: -L/usr/lib/x86_64-linux-gnu compilers: Checking arg -L/usr/lib/../lib compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/7/../../.. compilers: Checking arg /tmp/petsc-k0jR75/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-k0jR75/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Already in lflags: -lstdc++ compilers: Checking arg -ldl compilers: Already in lflags: -ldl compilers: Checking arg -lmpi_usempif08 compilers: Already in lflags: -lmpi_usempif08 compilers: Checking arg -lmpi_usempi_ignore_tkr compilers: Already in lflags: -lmpi_usempi_ignore_tkr compilers: Checking arg -lmpi_mpifh compilers: Already in lflags: -lmpi_mpifh compilers: Checking arg -lmpi compilers: Already in lflags: -lmpi compilers: Checking arg -lgfortran compilers: Found library: -lgfortran compilers: Checking arg -lm compilers: Found library: -lm compilers: Checking arg -lgcc_s compilers: Found library: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lquadmath compilers: Found library: -lquadmath compilers: Checking arg -lm compilers: Already in lflags: -lm compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lpthread compilers: Found library: -lpthread compilers: Checking arg -lc compilers: Found system library therefore skipping: -lc compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/crtendS.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/crtendS.o compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/crtn.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/crtn.o compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Libraries needed to link Fortran code with the C linker: ['-lstdc++', '-ldl', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib', '-L/usr/lib/x86_64-linux-gnu/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/7', '-L/usr/lib/gcc/x86_64-linux-gnu/7', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] compilers: Libraries needed to link Fortran main with the C linker: [] compilers: Check that Fortran libraries can be used with C as the linker Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest compilers: Check that Fortran libraries can be used with C++ as linker compilers: Fortran libraries can be used from C++ Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.setCompilers/conftest ================================================================================ TEST checkFortranLinkingCxx from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:1328) TESTING: checkFortranLinkingCxx from config.compilers(config/BuildSystem/config/compilers.py:1328) Check that Fortran can link C++ libraries Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void foo(void){d1chk_();} Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void d1chk_(void){return;} Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilers/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilers/conftest.o /tmp/petsc-k0jR75/config.compilers/cxxobj.o /tmp/petsc-k0jR75/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran can link C++ functions ================================================================================ TEST setupFrameworkCompilers from config.compilers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilers.py:1473) TESTING: setupFrameworkCompilers from config.compilers(config/BuildSystem/config/compilers.py:1473) child config.compilers 5.014990 ================================================================================ TEST configureClosure from config.utilities.closure(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/closure.py:17) TESTING: configureClosure from config.utilities.closure(config/BuildSystem/config/utilities/closure.py:17) Determine if Apple ^close syntax is supported in C All intermediate test results are stored in /tmp/petsc-k0jR75/config.utilities.closure Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.closure/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.utilities.closure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.closure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.utilities.closure/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.utilities.closure/conftest.c:6:6: error: expected identifier or ‘(’ before ‘^’ token int (^closure)(int);; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int (^closure)(int);; return 0; } Compile failed inside link child config.utilities.closure 0.043478 ================================================================================ TEST checkFortranTypeSizes from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:56) TESTING: checkFortranTypeSizes from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:56) Check whether real*8 is supported and suggest flags which will allow support All intermediate test results are stored in /tmp/petsc-k0jR75/config.compilersFortran Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90:2:21: real*8 variable 1 Warning: Unused variable ‘variable’ declared at (1) [-Wunused-variable] Source: program main real*8 variable end ================================================================================ TEST checkFortranPreprocessor from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:73) TESTING: checkFortranPreprocessor from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:73) Determine if Fortran handles preprocessing properly Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef dummy fooey #endif end compilers: Fortran uses preprocessor ================================================================================ TEST checkFortranDefineCompilerOption from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:96) TESTING: checkFortranDefineCompilerOption from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:96) Check if -WF,-Dfoobar or -Dfoobar is the compiler option to define a macro Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native -DTesting /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef Testing fooey #endif end Defined make macro "FC_DEFINE_FLAG" to "-D" compilers: Fortran uses -D for defining macro ================================================================================ TEST checkFortran90 from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:146) TESTING: checkFortran90 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:146) Determine whether the Fortran compiler handles F90 Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90:3:43: REAL(KIND=SELECTED_REAL_KIND(10)) d 1 Warning: Unused variable ‘d’ declared at (1) [-Wunused-variable] Source: program main REAL(KIND=SELECTED_REAL_KIND(10)) d INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8) INTEGER (KIND=int) :: ierr ierr = 1 end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -lstdc++ -ldl Fortran compiler supports F90 ================================================================================ TEST checkFortran90FreeForm from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:162) TESTING: checkFortran90FreeForm from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:162) Determine whether the Fortran compiler handles F90FreeForm We also require that the compiler handles lines longer than 132 characters Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8); INTEGER (KIND=int) :: ierr; ierr = 1 end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F90FREEFORM" to "1" Fortran compiler supports F90FreeForm ================================================================================ TEST checkFortran2003 from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:176) TESTING: checkFortran2003 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:176) Determine whether the Fortran compiler handles F2003 Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: module Base_module type, public :: base_type integer :: A contains procedure, public :: Print => BasePrint end type base_type contains subroutine BasePrint(this) class(base_type) :: this end subroutine BasePrint end module Base_module program main use,intrinsic :: iso_c_binding Type(C_Ptr),Dimension(:),Pointer :: CArray character(kind=c_char),pointer :: nullc => null() character(kind=c_char,len=5),dimension(:),pointer::list1 allocate(list1(5)) CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F2003" to "1" Fortran compiler supports F2003 ================================================================================ TEST checkFortran90Array from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:211) TESTING: checkFortran90Array from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:211) Check for F90 array interfaces Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void f90arraytest_(void* a1, void* a2,void* a3, void* i) { printf("arrays [%p %p %p]\n",a1,a2,a3); fflush(stdout); return; } void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void* p2, void* p3) { printf("arrays [%p %p %p]\n",a1,a2,a3); if ((p1 == p3) && (p1 != p2)) { printf("pointers match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); } else { printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); exit(111); } return; } Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: program main Interface Subroutine f90ptrtest(p1,p2,p3,i) integer, pointer :: p1(:,:) integer, pointer :: p2(:,:) integer, pointer :: p3(:,:) integer i End Subroutine End Interface integer, pointer :: ptr1(:,:),ptr2(:,:) integer, target :: array(6:8,9:21) integer in in = 25 ptr1 => array ptr2 => array call f90arraytest(ptr1,ptr2,ptr1,in) call f90ptrtest(ptr1,ptr2,ptr1,in) end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.o /tmp/petsc-k0jR75/config.compilersFortran/fooobj.o -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.compilersFortran/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.compilersFortran/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.compilersFortran/conftest stdout: arrays [0x7ffcfdc93820 0x7ffcfdc93820 0x7ffcfdc93820] arrays [0x7ffcfdc93740 0x7ffcfdc937c0 0x7ffcfdc93740] pointers do not match! [0x7f2e6d04a8c0 (nil)] [0x7f2e6d829740] ERROR while running executable: Could not execute "['/tmp/petsc-k0jR75/config.compilersFortran/conftest']": arrays [0x7ffcfdc93820 0x7ffcfdc93820 0x7ffcfdc93820] arrays [0x7ffcfdc93740 0x7ffcfdc937c0 0x7ffcfdc93740] pointers do not match! [0x7f2e6d04a8c0 (nil)] [0x7f2e6d829740] compilers: F90 uses a single argument for array pointers ================================================================================ TEST checkFortran90AssumedType from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:298) TESTING: checkFortran90AssumedType from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:298) Running Executable WITHOUT threads to time it out Executing: mpif90 -qversion ================================================================================ TEST checkFortranModuleInclude from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:303) TESTING: checkFortranModuleInclude from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:303) Figures out what flag is used to specify the include path for Fortran modules Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: program main use configtest write(*,*) testint end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilersFortran/conftest -I/tmp/petsc-k0jR75/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.o /tmp/petsc-k0jR75/config.compilersFortran/configtest.o -lstdc++ -ldl compilers: Fortran module include flag -I found ================================================================================ TEST checkFortranModuleOutput from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:369) TESTING: checkFortranModuleOutput from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:369) Figures out what flag is used to specify the include path for Fortran modules Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -module /tmp/petsc-k0jR75/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ‘-module’; did you mean ‘-mhle’? Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module compile failed Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -module:/tmp/petsc-k0jR75/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ‘-module:/tmp/petsc-k0jR75/config.compilersFortran/confdir’ Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module: compile failed Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fmod=/tmp/petsc-k0jR75/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ‘-fmod=/tmp/petsc-k0jR75/config.compilersFortran/confdir’ Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -fmod= compile failed Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -J/tmp/petsc-k0jR75/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -J found ================================================================================ TEST checkFortranTypeStar from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:135) TESTING: checkFortranTypeStar from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:135) Determine whether the Fortran compiler handles type(*) Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: program main interface subroutine a(b) type(*) :: b(:) end subroutine end interface end Defined "HAVE_FORTRAN_TYPE_STAR" to "1" Fortran compiler supports type(*) ================================================================================ TEST checkFortranTypeInitialize from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:125) TESTING: checkFortranTypeInitialize from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:125) Determines if PETSc objects in Fortran are initialized by default (doesn't work with common blocks) Defined "FORTRAN_TYPE_INITIALIZE" to " = -2" Initializing Fortran objects ================================================================================ TEST configureFortranFlush from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:116) TESTING: configureFortranFlush from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:116) Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.F90 Successful compile: Source: program main call flush(6) end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_FLUSH" to "1" ================================================================================ TEST checkDependencyGenerationFlag from config.compilersFortran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:414) TESTING: checkDependencyGenerationFlag from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:414) Check if -MMD works for dependency generation, and add it if it does Trying FC compiler flag -MMD -MP Defined make macro "FC_DEPFLAGS" to "-MMD -MP" Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.setCompilers/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native -MMD -MP /tmp/petsc-k0jR75/config.setCompilers/conftest.F90 Successful compile: Source: program main end child config.compilersFortran 1.403914 ================================================================================ TEST checkStdC from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:105) TESTING: checkStdC from config.headers(config/BuildSystem/config/headers.py:105) Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.headers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.headers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #define ISLOWER(c) ('a' <= (c) && (c) <= 'z') #define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main() { int i; for(i = 0; i < 256; i++) if (XOR(islower(i), ISLOWER(i)) || toupper(i) != TOUPPER(i)) exit(2); exit(0); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.headers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.headers/conftest.o -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.headers/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.headers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.headers/conftest ================================================================================ TEST checkStat from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:138) TESTING: checkStat from config.headers(config/BuildSystem/config/headers.py:138) Checks whether stat file-mode macros are broken, and defines STAT_MACROS_BROKEN if they are Preprocessing source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(S_ISBLK) && defined(S_IFDIR) # if S_ISBLK (S_IFDIR) You lose. # endif #endif #if defined(S_ISBLK) && defined(S_IFCHR) # if S_ISBLK (S_IFCHR) You lose. # endif #endif #if defined(S_ISLNK) && defined(S_IFREG) # if S_ISLNK (S_IFREG) You lose. # endif #endif #if defined(S_ISSOCK) && defined(S_IFREG) # if S_ISSOCK (S_IFREG) You lose. # endif #endif Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c ================================================================================ TEST checkSysWait from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:173) TESTING: checkSysWait from config.headers(config/BuildSystem/config/headers.py:173) Check for POSIX.1 compatible sys/wait.h, and defines HAVE_SYS_WAIT_H if found Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.headers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #ifndef WEXITSTATUS #define WEXITSTATUS(stat_val) ((unsigned)(stat_val) >> 8) #endif #ifndef WIFEXITED #define WIFEXITED(stat_val) (((stat_val) & 255) == 0) #endif int main() { int s; wait (&s); s = WIFEXITED (s) ? WEXITSTATUS (s) : 1; ; return 0; } Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST checkTime from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:195) TESTING: checkTime from config.headers(config/BuildSystem/config/headers.py:195) Checks if you can safely include both and , and if so defines TIME_WITH_SYS_TIME Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" Checking for header: sys/time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIME_H" to "1" ================================================================================ TEST checkMath from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:201) TESTING: checkMath from config.headers(config/BuildSystem/config/headers.py:201) Checks for the math headers and defines Checking for header: math.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.headers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double pi = M_PI; if (pi); ; return 0; } Found math #defines, like M_PI ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST checkRecursiveMacros from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:216) TESTING: checkRecursiveMacros from config.headers(config/BuildSystem/config/headers.py:216) Checks that the preprocessor allows recursive macros, and if not defines HAVE_BROKEN_RECURSIVE_MACRO Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.headers/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void a(int i, int j) {} #define a(b) a(b,__LINE__) int main() { a(0); ; return 0; } child config.headers 2.657714 ================================================================================ TEST configureCacheDetails from config.utilities.cacheDetails(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/cacheDetails.py:78) TESTING: configureCacheDetails from config.utilities.cacheDetails(config/BuildSystem/config/utilities/cacheDetails.py:78) Try to determine the size and associativity of the cache. All intermediate test results are stored in /tmp/petsc-k0jR75/config.utilities.cacheDetails Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { FILE *output = fopen("conftestval","w"); if (!output) return 1; fprintf(output,"%ld",getconf_LEVEL1_DCACHE_LINESIZE()); fclose(output);; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest.o -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest to see if it can be run Executing: /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-k0jR75/config.utilities.cacheDetails/conftest Defined "LEVEL1_DCACHE_LINESIZE" to "64" child config.utilities.cacheDetails 0.203807 ================================================================================ TEST check_struct_sigaction from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:43) TESTING: check_struct_sigaction from config.types(config/BuildSystem/config/types.py:43) Checks if "struct sigaction" exists in signal.h. This check is for C89 check. Checking for type: struct sigaction All intermediate test results are stored in /tmp/petsc-k0jR75/config.types Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:11:18: warning: unused variable ‘a’ [-Wunused-variable] struct sigaction a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { struct sigaction a;; return 0; } struct sigaction found Defined "HAVE_STRUCT_SIGACTION" to "1" ================================================================================ TEST check__int64 from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:49) TESTING: check__int64 from config.types(config/BuildSystem/config/types.py:49) Checks if __int64 exists. This is primarily for windows. Checking for type: __int64 Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:11:1: error: unknown type name ‘__int64’; did you mean ‘__int64_t’? __int64 a;; ^~~~~~~ __int64_t /tmp/petsc-k0jR75/config.types/conftest.c:11:9: warning: unused variable ‘a’ [-Wunused-variable] __int64 a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { __int64 a;; return 0; } __int64 found ================================================================================ TEST checkSizeTypes from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:55) TESTING: checkSizeTypes from config.types(config/BuildSystem/config/types.py:55) Checks for types associated with sizes, such as size_t. Checking for type: size_t Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:11:8: warning: unused variable ‘a’ [-Wunused-variable] size_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { size_t a;; return 0; } size_t found ================================================================================ TEST checkFileTypes from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:65) TESTING: checkFileTypes from config.types(config/BuildSystem/config/types.py:65) Checks for types associated with files, such as mode_t, off_t, etc. Checking for type: mode_t Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:11:8: warning: unused variable ‘a’ [-Wunused-variable] mode_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { mode_t a;; return 0; } mode_t found Checking for type: off_t Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:11:7: warning: unused variable ‘a’ [-Wunused-variable] off_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { off_t a;; return 0; } off_t found ================================================================================ TEST checkIntegerTypes from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:60) TESTING: checkIntegerTypes from config.types(config/BuildSystem/config/types.py:60) Checks for types associated with integers, such as int32_t. Checking for type: int32_t Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:11:9: warning: unused variable ‘a’ [-Wunused-variable] int32_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { int32_t a;; return 0; } int32_t found ================================================================================ TEST checkPID from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:71) TESTING: checkPID from config.types(config/BuildSystem/config/types.py:71) Checks for pid_t, and defines it if necessary Checking for type: pid_t Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:11:7: warning: unused variable ‘a’ [-Wunused-variable] pid_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { pid_t a;; return 0; } pid_t found ================================================================================ TEST checkUID from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:75) TESTING: checkUID from config.types(config/BuildSystem/config/types.py:75) Checks for uid_t and gid_t, and defines them if necessary Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.types/conftest.c ================================================================================ TEST checkC99Complex from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:82) TESTING: checkC99Complex from config.types(config/BuildSystem/config/types.py:82) Check for complex numbers in in C99 std Note that since PETSc source code uses _Complex we test specifically for that, not complex Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:6:17: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] double _Complex x; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:6:17: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] double _Complex x; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.types/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_C99_COMPLEX" to "1" ================================================================================ TEST checkCxxComplex from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:93) TESTING: checkCxxComplex from config.types(config/BuildSystem/config/types.py:93) Check for complex numbers in namespace std Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { std::complex x; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.types/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_CXX_COMPLEX" to "1" ================================================================================ TEST checkConst from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:104) TESTING: checkConst from config.types(config/BuildSystem/config/types.py:104) Checks for working const, and if not found defines it to empty string Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.types/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.types/conftest.c:25:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (x[0]); ^~ /tmp/petsc-k0jR75/config.types/conftest.c:26:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ { /* SCO 3.2v4 cc rejects this. */ ^ /tmp/petsc-k0jR75/config.types/conftest.c:25:10: warning: ‘x[0]’ is used uninitialized in this function [-Wuninitialized] if (x[0]); ~^~~ /tmp/petsc-k0jR75/config.types/conftest.c:30:9: warning: ‘t’ is used uninitialized in this function [-Wuninitialized] *t++ = 0; ~^~ /tmp/petsc-k0jR75/config.types/conftest.c:46:25: warning: ‘b’ is used uninitialized in this function [-Wuninitialized] struct s *b; b->j = 5; ~~~~~^~~ Source: #include "confdefs.h" #include "conffix.h" int main() { /* Ultrix mips cc rejects