Pushing language C Popping language C Pushing language CUDA Popping language CUDA Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC ================================================================================ ================================================================================ Starting Configure Run at Tue May 5 08:09:33 2015 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-mpi=1 --with-debugging=1 --download-fblaslapack=1 --download-superlu_dist=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-scalapack=1 --download-blacs=1 --download-moab=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-openmpi=1 --CXXFLAGS=-fno-vectorize -CFLAGS=-fno-vectorize --download-mumps=1 --download-ptscotch=1 Working directory: /opt/petsc Machine platform: ('Darwin', 'likask.local', '14.3.0', 'Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64', 'x86_64', 'i386') Python version: 2.7.6 (default, Sep 9 2014, 15:04:36) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] ================================================================================ Pushing language C Popping language C Pushing language CUDA Popping language CUDA Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC ================================================================================ TEST configureExternalPackagesDir from config.framework(/opt/petsc/config/BuildSystem/config/framework.py:832) TESTING: configureExternalPackagesDir from config.framework(config/BuildSystem/config/framework.py:832) All intermediate test results are stored in /tmp/petsc-UdhnXN Executing: cd /tmp/petsc-UdhnXN/config.programs/autoconfdir&&/usr/local/bin/autoreconf Executing: /usr/bin/sed -i s/sed/sd/g "/tmp/petsc-UdhnXN/config.programs/sed1" Executing: /usr/bin/sed -i "" s/sed/sd/g "/tmp/petsc-UdhnXN/config.programs/sed1" Executing: "/usr/bin/diff" -w "/tmp/petsc-UdhnXN/config.programs/diff1" "/tmp/petsc-UdhnXN/config.programs/diff2" ================================================================================ TEST configureMkdir from config.programs(/opt/petsc/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 /usr/texbin/mkdir...not found Checking for program mkdir...not found Checking for program /opt/local/bin/mkdir...not found Checking for program /opt/local/sbin/mkdir...not found Checking for program /usr/local/bin/mkdir...not found Checking for program /usr/bin/mkdir...not found Checking for program /bin/mkdir...found 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(/opt/petsc/config/BuildSystem/config/programs.py:44) TESTING: configureAutoreconf from config.programs(config/BuildSystem/config/programs.py:44) Check for autoreconf Checking for program /usr/texbin/autoreconf...not found Checking for program autoreconf...not found Checking for program /opt/local/bin/autoreconf...not found Checking for program /opt/local/sbin/autoreconf...not found Checking for program /usr/local/bin/autoreconf...found All intermediate test results are stored in /tmp/petsc-UdhnXN/config.programs autoreconf test successful! ================================================================================ TEST configurePrograms from config.programs(/opt/petsc/config/BuildSystem/config/programs.py:66) TESTING: configurePrograms from config.programs(config/BuildSystem/config/programs.py:66) Check for the programs needed to build and run PETSc Checking for program /usr/texbin/sh...not found Checking for program sh...not found Checking for program /opt/local/bin/sh...not found Checking for program /opt/local/sbin/sh...not found Checking for program /usr/local/bin/sh...not found Checking for program /usr/bin/sh...not found Checking for program /bin/sh...found Defined make macro "SHELL" to "/bin/sh" Checking for program /usr/texbin/sed...not found Checking for program sed...not found Checking for program /opt/local/bin/sed...not found Checking for program /opt/local/sbin/sed...not found Checking for program /usr/local/bin/sed...not found Checking for program /usr/bin/sed...found Defined make macro "SED" to "/usr/bin/sed" Rejected SEDINPLACE cmd: /usr/bin/sed -i Adding SEDINPLACE cmd: /usr/bin/sed -i "" Defined make macro "SEDINPLACE" to "/usr/bin/sed -i """ Checking for program /usr/texbin/mv...not found Checking for program mv...not found Checking for program /opt/local/bin/mv...not found Checking for program /opt/local/sbin/mv...not found Checking for program /usr/local/bin/mv...not found Checking for program /usr/bin/mv...not found Checking for program /bin/mv...found Defined make macro "MV" to "/bin/mv" Checking for program /usr/texbin/cp...not found Checking for program cp...not found Checking for program /opt/local/bin/cp...not found Checking for program /opt/local/sbin/cp...not found Checking for program /usr/local/bin/cp...not found Checking for program /usr/bin/cp...not found Checking for program /bin/cp...found Defined make macro "CP" to "/bin/cp" Checking for program /usr/texbin/grep...not found Checking for program grep...not found Checking for program /opt/local/bin/grep...not found Checking for program /opt/local/sbin/grep...not found Checking for program /usr/local/bin/grep...not found Checking for program /usr/bin/grep...found Defined make