this. */ typedef int charset[2]; const charset x; /* SunOS 4.1.1 cc rejects this. */ char const *const *ccp; char **p; /* NEC SVR4.0.2 mips cc rejects this. */ struct point {int x, y;}; static struct point const zero = {0,0}; /* AIX XL C 1.02.0.0 rejects this. It does not let you subtract one const X* pointer from another in an arm of an if-expression whose if-part is not a constant expression */ const char *g = "string"; ccp = &g + (g ? g-g : 0); /* HPUX 7.0 cc rejects these. */ ++ccp; p = (char**) ccp; ccp = (char const *const *) p; /* This section avoids unused variable warnings */ if (zero.x); if (x[0]); { /* SCO 3.2v4 cc rejects this. */ char *t; char const *s = 0 ? (char *) 0 : (char const *) 0; *t++ = 0; if (*s); } { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ int x[] = {25, 17}; const int *foo = &x[0]; ++foo; } { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ typedef const int *iptr; iptr p = 0; ++p; } { /* AIX XL C 1.02.0.0 rejects this saying "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ struct s { int j; const int *ap[3]; }; struct s *b; b->j = 5; } { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ const int foo = 10; /* Get rid of unused variable warning */ if (foo); } ; return 0; } ================================================================================ TEST checkSizeof from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:160) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:160) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: short Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(short)==2)*2-1]; Defined "SIZEOF_SHORT" to "2" ================================================================================ TEST checkSizeof from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:160) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:160) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: int Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(int)==4)*2-1]; Defined "SIZEOF_INT" to "4" ================================================================================ TEST checkSizeof from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:160) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:160) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: enum Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(enum{ENUM_DUMMY})==4)*2-1]; Defined "SIZEOF_ENUM" to "4" ================================================================================ TEST checkSizeof from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:160) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:160) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long)==8)*2-1]; Defined "SIZEOF_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:160) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:160) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: void * Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(void *)==8)*2-1]; Defined "SIZEOF_VOID_P" to "8" ================================================================================ TEST checkSizeof from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:160) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:160) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long long Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long long)==8)*2-1]; Defined "SIZEOF_LONG_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:160) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:160) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: size_t Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(size_t)==8)*2-1]; Defined "SIZEOF_SIZE_T" to "8" ================================================================================ TEST checkVisibility from config.types(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/types.py:194) TESTING: checkVisibility from config.types(config/BuildSystem/config/types.py:194) Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_C" to "1" Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.types/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_CXX" to "1" child config.types 1.666951 ================================================================================ TEST configureMemAlign from PETSc.options.memAlign(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/memAlign.py:29) TESTING: configureMemAlign from PETSc.options.memAlign(config/PETSc/options/memAlign.py:29) Choose alignment Defined "MEMALIGN" to "16" Memory alignment is 16 child PETSc.options.memAlign 0.000991 ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST checkMath from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:264) TESTING: checkMath from config.libraries(config/BuildSystem/config/libraries.py:264) Check for sin() in libm, the math library Checking for functions [sin floor log10 pow] in library [''] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_sin’: /tmp/petsc-k0jR75/config.libraries/conftest.c:6:40: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ^~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_floor’: /tmp/petsc-k0jR75/config.libraries/conftest.c:10:42: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ^~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_log10’: /tmp/petsc-k0jR75/config.libraries/conftest.c:14:42: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ^~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_pow’: /tmp/petsc-k0jR75/config.libraries/conftest.c:18:40: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ^~~~~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x22): undefined reference to `sin' conftest.c:(.text.startup+0x88): undefined reference to `log10' conftest.c:(.text.startup+0xbe): undefined reference to `pow' collect2: error: ld returned 1 exit status Checking for functions [sin floor log10 pow] in library ['m'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_sin’: /tmp/petsc-k0jR75/config.libraries/conftest.c:6:40: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ^~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_floor’: /tmp/petsc-k0jR75/config.libraries/conftest.c:10:42: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ^~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_log10’: /tmp/petsc-k0jR75/config.libraries/conftest.c:14:42: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ^~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_pow’: /tmp/petsc-k0jR75/config.libraries/conftest.c:18:40: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ^~~~~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" CheckMath: using math library ['libm.a'] ================================================================================ TEST checkMathErf from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:283) TESTING: checkMathErf from config.libraries(config/BuildSystem/config/libraries.py:283) Check for erf() in libm, the math library Checking for functions [erf] in library ['libm.a'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_erf’: /tmp/petsc-k0jR75/config.libraries/conftest.c:5:74: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } int main() { _check_erf();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" erf() found Defined "HAVE_ERF" to "1" ================================================================================ TEST checkMathTgamma from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:292) TESTING: checkMathTgamma from config.libraries(config/BuildSystem/config/libraries.py:292) Check for tgamma() in libm, the math library Checking for functions [tgamma] in library ['libm.a'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_tgamma’: /tmp/petsc-k0jR75/config.libraries/conftest.c:5:83: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } int main() { _check_tgamma();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" tgamma() found Defined "HAVE_TGAMMA" to "1" ================================================================================ TEST checkMathLgamma from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:301) TESTING: checkMathLgamma from config.libraries(config/BuildSystem/config/libraries.py:301) Check for lgamma() in libm, the math library Checking for functions [lgamma] in library ['libm.a'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include #include static void _check_lgamma() { double (*checkLgamma)(double) = lgamma;double x = 1,y; y = (*checkLgamma)(x);if (y != 0.) abort(); } int main() { _check_lgamma();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" lgamma() found Defined "HAVE_LGAMMA" to "1" ================================================================================ TEST checkMathFenv from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:314) TESTING: checkMathFenv from config.libraries(config/BuildSystem/config/libraries.py:314) Checks if can be used with FE_DFL_ENV Checking for functions [fesetenv] in library ['libm.a'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_fesetenv() { fesetenv(FE_DFL_ENV);; } int main() { _check_fesetenv();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" Defined "HAVE_FENV_H" to "1" ================================================================================ TEST checkMathLog2 from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:322) TESTING: checkMathLog2 from config.libraries(config/BuildSystem/config/libraries.py:322) Check for log2() in libm, the math library Checking for functions [log2] in library ['libm.a'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_log2’: /tmp/petsc-k0jR75/config.libraries/conftest.c:5:81: warning: unused variable ‘y’ [-Wunused-variable] static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } int main() { _check_log2();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" log2() found Defined "HAVE_LOG2" to "1" ================================================================================ TEST checkRealtime from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:331) TESTING: checkRealtime from config.libraries(config/BuildSystem/config/libraries.py:331) Check for presence of clock_gettime() in realtime library (POSIX Realtime extensions) Checking for functions [clock_gettime] in library [''] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } int main() { _check_clock_gettime();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lstdc++ -ldl realtime functions are linked in by default ================================================================================ TEST checkDynamic from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:347) TESTING: checkDynamic from config.libraries(config/BuildSystem/config/libraries.py:347) Check for the header and libraries necessary for dynamic library manipulation Checking for functions [dlopen] in library ['dl'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } int main() { _check_dlopen();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -ldl -lstdc++ -ldl Defined "HAVE_LIBDL" to "1" Checking for header: dlfcn.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" child config.libraries 1.575436 ================================================================================ TEST configureLibraryOptions from PETSc.options.libraryOptions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/libraryOptions.py:37) TESTING: configureLibraryOptions from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:37) Sets PETSC_USE_DEBUG, PETSC_USE_INFO, PETSC_USE_LOG, PETSC_USE_CTABLE, PETSC_USE_FORTRAN_KERNELS, and PETSC_USE_AVX512_KERNELS Defined "USE_LOG" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -qversion Defined "USE_MALLOC_COALESCED" to "1" Defined "USE_INFO" to "1" Defined "USE_CTABLE" to "1" Defined "USE_BACKWARD_LOOP" to "1" **********Checking if running on BGL/IBM detected Checking for functions [bgl_perfctr_void] in library [''] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char bgl_perfctr_void(); static void _check_bgl_perfctr_void() { bgl_perfctr_void(); } int main() { _check_bgl_perfctr_void();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `bgl_perfctr_void' collect2: error: ld returned 1 exit status Checking for functions [ADIOI_BGL_Open] in library [''] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ADIOI_BGL_Open(); static void _check_ADIOI_BGL_Open() { ADIOI_BGL_Open(); } int main() { _check_ADIOI_BGL_Open();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `ADIOI_BGL_Open' collect2: error: ld returned 1 exit status *********BGL/IBM test failure Defined "USE_AVX512_KERNELS" to "1" Defined "Alignx(a,b)" to " " ================================================================================ TEST configureISColorValueType from PETSc.options.libraryOptions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/libraryOptions.py:95) TESTING: configureISColorValueType from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:95) Sets PETSC_IS_COLOR_VALUE_TYPE, MPIU_COLORING_VALUE, IS_COLORING_MAX required by ISColor Defined "MPIU_COLORING_VALUE" to "MPI_UNSIGNED_SHORT" Defined "IS_COLORING_MAX" to "USHRT_MAX" Defined "IS_COLOR_VALUE_TYPE" to "short" Defined "IS_COLOR_VALUE_TYPE_F" to "integer2" child PETSc.options.libraryOptions 0.257994 child config.atomics 0.000025 ================================================================================ TEST checkSysinfo from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:106) TESTING: checkSysinfo from config.functions(config/BuildSystem/config/functions.py:106) Check whether sysinfo takes three arguments, and if it does define HAVE_SYSINFO_3ARG Checking for functions [sysinfo] All intermediate test results are stored in /tmp/petsc-k0jR75/config.functions Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sysinfo(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sysinfo) || defined (__stub___sysinfo) sysinfo_will_always_fail_with_ENOSYS(); #else sysinfo(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SYSINFO" to "1" Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.c:9:4: error: #error "Cannot check sysinfo without special headers" # error "Cannot check sysinfo without special headers" ^~~~~ /tmp/petsc-k0jR75/config.functions/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.functions/conftest.c:13:30: warning: implicit declaration of function ‘sysinfo’ [-Wimplicit-function-declaration] char buf[10]; long count=10; sysinfo(1, buf, count); ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #ifdef HAVE_SYS_SYSINFO_H # include #elif defined(HAVE_SYS_SYSTEMINFO_H) # include #else # error "Cannot check sysinfo without special headers" #endif int main() { char buf[10]; long count=10; sysinfo(1, buf, count); ; return 0; } Compile failed inside link ================================================================================ TEST checkVPrintf from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:125) TESTING: checkVPrintf from config.functions(config/BuildSystem/config/functions.py:125) Checks whether vprintf requires a char * last argument, and if it does defines HAVE_VPRINTF_CHAR Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vprintf( "%d", Argp ); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVFPrintf from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:131) TESTING: checkVFPrintf from config.functions(config/BuildSystem/config/functions.py:131) Checks whether vfprintf requires a char * last argument, and if it does defines HAVE_VFPRINTF_CHAR Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vfprintf(stdout, "%d", Argp ); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVSNPrintf from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:137) TESTING: checkVSNPrintf from config.functions(config/BuildSystem/config/functions.py:137) Checks whether vsnprintf requires a char * last argument, and if it does defines HAVE_VSNPRINTF_CHAR Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp;char str[6]; vsnprintf(str,5, "%d", Argp ); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VSNPRINTF" to "1" ================================================================================ TEST checkNanosleep from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:167) TESTING: checkNanosleep from config.functions(config/BuildSystem/config/functions.py:167) Check for functional nanosleep() - as time.h behaves differently for different compiler flags - like -std=c89 Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { struct timespec tp; tp.tv_sec = 0; tp.tv_nsec = (long)(1e9); nanosleep(&tp,0); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_NANOSLEEP" to "1" ================================================================================ TEST checkMemmove from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:173) TESTING: checkMemmove from config.functions(config/BuildSystem/config/functions.py:173) Check for functional memmove() - as MS VC requires correct includes to for this test Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char c1[1], c2[1] = "c"; size_t n=1; memmove(c1,c2,n); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MEMMOVE" to "1" ================================================================================ TEST checkSignalHandlerType from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:143) TESTING: checkSignalHandlerType from config.functions(config/BuildSystem/config/functions.py:143) Checks the type of C++ signals handlers, and defines SIGNAL_CAST to the correct value Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.functions/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include static void myhandler(int sig) {} int main() { signal(SIGFPE,myhandler); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.functions/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "SIGNAL_CAST" to " " ================================================================================ TEST checkFreeReturnType from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:153) TESTING: checkFreeReturnType from config.functions(config/BuildSystem/config/functions.py:153) Checks whether free returns void or int, and defines HAVE_FREE_RETURN_INT Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.functions/conftest.c:6:25: error: void value not ignored as it ought to be int ierr; void *p; ierr = free(p); return 0; ^ /tmp/petsc-k0jR75/config.functions/conftest.c:6:5: warning: variable ‘ierr’ set but not used [-Wunused-but-set-variable] int ierr; void *p; ierr = free(p); return 0; ^~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ierr; void *p; ierr = free(p); return 0; ; return 0; } Compile failed inside link ================================================================================ TEST checkVariableArgumentLists from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:159) TESTING: checkVariableArgumentLists from config.functions(config/BuildSystem/config/functions.py:159) Checks whether the variable argument list functionality is working Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { va_list l1, l2; va_copy(l1, l2); return 0; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VA_COPY" to "1" ================================================================================ TEST checkClassify from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:85) TESTING: checkClassify from config.functions(config/BuildSystem/config/functions.py:85) Recursive decompose to rapidly classify functions as found or missing To confirm that a function is missing, we require a compile/link failure with only that function in a compilation unit. In contrast, we can confirm that many functions are present by compiling them all together in a large compilation unit. We optimistically compile everything together, then trim all functions that were named in the error message and bisect the result. The trimming is only an optimization to increase the likelihood of a big-batch compile succeeding; we do not rely on the compiler naming missing functions. Checking for functions [rand getdomainname _access snprintf realpath dlsym bzero _getcwd _pipe getwd uname _lseek sleep _sleep lseek usleep dlclose gethostname clock access _snprintf dlerror fork getpagesize sbreak memalign getcwd gethostbyname readlink _set_output_format PXFGETARG strcasecmp dlopen drand48 socket popen getrusage _mkdir time stricmp] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.functions/conftest.c:16:6: warning: conflicting types for built-in function ‘snprintf’ [-Wbuiltin-declaration-mismatch] char snprintf(); ^~~~~~~~ /tmp/petsc-k0jR75/config.functions/conftest.c:19:6: warning: conflicting types for built-in function ‘bzero’ [-Wbuiltin-declaration-mismatch] char bzero(); ^~~~~ /tmp/petsc-k0jR75/config.functions/conftest.c:35:6: warning: conflicting types for built-in function ‘fork’ [-Wbuiltin-declaration-mismatch] char fork(); ^~~~ /tmp/petsc-k0jR75/config.functions/conftest.c:44:6: warning: conflicting types for built-in function ‘strcasecmp’ [-Wbuiltin-declaration-mismatch] char strcasecmp(); ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char _access(); char snprintf(); char realpath(); char dlsym(); char bzero(); char _getcwd(); char _pipe(); char getwd(); char uname(); char _lseek(); char sleep(); char _sleep(); char lseek(); char usleep(); char dlclose(); char gethostname(); char clock(); char access(); char _snprintf(); char dlerror(); char fork(); char getpagesize(); char sbreak(); char memalign(); char getcwd(); char gethostbyname(); char readlink(); char _set_output_format(); char PXFGETARG(); char strcasecmp(); char dlopen(); char drand48(); char socket(); char popen(); char getrusage(); char _mkdir(); char time(); char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif #if defined (__stub__pipe) || defined (__stub____pipe) _pipe_will_always_fail_with_ENOSYS(); #else _pipe(); #endif #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x46): warning: the `getwd' function is dangerous and should not be used. conftest.c:(.text.startup+0x15): undefined reference to `_access' conftest.c:(.text.startup+0x38): undefined reference to `_getcwd' conftest.c:(.text.startup+0x3f): undefined reference to `_pipe' conftest.c:(.text.startup+0x54): undefined reference to `_lseek' conftest.c:(.text.startup+0x62): undefined reference to `_sleep' conftest.c:(.text.startup+0x93): undefined reference to `_snprintf' conftest.c:(.text.startup+0xaf): undefined reference to `sbreak' conftest.c:(.text.startup+0xd2): undefined reference to `_set_output_format' conftest.c:(.text.startup+0xd9): undefined reference to `PXFGETARG' conftest.c:(.text.startup+0x10a): undefined reference to `_mkdir' conftest.c:(.text.startup+0x118): undefined reference to `stricmp' collect2: error: ld returned 1 exit status Checking for functions [rand getdomainname realpath dlsym bzero uname usleep dlclose gethostname clock dlerror] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.functions/conftest.c:17:6: warning: conflicting types for built-in function ‘bzero’ [-Wbuiltin-declaration-mismatch] char bzero(); ^~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char realpath(); char dlsym(); char bzero(); char uname(); char usleep(); char dlclose(); char gethostname(); char clock(); char dlerror(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_RAND" to "1" Defined "HAVE_GETDOMAINNAME" to "1" Defined "HAVE_REALPATH" to "1" Defined "HAVE_DLSYM" to "1" Defined "HAVE_BZERO" to "1" Defined "HAVE_UNAME" to "1" Defined "HAVE_USLEEP" to "1" Defined "HAVE_DLCLOSE" to "1" Defined "HAVE_GETHOSTNAME" to "1" Defined "HAVE_CLOCK" to "1" Defined "HAVE_DLERROR" to "1" Checking for functions [fork getpagesize memalign gethostbyname readlink strcasecmp dlopen drand48 socket popen getrusage time] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.functions/conftest.c:13:6: warning: conflicting types for built-in function ‘fork’ [-Wbuiltin-declaration-mismatch] char fork(); ^~~~ /tmp/petsc-k0jR75/config.functions/conftest.c:18:6: warning: conflicting types for built-in function ‘strcasecmp’ [-Wbuiltin-declaration-mismatch] char strcasecmp(); ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char fork(); char getpagesize(); char memalign(); char gethostbyname(); char readlink(); char strcasecmp(); char dlopen(); char drand48(); char socket(); char popen(); char getrusage(); char time(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_FORK" to "1" Defined "HAVE_GETPAGESIZE" to "1" Defined "HAVE_MEMALIGN" to "1" Defined "HAVE_GETHOSTBYNAME" to "1" Defined "HAVE_READLINK" to "1" Defined "HAVE_STRCASECMP" to "1" Defined "HAVE_DLOPEN" to "1" Defined "HAVE_DRAND48" to "1" Defined "HAVE_SOCKET" to "1" Defined "HAVE_POPEN" to "1" Defined "HAVE_GETRUSAGE" to "1" Defined "HAVE_TIME" to "1" Checking for functions [_access] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_access' collect2: error: ld returned 1 exit status Checking for functions [snprintf] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.functions/conftest.c:13:6: warning: conflicting types for built-in function ‘snprintf’ [-Wbuiltin-declaration-mismatch] char snprintf(); ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SNPRINTF" to "1" Checking for functions [_getcwd] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_getcwd' collect2: error: ld returned 1 exit status Checking for functions [_pipe] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _pipe(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__pipe) || defined (__stub____pipe) _pipe_will_always_fail_with_ENOSYS(); #else _pipe(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_pipe' collect2: error: ld returned 1 exit status Checking for functions [getwd] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): warning: the `getwd' function is dangerous and should not be used. Defined "HAVE_GETWD" to "1" Checking for functions [_lseek] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_lseek' collect2: error: ld returned 1 exit status Checking for functions [sleep] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SLEEP" to "1" Checking for functions [_sleep] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_sleep' collect2: error: ld returned 1 exit status Checking for functions [lseek] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_LSEEK" to "1" Checking for functions [access] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_ACCESS" to "1" Checking for functions [_snprintf] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_snprintf' collect2: error: ld returned 1 exit status Checking for functions [sbreak] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sbreak(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `sbreak' collect2: error: ld returned 1 exit status Checking for functions [getcwd] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_GETCWD" to "1" Checking for functions [_set_output_format] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _set_output_format(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_set_output_format' collect2: error: ld returned 1 exit status Checking for functions [PXFGETARG] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char PXFGETARG(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `PXFGETARG' collect2: error: ld returned 1 exit status Checking for functions [_mkdir] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _mkdir(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_mkdir' collect2: error: ld returned 1 exit status Checking for functions [stricmp] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `stricmp' collect2: error: ld returned 1 exit status ================================================================================ TEST checkMmap from config.functions(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/functions.py:179) TESTING: checkMmap from config.functions(config/BuildSystem/config/functions.py:179) Check for functional mmap() to allocate shared memory and define HAVE_MMAP Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.functions/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { int fd; fd=open("/tmp/file",O_RDWR); mmap((void*)0,100,PROT_READ|PROT_WRITE,MAP_SHARED,fd,0); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MMAP" to "1" child config.functions 3.580269 ================================================================================ TEST configureMemorySize from config.utilities.getResidentSetSize(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/getResidentSetSize.py:31) TESTING: configureMemorySize from config.utilities.getResidentSetSize(config/BuildSystem/config/utilities/getResidentSetSize.py:31) Try to determine how to measure the memory usage Defined "USE_PROC_FOR_SIZE" to "1" Using /proc for PetscMemoryGetCurrentUsage() child config.utilities.getResidentSetSize 0.001423 ================================================================================ TEST configureFortranCommandLine from config.utilities.fortranCommandLine(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/fortranCommandLine.py:27) TESTING: configureFortranCommandLine from config.utilities.fortranCommandLine(config/BuildSystem/config/utilities/fortranCommandLine.py:27) Check for the mechanism to retrieve command line arguments in Fortran Checking for functions [] in library [''] [] Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.F90 Successful compile: Source: program main integer i character*(80) arg i = command_argument_count() call get_command_argument(i,arg) end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_GET_COMMAND_ARGUMENT" to "1" child config.utilities.fortranCommandLine 0.135944 ================================================================================ TEST configureFeatureTestMacros from config.utilities.featureTestMacros(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/featureTestMacros.py:13) TESTING: configureFeatureTestMacros from config.utilities.featureTestMacros(config/BuildSystem/config/utilities/featureTestMacros.py:13) Checks if certain feature test macros are support All intermediate test results are stored in /tmp/petsc-k0jR75/config.utilities.featureTestMacros Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.c:4:10: fatal error: sysctl.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #define _POSIX_C_SOURCE 200112L #include int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.c Possible ERROR while running compiler: stderr: In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33:0, from /usr/include/stdlib.h:25, from /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.c:4: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #define _BSD_SOURCE #include int main() { ; return 0; } Defined "_BSD_SOURCE" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _DEFAULT_SOURCE #include int main() { ; return 0; } Defined "_DEFAULT_SOURCE" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include int main() { cpu_set_t mset; CPU_ZERO(&mset);; return 0; } Defined "_GNU_SOURCE" to "1" child config.utilities.featureTestMacros 0.231159 ================================================================================ TEST configureMissingUtypeTypedefs from config.utilities.missing(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/missing.py:55) TESTING: configureMissingUtypeTypedefs from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:55) Checks if u_short is undefined All intermediate test results are stored in /tmp/petsc-k0jR75/config.utilities.missing Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.utilities.missing/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.utilities.missing/conftest.c:6:9: warning: unused variable ‘foo’ [-Wunused-variable] u_short foo; ^~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { u_short foo; ; return 0; } ================================================================================ TEST configureMissingFunctions from config.utilities.missing(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/missing.py:61) TESTING: configureMissingFunctions from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:61) Checks for SOCKETS ================================================================================ TEST configureMissingSignals from config.utilities.missing(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/missing.py:79) TESTING: configureMissingSignals from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:79) Check for missing signals, and define MISSING_ if necessary Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGABRT; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGALRM; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGBUS; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCHLD; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCONT; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGFPE; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGHUP; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGILL; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGINT; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGKILL; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGPIPE; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGQUIT; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSEGV; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSTOP; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSYS; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTERM; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTRAP; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTSTP; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGURG; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR1; if (i); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR2; if (i); ; return 0; } ================================================================================ TEST configureMissingGetdomainnamePrototype from config.utilities.missing(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/missing.py:96) TESTING: configureMissingGetdomainnamePrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:96) Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -lstdc++ -ldl ================================================================================ TEST configureMissingSrandPrototype from config.utilities.missing(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/missing.py:121) TESTING: configureMissingSrandPrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:121) Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.utilities.missing/conftest.o -lstdc++ -ldl child config.utilities.missing 1.819047 ================================================================================ TEST configureFPTrap from config.utilities.FPTrap(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/utilities/FPTrap.py:27) TESTING: configureFPTrap from config.utilities.FPTrap(config/BuildSystem/config/utilities/FPTrap.py:27) Checking the handling of floating point traps Checking for header: sigfpe.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: Checking for header: fpxcp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~compilation terminated.: Checking for header: floatingpoint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conftest.c" # 1 "/tmp/petsc-k0jR75/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 # 1 "/tmp/petsc-k0jR75/config.headers/conffix.h" 1 # 3 "/tmp/petsc-k0jR75/config.headers/conftest.c" 2 stderr: /tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-k0jR75/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~compilation terminated.: child config.utilities.FPTrap 0.075544 ================================================================================ TEST configureScalarType from PETSc.options.scalarTypes(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/scalarTypes.py:40) TESTING: configureScalarType from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:40) Choose between real and complex numbers Scalar type is real All intermediate test results are stored in /tmp/petsc-k0jR75/PETSc.options.scalarTypes Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ‘a’ [-Wunused-variable] double b = 2.0; int a = isnormal(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnormal(b); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNORMAL" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ‘a’ [-Wunused-variable] double b = 2.0; int a = isnan(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnan(b); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNAN" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ‘a’ [-Wunused-variable] double b = 2.0; int a = isinf(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isinf(b); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISINF" to "1" ================================================================================ TEST configurePrecision from PETSc.options.scalarTypes(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/PETSc/options/scalarTypes.py:81) TESTING: configurePrecision from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:81) Set the default real number precision for PETSc objects Checking C compiler works with __float128 Checking for functions [logq] in library ['quadmath'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_logq’: /tmp/petsc-k0jR75/config.libraries/conftest.c:5:43: warning: ‘f’ is used uninitialized in this function [-Wuninitialized] static void _check_logq() { __float128 f; logq(f);; } ^~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c:5:40: note: ‘f’ was declared here static void _check_logq() { __float128 f; logq(f);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" C compiler with quadmath library Checking Fortran works with quadmath library Checking for functions [ ] in library ['quadmath'] [] Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.F90 Successful compile: Source: program main real*16 s,w; w = 2.0 ;s = cos(w) end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Fortran works with quadmath library Checking for functions [logq] in library ['quadmath'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.c: In function ‘_check_logq’: /tmp/petsc-k0jR75/config.libraries/conftest.c:5:43: warning: ‘f’ is used uninitialized in this function [-Wuninitialized] static void _check_logq() { __float128 f; logq(f);; } ^~~~~~~ /tmp/petsc-k0jR75/config.libraries/conftest.c:5:40: note: ‘f’ was declared here static void _check_logq() { __float128 f; logq(f);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Adding ['quadmath'] to LIBS Defined "HAVE_REAL___FLOAT128" to "1" Defined "USE_REAL_DOUBLE" to "1" Defined make macro "PETSC_SCALAR_SIZE" to "64" Precision is double child PETSc.options.scalarTypes 0.772335 ================================================================================ TEST configureMkdir from config.programs(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/programs.py:22) TESTING: configureMkdir from config.programs(config/BuildSystem/config/programs.py:22) Make sure we can have mkdir automatically make intermediate directories Checking for program /home/santiago/usr/local/bin/mkdir...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mkdir...not found Checking for program /usr/local/sbin/mkdir...not found Checking for program /usr/local/bin/mkdir...not found Checking for program /usr/sbin/mkdir...not found Checking for program /usr/bin/mkdir...not found Checking for program /sbin/mkdir...not found Checking for program /bin/mkdir...found Running Executable WITHOUT threads to time it out Executing: /bin/mkdir -p .conftest/tmp Adding -p flag to /bin/mkdir -p to automatically create directories Defined make macro "MKDIR" to "/bin/mkdir -p" ================================================================================ TEST configureAutoreconf from config.programs(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/programs.py:44) TESTING: configureAutoreconf from config.programs(config/BuildSystem/config/programs.py:44) Check for autoreconf Checking for program /home/santiago/usr/local/bin/autoreconf...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/autoreconf...not found Checking for program /usr/local/sbin/autoreconf...not found Checking for program /usr/local/bin/autoreconf...not found Checking for program /usr/sbin/autoreconf...not found Checking for program /usr/bin/autoreconf...not found Checking for program /sbin/autoreconf...not found Checking for program /bin/autoreconf...not found Checking for program /usr/games/autoreconf...not found Checking for program /usr/local/games/autoreconf...not found Checking for program /snap/bin/autoreconf...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/autoreconf...not found Unable to find programs ['autoreconf'] providing listing of each search directory to help debug Path provided in Python program Path provided by default path ['adiforfix.py', 'petsc_conf.py', 'petscnagupgrade.py', 'win32fe', 'petscdiff', 'petsc-mpiexec.uni', 'configVars.py', 'PetscBinaryIO.py', 'petsclogformat.py', 'PetscBinaryIOTrajectory.py', 'FASTMathInstaller.py', 'parseargs.py', 'petsc_gen_xdmf.py', 'PetscBinaryIO_tests.py', 'update.py', 'petscnagupgrade.pyc', 'popup', 'petscmpiexec', 'TOPSGenerator.py', 'saws', 'sendToJenkins', 'portabilitycheck.py', 'uncrustify.cfg', 'taucc.py'] ['cat_range_funcs.sh~', 'zip_postproc_yfrac.sh', 'nano', 'rsync_sh.zip', 'utils', 'test_diff.sh', 'set_file_datetime.sh', 'rsync_yfracrun_filelist_base.dat', 'nproc-alt.sh', 'linux_signing_key.pub', 'rsync_yfraccode_filelist_base.dat', 'homedir_generic', 'rsync_bkp_all_msys.sh', 'remove_odd_steps_explicit.sh', 'ubuntu-rdp', 'automated_email', 'rsync_yfracrun_funcs.sh', 'ncpus.sh', 'diffmult.sh', 'unset_proxy.sh', 'ls_dirs.sh', 'rsync_bkp_all.sh', 'au_946492_backspace-doesnt-work-inside-running-bash-script.sh', 'cat_range_funcs.sh', 'img_resize_batch.sh', 'kdeui_shortcuts_print_example.pdf', 'manage_path.sh', 'useful_commands.txt', 'gcc', 'remove_odd_steps.sh', 'zip_yfraccode.sh', 'du1sort.sh', 'split_string_funcs.sh', 'zip_run.sh', 'rsync_utils_msys.sh', 'zip_gmsh_yfrac.sh', 'xlsfonts.dat', 'rsync_delete.sh~', 'double_boot_grub', 'sensors.sh', 'bash_completion.txt', 'rsync_yfracrun.sh', 'echo_command.sh', 'll_dirs.sh', 'rsync_delete.sh', 'rsync_utils.sh', 'utils2017-12.zip', 'apt-get.txt', 'set_proxy.sh', 'rt.bashrc', 'gzip_run.sh', 'rsync_yfraccode_funcs.sh', 'rsync_yfraccode.sh', 'zip_utils.sh', 'inputrc', 'os_distro_funcs.sh', '.directory', 'rm_fast.sh'] [] [] ['apparmor_status', 'pppoe-discovery', 'irqbalance', 'update-default-aspell', 'newusers', 'filefrag', 'update-texmf', 'nfnl_osf', 'ufw', 'add-shell', 'ownership', 'usbmuxd', 'update-passwd', 'chroot', 'rtcwake', 'rtkitctl', 'aptd', 'ippserver', 'biosdecode', 'cups-browsed', 'popcon-largest-unused', 'NetworkManager', 'userdel', 'reject', 'lpc', 'update-dictcommon-hunspell', 'pptp', 'invoke-rc.d', 'genl', 'service', 'grpconv', 'gensprep', 'select-default-wordlist', 'chpasswd', 'avahi-daemon', 'update-dictcommon-aspell', 'grub-set-default', 'update-language-lua', 'update-info-dir', 'update-fmtutil', 'iucode_tool', 'grub-mkdevicemap', 'grpck', 'cppw', 'mklost+found', 'grpunconv', 'lpadmin', 'iio-sensor-proxy', 'create-cracklib-dict', 'groupmems', 'tzconfig', 'spice-vdagentd', 'getweb', 'delgroup', 'usb_modeswitch_dispatcher', 'update-texmf-config', 'aa-remove-unknown', 'iucode-tool', 'update-mime', 'genccode', 'e2freefrag', 'addgroup', 'upgrade-from-grub-legacy', 'update-tl-stacked-conffile', 'lpmove', 'rmt-tar', 'gdm3', 'select-default-ispell', 'escapesrc', 'gencmn', 'grub-bios-setup', 'e4crypt', 'cracklib-packer', 'pwconv', 'lpinfo', 'chat', 'arpd', 'chmem', 'pppoeconf', 'popularity-contest', 'alsa-info', 'make-ssl-cert', 'update-updmap', 'uuidd', 'irqbalance-ui', 'ippusbxd', 'cupsd', 'ispell-autobuildhash', 'alsabat-test', 'dmidecode', 'locale-gen', 'sshd', 'update-java-alternatives', 'pam_timestamp_check', 'cpgr', 'applygnupgdefaults', 'cupsreject', 'cron', 'gconf-schemas', 'update-icon-caches', 'pppstats', 'cupsenable', 'pam_getenv', 'remove-shell', 'vigr', 'usb_modeswitch', 'dpkg-preconfigure', 'cupsaddsmb', 'vpddecode', 'alsactl', 'rmt', 'update-fonts-scale', 'update-pciids', 'pppconfig', 'ModemManager', 'visudo', 'fdformat', 'cupsaccept', 'update-language-def', 'remove-default-ispell', 'rsyslogd', 'e4defrag', 'adduser', 'rfkill', 'update-fonts-alias', 'update-ca-certificates', 'netplan', 'update-default-ispell', 'grub-macbless', 'xrdp', 'cracklib-format', 'acpid', 'bluetoothd', 'nologin', 'cupsctl', 'chgpasswd', 'thermald', 'update-locale', 'readprofile', 'groupdel', 'update-initramfs', 'avahi-autoipd', 'groupadd', 'zic', 'groupmod', 'gennorm2', 'tarcat', 'cracklib-check', 'remove-default-wordlist', 'dpkg-reconfigure', 'logrotate', 'libgvc6-config-update', 'icupkg', 'grub-install', 'pam-auth-update', 'pppd', 'update-fonts-dir', 'xrdp-chansrv', 'useradd', 'paperconfig', 'arp', 'aa-status', 'pptpsetup', 'kerneloops', 'ldattach', 'pppdump', 'cracklib-unpacker', 'iptables-apply', 'vcstime', 'update-usbids', 'update-inetd', 'update-grub2', 'grub-mkconfig', 'cupsfilter', 'addgnupghome', 'setvesablank', 'grub-probe', 'anacron', 'update-grub', 'update-rc.d', 'xrdp-sesman', 'ip6tables-apply', 'update-cracklib', 'pwunconv', 'accessdb', 'update-default-wordlist', 'deluser', 'validlocale', 'cups-genppdupdate', 'grub-reboot', 'iconvconfig', 'update-language-dat', 'saned', 'tcpdump', 'mkinitramfs', 'accept', 'aspell-autobuildhash', 'dnsmasq', 'update-gsfontmap', 'pwck', 'update-grub-gfxpayload', 'usermod', 'vipw', 'cupsdisable', 'gnome-menus-blacklist', 'update-language'] ['ico', 'glib-genmarshal', 'ppmcolors', 'dvipdf', 'ppmtopi1', 'shred', 'findhyph', 'locate', 'htop', 'compare-im6', 'xdg-email', 'savelog', 'envsubst', 'vtkHashSource-7.1', 'mren', 'nad2bin', 'word-list-compress', 'gpgparsemail', 'avahi-resolve-host-name', 'usb-creator-gtk', 'nm-applet', 'dh_autotools-dev_restoreconfig', 'gnome-keyring', 'pslatex', 'passwd', 'routel', 'ppmtoyuvsplit', 'kpsestat', 'cs2cs', 'xgettext', 'traceroute6', 'pnmalias', 'psnup', 'uniq', 'rstart', 'qmlviewer', 'sha512sum', 'qr', 'lsinitramfs', 'gpmetis', 'python3-config', 'automat-visualize3', 'weave', 'gcov-tool-7', 'eps2eps', 'aconnect', 'dpkg-vendor', 'xrdp-keygen', 'oclock', 'qdbusxml2cpp', 'aplaymidi', 'tangle', 'fi_strerror', 'dviinfox', 'leaftoppm', 'pnmtopng', 'apport-bug', 'luit', 'import-im6', 'pod2html', 'corelist', 'gnome-session', 'dviselect', 'sftp', 'xwud', 'de-macro', 'mesg', 'update-notifier', 'pdfxup', 'mandb', 'opl2ofm', 'mkmanifest', 'kernel-install', 'zipnote', 'pr', 'listings-ext', 'make', 'sessreg', 'elfedit', 'xinit', 'lintian', 'ppmtojpeg', 'laptop-detect', 'gvfs-monitor-file', 'gpg', 'tabs', 'dpkg-query', 'xkbvleds', 'makeconv', 'makedtx', 'ps2txt', 'update-perl-sax-parsers', 'kpsewhere', 'whoopsie-preferences', 'sputoppm', 'ntfsdecrypt', 'fc-query', 'pnmtopalm', 'texosquery', 'ppmtouil', 'vpe', 'lsb_release', 'py3versions', 'autoinst', 'pgmbentley', 'mpiexec.openmpi', 'tie', 'showkey', 'grub-glue-efi', 'ubuntu-core-launcher', 'gnome-software-editor', 'lzma', 'gnome-terminal.wrapper', 'aptdcon', 'pbmtowbmp', 'libtoolize', 'mcomp', 'qmlcachegen', 'ckeygen', 'gst-launch-1.0', 'x86_64-linux-gnu-gprof', 'neqn', 'hp-info', 'otangle', 'gpg-zip', 'ps2frag', 'mkocp', 'eject', 'ltxfileinfo', 'pnmflip', 'x86_64-linux-gnu-gcc-ar', 'foo2xqx-wrapper', 'update-desktop-database', 'mpiCC.openmpi', 'baobab', 'qmljs', 'dh_doxygen', 'trial', 'orca-dm-wrapper', 'pod2usage', 'iecset', 'pnmpsnr', 'gpic', 'httex', 'dvitodvi', 'fixcvsdiff', 'spd-conf', 'assistant', 'sudoreplay', 'x-www-browser', 'dpkg-name', 'toe', 'palmtopnm', 'gio', 'dbus-send', 'gsnd', 'patchwork', 'firefox', 'pgmtolispm', 'recode-sr-latin', 'pdf180', 'ndmetis', 'xfd', 'montage', 'vmstat', 'gcov-tool', 'transmission-gtk', 'free', 'import', 'rtstat', 'logname', 'pbibtex', 'pygettext', 'mbadblocks', 'odbcinst', 'dot_builtins', 'gvfs-open', 'apgbfm', 'cpack', 'lp', 'gdal-config', 'syslinux', 'lzegrep', 'pf2afm', 'pdffonts', 'x86_64-linux-gnu-ranlib', 'ppmtoyuv', 'dh_installtex', 'pnmtotiffcmyk', 'mogrify', 't1mac', 'bluetoothctl', 'pnmmontage', 'mawk', 'pnm2ppa', 'qmlimportscanner', 'cmp', 'x86_64', 'pbmtopsg3', 'cpp-7', 'ybmtopbm', 'mingle', 'mfluajit', 'sotruss', 'pdflatexpicscale', 'updatedb', 'ppmshift', 'wc', 'kpsexpand', 'xeyes', 'rename', 'gemtopnm', 'bsd-write', 'updvitype', 'x86_64-linux-gnu-ld', 'run-mailcap', 'cweave', 'pnmgamma', 'isovfy', 'hp-logcapture', 'proxy', 'pdftotext', 'pbmtoepson', 'mdir', 'pdfdetach', 'localc', 'uuidparse', 'fc-list', 'timeout', 'tsort', 'system-config-printer-applet', 'h5fc', 'tred', 'mapscrn', 'prezip', 'objdump', 'pkfix', 'gettext', 'dpkg-distaddfile', 'fc-cache', 'alsabat', 'ibus-daemon', 'h5pcc', 'teckit_compile', 'tgatoppm', 'xauth', 'mathspic', 'dc', 'pbmtomgr', 'mech-dump', 'ps2pdf', 'soelim', 'gcc-ar', 'odvitype', 'xwd', 'telnet.netkit', 'captoinfo', 'rpdfcrop', 'gcov', 'vtkParseOGLExt-7.1', 'lspci', 'dvipdfm', 'gcov-dump', 'avahi-publish', 'kmodsign', 'dbus-update-activation-environment', 'rename.ul', 'fixwpps', 'x86_64-linux-gnu-python3m-config', 'pnmconvol', 'ipod-time-sync', 'gnome-shell', 'ssh-keyscan', 'debconf', 'file', 'pinky', 'foo2hbpl2-wrapper', 'texmaker', 'tbl', 'xrandr', 'cpp', 'wpa_passphrase', 'broadwayd', 'cachepic', 'namei', 'kdeinit5_wrapper', 'httexi', 'ptex', 'dvilj4l', 'xzcmp', 'xzfgrep', 'pnmsplit', 'gdbus', 'pamcut', 'spellintian', 'ppdi', 'dvips', 'pbmpscale', 'systemd-cgls', 'mgrtopbm', 'shasum', 'deallocvt', 'tpic2pdftex', 'getfacl', 'dumpkeys', 'python3m', 'lessfile', 'ttf2pk', 'delpart', 'pgmnoise', 'x86_64-linux-gnu-ld.gold', 'mpost', 'lsipc', 'resizepart', 'gnome-terminal.real', 'extractbb', 'ssh-import-id-gh', 'cd-it8', 'calendar', 'flock', 'qmlprofiler', 'nmtui-connect', 'fiascotopnm', 'rvim', 'i686-linux-gnu-pkg-config', 'cygdb3', 'dh_python2', 'xkeystone', 'pacmd', 'rdoc2.5', 'python2-config', 'fmt', 'totem', 'systemd-delta', 'rletopnm', 'exceltex', 'composite-im6.q16', 'vtkParseJava-7.1', 'xpmtoppm', 'funzip', 'latex2nemeth', 'paplay', 'tracepath', 'poff', 'logger', 'faked-sysv', 'dirmngr-client', 'mxtar', 'pnmcolormap', 'pngtopnm', 'pi1toppm', 'ctstat', 'h5pcc.openmpi', 'podchecker', 'gdb', 'pbmtoepsi', 'disdvi', 'oshrun', 'oshfort', 'vstp', 'plog', 'aa-enabled', 'dbus-cleanup-sockets', 'upower', 'ppmqvga', 'pvserver', 'qlalr', 'ps2pdfwr', 'fakeroot', 'x86_64-linux-gnu-g++', 'perldoc', 'genbrk', 'mkfifo', 'apport-collect', 'kpackagelauncherqml', 'locale', 'brltty-ctb', 'dpkg-trigger', 'avahi-browse', 'ipod-read-sysinfo-extended', 'xzmore', 'pico', 'arecord', 'pyhtmlizer3', 'vtk6python', 'ppmtopcx', 'kbuildsycoca5', 'gnome-session-custom-session', 'tload', 'ttfread', 'kolourpaint', 'lispmtopgm', 'dvipos', 'vlna', 'gtk-update-icon-cache', 'xstdcmap', 'oakdecode', 'dpkg-genbuildinfo', 'sha384sum', 'python-config', 'mdatopbm', 'rstartd', 'xwdtopnm', 'enchant-lsmod', 'rake', 'splitindex', 'xbrlapi', 'wall', 'pgmenhance', 'xkbevd', 'g++', 'select-editor', 'gjs', 'h5c++', 'gc', 'ionice', 'cupstestdsc', 'linux-boot-prober', 'systemd-cgtop', 'xwininfo', 'spd-say', 'e2pall', 'icontopbm', 'pstops', 'eyuvtoppm', 'fontinst', 'Xorg', 'sbkeysync', 'ccomps', 'ischroot', 'nproc', 'dpkg-statoverride', 'zeisstopnm', 'X', 'xman', 'pnmtotiff', 'kbxutil', 'pnmcat', 'mtrace', 'gmsh', 'spice-vdagent', 'gnome-disks', 'gemtopbm', 'libwacom-list-local-devices', 'mattrib', 'python3-qr', 'systemd-mount', 'kshell5', 'texfot', 'x86_64-linux-gnu-python3-config', 'xrefresh', 'gvfs-mkdir', 'pbmtobbnbg', 'ispell-wrapper', 'uic', 'opldecode', 'mdu', 'pnmscalefixed', 'pyversions', 'gtester', 'xclipboard', 'wofm2opl', 'conch', 'mtvtoppm', 'mdel', 'parsechangelog', 'twistd3', 'acpi_listen', 'apport-unpack', 'texdirflatten', 'scor2prt', 'pythontex3', 'glib-gettextize', 'setkeycodes', 'animate-im6', 'grog', 'xdvi-xaw', 'xvminitoppm', 'dt2dv', 'fc-scan', 'evince', 'kwriteconfig5', 'latex-wordcount', 'convert', 'gsdj500', 'scriptreplay', 'driverless', 'taskset', 'showrgb', 'geqn', 'pdfimages', 'pnmnorm', 'kcachegrind', 'snice', 'lsof', 'sbvarsign', 'filterdiff', 'ktrash5', 'lupdate', 'pgmhist', 'mysql_config', 'xzcat', 'arecordmidi', 'pnminvert', 'flipdiff', 'pstree', 'gtf', 'ppmchange', 'unmkinitramfs', 'sfdp', 'updmap-sys', 'lzgrep', 'pdfnup', 'x86_64-linux-gnu-ld.bfd', 'mkindex', 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'isdv4-serial-debugger', 'rcc', 'ppmdist', 'x86_64-linux-gnu-gcov-dump-7', 'screendump', 'qtchooser', 'ppmtobmp', 'colormgr', 'pslog', 'tput', 'depythontex', 'pip', 'boltctl', 'gnome-help', 'md5sum', 'cmuwmtopbm', 'pkg-config', 'gipddecode', 'pnmenlarge', 'ppdpo', 'mpicc.openmpi', 'peekfd', 'automat-visualize', 'skill', 'pgmcrater', 'xrdb', 'chcon', 'sane-find-scanner', 'python2.7-config', 