macro "GREP" to "/usr/bin/grep" Checking for program /usr/texbin/rm...not found Checking for program rm...not found Checking for program /opt/local/bin/rm...not found Checking for program /opt/local/sbin/rm...not found Checking for program /usr/local/bin/rm...not found Checking for program /usr/bin/rm...not found Checking for program /bin/rm...found Defined make macro "RM" to "/bin/rm -f" Checking for program /usr/texbin/diff...not found Checking for program diff...not found Checking for program /opt/local/bin/diff...not found Checking for program /opt/local/sbin/diff...not found Checking for program /usr/local/bin/diff...not found Checking for program /usr/bin/diff...found 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 /Users/likask/ps...not found Checking for program /usr/texbin/gzip...not found Checking for program gzip...not found Checking for program /opt/local/bin/gzip...not found Checking for program /opt/local/sbin/gzip...not found Checking for program /usr/local/bin/gzip...not found Checking for program /usr/bin/gzip...found Defined make macro "GZIP" to "/usr/bin/gzip" Defined "HAVE_GZIP" to "1" Defined make macro "PYTHON" to "/usr/bin/python" ================================================================================ TEST configureDirectories from PETSc.options.petscdir(/opt/petsc/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 0 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 5 #define PETSC_VERSION_SUBMINOR 3 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "unknown" #define PETSC_VERSION_GIT "unknown" #define PETSC_VERSION_DATE_GIT "unknown" #define PETSC_VERSION_(MAJOR,MINOR,SUBMINOR) \ #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) \ Defined make macro "DIR" to "/opt/petsc" C language is C ================================================================================ TEST configureCLanguage from PETSc.options.languages(/opt/petsc/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 Defined "CLANGUAGE_C" to "1" Executing: git --version stdout: git version 2.3.2 (Apple Git-55) ================================================================================ TEST configureGit from config.sourceControl(/opt/petsc/config/BuildSystem/config/sourceControl.py:24) TESTING: configureGit from config.sourceControl(config/BuildSystem/config/sourceControl.py:24) Find the Git executable Checking for program /usr/texbin/git...not found Checking for program git...not found Checking for program /opt/local/bin/git...not found Checking for program /opt/local/sbin/git...not found Checking for program /usr/local/bin/git...not found Checking for program /usr/bin/git...found Defined make macro "GIT" to "git" ================================================================================ TEST configureDebuggers from config.utilities.debuggers(/opt/petsc/config/BuildSystem/config/utilities/debuggers.py:22) TESTING: configureDebuggers from config.utilities.debuggers(config/BuildSystem/config/utilities/debuggers.py:22) Find a default debugger and determine its arguments Checking for program /usr/texbin/gdb...not found Checking for program gdb...not found Checking for program /opt/local/bin/gdb...not found Checking for program /opt/local/sbin/gdb...not found Checking for program /usr/local/bin/gdb...not found Checking for program /usr/bin/gdb...found Defined make macro "GDB" to "/usr/bin/gdb" Checking for program /usr/texbin/dbx...not found Checking for program dbx...not found Checking for program /opt/local/bin/dbx...not found Checking for program /opt/local/sbin/dbx...not found Checking for program /usr/local/bin/dbx...not found Checking for program /usr/bin/dbx...not found Checking for program /bin/dbx...not found Checking for program /usr/sbin/dbx...not found Checking for program /sbin/dbx...not found Checking for program /opt/X11/bin/dbx...not found Checking for program /usr/texbin/dbx...not found Checking for program /Users/likask/dbx...not found Checking for program /opt/petsc/bin/win32fe/dbx...not found Checking for program /usr/texbin/xdb...not found Checking for program xdb...not found Checking for program /opt/local/bin/xdb...not found Checking for program /opt/local/sbin/xdb...not found Checking for program /usr/local/bin/xdb...not found Checking for program /usr/bin/xdb...not found Checking for program /bin/xdb...not found Checking for program /usr/sbin/xdb...not found Checking for program /sbin/xdb...not found Checking for program /opt/X11/bin/xdb...not found Checking for program /usr/texbin/xdb...not found Checking for program /Users/likask/xdb...not found Checking for program /opt/petsc/bin/win32fe/xdb...not found Checking for program /usr/texbin/dsymutil...not found Checking for program dsymutil...not found Checking for program /opt/local/bin/dsymutil...not found Checking for program /opt/local/sbin/dsymutil...not found Checking for program /usr/local/bin/dsymutil...not found Checking for program /usr/bin/dsymutil...found Defined make macro "DSYMUTIL" to "/usr/bin/dsymutil" Defined make macro "DSYMUTIL" to "/usr/bin/dsymutil" Defined "USE_GDB_DEBUGGER" to "1" ================================================================================ TEST configureArchitecture from