'x86_64-linux-gnu-gcc-nm', 'vtkWrapJava-7.1', 'unwrapdiff', 'dh_pypy', 'bmptoppm', 'gml2gv', 'foo2oak', 'gresource', 'msgcat', 'ltximg', 'dvipdfmx', 'ssh-copy-id', 'pjtoppm', 'syslinux-legacy', 'pixeltool', 'whoopsie', 'xdg-open', 'pbmmake', 'rasttopnm', 'ms_print', 'fixtpps', 'convert-im6.q16', 'preconv', 'pdf270', 'ssh-import-id-lp', 'afm2pl', 'ps2eps', 'Xwayland', 'sensible-editor', 'pamstretch-gen', 'gettext.sh', 'srcredact', 'pnmtorle', 'setfacl', 'pdfunite', 'gvgen', 'pydoc', 'mcopy', 'dconf', 'oshmem_info', 'whoami', 'infocmp', 'pgmkernel', 'obexctl', 'x86_64-linux-gnu-gold', 'mrd', 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'pbmupc', 'installfont-tl', 'stream-im6', 'convert-im6', 'volname', 'readelf', 'pftp', 'im-launch', 'hp-firmware', 'gnome-session-properties', 'browse', 'test', 'gvfs-rm', 'mkpic', 'xset', 'gcc-nm', 'sensible-browser', 'lscpu', 'x-terminal-emulator', 'arlatex', 'tex4ebook', 'rediff', 'gencat', 'x86_64-linux-gnu-size', 'lwp-download', 'qdbusviewer', 'pinentry-x11', 'identify-im6', 'pfbtopfa', 'foo2zjs-wrapper', 'xmore', 'gpg-connect-agent', 'freetype-config', 'python3m-config', 'vimdiff', 'on_ac_power', 'kate', 'csplit', 'conjure', 'pkexec', 'pic', 'pbmtoptx', 'twist3', 'pygmentize', 'vim.tiny', 'mpic++', 'pdfpun', 'systemd-detect-virt', 'ppmtopj', 'edit', 'gnome-text-editor', 'msgfilter', 'cheese', 'dvi2tty', 'qvkgen', 'cg_merge', 'l2ping', 'desktop-file-edit', 'mf', 'ppltotf', 'setarch', 'gconf-merge-tree', 'groups', 'pvtkpython', 'bundledoc', 'pycompile', 'eptex', 'hp-query', 'pgmtofs', 'sbverify', 'sccmap', 'tic', 'pbmtoatk', 'identify', 'gcc-ar-7', 'foo2hp', 'repc', 'unxz', 'pvpython', 'qmlmin', 'gvfs-monitor-dir', 'f2py3.6', 'zjsdecode', 'pn2pdf', 'opalc++', 'mflua', 'pkcon', 'debconf-apt-progress', 'icuinfo', 'ttf2tfm', 'pyhtmlizer', 'fixdlsrps', 'grub-mount', 'splitfont', 'realpath', 'ld.gold', 'dpkg-architecture', 'libpng16-config', 'hipercdecode', 'migrate-pubring-from-classic-gpg', 'ua', 'apt-mark', 'nc-config', 'printer-profile', 'hp-testpage', 'deb-systemd-helper', 'hp-colorcal', 'ubuntu-support-status', 'xcutsel', 'libpng-config', 'uuidgen', 'monitor-sensor', 'rhythmbox-client', 'prove', 'lwp-dump', 'makeglossaries-lite', 'rmiregistry', 'systemd-run', 'parec', 'timedatectl', 'ps2ps2', 'erb2.5', 'prepmx', 'cpan5.26-x86_64-linux-gnu', 'ppmrainbow', 'gnome-terminal', 'paste', 'bc', 'editor', 'gtscompare', 'gxl2gv', 'gvfs-set-attribute', 'addr2line', 'unattended-upgrade', 'groff', 'gslj', 'parecord', 'bbox', 'sdptool', 'linguist', 'tr', 'gnome-todo', 'ppmcolormask', 'xdg-desktop-menu', 'simple-scan', 'gcc-7', 'ompi-top', 'mpicxx', 'chardetect3', 'simpdftex', 'vtkWrapPythonInit-6.3', 'repstopdf', 'upbibtex', 'ctanupload', 'msgcomm', 'x86_64-linux-gnu-gcc-ranlib', 'epstopdf', 'bibtex.original', 'pg_config', 'vtkEncodeString-7.1', 'grub-editenv', 'shuf', 'pdfseparate', 'last', 'upmendex', 'htmex', 'systemd-socket-activate', 'install-printerdriver', 'python3.6', 'xdg-icon-resource', 'prune', 'update-manager', 'faillog', 'tac', 'kwalletd5', 'codepage', 'lzcat', 'x86_64-linux-gnu-gcov-tool', 'qmlplugindump', 'users', 'dpkg-parsechangelog', 'libnetcfg', 'renice', 'pnmtosgi', 'touch', 'composite', 'unattended-upgrades', 'apt-sortpkgs', 'ctie', 'gdbtui', 'neato', 'pdb3', 'gtscheck', 'pvrenderserver', 'gmock_gen', 'x86_64-linux-gnu-cpp-7', 'xlsatoms', 'crontab', 'nmtui', 'x11perfcomp', 'pbmtoxbm', 'install-info', 'gvcolor', 'bmtoa', 'f2py3', 'gftodvi', 'expiry', 'gpgsm', 'pmpost', 'ginstall-info', 'newgrp', 'tlmgr', 'iptables-xml', 'esc-m', 'printerbanner', 'vtk7', 'gconftool-2', 'lzmore', 'unity-scope-loader', 'telnet', 'xsubpp', 'bibtex', 'x86_64-linux-gnu-pkg-config', 'systemd-path', 'xmlpatternsvalidator', 'chage', 'dpkg', 'pamdeinterlace', 'mfplain', 'python', 'gstreamer-codec-install', 'lcf', 'xhost', 'partx', 'setterm', 'xconsole', 'makejvf', 'gpgv', 'lpstat', 'hp-levels', 'stream-im6.q16', 'valgrind', 'install', 'valgrind.bin', 'orte-top', 'adhocfilelist', 'arping', 'psmerge', 'doxysearch.cgi', 'rhythmbox', 'dehtmldiff', 'encguess', 'pgmedge', 'ppmpat', 'ncal', 'scp1', 'gtbl', 'pax11publish', 'gnome-thumbnail-font', 'xdg-user-dir', 'tkconch', 'xmag', 'perltex', 'avahi-publish-service', 'keyring', 'ssh-keygen1', 'infotocap', 'isoinfo', 'w', 'match_parens', 'otp2ocp', 'mscompress', 'montage-im6.q16', 'gobject-query', 'a5toa4', 'pgmoil', 'sldtoppm', 'prezip-bin', 'ctest', 'texluajit', 'yuvsplittoppm', 'includeres', 'mendex', 'ppmtoleaf', 'pgmtopbm', 'pnmscale', 'preunzip', 'gts2oogl', 'imagetops', 'qtpaths', 'h5pfc.openmpi', 'openssl', 'mshortname', 'psfxtable', 'tkconch3', 'gdialog', 'yuvtoppm', 'prtstat', 'tftopl', 'ppmcie', 'htxelatex', 'hostid', 'pbmtomda', 'strace-log-merge', 'designer', 'makeglossaries', 'xbmtopbm', 'fmtutil-sys', 'sudoedit', 'gsbj', 'appres', 'unicode_stop', 'jexec', 'gnome-keyring-3', 'curl-config', 'libreoffice', 'icu-config', 'expand', 'genisoimage', 'updvitomp', 'pdfjam-pocketmod', 'foo2hp2600-wrapper', 'f95', 'utmpdump', 'rcp', 'msexpand', 'gftype', 'fmtutil', 'fi_pingpong', 'ps2pk', 'pcxtoppm', 'psfaddtable', 'ktelnetservice5', 'autosp', 'foo2slx-wrapper', 'pythontex', 'getmapdl', 'oshcc', 'ckeygen3', 'zipcloak', 'scp', 'c++', 'pfb2pfa', 'pnmmargin', 'psicc', 'helpztags', 'gtk-builder-tool', 'fonttosfnt', 'pamstack', 'gpg-agent', 'software-properties-gtk', 'python3.6m', 'numfmt', 'orte-ps', 'updmap-user', 'lshw', 'pnmtojpeg', 'cal', 'texdiff', 'pdfatfi', 'ppmmake', 'xsetwacom', 'pamstretch', 'xkill', 'gvfs-tree', 'ppmhist', 'pamon', 't1binary', 'fwupdate', 'pnminterp', 'zipdetails', 't4ht', 'smproxy', 'perli11ndoc', 'iceauth', 'snapctl', 'perl5.26.1', 'pnmnlfilt', 'pon', 'grub-mkpasswd-pbkdf2', 'mcookie', 'check-language-support', 'pdftocairo', 'yes', 'vtkWrapPythonInit-7.1', 'pkcheck', 'pldd', 'lslogins', 'hp-makeuri', 'latexdef', 'gnome-font-viewer', 'mousetweaks', 'pnmpaste', 'm2400w', 'pbmtext', 'printf', 'etex', 'base64', 'gslp', 'totem-video-thumbnailer', 'pgrep', 'showconsolefont', 'kpsetool', 'python2-qr', 'twistd', 'fwupdmgr', 'col', 'l2test', 'rfcomm', 'mkzftree', 'pbmtopi3', 'nroff', 'c89', 'editdiff', 'fixscribeps', 'gcov-dump-7', 'ovp2ovf', 'tee', 'gst-play-1.0', 'pbmtocmuwm', 'rawtopgm', 'keytool', 'anytopnm', 'nohup', 'luajittex', 'gnome-www-browser', 'dbus-uuidgen', 'pybuild', 'mf-nowin', 'linux-version', 'host', 'nm-connection-editor', 'erb', 'mpic++.openmpi', 'diff', 'xsm', 'vtkWrapPython-6.3', 'thunderbird', 'makeindex', 'sha224sum', 'xdg-user-dirs-gtk-update', 'xdpyinfo', 'gts2xyz', 'remmina', 'pacat', 'pbmtog3', 'localectl', 'mktexfmt', 'pnmtosir', 'qmlscene', 'mcd', 'ptx', 'dtxgen', 'x86_64-linux-gnu-gcc', 'psfgettable', 'ddstdecode', 'uconv', 'xdriinfo', 'dotty', 'aa-exec', 'pnmhisteq', 'circo', 'checklistings', 'avahi-browse-domains', 'GET', 'mflua-nowin', 'perl5.26-x86_64-linux-gnu', 'ppmtorgb3', 'gvfs-ls', 'foomatic-rip', 'ppmntsc', 'gpgsplit', 'fi_info', 'qmake', 'acyclic', 'zipinfo', 't1unmac', 'mclasserase', 'mpif90', 'cmake', 'hcitool', 'kactivities-cli', 'pedigree', 'gvfs-cat', 'identify-im6.q16', 'ps2epsi', 'foo2lava', 'tl-paper', 'sirtopnm', 'svn-multi', 'catman', 'dosepsbin', 'dig', 'pdb', 'b2sum', 'diff3', 'texdoctk', 'ld.bfd', 'pnmcrop', 'ptargrep', 'x86_64-linux-gnu-readelf', 'valgrind-listener', 'update-gconf-defaults', 'dap-config', 'apturl', 'brltty-trtxt', 'pygmentex', 'dvipdft'] ['dumpe2fs', 'pam_extrausers_update', 'apm_available', 'mount.ntfs-3g', 'cfdisk', 'setvtrgb', 'mii-tool', 'xtables-multi', 'crda', 'wipefs', 'hdparm', 'ldconfig', 'dosfslabel', 'hwclock', 'halt', 'switch_root', 'blockdev', 'unix_update', 'isosize', 'chcpu', 'e2label', 'modinfo', 'blkid', 'mke2fs', 'ntfsresize', 'ifdown', 'fsck.ext4', 'rtacct', 'fatlabel', 'rtmon', 'sfdisk', 'reboot', 'pccardctl', 'mkfs.ntfs', 'pivot_root', 'fixparts', 'brltty', 'mount.lowntfs-3g', 'ipmaddr', 'shadowconfig', 'zramctl', 'swapon', 'getty', 'modprobe', 'mkfs.bfs', 'iwpriv', 'agetty', 'kbdrate', 'capsh', 'ifquery', 'start-stop-daemon', 'pam_tally', 'findfs', 'losetup', 'debugfs', 'poweroff', 'ntfscp', 'iw', 'getpcaps', 'dhclient', 'regdbdump', 'plipconfig', 'fsfreeze', 'alsa', 'slattach', 'rmmod', 'nameif', 'badblocks', 'sgdisk', 'udevadm', 'mkfs', 'dmsetup', 'sulogin', 'e2undo', 'acpi_available', 'iwconfig', 'u-d-c-print-pci-ids', 'killall5', 'ntfsundelete', 'installkernel', 'mount.ntfs', 'iptables', 'fdisk', 'shutdown', 'mkdosfs', 'runlevel', 'blkdeactivate', 'rarp', 'fsck.msdos', 'pam_extrausers_chkpwd', 'brltty-setup', 'ntfsclone', 'setcap', 'iptunnel', 'parted', 'blkdiscard', 'plymouthd', 'ldconfig.real', 'umount.udisks2', 'fsck.vfat', 'mkfs.msdos', 'partprobe', 'mkfs.cramfs', 'wpa_action', 'ifconfig', 'e2fsck', 'iwlist', 'iptables-restore', 'mkswap', 'ifup', 'devlink', 'mkfs.vfat', 'dosfsck', 'mount.fuse', 'cgdisk', 'unix_chkpwd', 'fstab-decode', 'iptables-save', 'ip6tables-restore', 'ip6tables-save', 'iwspy', 'sysctl', 'wpa_supplicant', 'lspcmcia', 'tipc', 'ureadahead', 'mkfs.ext4', 'telinit', 'swapoff', 'lsmod', 'raw', 'iwgetid', 'fsck.ext2', 'depmod', 'e2image', 'init', 'on_ac_power', 'fsck', 'ip6tables', 'mkfs.ext3', 'mkhomedir_helper', 'getcap', 'logsave', 'fsck.ext3', 'resize2fs', 'tc', 'pam_tally2', 'ctrlaltdel', 'runuser', 'swaplabel', 'ip', 'apparmor_parser', 'fsck.minix', 'ntfslabel', 'gdisk', 'dhclient-script', 'iwevent', 'insmod', 'route', 'tune2fs', 'mkfs.ext2', 'fsck.fat', 'dmstats', 'wpa_cli', 'mkntfs', 'mkfs.fat', 'fsck.cramfs', 'bridge', 'mkfs.minix', 'fstrim'] ['cp', 'more', 'chmod', 'systemd', 'gzexe', 'systemd-hwdb', 'nc.openbsd', 'mknod', 'bzegrep', 'mt-gnu', 'sh', 'zmore', 'setupcon', 'true', 'rm', 'nano', 'false', 'fgconsole', 'ntfsfallocate', 'sed', 'ntfscmp', 'getfacl', 'dumpkeys', 'lessfile', 'zgrep', 'bzdiff', 'tar', 'fgrep', 'wdctl', 'systemd-inhibit', 'bzip2recover', 'ed', 'static-sh', 'rnano', 'open', 'systemd-escape', 'ntfsusermap', 'nc', 'mktemp', 'zfgrep', 'bzgrep', 'whiptail', 'chgrp', 'systemctl', 'sh.distrib', 'brltty', 'red', 'zforce', 'dash', 'lowntfs-3g', 'kmod', 'rbash', 'rmdir', 'chvt', 'tempfile', 'ls', 'ypdomainname', 'zegrep', 'dd', 'ntfsls', 'lessecho', 'ntfscat', 'dnsdomainname', 'ln', 'loadkeys', 'znew', 'chacl', 'cat', 'udevadm', 'ping4', 'run-parts', 'gunzip', 'date', 'efibootmgr', 'lesskey', 'journalctl', 'lesspipe', 'systemd-tty-ask-password-agent', 'zcat', 'mountpoint', 'systemd-tmpfiles', 'echo', 'mount', 'login', 'ntfsinfo', 'ss', 'bzcmp', 'uncompress', 'ntfs-3g.probe', 'mv', 'ntfsrecover', 'netstat', 'bzless', 'dir', 'ntfssecaudit', 'mt', 'bzip2', 'ntfscluster', 'less', 'openvt', 'sync', 'ntfstruncate', 'bzmore', 'which', 'egrep', 'systemd-ask-password', 'ntfsmove', 'bzcat', 'bzfgrep', 'bzexe', 'ping', 'kbd_mode', 'zdiff', 'bash', 'bunzip2', 'findmnt', 'gzip', 'netcat', 'mkdir', 'ping6', 'hciconfig', 'setfont', 'su', 'unicode_start', 'networkctl', 'ntfsfix', 'loginctl', 'setfacl', 'df', 'lsmod', 'grep', 'chown', 'domainname', 'plymouth', 'cpio', 'vdir', 'fusermount', 'systemd-notify', 'pwd', 'nisdomainname', 'umount', 'ntfswipe', 'systemd-machine-id-setup', 'pidof', 'efibootdump', 'touch', 'sleep', 'readlink', 'ip', 'systemd-sysusers', 'ps', 'uname', 'zcmp', 'hostname', 'fuser', 'ntfs-3g', 'stty', 'ulockmgr_server', 'dmesg', 'busybox', 'zless', 'lsblk', 'kill'] ['gnome-mahjongg', 'gnome-sudoku', 'sol', 'gnome-mines', 'espdiff'] [] ['gnome-calculator', 'gnome-system-monitor', 'gnome-logs', 'gnome-characters'] Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] Checking for program /home/santiago/usr/local/bin/libtoolize...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/libtoolize...not found Checking for program /usr/local/sbin/libtoolize...not found Checking for program /usr/local/bin/libtoolize...not found Checking for program /usr/sbin/libtoolize...not found Checking for program /usr/bin/libtoolize...found ================================================================================ TEST configurePrograms from config.programs(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/programs.py:71) TESTING: configurePrograms from config.programs(config/BuildSystem/config/programs.py:71) Check for the programs needed to build and run PETSc Checking for program /home/santiago/usr/local/bin/sh...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/sh...not found Checking for program /usr/local/sbin/sh...not found Checking for program /usr/local/bin/sh...not found Checking for program /usr/sbin/sh...not found Checking for program /usr/bin/sh...not found Checking for program /sbin/sh...not found Checking for program /bin/sh...found Defined make macro "SHELL" to "/bin/sh" Checking for program /home/santiago/usr/local/bin/sed...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/sed...not found Checking for program /usr/local/sbin/sed...not found Checking for program /usr/local/bin/sed...not found Checking for program /usr/sbin/sed...not found Checking for program /usr/bin/sed...not found Checking for program /sbin/sed...not found Checking for program /bin/sed...found Defined make macro "SED" to "/bin/sed" All intermediate test results are stored in /tmp/petsc-k0jR75/config.programs Running Executable WITHOUT threads to time it out Executing: /bin/sed -i s/sed/sd/g "/tmp/petsc-k0jR75/config.programs/sed1" Adding SEDINPLACE cmd: /bin/sed -i Defined make macro "SEDINPLACE" to "/bin/sed -i" Checking for program /home/santiago/usr/local/bin/mv...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mv...not found Checking for program /usr/local/sbin/mv...not found Checking for program /usr/local/bin/mv...not found Checking for program /usr/sbin/mv...not found Checking for program /usr/bin/mv...not found Checking for program /sbin/mv...not found Checking for program /bin/mv...found Defined make macro "MV" to "/bin/mv" Checking for program /home/santiago/usr/local/bin/cp...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/cp...not found Checking for program /usr/local/sbin/cp...not found Checking for program /usr/local/bin/cp...not found Checking for program /usr/sbin/cp...not found Checking for program /usr/bin/cp...not found Checking for program /sbin/cp...not found Checking for program /bin/cp...found Defined make macro "CP" to "/bin/cp" Checking for program /home/santiago/usr/local/bin/grep...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/grep...not found Checking for program /usr/local/sbin/grep...not found Checking for program /usr/local/bin/grep...not found Checking for program /usr/sbin/grep...not found Checking for program /usr/bin/grep...not found Checking for program /sbin/grep...not found Checking for program /bin/grep...found Defined make macro "GREP" to "/bin/grep" Checking for program /home/santiago/usr/local/bin/rm...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/rm...not found Checking for program /usr/local/sbin/rm...not found Checking for program /usr/local/bin/rm...not found Checking for program /usr/sbin/rm...not found Checking for program /usr/bin/rm...not found Checking for program /sbin/rm...not found Checking for program /bin/rm...found Defined make macro "RM" to "/bin/rm -f" Checking for program /home/santiago/usr/local/bin/diff...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/diff...not found Checking for program /usr/local/sbin/diff...not found Checking for program /usr/local/bin/diff...not found Checking for program /usr/sbin/diff...not found Checking for program /usr/bin/diff...found Running Executable WITHOUT threads to time it out Executing: "/usr/bin/diff" -w "/tmp/petsc-k0jR75/config.programs/diff1" "/tmp/petsc-k0jR75/config.programs/diff2" Defined make macro "DIFF" to "/usr/bin/diff -w" Checking for program /usr/ucb/ps...not found Checking for program /usr/usb/ps...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/ps...not found Unable to find programs ['ps'] providing listing of each search directory to help debug Path provided in Python program Warning accessing /usr/ucb gives errors: [Errno 2] No such file or directory: '/usr/ucb' Warning accessing /usr/usb gives errors: [Errno 2] No such file or directory: '/usr/usb' Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] Defined make macro "PYTHON" to "/usr/bin/python" Checking for program /home/santiago/usr/local/bin/m4...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/m4...not found Checking for program /usr/local/sbin/m4...not found Checking for program /usr/local/bin/m4...not found Checking for program /usr/sbin/m4...not found Checking for program /usr/bin/m4...not found Checking for program /sbin/m4...not found Checking for program /bin/m4...not found Checking for program /usr/games/m4...not found Checking for program /usr/local/games/m4...not found Checking for program /snap/bin/m4...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/m4...not found Unable to find programs ['m4'] providing listing of each search directory to help debug Path provided in Python program Path provided by default path ['adiforfix.py', 'petsc_conf.py', 'petscnagupgrade.py', 'win32fe', 'petscdiff', 'petsc-mpiexec.uni', 'configVars.py', 'PetscBinaryIO.py', 'petsclogformat.py', 'PetscBinaryIOTrajectory.py', 'FASTMathInstaller.py', 'parseargs.py', 'petsc_gen_xdmf.py', 'PetscBinaryIO_tests.py', 'update.py', 'petscnagupgrade.pyc', 'popup', 'petscmpiexec', 'TOPSGenerator.py', 'saws', 'sendToJenkins', 'portabilitycheck.py', 'uncrustify.cfg', 'taucc.py'] ['cat_range_funcs.sh~', 'zip_postproc_yfrac.sh', 'nano', 'rsync_sh.zip', 'utils', 'test_diff.sh', 'set_file_datetime.sh', 'rsync_yfracrun_filelist_base.dat', 'nproc-alt.sh', 'linux_signing_key.pub', 'rsync_yfraccode_filelist_base.dat', 'homedir_generic', 'rsync_bkp_all_msys.sh', 'remove_odd_steps_explicit.sh', 'ubuntu-rdp', 'automated_email', 'rsync_yfracrun_funcs.sh', 'ncpus.sh', 'diffmult.sh', 'unset_proxy.sh', 'ls_dirs.sh', 'rsync_bkp_all.sh', 'au_946492_backspace-doesnt-work-inside-running-bash-script.sh', 'cat_range_funcs.sh', 'img_resize_batch.sh', 'kdeui_shortcuts_print_example.pdf', 'manage_path.sh', 'useful_commands.txt', 'gcc', 'remove_odd_steps.sh', 'zip_yfraccode.sh', 'du1sort.sh', 'split_string_funcs.sh', 'zip_run.sh', 'rsync_utils_msys.sh', 'zip_gmsh_yfrac.sh', 'xlsfonts.dat', 'rsync_delete.sh~', 'double_boot_grub', 'sensors.sh', 'bash_completion.txt', 'rsync_yfracrun.sh', 'echo_command.sh', 'll_dirs.sh', 'rsync_delete.sh', 'rsync_utils.sh', 'utils2017-12.zip', 'apt-get.txt', 'set_proxy.sh', 'rt.bashrc', 'gzip_run.sh', 'rsync_yfraccode_funcs.sh', 'rsync_yfraccode.sh', 'zip_utils.sh', 'inputrc', 'os_distro_funcs.sh', '.directory', 'rm_fast.sh'] [] [] ['apparmor_status', 'pppoe-discovery', 'irqbalance', 'update-default-aspell', 'newusers', 'filefrag', 'update-texmf', 'nfnl_osf', 'ufw', 'add-shell', 'ownership', 'usbmuxd', 'update-passwd', 'chroot', 'rtcwake', 'rtkitctl', 'aptd', 'ippserver', 'biosdecode', 'cups-browsed', 'popcon-largest-unused', 'NetworkManager', 'userdel', 'reject', 'lpc', 'update-dictcommon-hunspell', 'pptp', 'invoke-rc.d', 'genl', 'service', 'grpconv', 'gensprep', 'select-default-wordlist', 'chpasswd', 'avahi-daemon', 'update-dictcommon-aspell', 'grub-set-default', 'update-language-lua', 'update-info-dir', 'update-fmtutil', 'iucode_tool', 'grub-mkdevicemap', 'grpck', 'cppw', 'mklost+found', 'grpunconv', 'lpadmin', 'iio-sensor-proxy', 'create-cracklib-dict', 'groupmems', 'tzconfig', 'spice-vdagentd', 'getweb', 'delgroup', 'usb_modeswitch_dispatcher', 'update-texmf-config', 'aa-remove-unknown', 'iucode-tool', 'update-mime', 'genccode', 'e2freefrag', 'addgroup', 'upgrade-from-grub-legacy', 'update-tl-stacked-conffile', 'lpmove', 'rmt-tar', 'gdm3', 'select-default-ispell', 'escapesrc', 'gencmn', 'grub-bios-setup', 'e4crypt', 'cracklib-packer', 'pwconv', 'lpinfo', 'chat', 'arpd', 'chmem', 'pppoeconf', 'popularity-contest', 'alsa-info', 'make-ssl-cert', 'update-updmap', 'uuidd', 'irqbalance-ui', 'ippusbxd', 'cupsd', 'ispell-autobuildhash', 'alsabat-test', 'dmidecode', 'locale-gen', 'sshd', 'update-java-alternatives', 'pam_timestamp_check', 'cpgr', 'applygnupgdefaults', 'cupsreject', 'cron', 'gconf-schemas', 'update-icon-caches', 'pppstats', 'cupsenable', 'pam_getenv', 'remove-shell', 'vigr', 'usb_modeswitch', 'dpkg-preconfigure', 'cupsaddsmb', 'vpddecode', 'alsactl', 'rmt', 'update-fonts-scale', 'update-pciids', 'pppconfig', 'ModemManager', 'visudo', 'fdformat', 'cupsaccept', 'update-language-def', 'remove-default-ispell', 'rsyslogd', 'e4defrag', 'adduser', 'rfkill', 'update-fonts-alias', 'update-ca-certificates', 'netplan', 'update-default-ispell', 'grub-macbless', 'xrdp', 'cracklib-format', 'acpid', 'bluetoothd', 'nologin', 'cupsctl', 'chgpasswd', 'thermald', 'update-locale', 'readprofile', 'groupdel', 'update-initramfs', 'avahi-autoipd', 'groupadd', 'zic', 'groupmod', 'gennorm2', 'tarcat', 'cracklib-check', 'remove-default-wordlist', 'dpkg-reconfigure', 'logrotate', 'libgvc6-config-update', 'icupkg', 'grub-install', 'pam-auth-update', 'pppd', 'update-fonts-dir', 'xrdp-chansrv', 'useradd', 'paperconfig', 'arp', 'aa-status', 'pptpsetup', 'kerneloops', 'ldattach', 'pppdump', 'cracklib-unpacker', 'iptables-apply', 'vcstime', 'update-usbids', 'update-inetd', 'update-grub2', 'grub-mkconfig', 'cupsfilter', 'addgnupghome', 'setvesablank', 'grub-probe', 'anacron', 'update-grub', 'update-rc.d', 'xrdp-sesman', 'ip6tables-apply', 'update-cracklib', 'pwunconv', 'accessdb', 'update-default-wordlist', 'deluser', 'validlocale', 'cups-genppdupdate', 'grub-reboot', 'iconvconfig', 'update-language-dat', 'saned', 'tcpdump', 'mkinitramfs', 'accept', 'aspell-autobuildhash', 'dnsmasq', 'update-gsfontmap', 'pwck', 'update-grub-gfxpayload', 'usermod', 'vipw', 'cupsdisable', 'gnome-menus-blacklist', 'update-language'] ['ico', 'glib-genmarshal', 'ppmcolors', 'dvipdf', 'ppmtopi1', 'shred', 'findhyph', 'locate', 'htop', 'compare-im6', 'xdg-email', 'savelog', 'envsubst', 'vtkHashSource-7.1', 'mren', 'nad2bin', 'word-list-compress', 'gpgparsemail', 'avahi-resolve-host-name', 'usb-creator-gtk', 'nm-applet', 'dh_autotools-dev_restoreconfig', 'gnome-keyring', 'pslatex', 'passwd', 'routel', 'ppmtoyuvsplit', 'kpsestat', 'cs2cs', 'xgettext', 'traceroute6', 'pnmalias', 'psnup', 'uniq', 'rstart', 'qmlviewer', 'sha512sum', 'qr', 'lsinitramfs', 'gpmetis', 'python3-config', 'automat-visualize3', 'weave', 'gcov-tool-7', 'eps2eps', 'aconnect', 'dpkg-vendor', 'xrdp-keygen', 'oclock', 'qdbusxml2cpp', 'aplaymidi', 'tangle', 'fi_strerror', 'dviinfox', 'leaftoppm', 'pnmtopng', 'apport-bug', 'luit', 'import-im6', 'pod2html', 'corelist', 'gnome-session', 'dviselect', 'sftp', 'xwud', 'de-macro', 'mesg', 'update-notifier', 'pdfxup', 'mandb', 'opl2ofm', 'mkmanifest', 'kernel-install', 'zipnote', 'pr', 'listings-ext', 'make', 'sessreg', 'elfedit', 'xinit', 'lintian', 'ppmtojpeg', 'laptop-detect', 'gvfs-monitor-file', 'gpg', 'tabs', 'dpkg-query', 'xkbvleds', 'makeconv', 'makedtx', 'ps2txt', 'update-perl-sax-parsers', 'kpsewhere', 'whoopsie-preferences', 'sputoppm', 'ntfsdecrypt', 'fc-query', 'pnmtopalm', 'texosquery', 'ppmtouil', 'vpe', 'lsb_release', 'py3versions', 'autoinst', 'pgmbentley', 'mpiexec.openmpi', 'tie', 'showkey', 'grub-glue-efi', 'ubuntu-core-launcher', 'gnome-software-editor', 'lzma', 'gnome-terminal.wrapper', 'aptdcon', 'pbmtowbmp', 'libtoolize', 'mcomp', 'qmlcachegen', 'ckeygen', 'gst-launch-1.0', 'x86_64-linux-gnu-gprof', 'neqn', 'hp-info', 'otangle', 'gpg-zip', 'ps2frag', 'mkocp', 'eject', 'ltxfileinfo', 'pnmflip', 'x86_64-linux-gnu-gcc-ar', 'foo2xqx-wrapper', 'update-desktop-database', 'mpiCC.openmpi', 'baobab', 'qmljs', 'dh_doxygen', 'trial', 'orca-dm-wrapper', 'pod2usage', 'iecset', 'pnmpsnr', 'gpic', 'httex', 'dvitodvi', 'fixcvsdiff', 'spd-conf', 'assistant', 'sudoreplay', 'x-www-browser', 'dpkg-name', 'toe', 'palmtopnm', 'gio', 'dbus-send', 'gsnd', 'patchwork', 'firefox', 'pgmtolispm', 'recode-sr-latin', 'pdf180', 'ndmetis', 'xfd', 'montage', 'vmstat', 'gcov-tool', 'transmission-gtk', 'free', 'import', 'rtstat', 'logname', 'pbibtex', 'pygettext', 'mbadblocks', 'odbcinst', 'dot_builtins', 'gvfs-open', 'apgbfm', 'cpack', 'lp', 'gdal-config', 'syslinux', 'lzegrep', 'pf2afm', 'pdffonts', 'x86_64-linux-gnu-ranlib', 'ppmtoyuv', 'dh_installtex', 'pnmtotiffcmyk', 'mogrify', 't1mac', 'bluetoothctl', 'pnmmontage', 'mawk', 'pnm2ppa', 'qmlimportscanner', 'cmp', 'x86_64', 'pbmtopsg3', 'cpp-7', 'ybmtopbm', 'mingle', 'mfluajit', 'sotruss', 'pdflatexpicscale', 'updatedb', 'ppmshift', 'wc', 'kpsexpand', 'xeyes', 'rename', 'gemtopnm', 'bsd-write', 'updvitype', 'x86_64-linux-gnu-ld', 'run-mailcap', 'cweave', 'pnmgamma', 'isovfy', 'hp-logcapture', 'proxy', 'pdftotext', 'pbmtoepson', 'mdir', 'pdfdetach', 'localc', 'uuidparse', 'fc-list', 'timeout', 'tsort', 'system-config-printer-applet', 'h5fc', 'tred', 'mapscrn', 'prezip', 'objdump', 'pkfix', 'gettext', 'dpkg-distaddfile', 'fc-cache', 'alsabat', 'ibus-daemon', 'h5pcc', 'teckit_compile', 'tgatoppm', 'xauth', 'mathspic', 'dc', 'pbmtomgr', 'mech-dump', 'ps2pdf', 'soelim', 'gcc-ar', 'odvitype', 'xwd', 'telnet.netkit', 'captoinfo', 'rpdfcrop', 'gcov', 'vtkParseOGLExt-7.1', 'lspci', 'dvipdfm', 'gcov-dump', 'avahi-publish', 'kmodsign', 'dbus-update-activation-environment', 'rename.ul', 'fixwpps', 'x86_64-linux-gnu-python3m-config', 'pnmconvol', 'ipod-time-sync', 'gnome-shell', 'ssh-keyscan', 'debconf', 'file', 'pinky', 'foo2hbpl2-wrapper', 'texmaker', 'tbl', 'xrandr', 'cpp', 'wpa_passphrase', 'broadwayd', 'cachepic', 'namei', 'kdeinit5_wrapper', 'httexi', 'ptex', 'dvilj4l', 'xzcmp', 'xzfgrep', 'pnmsplit', 'gdbus', 'pamcut', 'spellintian', 'ppdi', 'dvips', 'pbmpscale', 'systemd-cgls', 'mgrtopbm', 'shasum', 'deallocvt', 'tpic2pdftex', 'getfacl', 'dumpkeys', 'python3m', 'lessfile', 'ttf2pk', 'delpart', 'pgmnoise', 'x86_64-linux-gnu-ld.gold', 'mpost', 'lsipc', 'resizepart', 'gnome-terminal.real', 'extractbb', 'ssh-import-id-gh', 'cd-it8', 'calendar', 'flock', 'qmlprofiler', 'nmtui-connect', 'fiascotopnm', 'rvim', 'i686-linux-gnu-pkg-config', 'cygdb3', 'dh_python2', 'xkeystone', 'pacmd', 'rdoc2.5', 'python2-config', 'fmt', 'totem', 'systemd-delta', 'rletopnm', 'exceltex', 'composite-im6.q16', 'vtkParseJava-7.1', 'xpmtoppm', 'funzip', 'latex2nemeth', 'paplay', 'tracepath', 'poff', 'logger', 'faked-sysv', 'dirmngr-client', 'mxtar', 'pnmcolormap', 'pngtopnm', 'pi1toppm', 'ctstat', 'h5pcc.openmpi', 'podchecker', 'gdb', 'pbmtoepsi', 'disdvi', 'oshrun', 'oshfort', 'vstp', 'plog', 'aa-enabled', 'dbus-cleanup-sockets', 'upower', 'ppmqvga', 'pvserver', 'qlalr', 'ps2pdfwr', 'fakeroot', 'x86_64-linux-gnu-g++', 'perldoc', 'genbrk', 'mkfifo', 'apport-collect', 'kpackagelauncherqml', 'locale', 'brltty-ctb', 'dpkg-trigger', 'avahi-browse', 'ipod-read-sysinfo-extended', 'xzmore', 'pico', 'arecord', 'pyhtmlizer3', 'vtk6python', 'ppmtopcx', 'kbuildsycoca5', 'gnome-session-custom-session', 'tload', 'ttfread', 'kolourpaint', 'lispmtopgm', 'dvipos', 'vlna', 'gtk-update-icon-cache', 'xstdcmap', 'oakdecode', 'dpkg-genbuildinfo', 'sha384sum', 'python-config', 'mdatopbm', 'rstartd', 'xwdtopnm', 'enchant-lsmod', 'rake', 'splitindex', 'xbrlapi', 'wall', 'pgmenhance', 'xkbevd', 'g++', 'select-editor', 'gjs', 'h5c++', 'gc', 'ionice', 'cupstestdsc', 'linux-boot-prober', 'systemd-cgtop', 'xwininfo', 'spd-say', 'e2pall', 'icontopbm', 'pstops', 'eyuvtoppm', 'fontinst', 'Xorg', 'sbkeysync', 'ccomps', 'ischroot', 'nproc', 'dpkg-statoverride', 'zeisstopnm', 'X', 'xman', 'pnmtotiff', 'kbxutil', 'pnmcat', 'mtrace', 'gmsh', 'spice-vdagent', 'gnome-disks', 'gemtopbm', 'libwacom-list-local-devices', 'mattrib', 'python3-qr', 'systemd-mount', 'kshell5', 'texfot', 'x86_64-linux-gnu-python3-config', 'xrefresh', 'gvfs-mkdir', 'pbmtobbnbg', 'ispell-wrapper', 'uic', 'opldecode', 'mdu', 'pnmscalefixed', 'pyversions', 'gtester', 'xclipboard', 'wofm2opl', 'conch', 'mtvtoppm', 'mdel', 'parsechangelog', 'twistd3', 'acpi_listen', 'apport-unpack', 'texdirflatten', 'scor2prt', 'pythontex3', 'glib-gettextize', 'setkeycodes', 'animate-im6', 'grog', 'xdvi-xaw', 'xvminitoppm', 'dt2dv', 'fc-scan', 'evince', 'kwriteconfig5', 'latex-wordcount', 'convert', 'gsdj500', 'scriptreplay', 'driverless', 'taskset', 'showrgb', 'geqn', 'pdfimages', 'pnmnorm', 'kcachegrind', 'snice', 'lsof', 'sbvarsign', 'filterdiff', 'ktrash5', 'lupdate', 'pgmhist', 'mysql_config', 'xzcat', 'arecordmidi', 'pnminvert', 'flipdiff', 'pstree', 'gtf', 'ppmchange', 'unmkinitramfs', 'sfdp', 'updmap-sys', 'lzgrep', 'pdfnup', 'x86_64-linux-gnu-ld.bfd', 'mkindex', 'luatex', 'mpirun', 'hp-plugin', 'proj', 'apport-cli', 'pnmfile', 'ri', 'setxkbmap', 'lwarpmk', 'sort', 'psbook', 'lastlog', 'lexgrog', 'udisksctl', 'pbmto10x', 'lorder', 'xlsclients', 'kpsewhich', 'uptime', 'clear_console', 'h2ph', 'recountdiff', 'symcryptrun', 'mmcli', 'fc-cat', 'faked-tcp', 'dv2dt', 'gnome-shell-extension-prefs', 'msgmerge', 'dpkg-genchanges', 'lsns', 'gem2.5', 'view', 'gcc-ranlib-7', 'bzr', 'pgmramp', 'msgfmt', 'dvilj6', 'mpicc', 'epspdf', 'dpkg-buildflags', 'gconftool', 'eutp', 'pbmlife', 'listres', 'ex', 'join', 'ppmtopuzz', 'qtconfig', 'foo2lava-wrapper', 'gnome-screenshot', 'lsmem', 'kwrapper5', 'gnome-session-inhibit', 'xclock', 'afm2afm', 'geos-config', 'grub-mkimage', 'rawtoppm', 'ppmtomap', 'from', 'perlbug', 'gvmap', 'xfontsel', 'python3', 'gnome-session-quit', 'dvisvgm', 'msgexec', 'perlivp', 'dfu-tool', 'grops', 'mkisofs', 'dot', 'pfarrei', 'mpiexec', 'pydoc3', 'nice', 'st4topgm', 'ckbcomp', 'cut', 'ipcrm', 'as', 'latexfileversion', 'psjoin', 'pnmnoraw', 'msginit', 'pnmindex', 'm2300w-wrapper', 'gdm-screenshot', 'texhash', 'wish', 'minfo', 'tzselect', 'euptex', 'dbus-daemon', 'bdftopcf', 'id', 'fc-match', 'ogdi-config', 'gsftopk', 'ubuntu-software', 'pdftohtml', 'interdiff', 'hex2hcd', 'x-session-manager', 'gnome-software', 'mf2pt1', 'mpicxx.openmpi', 'mtoolstest', 'dpkg-scansources', 'xzegrep', 'texluac', 'h5pfc', 'hp-doctor', 'pwdx', 'lofromtemplate', 'pnmtofits', 'gcc', 'gpu-manager', 'lzfgrep', 'combinediff', 'bioradtopgm', 'giftopnm', 'isdv4-serial-inputattach', 'dviluatex', 'fc-pattern', 'fixwwps', 'kpsepath', 'pdfetex', 'isodump', 'startx', 'ppmtoneo', 'comm', 'pcre-config', 'yplan', 'mcat', 'latex', 'resizecons', 'orted', 'xload', 'snapfuse', 'mkt1font', 'valgrind-di-server', 'gftopk', 'gnome-shell-extension-tool', 'ttfdump', 'nawk', 'unflatten', 'gvfs-move', 'lpq', 'Xephyr', 'msgcmp', 'linux-update-symlinks', 'ppm3d', 'mzip', 'trial3', 'qpdf', 'speech-dispatcher', 'sg', 'hp-align', 'soffice', 'genrb', 'ximtoppm', 'nvidia-detector', 'lastb', '[', 'gvfs-less', 'gst-discoverer-1.0', 'xlogo', 'ppmtoilbm', 'fmtutil-user', 'sbigtopgm', 'gnome-power-statistics', 'xgamma', 'pdf2ps', 'ps2pdf13', 'latexpand', 'whatis', 'gsdj', 'amidi', 'x86_64-linux-gnu-objdump', 'nstat', 'ssh-import-id', 'depythontex3', 'cc', 'ipcmk', 'unzip', 'xkbwatch', 'ptardiff', 'gregorio', 'splain', 'pydoc2.7', 'kreadconfig5', 'wbmptopbm', 'gamma4scanimage', 'fakeroot-tcp', 'hwe-support-status', 'jpegtopnm', 'mailmail', 'ppmtoacad', 'atobm', 'deja-dup', 'canberra-gtk-play', 'uz', 'x86_64-linux-gnu-python-config', 'lzmainfo', 'rgb3toppm', 'colordiff', 'xargs', 'netkit-ftp', 'irb', 'x86_64-linux-gnu-nm', 'apt-config', 'zipgrep', 'xrdp-sesadmin', 'ppmflash', 'lualatex', '411toppm', 'qhelpconverter', 't1ascii', 'systemd-stdio-bridge', 'dh_perl_openssl', 'lspgpot', 'cg_annotate', 'latex-papersize', 'dwp', 'kbdinfo', 'ompi-clean', 't1disasm', 'allec', 'nsupdate', 'ibus-table-createdb', 'pbmtoybm', 'mtype', 'derb', 'm2300w', 'fallocate', 'pstopnm', 'dpkg-checkbuilddeps', 'unlzma', 'systemd-resolve', 'ipcs', 'asciitopgm', 'shotwell', 'xdvi', 'pdflatex', 'g++-7', 'watch', 'gsettings', 'chsh', 'apt', 'avahi-publish-address', 'cmpfillin', 'hp-clean', 'foo2oak-wrapper', 'gcr-viewer', 'transicc', 'pkill', 'who', 'aspell-import', 'pinentry', 'pbmtonokia', 'pager', 'ot2kpx', 'texdoc', 'printafm', 'x86_64-linux-gnu-ar', 'od', 'python2', 'grub-mkstandalone', 'file2brl', 'ruby2.5', 'lnstat', 'lintian-lab-tool', 'mpif77', 'qdoc', 'vi', 'uic3', 'gvfs-save', 'ompi-ps', 'gnome-calendar', 'aleph', 'sgitopnm', 'pbmtolj', 'getkeycodes', 'calibrate_ppa', 'foo2ddst', 'ebb', 'ssh-add', 'kdebugdialog5', 'xdot', 'dpkg-mergechangelogs', 'head', 'compare-im6.q16', 'jpgicc', 'x86_64-linux-gnu-as', 'cd-iccdump', 'avahi-resolve', 'min12xxw', 'dh_bash-completion', 'appstreamcli', 'catchsegv', 'transform', 'ppdmerge', 'unopkg', 'pkmon', 'top', 'mogrify-im6.q16', 'pnmcut', 'hp-pkservice', 'brltty-ttb', 'pygettext3', 'x86_64-linux-gnu-gcc-7', 'gnome-language-selector', 'ptar', 'gpgconf', 'qdbus', 'ri2.5', 'pdfbook2', 'callgrind_annotate', 'h5cc', 'nautilus-desktop', 'pinentry-curses', 'unlink', 'ppmtompeg', 'dviconcat', 'hp-check', 'dvitype', 'gdb-add-index', 'orte-clean', 'getent', 'perl', 'ftp', 'piconv', 'texosquery-jre5', 'ubuntu-advantage', 'eog', 'x86_64-linux-gnu-addr2line', 'manpath', 'pnmpad', 'twist', 'kdeinit5_shutdown', 'allneeded', 'ppmmix', 'mlocate', 'gdbserver', 'epspdftk', 'gtstemplate', 'xetex', 'lessecho', 'opalcc', 'fitstopnm', 'mpif77.openmpi', 'ssh-askpass', 'ctan-o-mat', 'tail', 'x86_64-linux-gnu-cpp', 'pnmarith', 'xml2-config', 'xbiff', 'ibus', 'sha1sum', 'x86_64-linux-gnu-gfortran-7', 'dpkg-maintscript-helper', 'epsffit', 'xdg-desktop-icon', 'debconf-show', 'edgepaint', 'rsh', 'pstree.x11', 'ubuntu-drivers', 'instmodsh', 'nmtui-edit', 'vimdot', 'conjure-im6.q16', 'ppdc', 'htxetex', 'kdeinit5', 'xgc', 'x86_64-linux-gnu-gcov-dump', 'dijkstra', 'mlabel', 'ppmtv', 'qcollectiongenerator', 'debconf-escape', 'pdfbook', 'do-release-upgrade', 'alsamixer', 'bibtexu', 'x86_64-linux-gnu-gcc-ar-7', 'dvired', 'mktexpk', 'xcalc', 'runcon', 'getconf', 'pdfclose', 'f2py2.7', 'basename', 'gvfs-trash', 'ltrace', 'lpoptions', 'gnome-control-center', 'loadkeys', 'pi3topbm', 'bashbug', 'py3compile', 'arara', 'gnome-disk-image-mounter', 'pkaction', 'mk_modmap', 'unzipsfx', 'xinput', 'fstopgm', 'clear', 'iconv', 'foo2qpdl', 'apt-add-repository', 'chacl', 'vptovf', 'nmcli', 'imgtoppm', 'debconf-communicate', 'lowriter', 'vpl2vpl', 'ipptool', 'env', 'authorindex', 'ht', 'fixpsditps', 'dvilj2p', 'python2.7', 'protocoltojson', 'unexpand', 'pnmtoxwd', 'gcov-7', 'scanimage', 'x-window-manager', 'foo2zjs-pstops', 'cg_diff', 'lslocks', 'gcore', 'ppmtotga', 'mtr', 'msgunfmt', 'ps4pdf', 'grub-mkfont', 'pydoc3.6', 'foo2hiperc', 'eqn', 'slxdecode', 'tty', 'alsatplg', 'mpmetis', 'lomath', 'hciattach', 'pdfopen', 'c99-gcc', 'stl2gts', 'snap', 'mft', 'psfstriptable', 'qmleasing', 'info', 'x86_64-linux-gnu-c++filt', 'gio-querymodules', 'orte-server', 'shutter', 'foo2qpdl-wrapper', 'zipsplit', 'vtkWrapHierarchy-7.1', 'display-im6', 'ppmforge', 'cd-fix-profile', 'btmgmt', 'vftovp', 'lneato', 'fix-qdf', 'dpkg-shlibdeps', 'msggrep', 'xprop', 'lwp-mirror', 'x86_64-linux-gnu-gcov-tool-7', 'gvpr', 'ppmnorm', 'x86_64-linux-gnu-gcov', 'grub-render-label', 'print', 'foo2xqx', 'start-pulseaudio-x11', 'lpr', 'opal_wrapper', 'apt-key', 'yelp', 'truncate', 'qml1plugindump', 'ppmdither', 'msgen', 'x86_64-linux-gnu-elfedit', 'hp-probe', 'foo2zjs-icc2ps', 'pdfjam', 'ptftopl', 'splitdiff', 'ppmtogif', 'mkjobtexmf', 'xzdiff', 'arch', 'delv', 'mogrify-im6', 'fixpspps', 'link', 'pnmshear', 'doxyindexer', 'ucfq', 'rdoc', 'xz', 'rdma', 'apt-cache', 'qmltestrunner', 'seq', 'compose', 'afm2tfm', 'pmxab', 'fc-validate', 'linkicc', 'pdftosrc', 'gapplication', 'arm2hpdl', 'lesskey', 'pamoil', 'hexdump', 'cdiff', 'mcheck', 'aspell', 'dvilj', 'winicontoppm', 'gv2gxl', 'lzless', 'fig4latex', 'dirname', 'pamfile', 'ld', 'apt-cdrom', 'pk2bm', 'qhelpgenerator', 'lzcmp', 'size', 'kactivitymanagerd', 'gfortran-7', 'x86_64-linux-gnu-gfortran', 'brushtopbm', 'inimf', 'ldd', 'pod2text', 'gvfs-mime', 'gold', 'ilbmtoppm', 'grub-mkrescue', 'ppmquant', 'mktextfm', 'lavadecode', 'dvitomp', 'gdk-pixbuf-thumbnailer', 'dpkg-buildpackage', 'gedit', 'xvinfo', 'chardetect', 'texcount', 'lesspipe', 'allcm', 'xditview', 'viewres', 'glib-compile-resources', 'pst2pdf', 'initex', 'diffimg', 'setsid', 'pnmcomp', 'psresize', 'pdftex', 'ijs_pxljr', 'omfonts', 'grub-mknetdir', 'montage-im6', 'deb-systemd-invoke', 'gnome-shell-perf-tool', 'pdf2dsc', 'debconf-copydb', 'kpseaccess', 'ssh-argv0', 'typeoutfileinfo', 'ppmtomitsu', 'usb-devices', 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'pnmtojpeg', 'cal', 'texdiff', 'pdfatfi', 'ppmmake', 'xsetwacom', 'pamstretch', 'xkill', 'gvfs-tree', 'ppmhist', 'pamon', 't1binary', 'fwupdate', 'pnminterp', 'zipdetails', 't4ht', 'smproxy', 'perli11ndoc', 'iceauth', 'snapctl', 'perl5.26.1', 'pnmnlfilt', 'pon', 'grub-mkpasswd-pbkdf2', 'mcookie', 'check-language-support', 'pdftocairo', 'yes', 'vtkWrapPythonInit-7.1', 'pkcheck', 'pldd', 'lslogins', 'hp-makeuri', 'latexdef', 'gnome-font-viewer', 'mousetweaks', 'pnmpaste', 'm2400w', 'pbmtext', 'printf', 'etex', 'base64', 'gslp', 'totem-video-thumbnailer', 'pgrep', 'showconsolefont', 'kpsetool', 'python2-qr', 'twistd', 'fwupdmgr', 'col', 'l2test', 'rfcomm', 'mkzftree', 'pbmtopi3', 'nroff', 'c89', 'editdiff', 'fixscribeps', 'gcov-dump-7', 'ovp2ovf', 'tee', 'gst-play-1.0', 'pbmtocmuwm', 'rawtopgm', 'keytool', 'anytopnm', 'nohup', 'luajittex', 'gnome-www-browser', 'dbus-uuidgen', 'pybuild', 'mf-nowin', 'linux-version', 'host', 'nm-connection-editor', 'erb', 'mpic++.openmpi', 'diff', 'xsm', 'vtkWrapPython-6.3', 'thunderbird', 'makeindex', 'sha224sum', 'xdg-user-dirs-gtk-update', 'xdpyinfo', 'gts2xyz', 'remmina', 'pacat', 'pbmtog3', 'localectl', 'mktexfmt', 'pnmtosir', 'qmlscene', 'mcd', 'ptx', 'dtxgen', 'x86_64-linux-gnu-gcc', 'psfgettable', 'ddstdecode', 'uconv', 'xdriinfo', 'dotty', 'aa-exec', 'pnmhisteq', 'circo', 'checklistings', 'avahi-browse-domains', 'GET', 'mflua-nowin', 'perl5.26-x86_64-linux-gnu', 'ppmtorgb3', 'gvfs-ls', 'foomatic-rip', 'ppmntsc', 'gpgsplit', 'fi_info', 'qmake', 'acyclic', 'zipinfo', 't1unmac', 'mclasserase', 'mpif90', 'cmake', 'hcitool', 'kactivities-cli', 'pedigree', 'gvfs-cat', 'identify-im6.q16', 'ps2epsi', 'foo2lava', 'tl-paper', 'sirtopnm', 'svn-multi', 'catman', 'dosepsbin', 'dig', 'pdb', 'b2sum', 'diff3', 'texdoctk', 'ld.bfd', 'pnmcrop', 'ptargrep', 'x86_64-linux-gnu-readelf', 'valgrind-listener', 'update-gconf-defaults', 'dap-config', 'apturl', 'brltty-trtxt', 'pygmentex', 'dvipdft'] ['dumpe2fs', 'pam_extrausers_update', 'apm_available', 'mount.ntfs-3g', 'cfdisk', 'setvtrgb', 'mii-tool', 'xtables-multi', 'crda', 'wipefs', 'hdparm', 'ldconfig', 'dosfslabel', 'hwclock', 'halt', 'switch_root', 'blockdev', 'unix_update', 'isosize', 'chcpu', 'e2label', 'modinfo', 'blkid', 'mke2fs', 'ntfsresize', 'ifdown', 'fsck.ext4', 'rtacct', 'fatlabel', 'rtmon', 'sfdisk', 'reboot', 'pccardctl', 'mkfs.ntfs', 'pivot_root', 'fixparts', 'brltty', 'mount.lowntfs-3g', 'ipmaddr', 'shadowconfig', 'zramctl', 'swapon', 'getty', 'modprobe', 'mkfs.bfs', 'iwpriv', 'agetty', 'kbdrate', 'capsh', 'ifquery', 'start-stop-daemon', 'pam_tally', 'findfs', 'losetup', 'debugfs', 'poweroff', 'ntfscp', 'iw', 'getpcaps', 'dhclient', 'regdbdump', 'plipconfig', 'fsfreeze', 'alsa', 'slattach', 'rmmod', 'nameif', 'badblocks', 'sgdisk', 'udevadm', 'mkfs', 'dmsetup', 'sulogin', 'e2undo', 'acpi_available', 'iwconfig', 'u-d-c-print-pci-ids', 'killall5', 'ntfsundelete', 'installkernel', 'mount.ntfs', 'iptables', 'fdisk', 'shutdown', 'mkdosfs', 'runlevel', 'blkdeactivate', 'rarp', 'fsck.msdos', 'pam_extrausers_chkpwd', 'brltty-setup', 'ntfsclone', 'setcap', 'iptunnel', 'parted', 'blkdiscard', 'plymouthd', 'ldconfig.real', 'umount.udisks2', 'fsck.vfat', 'mkfs.msdos', 'partprobe', 'mkfs.cramfs', 'wpa_action', 'ifconfig', 'e2fsck', 'iwlist', 'iptables-restore', 'mkswap', 'ifup', 'devlink', 'mkfs.vfat', 'dosfsck', 'mount.fuse', 'cgdisk', 'unix_chkpwd', 'fstab-decode', 'iptables-save', 'ip6tables-restore', 'ip6tables-save', 'iwspy', 'sysctl', 'wpa_supplicant', 'lspcmcia', 'tipc', 'ureadahead', 'mkfs.ext4', 'telinit', 'swapoff', 'lsmod', 'raw', 'iwgetid', 'fsck.ext2', 'depmod', 'e2image', 'init', 'on_ac_power', 'fsck', 'ip6tables', 'mkfs.ext3', 'mkhomedir_helper', 'getcap', 'logsave', 'fsck.ext3', 'resize2fs', 'tc', 'pam_tally2', 'ctrlaltdel', 'runuser', 'swaplabel', 'ip', 'apparmor_parser', 'fsck.minix', 'ntfslabel', 'gdisk', 'dhclient-script', 'iwevent', 'insmod', 'route', 'tune2fs', 'mkfs.ext2', 'fsck.fat', 'dmstats', 'wpa_cli', 'mkntfs', 'mkfs.fat', 'fsck.cramfs', 'bridge', 'mkfs.minix', 'fstrim'] ['cp', 'more', 'chmod', 'systemd', 'gzexe', 'systemd-hwdb', 'nc.openbsd', 'mknod', 'bzegrep', 'mt-gnu', 'sh', 'zmore', 'setupcon', 'true', 'rm', 'nano', 'false', 'fgconsole', 'ntfsfallocate', 'sed', 'ntfscmp', 'getfacl', 'dumpkeys', 'lessfile', 'zgrep', 'bzdiff', 'tar', 'fgrep', 'wdctl', 'systemd-inhibit', 'bzip2recover', 'ed', 'static-sh', 'rnano', 'open', 'systemd-escape', 'ntfsusermap', 'nc', 'mktemp', 'zfgrep', 'bzgrep', 'whiptail', 'chgrp', 'systemctl', 'sh.distrib', 'brltty', 'red', 'zforce', 'dash', 'lowntfs-3g', 'kmod', 'rbash', 'rmdir', 'chvt', 'tempfile', 'ls', 'ypdomainname', 'zegrep', 'dd', 'ntfsls', 'lessecho', 'ntfscat', 'dnsdomainname', 'ln', 'loadkeys', 'znew', 'chacl', 'cat', 'udevadm', 'ping4', 'run-parts', 'gunzip', 'date', 'efibootmgr', 'lesskey', 'journalctl', 'lesspipe', 'systemd-tty-ask-password-agent', 'zcat', 'mountpoint', 'systemd-tmpfiles', 'echo', 'mount', 'login', 'ntfsinfo', 'ss', 'bzcmp', 'uncompress', 'ntfs-3g.probe', 'mv', 'ntfsrecover', 'netstat', 'bzless', 'dir', 'ntfssecaudit', 'mt', 'bzip2', 'ntfscluster', 'less', 'openvt', 'sync', 'ntfstruncate', 'bzmore', 'which', 'egrep', 'systemd-ask-password', 'ntfsmove', 'bzcat', 'bzfgrep', 'bzexe', 'ping', 'kbd_mode', 'zdiff', 'bash', 'bunzip2', 'findmnt', 'gzip', 'netcat', 'mkdir', 'ping6', 'hciconfig', 'setfont', 'su', 'unicode_start', 'networkctl', 'ntfsfix', 'loginctl', 'setfacl', 'df', 'lsmod', 'grep', 'chown', 'domainname', 'plymouth', 'cpio', 'vdir', 'fusermount', 'systemd-notify', 'pwd', 'nisdomainname', 'umount', 'ntfswipe', 'systemd-machine-id-setup', 'pidof', 'efibootdump', 'touch', 'sleep', 'readlink', 'ip', 'systemd-sysusers', 'ps', 'uname', 'zcmp', 'hostname', 'fuser', 'ntfs-3g', 'stty', 'ulockmgr_server', 'dmesg', 'busybox', 'zless', 'lsblk', 'kill'] ['gnome-mahjongg', 'gnome-sudoku', 'sol', 'gnome-mines', 'espdiff'] [] ['gnome-calculator', 'gnome-system-monitor', 'gnome-logs', 'gnome-characters'] Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] child config.programs 0.043978 ================================================================================ TEST configureMake from config.packages.make(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/make.py:87) TESTING: configureMake from config.packages.make(config/BuildSystem/config/packages/make.py:87) Check Guesses for GNU make Running Executable WITHOUT threads to time it out Executing: gmake --version GNUMake check failed: Could not execute "['gmake --version']": /bin/sh: 1: gmake: not found Running Executable WITHOUT threads to time it out Executing: make --version stdout: GNU Make 4.1 Built for x86_64-pc-linux-gnu Copyright (C) 1988-2014 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Checking for program /home/santiago/usr/local/bin/make...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/make...not found Checking for program /usr/local/sbin/make...not found Checking for program /usr/local/bin/make...not found Checking for program /usr/sbin/make...not found Checking for program /usr/bin/make...found Defined make macro "MAKE" to "/usr/bin/make" ================================================================================ TEST setupGNUMake from config.packages.make(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/make.py:121) TESTING: setupGNUMake from config.packages.make(config/BuildSystem/config/packages/make.py:121) Setup other GNU make stuff Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux Defined make rule "libc" with dependencies "${LIBNAME}(${OBJSC})" and code [] Defined make rule "libcxx" with dependencies "${LIBNAME}(${OBJSCXX})" and code [] Defined make rule "libcu" with dependencies "${LIBNAME}(${OBJSCU})" and code [] Defined make rule "libf" with dependencies "${OBJSF}" and code -${AR} ${AR_FLAGS} ${LIBNAME} ${OBJSF} Defined make macro "OMAKE_PRINTDIR " to "/usr/bin/make --print-directory" Defined make macro "OMAKE" to "/usr/bin/make --no-print-directory" Defined make macro "MAKE_PAR_OUT_FLG" to "--output-sync=recurse" ================================================================================ TEST configureMakeNP from config.packages.make(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/make.py:168) TESTING: configureMakeNP from config.packages.make(config/BuildSystem/config/packages/make.py:168) check no of cores on the build machine [perhaps to do make '-j ncores'] module multiprocessing found 48 cores: using make_np = 32 using user-provided make_np = 10 Defined make macro "MAKE_NP" to "10" Defined make macro "MAKE_TEST_NP" to "21" Defined make macro "MAKE_LOAD" to "72.0" Defined make macro "NPMAX" to "48" child config.packages.make 0.036372 ================================================================================ TEST alternateConfigureLibrary from config.packages.OpenMPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.OpenMPI(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.OpenMPI 0.001461 Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux ================================================================================ TEST alternateConfigureLibrary from config.packages.MPICH(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.MPICH(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.MPICH 0.008763 ================================================================================ TEST checkDependencies from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:843) TESTING: checkDependencies from config.packages.MPI(config/BuildSystem/config/package.py:843) ================================================================================ TEST configureLibrary from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:617) TESTING: configureLibrary from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:617) ================================================================================== Checking for a functional MPI Checking for library in Compiler specific search MPI: [] ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [MPI_Init MPI_Comm_create] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Init(); static void _check_MPI_Init() { MPI_Init(); } char MPI_Comm_create(); static void _check_MPI_Comm_create() { MPI_Comm_create(); } int main() { _check_MPI_Init(); _check_MPI_Comm_create();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for optional headers [] in Compiler specific search MPI: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Found header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking for headers ['mpi.h'] in Compiler specific search MPI: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['mpi.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['mpi.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkMPIDistro from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:478) TESTING: checkMPIDistro from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:478) Determine if MPICH_NUMVERSION, OMPI_MAJOR_VERSION or MSMPI_VER exist in mpi.h Used for consistency checking of MPI installation at compile time All intermediate test results are stored in /tmp/petsc-k0jR75/config.packages.MPI Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:4:25: error: ‘I_MPI_VERSION’ undeclared here (not in a function); did you mean ‘MPI_VERSION’? const char *mpich_ver = I_MPI_VERSION; ^~~~~~~~~~~~~ MPI_VERSION Source: #include "confdefs.h" #include "conffix.h" #include const char *mpich_ver = I_MPI_VERSION; int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:4:17: error: ‘I_MPI_NUMVERSION’ undeclared here (not in a function); did you mean ‘MPI_SUBVERSION’? int mpich_ver = I_MPI_NUMVERSION; ^~~~~~~~~~~~~~~~ MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = I_MPI_NUMVERSION; int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:4:17: error: ‘MVAPICH2_NUMVERSION’ undeclared here (not in a function); did you mean ‘MPI_SUBVERSION’? int mpich_ver = MVAPICH2_NUMVERSION; ^~~~~~~~~~~~~~~~~~~ MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MVAPICH2_NUMVERSION; int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:4:17: error: ‘MPICH_NUMVERSION’ undeclared here (not in a function); did you mean ‘MPI_SUBVERSION’? int mpich_ver = MPICH_NUMVERSION; ^~~~~~~~~~~~~~~~ MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MPICH_NUMVERSION; int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int ompi_major = OMPI_MAJOR_VERSION; int ompi_minor = OMPI_MINOR_VERSION; int ompi_release = OMPI_RELEASE_VERSION; int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include int ompi_major = OMPI_MAJOR_VERSION; int ompi_minor = OMPI_MINOR_VERSION; int ompi_release = OMPI_RELEASE_VERSION; Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.headers /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Defined "HAVE_OMPI_MAJOR_VERSION" to "2" Defined "HAVE_OMPI_MINOR_VERSION" to "1" Defined "HAVE_OMPI_RELEASE_VERSION" to "1" Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux ================================================================================ TEST configureMPI2 from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:253) TESTING: configureMPI2 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:253) Check for functions added to the interface in MPI-2 Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int flag;if (MPI_Finalized(&flag)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_FINALIZED" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Allreduce(MPI_IN_PLACE,0, 1, MPI_INT, MPI_SUM, MPI_COMM_SELF)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_IN_PLACE" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:6:94: warning: initialization makes pointer from integer without a cast [-Wint-conversion] int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={0,1}; MPI_Datatype *newtype = 0; ^ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:6:94: note: (near initialization for ‘old_types[1]’) Source: #include "confdefs.h" #include "conffix.h" #include int main() { int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={0,1}; MPI_Datatype *newtype = 0; if (MPI_Type_create_struct(count, blocklens, indices, old_types, newtype)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Comm_set_errhandler(MPI_COMM_WORLD,MPI_ERRORS_RETURN)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Reduce_local(0, 0, 0, MPI_INT, MPI_SUM));; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_REDUCE_LOCAL" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char version[MPI_MAX_LIBRARY_VERSION_STRING];int verlen;if (MPI_Get_library_version(version,&verlen)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_GET_LIBRARY_VERSION" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int base[100]; MPI_Win win; if (MPI_Win_create(base,100,4,MPI_INFO_NULL,MPI_COMM_WORLD,&win)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_WIN_CREATE" to "1" Defined "HAVE_MPI_ONE_SIDED" to "1" ================================================================================ TEST configureMPI3 from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:298) TESTING: configureMPI3 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:298) Check for functions added to the interface in MPI-3 Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm scomm; MPI_Aint size=128; int disp_unit=8,*baseptr; MPI_Win win; if (MPI_Comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &scomm)); if (MPI_Win_allocate_shared(size,disp_unit,MPI_INFO_NULL,MPI_COMM_WORLD,&baseptr,&win)); if (MPI_Win_shared_query(win,0,&size,&disp_unit,&baseptr)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_PROCESS_SHARED_MEMORY" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:7:24: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); ^~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:8:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); ^~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int send=0,recv,counts[2]={1,1},displs[2]={1,2}; MPI_Request req; if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igather(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iallgather(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Iallgatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Ialltoall(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NONBLOCKING_COLLECTIVES" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm distcomm; MPI_Request req; if (MPI_Dist_graph_create_adjacent(MPI_COMM_WORLD,0,0,MPI_WEIGHTS_EMPTY,0,0,MPI_WEIGHTS_EMPTY,MPI_INFO_NULL,0,&distcomm)); if (MPI_Neighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm)); if (MPI_Ineighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm,&req)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NEIGHBORHOOD_COLLECTIVES" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:7:3: error: #error This OpenMPI is not CUDA-aware #error This OpenMPI is not CUDA-aware ^~~~~ Source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(MPIX_CUDA_AWARE_SUPPORT) && MPIX_CUDA_AWARE_SUPPORT #else #error This OpenMPI is not CUDA-aware #endif int main() { ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:6:30: warning: ‘win’ is used uninitialized in this function [-Wuninitialized] int ptr[1]; MPI_Win win; if (MPI_Get_accumulate(ptr,1,MPI_INT,ptr,1,MPI_INT,0,0,1,MPI_INT,MPI_SUM,win)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ptr[1]; MPI_Win win; if (MPI_Get_accumulate(ptr,1,MPI_INT,ptr,1,MPI_INT,0,0,1,MPI_INT,MPI_SUM,win)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_GET_ACCUMULATE" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:6:47: warning: ‘win’ is used uninitialized in this function [-Wuninitialized] int ptr[1]; MPI_Win win; MPI_Request req; if (MPI_Rget(ptr,1,MPI_INT,0,1,1,MPI_INT,win,&req)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ptr[1]; MPI_Win win; MPI_Request req; if (MPI_Rget(ptr,1,MPI_INT,0,1,1,MPI_INT,win,&req)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_RGET" to "1" ================================================================================ TEST configureMPIEXEC from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:175) TESTING: configureMPIEXEC from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:175) Checking for location of mpiexec Checking for program /home/santiago/usr/local/bin/mpiexec...not found Checking for program /home/santiago/usr/local/bin/mpirun...not found Checking for program /home/santiago/usr/local/bin/mprun...