PETSc.options.arch(/opt/petsc/config/PETSc/options/arch.py:25) TESTING: configureArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:25) Checks PETSC_ARCH and sets if not set Defined "ARCH" to ""arch-darwin-c-debug"" ================================================================================ TEST getDatafilespath from PETSc.options.dataFilesPath(/opt/petsc/config/PETSc/options/dataFilesPath.py:29) TESTING: getDatafilespath from PETSc.options.dataFilesPath(config/PETSc/options/dataFilesPath.py:29) Checks what DATAFILESPATH should be Executing: cd /opt/petsc && git describe stdout: v3.5.3-2812-gc9542f9 Executing: cd /opt/petsc && git log -1 --pretty=format:%H stdout: c9542f9ac1a4fbf9e686b1d5e2e739975907910f Executing: cd /opt/petsc && git log -1 --pretty=format:%ci stdout: 2015-05-03 22:34:15 +0300 Executing: cd /opt/petsc && git branch stdout: * master ================================================================================ TEST configureInstallationMethod from PETSc.options.petscclone(/opt/petsc/config/PETSc/options/petscclone.py:20) TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:20) bin/maint exists. This appears to be a repository clone .git directory exists Defined "VERSION_GIT" to ""v3.5.3-2812-gc9542f9"" Defined "VERSION_DATE_GIT" to ""2015-05-03 22:34:15 +0300"" Defined "VERSION_BRANCH_GIT" to ""master"" Changed persistence directory to /opt/petsc/arch-darwin-c-debug/lib/petsc/conf ================================================================================ TEST setInstallDir from PETSc.options.installDir(/opt/petsc/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 ================================================================================ TEST saveReconfigure from PETSc.options.installDir(/opt/petsc/config/PETSc/options/installDir.py:74) TESTING: saveReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:74) ================================================================================ TEST cleanInstallDir from PETSc.options.installDir(/opt/petsc/config/PETSc/options/installDir.py:67) TESTING: cleanInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:67) ================================================================================ TEST configureInstallDir from PETSc.options.installDir(/opt/petsc/config/PETSc/options/installDir.py:51) TESTING: configureInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:51) Makes installDir subdirectories if it does not exist for both prefix install location and PETSc work install location ================================================================================ TEST restoreReconfigure from PETSc.options.installDir(/opt/petsc/config/PETSc/options/installDir.py:87) TESTING: restoreReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:87) Pushing language C Popping language C Pushing language CUDA Popping language CUDA Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC Pushing language C Popping language C Pushing language C Popping language C Pushing language C Popping language C Preprocess stderr before filtering:: Preprocess stderr after filtering:: Pushing language C Popping language C Pushing language CUDA Popping language CUDA Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC Pushing language CXX Popping language CXX Pushing language CXX Popping language CXX Pushing language CXX Popping language CXX Preprocess stderr before filtering:: Preprocess stderr after filtering:: Pushing language C Popping language C Pushing language CUDA Popping language CUDA Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC Pushing language FC Popping language FC Pushing language FC Popping language FC Pushing language FC Popping language FC Executing: gcc --help stdout: OVERVIEW: clang LLVM compiler USAGE: clang [options] OPTIONS: -### Print (but do not run) the commands to run for this compilation --analyze Run the static analyzer -arcmt-migrate-emit-errors Emit ARC errors even if the migrator can fix them -arcmt-migrate-report-output Output path for the plist report -cxx-isystem Add directory to the C++ SYSTEM include search path -c Only run preprocess, compile, and assemble steps -dD Print macro definitions in -E mode in addition to normal output -dependency-dot Filename to write DOT-formatted header dependencies to -dependency-file Filename (or -) to write dependency output to -dM Print macro definitions in -E mode instead of normal output -emit-ast Emit Clang AST files for source inputs -emit-llvm Use the LLVM representation for assembler and object files -E Only run the preprocessor -faltivec Enable AltiVec vector initializer syntax -fansi-escape-codes Use ANSI escape codes for diagnostics -fapinotes-cache-path= Specify the API notes cache path -fapinotes Enable external API notes support -fapple-kext Use Apple's kernel extensions ABI -fapple-pragma-pack Enable Apple gcc-compatible #pragma pack handling -fapplication-extension Restrict code to those available for App Extensions -fblocks Enable the 'blocks' language feature -fborland-extensions Accept non-standard constructs supported by the Borland compiler -fbuild-session-file= Use the last modification time of as the build session timestamp -fbuild-session-timestamp=