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpiexec...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mpirun...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/mprun...not found Checking for program /usr/local/sbin/mpiexec...not found Checking for program /usr/local/sbin/mpirun...not found Checking for program /usr/local/sbin/mprun...not found Checking for program /usr/local/bin/mpiexec...not found Checking for program /usr/local/bin/mpirun...not found Checking for program /usr/local/bin/mprun...not found Checking for program /usr/sbin/mpiexec...not found Checking for program /usr/sbin/mpirun...not found Checking for program /usr/sbin/mprun...not found Checking for program /usr/bin/mpiexec...found Running Executable with threads to time it out at 60 Executing: mpiexec -n 1 printenv stdout: OMPI_MCA_pmix=^s1,s2,cray OMPI_COMMAND=printenv OMPI_MCA_orte_precondition_transports=e21d478a85863350-ca3d9aae6b517413 LESSOPEN=| /usr/bin/lesspipe %s HISTTIMEFORMAT=%d/%m/%y %T MAIL=/var/mail/santiago USER=santiago SSH_CLIENT=10.8.125.236 53694 22 LC_TIME=es_AR.UTF-8 HOSTFILE=/etc/hosts LD_LIBRARY_PATH= SHLVL=1 OLDPWD=/home/santiago/Documents/installers/petsc HOME=/home/santiago METIS_LIBDIR=/usr/lib/x86_64-linux-gnu SSH_TTY=/dev/pts/2 METIS_INCDIR=/usr/include PS1=\[\033[1;34m\][\[\033[1;32m\]\u\[\033[1;34m\]@\[\033[1;32m\]\h\[\033[1;34m\]:\[\033[1;32m\]\w\[\033[1;34m\]]\[\033[1;31m\]$\[\033[00m\] LC_MONETARY=es_AR.UTF-8 RED=\[\033[1;31m\] BASHPROFILEREAD=Yes DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1002/bus LOGNAME=santiago PETSC_ARCH=arch-linux2-c-opt _=./configure XDG_SESSION_ID=506 TERM=xterm COLUMNS=129 PATH=/home/santiago/usr/local/bin:/home/santiago/Documents/soft-hard-ware/linux-ubuntu:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin LC_ADDRESS=es_AR.UTF-8 XDG_RUNTIME_DIR=/run/user/1002 RESET=\[\033[00m\] DISPLAY=localhost:10.0 GREEN=\[\033[1;32m\] LANG=en_US.UTF-8 PYTHONSTARTUP=/home/santiago/.pythonrc LC_TELEPHONE=es_AR.UTF-8 LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36: SSH_AUTH_SOCK=/tmp/ssh-6IKS7MnE1D/agent.6417 BLUE=\[\033[1;34m\] LC_NAME=es_AR.UTF-8 SHELL=/bin/bash PROMPT_COMMAND=echo -ne "\033]0;Terminal - ${PWD}\007" LESSCLOSE=/usr/bin/lesspipe %s %s LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=es_AR.UTF-8 PETSC_DIR=/home/santiago/Documents/installers/petsc/petsc-3.13.0 PWD=/home/santiago/Documents/installers/petsc/petsc-3.13.0 SSH_CONNECTION=10.8.125.236 53694 10.129.62.17 22 XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop LC_NUMERIC=es_AR.UTF-8 PYTHONPATH=/usr/lib/python2.7/dist-packages/paraview LINES=36 LC_PAPER=es_AR.UTF-8 EDITOR=nano IPATH_NO_BACKTRACE=1 HFI_NO_BACKTRACE=1 OMPI_MCA_orte_local_daemon_uri=3488415744.0;usock;tcp://10.129.62.17:34809 OMPI_MCA_orte_hnp_uri=3488415744.0;usock;tcp://10.129.62.17:34809 OMPI_MCA_mpi_yield_when_idle=0 OMPI_MCA_orte_app_num=0 OMPI_UNIVERSE_SIZE=1 OMPI_MCA_orte_num_nodes=1 OMPI_MCA_shmem_RUNTIME_QUERY_hint=mmap OMPI_MCA_orte_bound_at_launch=1 OMPI_MCA_ess=pmi OMPI_MCA_orte_ess_num_procs=1 OMPI_COMM_WORLD_SIZE=1 OMPI_COMM_WORLD_LOCAL_SIZE=1 OMPI_MCA_orte_tmpdir_base=/tmp OMPI_NUM_APP_CTX=1 OMPI_FIRST_RANKS=0 OMPI_APP_CTX_NUM_PROCS=1 OMPI_MCA_initial_wdir=/home/santiago/Documents/installers/petsc/petsc-3.13.0 PMIX_NAMESPACE=3488415745 PMIX_RANK=0 PMIX_SERVER_URI=pmix-server:10064:/tmp/openmpi-sessions-1002@isaiasPrecision-7820_0/53229/pmix-10064 PMIX_SECURITY_MODE=native PMIX_DSTORE_ESH_BASE_PATH=/tmp/openmpi-sessions-1002@isaiasPrecision-7820_0/53229/pmix_dstor_10064 OMPI_MCA_orte_launch=1 OMPI_MCA_ess_base_jobid=3488415745 OMPI_MCA_ess_base_vpid=0 OMPI_COMM_WORLD_RANK=0 OMPI_COMM_WORLD_LOCAL_RANK=0 OMPI_COMM_WORLD_NODE_RANK=0 OMPI_MCA_orte_ess_node_rank=0 PMIX_ID=3488415745.0 OMPI_FILE_LOCATION=/tmp/openmpi-sessions-1002@isaiasPrecision-7820_0/53229/1/0 OPAL_OUTPUT_STDERR_FD=37 Defined "HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE" to "OMP" Defined make macro "MPIEXEC" to "mpiexec" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Init(0,0); MPI_Finalize(); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.packages.MPI/conftest to see if it can be run Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest Running Executable with threads to time it out at 60 Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest ================================================================================ TEST configureMPITypes from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:345) TESTING: configureMPITypes from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:345) Checking for MPI Datatype handles Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.packages.MPI/conftest to see if it can be run Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest Running Executable with threads to time it out at 60 Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest Defined "HAVE_MPI_LONG_DOUBLE" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.packages.MPI/conftest to see if it can be run Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest Running Executable with threads to time it out at 60 Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest Defined "HAVE_MPI_INT64_T" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.libraries -I/tmp/petsc-k0jR75/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-k0jR75/config.packages.MPI/conftest to see if it can be run Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest Running Executable with threads to time it out at 60 Executing: mpiexec -n 1 /tmp/petsc-k0jR75/config.packages.MPI/conftest Defined "HAVE_MPI_C_DOUBLE_COMPLEX" to "1" ================================================================================ TEST SGIMPICheck from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:406) TESTING: SGIMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:406) Returns true if SGI MPI is used Checking for functions [MPI_SGI_barrier] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_SGI_barrier(); static void _check_MPI_SGI_barrier() { MPI_SGI_barrier(); } int main() { _check_MPI_SGI_barrier();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `MPI_SGI_barrier' collect2: error: ld returned 1 exit status SGI MPI test failure ================================================================================ TEST CxxMPICheck from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:416) TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:416) Make sure C++ can compile and link Checking for header mpi.h Checking for C++ MPI_Finalize() Checking for functions [MPI_Finalize] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicxx -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/config.libraries -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native -fPIC /tmp/petsc-k0jR75/config.libraries/conftest.cc Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.libraries/conftest.cc: In function ‘void _check_MPI_Finalize()’: /tmp/petsc-k0jR75/config.libraries/conftest.cc:5:41: warning: variable ‘ierr’ set but not used [-Wunused-but-set-variable] static void _check_MPI_Finalize() { int ierr; ^~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_MPI_Finalize() { int ierr; ierr = MPI_Finalize();; } int main() { _check_MPI_Finalize();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicxx -o /tmp/petsc-k0jR75/config.libraries/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl ================================================================================ TEST FortranMPICheck from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:432) TESTING: FortranMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:432) Make sure fortran include [mpif.h] and library symbols are found Checking for fortran mpi_init() Checking for functions [] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.F90 Successful compile: Source: program main #include "mpif.h" integer ierr call mpi_init(ierr) end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for mpi.mod Checking for functions [] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpif90 -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.F90 Successful compile: Source: program main use mpi integer ierr,rank call mpi_init(ierr) call mpi_comm_rank(MPI_COMM_WORLD,rank,ierr) end Running Executable WITHOUT threads to time it out Executing: mpif90 -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_F90MODULE" to "1" ================================================================================ TEST configureIO from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:454) TESTING: configureIO from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:454) Check for the functions in MPI/IO - Define HAVE_MPIIO if they are present - Some older MPI 1 implementations are missing these Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:7:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); ^~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:9:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ MPI_File fh; ^~~~~~~~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:12:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); ^~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:14:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); ^~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:18:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); ^~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:20:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); ^~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:12:5: warning: ‘buf’ is used uninitialized in this function [-Wuninitialized] if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:18:5: warning: ‘disp’ is used uninitialized in this function [-Wuninitialized] if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:18:5: warning: ‘info’ is used uninitialized in this function [-Wuninitialized] Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Aint lb, extent; if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); MPI_File fh; void *buf; MPI_Status status; if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); MPI_Offset disp; MPI_Info info; if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); if (MPI_File_close(&fh)); ; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPIIO" to "1" ================================================================================ TEST findMPIInc from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:558) TESTING: findMPIInc from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:558) Find MPI include paths from "mpicc -show" and use with CUDAC_FLAGS ================================================================================ TEST PetscArchMPICheck from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/MPI.py:592) TESTING: PetscArchMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:592) Checking for functions [MPI_Type_get_envelope MPI_Type_dup MPI_Init_thread MPI_Iallreduce MPI_Ibarrier MPI_Finalized MPI_Exscan MPI_Reduce_scatter MPI_Reduce_scatter_block] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Type_get_envelope(); static void _check_MPI_Type_get_envelope() { MPI_Type_get_envelope(); } char MPI_Type_dup(); static void _check_MPI_Type_dup() { MPI_Type_dup(); } char MPI_Init_thread(); static void _check_MPI_Init_thread() { MPI_Init_thread(); } char MPI_Iallreduce(); static void _check_MPI_Iallreduce() { MPI_Iallreduce(); } char MPI_Ibarrier(); static void _check_MPI_Ibarrier() { MPI_Ibarrier(); } char MPI_Finalized(); static void _check_MPI_Finalized() { MPI_Finalized(); } char MPI_Exscan(); static void _check_MPI_Exscan() { MPI_Exscan(); } char MPI_Reduce_scatter(); static void _check_MPI_Reduce_scatter() { MPI_Reduce_scatter(); } char MPI_Reduce_scatter_block(); static void _check_MPI_Reduce_scatter_block() { MPI_Reduce_scatter_block(); } int main() { _check_MPI_Type_get_envelope(); _check_MPI_Type_dup(); _check_MPI_Init_thread(); _check_MPI_Iallreduce(); _check_MPI_Ibarrier(); _check_MPI_Finalized(); _check_MPI_Exscan(); _check_MPI_Reduce_scatter(); _check_MPI_Reduce_scatter_block();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_TYPE_GET_ENVELOPE" to "1" Defined "HAVE_MPI_TYPE_DUP" to "1" Defined "HAVE_MPI_INIT_THREAD" to "1" Defined "HAVE_MPI_IALLREDUCE" to "1" Defined "HAVE_MPI_IBARRIER" to "1" Defined "HAVE_MPI_FINALIZED" to "1" Defined "HAVE_MPI_EXSCAN" to "1" Defined "HAVE_MPI_REDUCE_SCATTER" to "1" Defined "HAVE_MPI_REDUCE_SCATTER_BLOCK" to "1" Checking for functions [MPIX_Iallreduce] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPIX_Iallreduce(); static void _check_MPIX_Iallreduce() { MPIX_Iallreduce(); } int main() { _check_MPIX_Iallreduce();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `MPIX_Iallreduce' collect2: error: ld returned 1 exit status Checking for functions [MPIX_Ibarrier] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPIX_Ibarrier(); static void _check_MPIX_Ibarrier() { MPIX_Ibarrier(); } int main() { _check_MPIX_Ibarrier();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `MPIX_Ibarrier' collect2: error: ld returned 1 exit status Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:6:5: warning: unused variable ‘combiner’ [-Wunused-variable] int combiner = MPI_COMBINER_DUP;; ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_DUP;; return 0; } Defined "HAVE_MPI_COMBINER_DUP" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:6:5: warning: unused variable ‘combiner’ [-Wunused-variable] int combiner = MPI_COMBINER_CONTIGUOUS;; ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_CONTIGUOUS;; return 0; } Defined "HAVE_MPI_COMBINER_CONTIGUOUS" to "1" Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.MPI/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-k0jR75/config.packages.MPI/conftest.c:6:5: warning: unused variable ‘combiner’ [-Wunused-variable] int combiner = MPI_COMBINER_NAMED;; ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_NAMED;; return 0; } Defined "HAVE_MPI_COMBINER_NAMED" to "1" ================================================================================ TEST checkVersion from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:992) TESTING: checkVersion from config.packages.MPI(config/BuildSystem/config/package.py:992) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version Preprocessing source: #include "confdefs.h" #include "conffix.h" #include "mpi.h" ;petscpkgver(MPI_VERSION); Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.packages.MPI /tmp/petsc-k0jR75/config.packages.MPI/conftest.c For mpi need 2 <= 3 <= ================================================================================ TEST checkSharedLibrary from config.packages.MPI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:926) TESTING: checkSharedLibrary from config.packages.MPI(config/BuildSystem/config/package.py:926) By default we don't care about checking if the library is shared child config.packages.MPI 6.605420 ================================================================================ TEST alternateConfigureLibrary from config.packages.zstd(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.zstd(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.zstd 0.000938 ================================================================================ TEST alternateConfigureLibrary from config.packages.yaml(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.yaml(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.yaml 0.000507 ================================================================================ TEST configureLibrary from config.packages.valgrind(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:868) TESTING: configureLibrary from config.packages.valgrind(config/BuildSystem/config/package.py:868) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional valgrind Not checking for library in Compiler specific search VALGRIND: [] because no functions given to check for ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library [] [] Checking for optional headers [] in Compiler specific search VALGRIND: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Found header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking for headers ['valgrind/valgrind.h'] in Compiler specific search VALGRIND: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['valgrind/valgrind.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.headers -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['valgrind/valgrind.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] All intermediate test results are stored in /tmp/petsc-k0jR75/config.packages.valgrind Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.packages.valgrind/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.packages.valgrind -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.packages.valgrind/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { RUNNING_ON_VALGRIND; ; return 0; } Defined "HAVE_VALGRIND" to "1" child config.packages.valgrind 0.098615 ================================================================================ TEST alternateConfigureLibrary from config.packages.ssl(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.ssl(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.ssl 0.001652 ================================================================================ TEST alternateConfigureLibrary from config.packages.sprng(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.sprng(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.sprng 0.001412 Not a clone of PETSc or no Fortran compiler or fortran-bindings disabled, don't need Sowing child config.packages.sowing 0.000330 ================================================================================ TEST alternateConfigureLibrary from config.packages.revolve(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.revolve(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.revolve 0.001428 ================================================================================ TEST alternateConfigureLibrary from config.packages.radau5(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.radau5(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.radau5 0.001334 ================================================================================ TEST alternateConfigureLibrary from config.packages.pami(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.pami(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.pami 0.001025 ================================================================================ TEST alternateConfigureLibrary from config.packages.opengles(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.opengles(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.opengles 0.000874 ================================================================================ TEST alternateConfigureLibrary from config.packages.opencl(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.opencl(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.opencl 0.000871 ================================================================================ TEST alternateConfigureLibrary from config.packages.muparser(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.muparser(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.muparser 0.001005 Defined "PYTHON_EXE" to ""/usr/bin/python"" Running Executable WITHOUT threads to time it out Executing: /usr/bin/python -c "import Cython" Running Executable WITHOUT threads to time it out Executing: /usr/bin/python -c "import numpy" child config.packages.python 0.090925 ================================================================================ TEST alternateConfigureLibrary from config.packages.petsc4py(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/petsc4py.py:97) TESTING: alternateConfigureLibrary from config.packages.petsc4py(config/BuildSystem/config/packages/petsc4py.py:97) Defined make rule "petsc4py-build" with dependencies "" and code [] Defined make rule "petsc4py-install" with dependencies "" and code [] child config.packages.petsc4py 0.002930 ================================================================================ TEST alternateConfigureLibrary from config.packages.mpi4py(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/mpi4py.py:74) TESTING: alternateConfigureLibrary from config.packages.mpi4py(config/BuildSystem/config/packages/mpi4py.py:74) Defined make rule "mpi4py-build" with dependencies "" and code [] Defined make rule "mpi4py-install" with dependencies "" and code [] child config.packages.mpi4py 0.001912 ================================================================================ TEST alternateConfigureLibrary from config.packages.mpe(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.mpe(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.mpe 0.001489 ================================================================================ TEST alternateConfigureLibrary from config.packages.memkind(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.memkind(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.memkind 0.001188 ================================================================================ TEST alternateConfigureLibrary from config.packages.libmesh(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/libmesh.py:76) TESTING: alternateConfigureLibrary from config.packages.libmesh(config/BuildSystem/config/packages/libmesh.py:76) Defined make rule "libmesh-build" with dependencies "" and code [] Defined make rule "libmesh-install" with dependencies "" and code [] child config.packages.libmesh 0.001684 ================================================================================ TEST alternateConfigureLibrary from config.packages.moose(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.moose(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.moose 0.001400 ================================================================================ TEST alternateConfigureLibrary from config.packages.libjpeg(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.libjpeg(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.libjpeg 0.001415 ================================================================================ TEST alternateConfigureLibrary from config.packages.libceed(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.libceed(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.libceed 0.001371 Not a clone of PETSc, don't need Lgrind child config.packages.lgrind 0.000265 ================================================================================ TEST alternateConfigureLibrary from config.packages.slepc(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/slepc.py:88) TESTING: alternateConfigureLibrary from config.packages.slepc(config/BuildSystem/config/packages/slepc.py:88) Defined make rule "slepc-build" with dependencies "" and code [] Defined make rule "slepc-install" with dependencies "" and code [] child config.packages.slepc 0.001657 ================================================================================ TEST alternateConfigureLibrary from config.packages.gmp(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.gmp(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.gmp 0.000879 ================================================================================ TEST alternateConfigureLibrary from config.packages.mpfr(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.mpfr(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.mpfr 0.000815 ================================================================================ TEST alternateConfigureLibrary from config.packages.giflib(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.giflib 0.000817 ================================================================================ TEST alternateConfigureLibrary from config.packages.egads(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.egads(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.egads 0.000823 ================================================================================ TEST alternateConfigureLibrary from config.packages.ctetgen(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.ctetgen(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.ctetgen 0.000810 ================================================================================ TEST alternateConfigureLibrary from config.packages.concurrencykit(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.concurrencykit(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.concurrencykit 0.000815 ================================================================================ TEST locateC2html from config.packages.c2html(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/c2html.py:33) TESTING: locateC2html from config.packages.c2html(config/BuildSystem/config/packages/c2html.py:33) Looking for default C2html executable Checking for program /home/santiago/usr/local/bin/c2html...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/c2html...not found Checking for program /usr/local/sbin/c2html...not found Checking for program /usr/local/bin/c2html...not found Checking for program /usr/sbin/c2html...not found Checking for program /usr/bin/c2html...not found Checking for program /sbin/c2html...not found Checking for program /bin/c2html...not found Checking for program /usr/games/c2html...not found Checking for program /usr/local/games/c2html...not found Checking for program /snap/bin/c2html...not found Checking for program /home/santiago/Documents/installers/petsc/petsc-3.13.0/lib/petsc/bin/win32fe/c2html...not found Unable to find programs ['c2html'] providing listing of each search directory to help debug Path provided in Python program Path provided by default path ['adiforfix.py', 'petsc_conf.py', 'petscnagupgrade.py', 'win32fe', 'petscdiff', 'petsc-mpiexec.uni', 'configVars.py', 'PetscBinaryIO.py', 'petsclogformat.py', 'PetscBinaryIOTrajectory.py', 'FASTMathInstaller.py', 'parseargs.py', 'petsc_gen_xdmf.py', 'PetscBinaryIO_tests.py', 'update.py', 'petscnagupgrade.pyc', 'popup', 'petscmpiexec', 'TOPSGenerator.py', 'saws', 'sendToJenkins', 'portabilitycheck.py', 'uncrustify.cfg', 'taucc.py'] ['cat_range_funcs.sh~', 'zip_postproc_yfrac.sh', 'nano', 'rsync_sh.zip', 'utils', 'test_diff.sh', 'set_file_datetime.sh', 'rsync_yfracrun_filelist_base.dat', 'nproc-alt.sh', 'linux_signing_key.pub', 'rsync_yfraccode_filelist_base.dat', 'homedir_generic', 'rsync_bkp_all_msys.sh', 'remove_odd_steps_explicit.sh', 'ubuntu-rdp', 'automated_email', 'rsync_yfracrun_funcs.sh', 'ncpus.sh', 'diffmult.sh', 'unset_proxy.sh', 'ls_dirs.sh', 'rsync_bkp_all.sh', 'au_946492_backspace-doesnt-work-inside-running-bash-script.sh', 'cat_range_funcs.sh', 'img_resize_batch.sh', 'kdeui_shortcuts_print_example.pdf', 'manage_path.sh', 'useful_commands.txt', 'gcc', 'remove_odd_steps.sh', 'zip_yfraccode.sh', 'du1sort.sh', 'split_string_funcs.sh', 'zip_run.sh', 'rsync_utils_msys.sh', 'zip_gmsh_yfrac.sh', 'xlsfonts.dat', 'rsync_delete.sh~', 'double_boot_grub', 'sensors.sh', 'bash_completion.txt', 'rsync_yfracrun.sh', 'echo_command.sh', 'll_dirs.sh', 'rsync_delete.sh', 'rsync_utils.sh', 'utils2017-12.zip', 'apt-get.txt', 'set_proxy.sh', 'rt.bashrc', 'gzip_run.sh', 'rsync_yfraccode_funcs.sh', 'rsync_yfraccode.sh', 'zip_utils.sh', 'inputrc', 'os_distro_funcs.sh', '.directory', 'rm_fast.sh'] [] [] ['apparmor_status', 'pppoe-discovery', 'irqbalance', 'update-default-aspell', 'newusers', 'filefrag', 'update-texmf', 'nfnl_osf', 'ufw', 'add-shell', 'ownership', 'usbmuxd', 'update-passwd', 'chroot', 'rtcwake', 'rtkitctl', 'aptd', 'ippserver', 'biosdecode', 'cups-browsed', 'popcon-largest-unused', 'NetworkManager', 'userdel', 'reject', 'lpc', 'update-dictcommon-hunspell', 'pptp', 'invoke-rc.d', 'genl', 'service', 'grpconv', 'gensprep', 'select-default-wordlist', 'chpasswd', 'avahi-daemon', 'update-dictcommon-aspell', 'grub-set-default', 'update-language-lua', 'update-info-dir', 'update-fmtutil', 'iucode_tool', 'grub-mkdevicemap', 'grpck', 'cppw', 'mklost+found', 'grpunconv', 'lpadmin', 'iio-sensor-proxy', 'create-cracklib-dict', 'groupmems', 'tzconfig', 'spice-vdagentd', 'getweb', 'delgroup', 'usb_modeswitch_dispatcher', 'update-texmf-config', 'aa-remove-unknown', 'iucode-tool', 'update-mime', 'genccode', 'e2freefrag', 'addgroup', 'upgrade-from-grub-legacy', 'update-tl-stacked-conffile', 'lpmove', 'rmt-tar', 'gdm3', 'select-default-ispell', 'escapesrc', 'gencmn', 'grub-bios-setup', 'e4crypt', 'cracklib-packer', 'pwconv', 'lpinfo', 'chat', 'arpd', 'chmem', 'pppoeconf', 'popularity-contest', 'alsa-info', 'make-ssl-cert', 'update-updmap', 'uuidd', 'irqbalance-ui', 'ippusbxd', 'cupsd', 'ispell-autobuildhash', 'alsabat-test', 'dmidecode', 'locale-gen', 'sshd', 'update-java-alternatives', 'pam_timestamp_check', 'cpgr', 'applygnupgdefaults', 'cupsreject', 'cron', 'gconf-schemas', 'update-icon-caches', 'pppstats', 'cupsenable', 'pam_getenv', 'remove-shell', 'vigr', 'usb_modeswitch', 'dpkg-preconfigure', 'cupsaddsmb', 'vpddecode', 'alsactl', 'rmt', 'update-fonts-scale', 'update-pciids', 'pppconfig', 'ModemManager', 'visudo', 'fdformat', 'cupsaccept', 'update-language-def', 'remove-default-ispell', 'rsyslogd', 'e4defrag', 'adduser', 'rfkill', 'update-fonts-alias', 'update-ca-certificates', 'netplan', 'update-default-ispell', 'grub-macbless', 'xrdp', 'cracklib-format', 'acpid', 'bluetoothd', 'nologin', 'cupsctl', 'chgpasswd', 'thermald', 'update-locale', 'readprofile', 'groupdel', 'update-initramfs', 'avahi-autoipd', 'groupadd', 'zic', 'groupmod', 'gennorm2', 'tarcat', 'cracklib-check', 'remove-default-wordlist', 'dpkg-reconfigure', 'logrotate', 'libgvc6-config-update', 'icupkg', 'grub-install', 'pam-auth-update', 'pppd', 'update-fonts-dir', 'xrdp-chansrv', 'useradd', 'paperconfig', 'arp', 'aa-status', 'pptpsetup', 'kerneloops', 'ldattach', 'pppdump', 'cracklib-unpacker', 'iptables-apply', 'vcstime', 'update-usbids', 'update-inetd', 'update-grub2', 'grub-mkconfig', 'cupsfilter', 'addgnupghome', 'setvesablank', 'grub-probe', 'anacron', 'update-grub', 'update-rc.d', 'xrdp-sesman', 'ip6tables-apply', 'update-cracklib', 'pwunconv', 'accessdb', 'update-default-wordlist', 'deluser', 'validlocale', 'cups-genppdupdate', 'grub-reboot', 'iconvconfig', 'update-language-dat', 'saned', 'tcpdump', 'mkinitramfs', 'accept', 'aspell-autobuildhash', 'dnsmasq', 'update-gsfontmap', 'pwck', 'update-grub-gfxpayload', 'usermod', 'vipw', 'cupsdisable', 'gnome-menus-blacklist', 'update-language'] ['ico', 'glib-genmarshal', 'ppmcolors', 'dvipdf', 'ppmtopi1', 'shred', 'findhyph', 'locate', 'htop', 'compare-im6', 'xdg-email', 'savelog', 'envsubst', 'vtkHashSource-7.1', 'mren', 'nad2bin', 'word-list-compress', 'gpgparsemail', 'avahi-resolve-host-name', 'usb-creator-gtk', 'nm-applet', 'dh_autotools-dev_restoreconfig', 'gnome-keyring', 'pslatex', 'passwd', 'routel', 'ppmtoyuvsplit', 'kpsestat', 'cs2cs', 'xgettext', 'traceroute6', 'pnmalias', 'psnup', 'uniq', 'rstart', 'qmlviewer', 'sha512sum', 'qr', 'lsinitramfs', 'gpmetis', 'python3-config', 'automat-visualize3', 'weave', 'gcov-tool-7', 'eps2eps', 'aconnect', 'dpkg-vendor', 'xrdp-keygen', 'oclock', 'qdbusxml2cpp', 'aplaymidi', 'tangle', 'fi_strerror', 'dviinfox', 'leaftoppm', 'pnmtopng', 'apport-bug', 'luit', 'import-im6', 'pod2html', 'corelist', 'gnome-session', 'dviselect', 'sftp', 'xwud', 'de-macro', 'mesg', 'update-notifier', 'pdfxup', 'mandb', 'opl2ofm', 'mkmanifest', 'kernel-install', 'zipnote', 'pr', 'listings-ext', 'make', 'sessreg', 'elfedit', 'xinit', 'lintian', 'ppmtojpeg', 'laptop-detect', 'gvfs-monitor-file', 'gpg', 'tabs', 'dpkg-query', 'xkbvleds', 'makeconv', 'makedtx', 'ps2txt', 'update-perl-sax-parsers', 'kpsewhere', 'whoopsie-preferences', 'sputoppm', 'ntfsdecrypt', 'fc-query', 'pnmtopalm', 'texosquery', 'ppmtouil', 'vpe', 'lsb_release', 'py3versions', 'autoinst', 'pgmbentley', 'mpiexec.openmpi', 'tie', 'showkey', 'grub-glue-efi', 'ubuntu-core-launcher', 'gnome-software-editor', 'lzma', 'gnome-terminal.wrapper', 'aptdcon', 'pbmtowbmp', 'libtoolize', 'mcomp', 'qmlcachegen', 'ckeygen', 'gst-launch-1.0', 'x86_64-linux-gnu-gprof', 'neqn', 'hp-info', 'otangle', 'gpg-zip', 'ps2frag', 'mkocp', 'eject', 'ltxfileinfo', 'pnmflip', 'x86_64-linux-gnu-gcc-ar', 'foo2xqx-wrapper', 'update-desktop-database', 'mpiCC.openmpi', 'baobab', 'qmljs', 'dh_doxygen', 'trial', 'orca-dm-wrapper', 'pod2usage', 'iecset', 'pnmpsnr', 'gpic', 'httex', 'dvitodvi', 'fixcvsdiff', 'spd-conf', 'assistant', 'sudoreplay', 'x-www-browser', 'dpkg-name', 'toe', 'palmtopnm', 'gio', 'dbus-send', 'gsnd', 'patchwork', 'firefox', 'pgmtolispm', 'recode-sr-latin', 'pdf180', 'ndmetis', 'xfd', 'montage', 'vmstat', 'gcov-tool', 'transmission-gtk', 'free', 'import', 'rtstat', 'logname', 'pbibtex', 'pygettext', 'mbadblocks', 'odbcinst', 'dot_builtins', 'gvfs-open', 'apgbfm', 'cpack', 'lp', 'gdal-config', 'syslinux', 'lzegrep', 'pf2afm', 'pdffonts', 'x86_64-linux-gnu-ranlib', 'ppmtoyuv', 'dh_installtex', 'pnmtotiffcmyk', 'mogrify', 't1mac', 'bluetoothctl', 'pnmmontage', 'mawk', 'pnm2ppa', 'qmlimportscanner', 'cmp', 'x86_64', 'pbmtopsg3', 'cpp-7', 'ybmtopbm', 'mingle', 'mfluajit', 'sotruss', 'pdflatexpicscale', 'updatedb', 'ppmshift', 'wc', 'kpsexpand', 'xeyes', 'rename', 'gemtopnm', 'bsd-write', 'updvitype', 'x86_64-linux-gnu-ld', 'run-mailcap', 'cweave', 'pnmgamma', 'isovfy', 'hp-logcapture', 'proxy', 'pdftotext', 'pbmtoepson', 'mdir', 'pdfdetach', 'localc', 'uuidparse', 'fc-list', 'timeout', 'tsort', 'system-config-printer-applet', 'h5fc', 'tred', 'mapscrn', 'prezip', 'objdump', 'pkfix', 'gettext', 'dpkg-distaddfile', 'fc-cache', 'alsabat', 'ibus-daemon', 'h5pcc', 'teckit_compile', 'tgatoppm', 'xauth', 'mathspic', 'dc', 'pbmtomgr', 'mech-dump', 'ps2pdf', 'soelim', 'gcc-ar', 'odvitype', 'xwd', 'telnet.netkit', 'captoinfo', 'rpdfcrop', 'gcov', 'vtkParseOGLExt-7.1', 'lspci', 'dvipdfm', 'gcov-dump', 'avahi-publish', 'kmodsign', 'dbus-update-activation-environment', 'rename.ul', 'fixwpps', 'x86_64-linux-gnu-python3m-config', 'pnmconvol', 'ipod-time-sync', 'gnome-shell', 'ssh-keyscan', 'debconf', 'file', 'pinky', 'foo2hbpl2-wrapper', 'texmaker', 'tbl', 'xrandr', 'cpp', 'wpa_passphrase', 'broadwayd', 'cachepic', 'namei', 'kdeinit5_wrapper', 'httexi', 'ptex', 'dvilj4l', 'xzcmp', 'xzfgrep', 'pnmsplit', 'gdbus', 'pamcut', 'spellintian', 'ppdi', 'dvips', 'pbmpscale', 'systemd-cgls', 'mgrtopbm', 'shasum', 'deallocvt', 'tpic2pdftex', 'getfacl', 'dumpkeys', 'python3m', 'lessfile', 'ttf2pk', 'delpart', 'pgmnoise', 'x86_64-linux-gnu-ld.gold', 'mpost', 'lsipc', 'resizepart', 'gnome-terminal.real', 'extractbb', 'ssh-import-id-gh', 'cd-it8', 'calendar', 'flock', 'qmlprofiler', 'nmtui-connect', 'fiascotopnm', 'rvim', 'i686-linux-gnu-pkg-config', 'cygdb3', 'dh_python2', 'xkeystone', 'pacmd', 'rdoc2.5', 'python2-config', 'fmt', 'totem', 'systemd-delta', 'rletopnm', 'exceltex', 'composite-im6.q16', 'vtkParseJava-7.1', 'xpmtoppm', 'funzip', 'latex2nemeth', 'paplay', 'tracepath', 'poff', 'logger', 'faked-sysv', 'dirmngr-client', 'mxtar', 'pnmcolormap', 'pngtopnm', 'pi1toppm', 'ctstat', 'h5pcc.openmpi', 'podchecker', 'gdb', 'pbmtoepsi', 'disdvi', 'oshrun', 'oshfort', 'vstp', 'plog', 'aa-enabled', 'dbus-cleanup-sockets', 'upower', 'ppmqvga', 'pvserver', 'qlalr', 'ps2pdfwr', 'fakeroot', 'x86_64-linux-gnu-g++', 'perldoc', 'genbrk', 'mkfifo', 'apport-collect', 'kpackagelauncherqml', 'locale', 'brltty-ctb', 'dpkg-trigger', 'avahi-browse', 'ipod-read-sysinfo-extended', 'xzmore', 'pico', 'arecord', 'pyhtmlizer3', 'vtk6python', 'ppmtopcx', 'kbuildsycoca5', 'gnome-session-custom-session', 'tload', 'ttfread', 'kolourpaint', 'lispmtopgm', 'dvipos', 'vlna', 'gtk-update-icon-cache', 'xstdcmap', 'oakdecode', 'dpkg-genbuildinfo', 'sha384sum', 'python-config', 'mdatopbm', 'rstartd', 'xwdtopnm', 'enchant-lsmod', 'rake', 'splitindex', 'xbrlapi', 'wall', 'pgmenhance', 'xkbevd', 'g++', 'select-editor', 'gjs', 'h5c++', 'gc', 'ionice', 'cupstestdsc', 'linux-boot-prober', 'systemd-cgtop', 'xwininfo', 'spd-say', 'e2pall', 'icontopbm', 'pstops', 'eyuvtoppm', 'fontinst', 'Xorg', 'sbkeysync', 'ccomps', 'ischroot', 'nproc', 'dpkg-statoverride', 'zeisstopnm', 'X', 'xman', 'pnmtotiff', 'kbxutil', 'pnmcat', 'mtrace', 'gmsh', 'spice-vdagent', 'gnome-disks', 'gemtopbm', 'libwacom-list-local-devices', 'mattrib', 'python3-qr', 'systemd-mount', 'kshell5', 'texfot', 'x86_64-linux-gnu-python3-config', 'xrefresh', 'gvfs-mkdir', 'pbmtobbnbg', 'ispell-wrapper', 'uic', 'opldecode', 'mdu', 'pnmscalefixed', 'pyversions', 'gtester', 'xclipboard', 'wofm2opl', 'conch', 'mtvtoppm', 'mdel', 'parsechangelog', 'twistd3', 'acpi_listen', 'apport-unpack', 'texdirflatten', 'scor2prt', 'pythontex3', 'glib-gettextize', 'setkeycodes', 'animate-im6', 'grog', 'xdvi-xaw', 'xvminitoppm', 'dt2dv', 'fc-scan', 'evince', 'kwriteconfig5', 'latex-wordcount', 'convert', 'gsdj500', 'scriptreplay', 'driverless', 'taskset', 'showrgb', 'geqn', 'pdfimages', 'pnmnorm', 'kcachegrind', 'snice', 'lsof', 'sbvarsign', 'filterdiff', 'ktrash5', 'lupdate', 'pgmhist', 'mysql_config', 'xzcat', 'arecordmidi', 'pnminvert', 'flipdiff', 'pstree', 'gtf', 'ppmchange', 'unmkinitramfs', 'sfdp', 'updmap-sys', 'lzgrep', 'pdfnup', 'x86_64-linux-gnu-ld.bfd', 'mkindex', 'luatex', 'mpirun', 'hp-plugin', 'proj', 'apport-cli', 'pnmfile', 'ri', 'setxkbmap', 'lwarpmk', 'sort', 'psbook', 'lastlog', 'lexgrog', 'udisksctl', 'pbmto10x', 'lorder', 'xlsclients', 'kpsewhich', 'uptime', 'clear_console', 'h2ph', 'recountdiff', 'symcryptrun', 'mmcli', 'fc-cat', 'faked-tcp', 'dv2dt', 'gnome-shell-extension-prefs', 'msgmerge', 'dpkg-genchanges', 'lsns', 'gem2.5', 'view', 'gcc-ranlib-7', 'bzr', 'pgmramp', 'msgfmt', 'dvilj6', 'mpicc', 'epspdf', 'dpkg-buildflags', 'gconftool', 'eutp', 'pbmlife', 'listres', 'ex', 'join', 'ppmtopuzz', 'qtconfig', 'foo2lava-wrapper', 'gnome-screenshot', 'lsmem', 'kwrapper5', 'gnome-session-inhibit', 'xclock', 'afm2afm', 'geos-config', 'grub-mkimage', 'rawtoppm', 'ppmtomap', 'from', 'perlbug', 'gvmap', 'xfontsel', 'python3', 'gnome-session-quit', 'dvisvgm', 'msgexec', 'perlivp', 'dfu-tool', 'grops', 'mkisofs', 'dot', 'pfarrei', 'mpiexec', 'pydoc3', 'nice', 'st4topgm', 'ckbcomp', 'cut', 'ipcrm', 'as', 'latexfileversion', 'psjoin', 'pnmnoraw', 'msginit', 'pnmindex', 'm2300w-wrapper', 'gdm-screenshot', 'texhash', 'wish', 'minfo', 'tzselect', 'euptex', 'dbus-daemon', 'bdftopcf', 'id', 'fc-match', 'ogdi-config', 'gsftopk', 'ubuntu-software', 'pdftohtml', 'interdiff', 'hex2hcd', 'x-session-manager', 'gnome-software', 'mf2pt1', 'mpicxx.openmpi', 'mtoolstest', 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'xcmsdb', 'debconf-set-selections', 'setleds', 'mmount', 'pooltype', 'ppmquantall', 'du', 'zenity', 'grub-kbdcomp', 'pasuspender', 'psselect', 'notify-send', 'ppmtoicr', 'ruby', 'HEAD', 'pnmtoddif', 'dirmngr', 'dh_autotools-dev_updateconfig', 'apturl-gtk', 'pnmrotate', 'pathchk', 'pbmtoicon', 'gdbus-codegen', 'xcursorgen', 'dvilualatex', 'wish8.6', 'x86_64-linux-gnu-strings', 'thumbpdf', 'linux64', 'run-with-aspell', 'sdiff', 'pnmsmooth', 'gsettings-schema-convert', 'x86_64-linux-gnu-g++-7', 'evince-thumbnailer', 'xedit', 'pcimodules', 'gvfs-mount', 'showchar', 'ssh-keygen', 'hp-setup', 'foo2hbpl2', 'grub-syslinux2cfg', 'mkfontscale', 'pbmupc', 'installfont-tl', 'stream-im6', 'convert-im6', 'volname', 'readelf', 'pftp', 'im-launch', 'hp-firmware', 'gnome-session-properties', 'browse', 'test', 'gvfs-rm', 'mkpic', 'xset', 'gcc-nm', 'sensible-browser', 'lscpu', 'x-terminal-emulator', 'arlatex', 'tex4ebook', 'rediff', 'gencat', 'x86_64-linux-gnu-size', 'lwp-download', 'qdbusviewer', 'pinentry-x11', 'identify-im6', 'pfbtopfa', 'foo2zjs-wrapper', 'xmore', 'gpg-connect-agent', 'freetype-config', 'python3m-config', 'vimdiff', 'on_ac_power', 'kate', 'csplit', 'conjure', 'pkexec', 'pic', 'pbmtoptx', 'twist3', 'pygmentize', 'vim.tiny', 'mpic++', 'pdfpun', 'systemd-detect-virt', 'ppmtopj', 'edit', 'gnome-text-editor', 'msgfilter', 'cheese', 'dvi2tty', 'qvkgen', 'cg_merge', 'l2ping', 'desktop-file-edit', 'mf', 'ppltotf', 'setarch', 'gconf-merge-tree', 'groups', 'pvtkpython', 'bundledoc', 'pycompile', 'eptex', 'hp-query', 'pgmtofs', 'sbverify', 'sccmap', 'tic', 'pbmtoatk', 'identify', 'gcc-ar-7', 'foo2hp', 'repc', 'unxz', 'pvpython', 'qmlmin', 'gvfs-monitor-dir', 'f2py3.6', 'zjsdecode', 'pn2pdf', 'opalc++', 'mflua', 'pkcon', 'debconf-apt-progress', 'icuinfo', 'ttf2tfm', 'pyhtmlizer', 'fixdlsrps', 'grub-mount', 'splitfont', 'realpath', 'ld.gold', 'dpkg-architecture', 'libpng16-config', 'hipercdecode', 'migrate-pubring-from-classic-gpg', 'ua', 'apt-mark', 'nc-config', 'printer-profile', 'hp-testpage', 'deb-systemd-helper', 'hp-colorcal', 'ubuntu-support-status', 'xcutsel', 'libpng-config', 'uuidgen', 'monitor-sensor', 'rhythmbox-client', 'prove', 'lwp-dump', 'makeglossaries-lite', 'rmiregistry', 'systemd-run', 'parec', 'timedatectl', 'ps2ps2', 'erb2.5', 'prepmx', 'cpan5.26-x86_64-linux-gnu', 'ppmrainbow', 'gnome-terminal', 'paste', 'bc', 'editor', 'gtscompare', 'gxl2gv', 'gvfs-set-attribute', 'addr2line', 'unattended-upgrade', 'groff', 'gslj', 'parecord', 'bbox', 'sdptool', 'linguist', 'tr', 'gnome-todo', 'ppmcolormask', 'xdg-desktop-menu', 'simple-scan', 'gcc-7', 'ompi-top', 'mpicxx', 'chardetect3', 'simpdftex', 'vtkWrapPythonInit-6.3', 'repstopdf', 'upbibtex', 'ctanupload', 'msgcomm', 'x86_64-linux-gnu-gcc-ranlib', 'epstopdf', 'bibtex.original', 'pg_config', 'vtkEncodeString-7.1', 'grub-editenv', 'shuf', 'pdfseparate', 'last', 'upmendex', 'htmex', 'systemd-socket-activate', 'install-printerdriver', 'python3.6', 'xdg-icon-resource', 'prune', 'update-manager', 'faillog', 'tac', 'kwalletd5', 'codepage', 'lzcat', 'x86_64-linux-gnu-gcov-tool', 'qmlplugindump', 'users', 'dpkg-parsechangelog', 'libnetcfg', 'renice', 'pnmtosgi', 'touch', 'composite', 'unattended-upgrades', 'apt-sortpkgs', 'ctie', 'gdbtui', 'neato', 'pdb3', 'gtscheck', 'pvrenderserver', 'gmock_gen', 'x86_64-linux-gnu-cpp-7', 'xlsatoms', 'crontab', 'nmtui', 'x11perfcomp', 'pbmtoxbm', 'install-info', 'gvcolor', 'bmtoa', 'f2py3', 'gftodvi', 'expiry', 'gpgsm', 'pmpost', 'ginstall-info', 'newgrp', 'tlmgr', 'iptables-xml', 'esc-m', 'printerbanner', 'vtk7', 'gconftool-2', 'lzmore', 'unity-scope-loader', 'telnet', 'xsubpp', 'bibtex', 'x86_64-linux-gnu-pkg-config', 'systemd-path', 'xmlpatternsvalidator', 'chage', 'dpkg', 'pamdeinterlace', 'mfplain', 'python', 'gstreamer-codec-install', 'lcf', 'xhost', 'partx', 'setterm', 'xconsole', 'makejvf', 'gpgv', 'lpstat', 'hp-levels', 'stream-im6.q16', 'valgrind', 'install', 'valgrind.bin', 'orte-top', 'adhocfilelist', 'arping', 'psmerge', 'doxysearch.cgi', 'rhythmbox', 'dehtmldiff', 'encguess', 'pgmedge', 'ppmpat', 'ncal', 'scp1', 'gtbl', 'pax11publish', 'gnome-thumbnail-font', 'xdg-user-dir', 'tkconch', 'xmag', 'perltex', 'avahi-publish-service', 'keyring', 'ssh-keygen1', 'infotocap', 'isoinfo', 'w', 'match_parens', 'otp2ocp', 'mscompress', 'montage-im6.q16', 'gobject-query', 'a5toa4', 'pgmoil', 'sldtoppm', 'prezip-bin', 'ctest', 'texluajit', 'yuvsplittoppm', 'includeres', 'mendex', 'ppmtoleaf', 'pgmtopbm', 'pnmscale', 'preunzip', 'gts2oogl', 'imagetops', 'qtpaths', 'h5pfc.openmpi', 'openssl', 'mshortname', 'psfxtable', 'tkconch3', 'gdialog', 'yuvtoppm', 'prtstat', 'tftopl', 'ppmcie', 'htxelatex', 'hostid', 'pbmtomda', 'strace-log-merge', 'designer', 'makeglossaries', 'xbmtopbm', 'fmtutil-sys', 'sudoedit', 'gsbj', 'appres', 'unicode_stop', 'jexec', 'gnome-keyring-3', 'curl-config', 'libreoffice', 'icu-config', 'expand', 'genisoimage', 'updvitomp', 'pdfjam-pocketmod', 'foo2hp2600-wrapper', 'f95', 'utmpdump', 'rcp', 'msexpand', 'gftype', 'fmtutil', 'fi_pingpong', 'ps2pk', 'pcxtoppm', 'psfaddtable', 'ktelnetservice5', 'autosp', 'foo2slx-wrapper', 'pythontex', 'getmapdl', 'oshcc', 'ckeygen3', 'zipcloak', 'scp', 'c++', 'pfb2pfa', 'pnmmargin', 'psicc', 'helpztags', 'gtk-builder-tool', 'fonttosfnt', 'pamstack', 'gpg-agent', 'software-properties-gtk', 'python3.6m', 'numfmt', 'orte-ps', 'updmap-user', 'lshw', 'pnmtojpeg', 'cal', 'texdiff', 'pdfatfi', 'ppmmake', 'xsetwacom', 'pamstretch', 'xkill', 'gvfs-tree', 'ppmhist', 'pamon', 't1binary', 'fwupdate', 'pnminterp', 'zipdetails', 't4ht', 'smproxy', 'perli11ndoc', 'iceauth', 'snapctl', 'perl5.26.1', 'pnmnlfilt', 'pon', 'grub-mkpasswd-pbkdf2', 'mcookie', 'check-language-support', 'pdftocairo', 'yes', 'vtkWrapPythonInit-7.1', 'pkcheck', 'pldd', 'lslogins', 'hp-makeuri', 'latexdef', 'gnome-font-viewer', 'mousetweaks', 'pnmpaste', 'm2400w', 'pbmtext', 'printf', 'etex', 'base64', 'gslp', 'totem-video-thumbnailer', 'pgrep', 'showconsolefont', 'kpsetool', 'python2-qr', 'twistd', 'fwupdmgr', 'col', 'l2test', 'rfcomm', 'mkzftree', 'pbmtopi3', 'nroff', 'c89', 'editdiff', 'fixscribeps', 'gcov-dump-7', 'ovp2ovf', 'tee', 'gst-play-1.0', 'pbmtocmuwm', 'rawtopgm', 'keytool', 'anytopnm', 'nohup', 'luajittex', 'gnome-www-browser', 'dbus-uuidgen', 'pybuild', 'mf-nowin', 'linux-version', 'host', 'nm-connection-editor', 'erb', 'mpic++.openmpi', 'diff', 'xsm', 'vtkWrapPython-6.3', 'thunderbird', 'makeindex', 'sha224sum', 'xdg-user-dirs-gtk-update', 'xdpyinfo', 'gts2xyz', 'remmina', 'pacat', 'pbmtog3', 'localectl', 'mktexfmt', 'pnmtosir', 'qmlscene', 'mcd', 'ptx', 'dtxgen', 'x86_64-linux-gnu-gcc', 'psfgettable', 'ddstdecode', 'uconv', 'xdriinfo', 'dotty', 'aa-exec', 'pnmhisteq', 'circo', 'checklistings', 'avahi-browse-domains', 'GET', 'mflua-nowin', 'perl5.26-x86_64-linux-gnu', 'ppmtorgb3', 'gvfs-ls', 'foomatic-rip', 'ppmntsc', 'gpgsplit', 'fi_info', 'qmake', 'acyclic', 'zipinfo', 't1unmac', 'mclasserase', 'mpif90', 'cmake', 'hcitool', 'kactivities-cli', 'pedigree', 'gvfs-cat', 'identify-im6.q16', 'ps2epsi', 'foo2lava', 'tl-paper', 'sirtopnm', 'svn-multi', 'catman', 'dosepsbin', 'dig', 'pdb', 'b2sum', 'diff3', 'texdoctk', 'ld.bfd', 'pnmcrop', 'ptargrep', 'x86_64-linux-gnu-readelf', 'valgrind-listener', 'update-gconf-defaults', 'dap-config', 'apturl', 'brltty-trtxt', 'pygmentex', 'dvipdft'] ['dumpe2fs', 'pam_extrausers_update', 'apm_available', 'mount.ntfs-3g', 'cfdisk', 'setvtrgb', 'mii-tool', 'xtables-multi', 'crda', 'wipefs', 'hdparm', 'ldconfig', 'dosfslabel', 'hwclock', 'halt', 'switch_root', 'blockdev', 'unix_update', 'isosize', 'chcpu', 'e2label', 'modinfo', 'blkid', 'mke2fs', 'ntfsresize', 'ifdown', 'fsck.ext4', 'rtacct', 'fatlabel', 'rtmon', 'sfdisk', 'reboot', 'pccardctl', 'mkfs.ntfs', 'pivot_root', 'fixparts', 'brltty', 'mount.lowntfs-3g', 'ipmaddr', 'shadowconfig', 'zramctl', 'swapon', 'getty', 'modprobe', 'mkfs.bfs', 'iwpriv', 'agetty', 'kbdrate', 'capsh', 'ifquery', 'start-stop-daemon', 'pam_tally', 'findfs', 'losetup', 'debugfs', 'poweroff', 'ntfscp', 'iw', 'getpcaps', 'dhclient', 'regdbdump', 'plipconfig', 'fsfreeze', 'alsa', 'slattach', 'rmmod', 'nameif', 'badblocks', 'sgdisk', 'udevadm', 'mkfs', 'dmsetup', 'sulogin', 'e2undo', 'acpi_available', 'iwconfig', 'u-d-c-print-pci-ids', 'killall5', 'ntfsundelete', 'installkernel', 'mount.ntfs', 'iptables', 'fdisk', 'shutdown', 'mkdosfs', 'runlevel', 'blkdeactivate', 'rarp', 'fsck.msdos', 'pam_extrausers_chkpwd', 'brltty-setup', 'ntfsclone', 'setcap', 'iptunnel', 'parted', 'blkdiscard', 'plymouthd', 'ldconfig.real', 'umount.udisks2', 'fsck.vfat', 'mkfs.msdos', 'partprobe', 'mkfs.cramfs', 'wpa_action', 'ifconfig', 'e2fsck', 'iwlist', 'iptables-restore', 'mkswap', 'ifup', 'devlink', 'mkfs.vfat', 'dosfsck', 'mount.fuse', 'cgdisk', 'unix_chkpwd', 'fstab-decode', 'iptables-save', 'ip6tables-restore', 'ip6tables-save', 'iwspy', 'sysctl', 'wpa_supplicant', 'lspcmcia', 'tipc', 'ureadahead', 'mkfs.ext4', 'telinit', 'swapoff', 'lsmod', 'raw', 'iwgetid', 'fsck.ext2', 'depmod', 'e2image', 'init', 'on_ac_power', 'fsck', 'ip6tables', 'mkfs.ext3', 'mkhomedir_helper', 'getcap', 'logsave', 'fsck.ext3', 'resize2fs', 'tc', 'pam_tally2', 'ctrlaltdel', 'runuser', 'swaplabel', 'ip', 'apparmor_parser', 'fsck.minix', 'ntfslabel', 'gdisk', 'dhclient-script', 'iwevent', 'insmod', 'route', 'tune2fs', 'mkfs.ext2', 'fsck.fat', 'dmstats', 'wpa_cli', 'mkntfs', 'mkfs.fat', 'fsck.cramfs', 'bridge', 'mkfs.minix', 'fstrim'] ['cp', 'more', 'chmod', 'systemd', 'gzexe', 'systemd-hwdb', 'nc.openbsd', 'mknod', 'bzegrep', 'mt-gnu', 'sh', 'zmore', 'setupcon', 'true', 'rm', 'nano', 'false', 'fgconsole', 'ntfsfallocate', 'sed', 'ntfscmp', 'getfacl', 'dumpkeys', 'lessfile', 'zgrep', 'bzdiff', 'tar', 'fgrep', 'wdctl', 'systemd-inhibit', 'bzip2recover', 'ed', 'static-sh', 'rnano', 'open', 'systemd-escape', 'ntfsusermap', 'nc', 'mktemp', 'zfgrep', 'bzgrep', 'whiptail', 'chgrp', 'systemctl', 'sh.distrib', 'brltty', 'red', 'zforce', 'dash', 'lowntfs-3g', 'kmod', 'rbash', 'rmdir', 'chvt', 'tempfile', 'ls', 'ypdomainname', 'zegrep', 'dd', 'ntfsls', 'lessecho', 'ntfscat', 'dnsdomainname', 'ln', 'loadkeys', 'znew', 'chacl', 'cat', 'udevadm', 'ping4', 'run-parts', 'gunzip', 'date', 'efibootmgr', 'lesskey', 'journalctl', 'lesspipe', 'systemd-tty-ask-password-agent', 'zcat', 'mountpoint', 'systemd-tmpfiles', 'echo', 'mount', 'login', 'ntfsinfo', 'ss', 'bzcmp', 'uncompress', 'ntfs-3g.probe', 'mv', 'ntfsrecover', 'netstat', 'bzless', 'dir', 'ntfssecaudit', 'mt', 'bzip2', 'ntfscluster', 'less', 'openvt', 'sync', 'ntfstruncate', 'bzmore', 'which', 'egrep', 'systemd-ask-password', 'ntfsmove', 'bzcat', 'bzfgrep', 'bzexe', 'ping', 'kbd_mode', 'zdiff', 'bash', 'bunzip2', 'findmnt', 'gzip', 'netcat', 'mkdir', 'ping6', 'hciconfig', 'setfont', 'su', 'unicode_start', 'networkctl', 'ntfsfix', 'loginctl', 'setfacl', 'df', 'lsmod', 'grep', 'chown', 'domainname', 'plymouth', 'cpio', 'vdir', 'fusermount', 'systemd-notify', 'pwd', 'nisdomainname', 'umount', 'ntfswipe', 'systemd-machine-id-setup', 'pidof', 'efibootdump', 'touch', 'sleep', 'readlink', 'ip', 'systemd-sysusers', 'ps', 'uname', 'zcmp', 'hostname', 'fuser', 'ntfs-3g', 'stty', 'ulockmgr_server', 'dmesg', 'busybox', 'zless', 'lsblk', 'kill'] ['gnome-mahjongg', 'gnome-sudoku', 'sol', 'gnome-mines', 'espdiff'] [] ['gnome-calculator', 'gnome-system-monitor', 'gnome-logs', 'gnome-characters'] Path provided by --with-executables-search-path ['win32feutils.dll', 'win32fe.exe'] child config.packages.c2html 0.004760 ================================================================================ TEST alternateConfigureLibrary from config.packages.boost(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.boost(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.boost 0.000637 ================================================================================ TEST alternateConfigureLibrary from config.packages.silo(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.silo(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.silo 0.000575 ================================================================================ TEST alternateConfigureLibrary from config.packages.Random123(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.Random123(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.Random123 0.000550 ================================================================================ TEST alternateConfigureLibrary from config.packages.PARTY(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.PARTY(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.PARTY 0.000549 ================================================================================ TEST alternateConfigureLibrary from config.packages.Matlab(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.Matlab(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.Matlab 0.000442 ================================================================================ TEST alternateConfigureLibrary from config.packages.MatlabEngine(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.MatlabEngine(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.MatlabEngine 0.000468 ================================================================================ TEST alternateConfigureLibrary from config.packages.Mathematica(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.Mathematica(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.Mathematica 0.000476 ================================================================================ TEST checkDependencies from config.packages.regex(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:843) TESTING: checkDependencies from config.packages.regex(config/BuildSystem/config/package.py:843) ================================================================================ TEST configureLibrary from config.packages.regex(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:868) TESTING: configureLibrary from config.packages.regex(config/BuildSystem/config/package.py:868) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional regex Checking for library in Compiler specific search REGEX: [] ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [regexec regcomp regfree] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.packages.valgrind -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char regexec(); static void _check_regexec() { regexec(); } char regcomp(); static void _check_regcomp() { regcomp(); } char regfree(); static void _check_regfree() { regfree(); } int main() { _check_regexec(); _check_regcomp(); _check_regfree();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for optional headers [] in Compiler specific search REGEX: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Found header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking for headers ['regex.h'] in Compiler specific search REGEX: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['regex.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.headers -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['regex.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkVersion from config.packages.regex(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:992) TESTING: checkVersion from config.packages.regex(config/BuildSystem/config/package.py:992) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.regex(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:926) TESTING: checkSharedLibrary from config.packages.regex(config/BuildSystem/config/package.py:926) By default we don't care about checking if the library is shared child config.packages.regex 0.152235 ================================================================================ TEST alternateConfigureLibrary from config.packages.opengl(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.opengl(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.opengl 0.002180 ================================================================================ TEST alternateConfigureLibrary from config.packages.glut(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.glut 0.001199 ================================================================================ TEST checkDependencies from config.packages.X(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:843) TESTING: checkDependencies from config.packages.X(config/BuildSystem/config/package.py:843) ================================================================================ TEST configureLibrary from config.packages.X(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:868) TESTING: configureLibrary from config.packages.X(config/BuildSystem/config/package.py:868) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional X Checking for library in Compiler specific search X: [] ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [XSetWMName] in library [] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.packages.valgrind -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char XSetWMName(); static void _check_XSetWMName() { XSetWMName(); } int main() { _check_XSetWMName();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-k0jR75/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `XSetWMName' collect2: error: ld returned 1 exit status Checking for library in Compiler specific search X: ['libX11.a'] ================================================================================ TEST check from config.libraries(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [XSetWMName] in library ['libX11.a'] [] Running Executable WITHOUT threads to time it out Executing: mpicc -c -o /tmp/petsc-k0jR75/config.libraries/conftest.o -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.compilers -I/tmp/petsc-k0jR75/config.utilities.closure -I/tmp/petsc-k0jR75/config.compilersFortran -I/tmp/petsc-k0jR75/config.headers -I/tmp/petsc-k0jR75/config.utilities.cacheDetails -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.functions -I/tmp/petsc-k0jR75/config.utilities.featureTestMacros -I/tmp/petsc-k0jR75/config.utilities.missing -I/tmp/petsc-k0jR75/PETSc.options.scalarTypes -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.packages.valgrind -I/tmp/petsc-k0jR75/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char XSetWMName(); static void _check_XSetWMName() { XSetWMName(); } int main() { _check_XSetWMName();; return 0; } Running Executable WITHOUT threads to time it out Executing: mpicc -o /tmp/petsc-k0jR75/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O -O3 -march=native -mtune=native /tmp/petsc-k0jR75/config.libraries/conftest.o -lX11 -lquadmath -lstdc++ -ldl Defined "HAVE_LIBX11" to "1" Checking for optional headers [] in Compiler specific search X: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Found header files [] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking for headers ['X11/Xlib.h'] in Compiler specific search X: ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['X11/Xlib.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Running Executable WITHOUT threads to time it out Executing: mpicc -E -I/tmp/petsc-k0jR75/config.setCompilers -I/tmp/petsc-k0jR75/config.types -I/tmp/petsc-k0jR75/config.packages.MPI -I/tmp/petsc-k0jR75/config.headers -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib /tmp/petsc-k0jR75/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['X11/Xlib.h'] in ['/usr/lib/x86_64-linux-gnu/openmpi/include', '/usr/lib/x86_64-linux-gnu/openmpi/lib'] ================================================================================ TEST checkVersion from config.packages.X(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:992) TESTING: checkVersion from config.packages.X(config/BuildSystem/config/package.py:992) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.X(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:926) TESTING: checkSharedLibrary from config.packages.X(config/BuildSystem/config/package.py:926) By default we don't care about checking if the library is shared child config.packages.X 0.281134 ================================================================================ TEST alternateConfigureLibrary from config.packages.GLVis(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.GLVis(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.GLVis 0.002251 ================================================================================ TEST alternateConfigureLibrary from config.packages.CoDiPack(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.CoDiPack(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.CoDiPack 0.001391 ================================================================================ TEST alternateConfigureLibrary from config.packages.adblaslapack(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.adblaslapack(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.adblaslapack 0.001325 ================================================================================ TEST alternateConfigureLibrary from config.packages.cuda(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.cuda(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.cuda 0.001187 child config.packages.cxxlibs 0.000031 ================================================================================ TEST alternateConfigureLibrary from config.packages.ADOLC(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.ADOLC(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.ADOLC 0.001356 ================================================================================ TEST locateCMake from config.packages.cmake(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/cmake.py:39) TESTING: locateCMake from config.packages.cmake(config/BuildSystem/config/packages/cmake.py:39) Looking for default CMake executable Checking for program /home/santiago/usr/local/bin/cmake...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/cmake...not found Checking for program /usr/local/sbin/cmake...not found Checking for program /usr/local/bin/cmake...not found Checking for program /usr/sbin/cmake...not found Checking for program /usr/bin/cmake...found Defined make macro "CMAKE" to "/usr/bin/cmake" Looking for default CTest executable Checking for program /home/santiago/usr/local/bin/ctest...not found Checking for program /home/santiago/Documents/soft-hard-ware/linux-ubuntu/ctest...not found Checking for program /usr/local/sbin/ctest...not found Checking for program /usr/local/bin/ctest...not found Checking for program /usr/sbin/ctest...not found Checking for program /usr/bin/ctest...found Defined make macro "CTEST" to "/usr/bin/ctest" Running Executable WITHOUT threads to time it out Executing: /usr/bin/cmake --version stdout: cmake version 3.10.2 CMake suite maintained and supported by Kitware (kitware.com/cmake). cmake version found 3.10.2 child config.packages.cmake 0.028764 ================================================================================ TEST alternateConfigureLibrary from config.packages.googletest(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.googletest(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.googletest 0.002463 ================================================================================ TEST alternateConfigureLibrary from config.packages.unittestcpp(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.unittestcpp(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.unittestcpp 0.001399 ================================================================================ TEST alternateConfigureLibrary from config.packages.eigen(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.eigen(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.eigen 0.001331 ================================================================================ TEST alternateConfigureLibrary from config.packages.szlib(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.szlib(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.szlib 0.001334 ================================================================================ TEST alternateConfigureLibrary from config.packages.zlib(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.zlib(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.zlib 0.001247 child config.packages.mathlib 0.000040 ================================================================================ TEST alternateConfigureLibrary from config.packages.tetgen(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.tetgen(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.tetgen 0.001039 ================================================================================ TEST alternateConfigureLibrary from config.packages.tchem(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.tchem(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.tchem 0.001005 ================================================================================ TEST alternateConfigureLibrary from config.packages.saws(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.saws(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.saws 0.001012 ================================================================================ TEST alternateConfigureLibrary from config.packages.libpng(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.libpng(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.libpng 0.001009 ================================================================================ TEST alternateConfigureLibrary from config.packages.combblas(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.combblas(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.combblas 0.001019 ================================================================================ TEST alternateConfigureLibrary from config.packages.Triangle(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.Triangle(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.Triangle 0.000999 ================================================================================ TEST alternateConfigureLibrary from config.packages.metis(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.metis(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.metis 0.001010 ================================================================================ TEST alternateConfigureLibrary from config.packages.pragmatic(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.pragmatic(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.pragmatic 0.001013 ================================================================================ TEST alternateConfigureLibrary from config.packages.parmetis(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.parmetis(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.parmetis 0.000904 ================================================================================ TEST alternateConfigureLibrary from config.packages.Chaco(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.Chaco(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.Chaco 0.000655 Running Executable WITHOUT threads to time it out Executing: uname -s stdout: Linux ================================================================================ TEST alternateConfigureLibrary from config.packages.hdf5(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.hdf5(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.hdf5 0.009012 ================================================================================ TEST alternateConfigureLibrary from config.packages.med(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.med(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.med 0.001453 ================================================================================ TEST alternateConfigureLibrary from config.packages.cgns(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.cgns(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.cgns 0.001202 ================================================================================ TEST alternateConfigureLibrary from config.packages.ascem-io(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.ascem-io(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.ascem-io 0.001375 ================================================================================ TEST alternateConfigureLibrary from config.packages.pflotran(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.pflotran(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.pflotran 0.001350 ================================================================================ TEST alternateConfigureLibrary from config.packages.alquimia(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.alquimia(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.alquimia 0.001196 ================================================================================ TEST alternateConfigureLibrary from config.packages.SAMRAI(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.SAMRAI(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.SAMRAI 0.001245 ================================================================================ TEST alternateConfigureLibrary from config.packages.ADIOS2(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.ADIOS2(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.ADIOS2 0.001237 child config.packages.flibs 0.000051 ================================================================================ TEST alternateConfigureLibrary from config.packages.pnetcdf(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.pnetcdf(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.pnetcdf 0.001206 ================================================================================ TEST alternateConfigureLibrary from config.packages.netcdf(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.netcdf(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.netcdf 0.001183 ================================================================================ TEST alternateConfigureLibrary from config.packages.exodusii(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:930) TESTING: alternateConfigureLibrary from config.packages.exodusii(config/BuildSystem/config/package.py:930) Called if --with-packagename=0; does nothing by default child config.packages.exodusii 0.001218 ================================================================================ TEST checkDependencies from config.packages.fblaslapack(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py:843) TESTING: checkDependencies from config.packages.fblaslapack(config/BuildSystem/config/package.py:843) ================================================================================ TEST configureLibrary from config.packages.fblaslapack(/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/fblaslapack.py:19) TESTING: configureLibrary from config.packages.fblaslapack(config/BuildSystem/config/packages/fblaslapack.py:19) ================================================================================== Checking for a functional fblaslapack Looking for FBLASLAPACK at git.fblaslapack, hg.fblaslapack or a directory starting with ['petsc-pkg-fblaslapack'] Could not locate an existing copy of FBLASLAPACK: ['fblaslapack-3.4.2'] Downloading fblaslapack =============================================================================== Trying to download file:///home/santiago/Documents/installers/petsc/fblaslapack-3.4.2.tar.gz for FBLASLAPACK =============================================================================== Downloading file:///home/santiago/Documents/installers/petsc/fblaslapack-3.4.2.tar.gz to /home/santiago/Documents/installers/petsc/petsc-3.13.0/arch-linux2-c-opt/externalpackages/_d_fblaslapack-3.4.2.tar.gz Extracting /home/santiago/Documents/installers/petsc/petsc-3.13.0/arch-linux2-c-opt/externalpackages/_d_fblaslapack-3.4.2.tar.gz Running Executable WITHOUT threads to time it out Executing: cd /home/santiago/Documents/installers/petsc/petsc-3.13.0/arch-linux2-c-opt/externalpackages; chmod -R a+r fblaslapack-3.4.2;find fblaslapack-3.4.2 -type d -name "*" -exec chmod a+rx {} \; Looking for FBLASLAPACK at git.fblaslapack, hg.fblaslapack or a directory starting with ['petsc-pkg-fblaslapack'] Could not locate an existing copy of FBLASLAPACK: ['fblaslapack-3.4.2'] ERROR: Could not locate downloaded package FBLASLAPACK in /home/santiago/Documents/installers/petsc/petsc-3.13.0/arch-linux2-c-opt/externalpackages **** Configure header /tmp/petsc-k0jR75/confdefs.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #define IS_COLORING_MAX USHRT_MAX #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT #define PETSC_CLANGUAGE_C 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_LGAMMA 1 #define PETSC_HAVE_LOG2 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_CXX_INLINE inline #define PETSC_CXX_RESTRICT __restrict #define PETSC_C_INLINE inline #define PETSC_C_RESTRICT __restrict #define PETSC_FORTRAN_CHARLEN_T int #define PETSC_HAVE_C99 1 #define PETSC_HAVE_CXX_DIALECT_CXX11 1 #define PETSC_HAVE_CXX_DIALECT_CXX14 1 #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_RTLD_GLOBAL 1 #define PETSC_HAVE_RTLD_LAZY 1 #define PETSC_HAVE_RTLD_LOCAL 1 #define PETSC_HAVE_RTLD_NOW 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_IMMINTRIN_H 1 #define PETSC_HAVE_INTTYPES_H 1 #define PETSC_HAVE_MALLOC_H 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_SETJMP_H 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_SYS_PROCFS_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_SYS_SYSINFO_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_HAVE_ISNORMAL 1 #define PETSC_HAVE_REAL___FLOAT128 1 #define PETSC_USE_REAL_DOUBLE 1 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_HAVE_CXX_COMPLEX 1 #define PETSC_HAVE_STRUCT_SIGACTION 1 #define PETSC_SIZEOF_ENUM 4 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG 8 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_USE_VISIBILITY_C 1 #define PETSC_USE_VISIBILITY_CXX 1 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_MEMALIGN 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE_MMAP 1 #define PETSC_HAVE_NANOSLEEP 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_SYSINFO 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_SIGNAL_CAST #define PETSC_FORTRAN_TYPE_INITIALIZE = -2 #define PETSC_HAVE_FORTRAN_FLUSH 1 #define PETSC_HAVE_FORTRAN_TYPE_STAR 1 #define PETSC_USING_F2003 1 #define PETSC_USING_F90FREEFORM 1 #define PETSC_HAVE_DYNAMIC_LIBRARIES 1 #define PETSC_USE_SHARED_LIBRARIES 1 #define PETSC_USE_DEBUGGER "gdb" #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE OMP #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_COMBINER_CONTIGUOUS 1 #define PETSC_HAVE_MPI_COMBINER_DUP 1 #define PETSC_HAVE_MPI_COMBINER_NAMED 1 #define PETSC_HAVE_MPI_C_DOUBLE_COMPLEX 1 #define PETSC_HAVE_MPI_EXSCAN 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_GET_ACCUMULATE 1 #define PETSC_HAVE_MPI_GET_LIBRARY_VERSION 1 #define PETSC_HAVE_MPI_IALLREDUCE 1 #define PETSC_HAVE_MPI_IBARRIER 1 #define PETSC_HAVE_MPI_INIT_THREAD 1 #define PETSC_HAVE_MPI_INT64_T 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_HAVE_MPI_LONG_DOUBLE 1 #define PETSC_HAVE_MPI_NEIGHBORHOOD_COLLECTIVES 1 #define PETSC_HAVE_MPI_NONBLOCKING_COLLECTIVES 1 #define PETSC_HAVE_MPI_ONE_SIDED 1 #define PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY 1 #define PETSC_HAVE_MPI_REDUCE_LOCAL 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER_BLOCK 1 #define PETSC_HAVE_MPI_RGET 1 #define PETSC_HAVE_MPI_TYPE_DUP 1 #define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_HAVE_OMPI_MAJOR_VERSION 2 #define PETSC_HAVE_OMPI_MINOR_VERSION 1 #define PETSC_HAVE_OMPI_RELEASE_VERSION 1 #define PETSC_Alignx(a,b) #define PETSC_IS_COLOR_VALUE_TYPE short #define PETSC_IS_COLOR_VALUE_TYPE_F integer2 #define PETSC_USE_AVX512_KERNELS 1 #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_CTABLE 1 #define PETSC_USE_INFO 1 #define PETSC_USE_LOG 1 #define PETSC_USE_MALLOC_COALESCED 1 #define PETSC_MEMALIGN 16 #define PETSC_LEVEL1_DCACHE_LINESIZE 64 #define PETSC__BSD_SOURCE 1 #define PETSC__DEFAULT_SOURCE 1 #define PETSC__GNU_SOURCE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_USE_PROC_FOR_SIZE 1 #define PETSC_PYTHON_EXE "/usr/bin/python" #define PETSC_HAVE_VALGRIND 1 #endif **** C specific Configure header /tmp/petsc-k0jR75/conffix.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #if defined(__cplusplus) extern "C" { } #else #endif #endif ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error during download/extract/detection of FBLASLAPACK: Could not locate downloaded package FBLASLAPACK in /home/santiago/Documents/installers/petsc/petsc-3.13.0/arch-linux2-c-opt/externalpackages ******************************************************************************* File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/configure.py", line 440, in petsc_configure framework.configure(out = sys.stdout) File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/framework.py", line 1229, in configure self.processChildren() File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/framework.py", line 1218, in processChildren self.serialEvaluation(self.childGraph) File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/framework.py", line 1193, in serialEvaluation child.configure() File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 1110, in configure self.executeTest(self.configureLibrary) File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/base.py", line 139, in executeTest ret = test(*args,**kargs) File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/packages/fblaslapack.py", line 24, in configureLibrary config.package.Package.configureLibrary(self) File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 875, in configureLibrary for location, directory, lib, incl in self.generateGuesses(): File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 453, in generateGuesses d = self.checkDownload() File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 587, in checkDownload return self.getInstallDir() File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 331, in getInstallDir if not self.packageDir: self.packageDir = self.downLoad() File "/home/santiago/Documents/installers/petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 792, in downLoad raise RuntimeError('Error during download/extract/detection of '+self.PACKAGE+':\n'+err) ================================================================================ Finishing configure run at Fri, 17 Apr 2020 16:12:04 -0300 ================================================================================