================================================================================ ================================================================================ Starting configure run at Thu, 12 Mar 2020 16:38:35 -0600 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --download-hypre=1 --with-debugging=no --with-shared-libraries=1 --download-fblaslapack=1 --download-metis=1 --download-ptscotch=1 --download-parmetis=1 --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1 --download-slepc=git://https://gitlab.com/slepc/slepc.git --download-slepc-commit= 59ff81b --with-mpi=1 --with-cxx-dialect=C++11 --with-fortran-bindings=0 --with-sowing=0 Working directory: /home/kongf/workhome/rod/moose/petsc Machine platform: uname_result(system='Linux', node='rod', release='4.15.0-70-generic', version='#79-Ubuntu SMP Tue Nov 12 10:36:11 UTC 2019', machine='x86_64', processor='x86_64') Python version: 3.7.6 (default, Jan 8 2020, 19:59:22) [GCC 7.3.0] ================================================================================ ================================================================================ TEST configureExternalPackagesDir from config.framework(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/framework.py:911) TESTING: configureExternalPackagesDir from config.framework(config/BuildSystem/config/framework.py:911) ================================================================================ TEST configureDebuggers from config.utilities.debuggers(/home/kongf/workhome/rod/moose/petsc/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 Executing: uname -s stdout: Linux Checking for program /home/kongf/workhome/rod/miniconda3/bin/gdb...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/gdb...not found Checking for program /home/kongf/workhome/rod/miniconda3/condabin/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"" Executing: uname -s stdout: Linux Defined make macro "DSYMUTIL" to "true" child config.utilities.debuggers 0.010668 ================================================================================ TEST configureDirectories from PETSc.options.petscdir(/home/kongf/workhome/rod/moose/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 1 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 12 #define PETSC_VERSION_SUBMINOR 4 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "unknown" #define PETSC_VERSION_GIT "unknown" #define PETSC_VERSION_DATE_GIT "unknown" #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 0.003588 ================================================================================ TEST getDatafilespath from PETSc.options.dataFilesPath(/home/kongf/workhome/rod/moose/petsc/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 0.000308 ================================================================================ TEST configureGit from config.sourceControl(/home/kongf/workhome/rod/moose/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 /home/kongf/workhome/rod/miniconda3/bin/git...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/git...not found Checking for program /home/kongf/workhome/rod/miniconda3/condabin/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...found Defined make macro "GIT" to "git" Executing: git --version stdout: git version 2.17.1 child config.sourceControl 0.005860 ================================================================================ TEST configureInstallationMethod from PETSc.options.petscclone(/home/kongf/workhome/rod/moose/petsc/config/PETSc/options/petscclone.py:20) TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:20) lib/petsc/bin/maint exists. This appears to be a repository clone .git directory exists Executing: ['git', 'describe', '--match=v*'] stdout: v3.12.4-96-gf413fdba98 Executing: ['git', 'log', '-1', '--pretty=format:%H'] stdout: f413fdba984f8aa86152bf1d2905ebbce2ddc31e Executing: ['git', 'log', '-1', '--pretty=format:%ci'] stdout: 2020-03-11 17:29:20 +0000 Executing: ['git', 'branch'] stdout: * maint master Defined "VERSION_GIT" to ""v3.12.4-96-gf413fdba98"" Defined "VERSION_DATE_GIT" to ""2020-03-11 17:29:20 +0000"" Defined "VERSION_BRANCH_GIT" to ""maint"" child PETSc.options.petscclone 0.051088 ================================================================================ TEST setNativeArchitecture from PETSc.options.arch(/home/kongf/workhome/rod/moose/petsc/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/kongf/workhome/rod/moose/petsc/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-moose/lib/petsc/conf/configure-hash Deleting configure hash file: arch-moose/lib/petsc/conf/configure-hash Unable to delete configure hash file: arch-moose/lib/petsc/conf/configure-hash child PETSc.options.arch 0.069583 ================================================================================ TEST setInstallDir from PETSc.options.installDir(/home/kongf/workhome/rod/moose/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 Defined make macro "PREFIXDIR" to "/home/kongf/workhome/rod/moose/petsc/arch-moose" ================================================================================ TEST saveReconfigure from PETSc.options.installDir(/home/kongf/workhome/rod/moose/petsc/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/kongf/workhome/rod/moose/petsc/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/kongf/workhome/rod/moose/petsc/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/kongf/workhome/rod/moose/petsc/arch-moose/lib/petsc/conf ================================================================================ TEST restoreReconfigure from PETSc.options.installDir(/home/kongf/workhome/rod/moose/petsc/config/PETSc/options/installDir.py:93) TESTING: restoreReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:93) child PETSc.options.installDir 0.009420 ================================================================================ TEST setExternalPackagesDir from PETSc.options.externalpackagesdir(/home/kongf/workhome/rod/moose/petsc/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/kongf/workhome/rod/moose/petsc/config/PETSc/options/externalpackagesdir.py:22) TESTING: cleanExternalpackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:22) child PETSc.options.externalpackagesdir 0.000442 ================================================================================ TEST configureCLanguage from PETSc.options.languages(/home/kongf/workhome/rod/moose/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 C language is C Defined "CLANGUAGE_C" to "1" child PETSc.options.languages 0.001113 ================================================================================ TEST printEnvVariables from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1700) TESTING: printEnvVariables from config.setCompilers(config/BuildSystem/config/setCompilers.py:1700) **** printenv **** CONDA_SHLVL=2 CONDA_EXE=/home/kongf/workhome/rod/miniconda3/bin/conda SSH_CONNECTION=141.221.41.246 54621 141.221.75.240 22 GPROF=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gprof MOOSE_NO_CODESIGN=true LANG=en_US.UTF-8 GXX=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-g++ hostname=hostname CCACHE_SLOPPINESS=time_macros OLDPWD=/home/kongf/workhome/rod/moose LD_GOLD=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-ld.gold DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include MPIHOME=/home/kongf/workhome/rod/miniconda3/envs/moose DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include GCC_NM=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gcc-nm PETSC_ARCH=arch-moose CONDA_PREFIX=/home/kongf/workhome/rod/miniconda3/envs/moose GCC_RANLIB=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include GCC_AR=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gcc-ar S_COLORS=auto _CE_M= CC=ccache mpicc READELF=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-readelf XDG_SESSION_ID=4702 USER=kongf CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include CONDA_PREFIX_1=/home/kongf/workhome/rod/miniconda3 MODULE_VERSION=3.2.10 STRIP=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-strip DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe OBJCOPY=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-objcopy _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu PWD=/home/kongf/workhome/rod/moose/petsc HOME=/home/kongf CONDA_PYTHON_EXE=/home/kongf/workhome/rod/miniconda3/bin/python ADDR2LINE=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-addr2line CMAKE_PREFIX_PATH=/home/kongf/workhome/rod/miniconda3/envs/moose:/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/usr HOST=x86_64-conda_cos6-linux-gnu SSH_CLIENT=141.221.41.246 54621 22 hpc_bash_loaded=Yes F77=mpif77 FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop RANLIB=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-ranlib OBJDUMP=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-objdump AS=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-as AR=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-ar GFORTRAN=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gfortran CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu _CE_CONDA= DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe LOADEDMODULES= FC=mpif90 NM=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-nm CONDA_PROMPT_MODIFIER=(moose) SSH_TTY=/dev/pts/7 CONDA_BUILD_SYSROOT=/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot MAIL=/var/mail/kongf DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include CXX=ccache mpicxx SHELL=/bin/bash TERM=xterm-256color CXXFILT=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-c++filt myhost=rod ELFEDIT=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-elfedit SHLVL=2 FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include MANPATH=:/opt/pbs/share/man CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib STRINGS=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-strings F90=mpif90 F95=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-f95 MODULEPATH=/opt/Modules/versions:/opt/Modules/$MODULE_VERSION/modulefiles:/opt/Modules/modulefiles LOGNAME=kongf DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/24746/bus XDG_RUNTIME_DIR=/run/user/24746 MODULE_VERSION_STACK=3.2.10 LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib PATH=/home/kongf/workhome/rod/miniconda3/bin:/home/kongf/workhome/rod/miniconda3/envs/moose/bin:/home/kongf/workhome/rod/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/pbs/bin GCC=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gcc MODULESHOME=/opt/Modules/3.2.10 CONDA_DEFAULT_ENV=moose PETSC_DIR=/home/kongf/workhome/rod/moose/scripts/../petsc SIZE=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-size CPP=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-cpp LD=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-ld BASH_FUNC_module%%=() { eval `/opt/Modules/$MODULE_VERSION/bin/modulecmd bash $*` } _=./configure ================================================================================ TEST resetEnvCompilers from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1707) TESTING: resetEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1707) =============================================================================== ***** WARNING: CC (set to ccache mpicc) found in environment variables - ignoring use ./configure CC=$CC if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CXX (set to ccache mpicxx) found in environment variables - ignoring use ./configure CXX=$CXX if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: FC (set to mpif90) found in environment variables - ignoring use ./configure FC=$FC if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: F77 (set to mpif77) found in environment variables - ignoring use ./configure F77=$F77 if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: F90 (set to mpif90) found in environment variables - ignoring use ./configure F90=$F90 if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CFLAGS (set to -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include) found in environment variables - ignoring use ./configure CFLAGS=$CFLAGS if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CXXFLAGS (set to -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include) found in environment variables - ignoring use ./configure CXXFLAGS=$CXXFLAGS if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: FFLAGS (set to -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include) found in environment variables - ignoring use ./configure FFLAGS=$FFLAGS if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CPP (set to /home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-cpp) found in environment variables - ignoring use ./configure CPP=$CPP if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CPPFLAGS (set to -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/kongf/workhome/rod/miniconda3/envs/moose/include) found in environment variables - ignoring use ./configure CPPFLAGS=$CPPFLAGS if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: LDFLAGS (set to -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib) found in environment variables - ignoring use ./configure LDFLAGS=$LDFLAGS if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: AR (set to /home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-ar) found in environment variables - ignoring use ./configure AR=$AR if you really want to use that value ****** =============================================================================== ================================================================================ TEST checkEnvCompilers from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1737) TESTING: checkEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1737) ================================================================================ TEST checkMPICompilerOverride from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1670) TESTING: checkMPICompilerOverride from config.setCompilers(config/BuildSystem/config/setCompilers.py:1670) 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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1691) TESTING: requireMpiLdPath from config.setCompilers(config/BuildSystem/config/setCompilers.py:1691) OpenMPI wrappers require LD_LIBRARY_PATH set ================================================================================ TEST checkInitialFlags from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:435) TESTING: checkInitialFlags from config.setCompilers(config/BuildSystem/config/setCompilers.py:435) 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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:605) TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:605) Locate a functional C compiler Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpicc...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpicc...found Defined make macro "CC" to "mpicc" All intermediate test results are stored in /tmp/petsc-uw1fxxf1 All intermediate test results are stored in /tmp/petsc-uw1fxxf1/config.setCompilers Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Testing executable /tmp/petsc-uw1fxxf1/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest Executing: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest Executing: mpicc --version stdout: x86_64-conda_cos6-linux-gnu-cc (crosstool-NG 1.23.0.450-d54ae) 7.3.0 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 checkCPreprocessor from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:642) TESTING: checkCPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:642) Locate a functional C preprocessor Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpicc...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpicc...found Defined make macro "CPP" to "mpicc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkCUDACompiler from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:680) TESTING: checkCUDACompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:680) Locate a functional CUDA compiler Checking for program /home/kongf/workhome/rod/miniconda3/bin/nvcc...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/nvcc...not found Checking for program /home/kongf/workhome/rod/miniconda3/condabin/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 /opt/pbs/bin/nvcc...not found Checking for program /home/kongf/workhome/rod/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found Checking for program /Developer/NVIDIA/CUDA-6.5/bin/nvcc...not found Checking for program /home/kongf/workhome/rod/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found Checking for program /usr/local/cuda/bin/nvcc...not found Checking for program /home/kongf/workhome/rod/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found ================================================================================ TEST checkCUDAPreprocessor from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:720) TESTING: checkCUDAPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:720) Locate a functional CUDA preprocessor ================================================================================ TEST checkCxxCompiler from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:820) TESTING: checkCxxCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:820) Locate a functional Cxx compiler Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpicxx...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpicxx...found Defined make macro "CXX" to "mpicxx" Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Testing executable /tmp/petsc-uw1fxxf1/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest Executing: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest Executing: mpicxx --version stdout: x86_64-conda_cos6-linux-gnu-c++ (crosstool-NG 1.23.0.450-d54ae) 7.3.0 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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:862) TESTING: checkCxxPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:862) Locate a functional Cxx preprocessor Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpicxx...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpicxx...found Defined make macro "CXXPP" to "mpicxx -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicxx -E -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkFortranCompiler from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:965) TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:965) Locate a functional Fortran compiler Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpif90...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpif90...found Defined make macro "FC" to "mpif90" Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Testing executable /tmp/petsc-uw1fxxf1/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest Executing: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest Executing: mpif90 --version stdout: GNU Fortran (crosstool-NG 1.23.0.450-d54ae) 7.3.0 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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1002) TESTING: checkFortranPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:1002) Locate a functional Fortran preprocessor Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpif90...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpif90...found Defined make macro "FPP" to "mpif90 -E" Deleting "FPP" Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpif90...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpif90...found Defined make macro "FPP" to "mpif90 --use cpp32" Deleting "FPP" ================================================================================ TEST checkFortranComments from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1025) TESTING: checkFortranComments from config.setCompilers(config/BuildSystem/config/setCompilers.py:1025) Make sure fortran comment "!" works Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main ! comment end Fortran comments can use ! in column 1 ================================================================================ TEST checkLargeFileIO from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1156) TESTING: checkLargeFileIO from config.setCompilers(config/BuildSystem/config/setCompilers.py:1156) ================================================================================ TEST checkArchiver from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1255) TESTING: checkArchiver from config.setCompilers(config/BuildSystem/config/setCompilers.py:1255) Check that the archiver exists and can make a library usable by the compiler 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. 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" Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /home/kongf/workhome/rod/miniconda3/bin/ar...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/ar...not found Checking for program /home/kongf/workhome/rod/miniconda3/condabin/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/kongf/workhome/rod/miniconda3/bin/ranlib...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/ranlib...not found Checking for program /home/kongf/workhome/rod/miniconda3/condabin/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" Executing: /usr/bin/ar cr /tmp/petsc-uw1fxxf1/config.setCompilers/libconf1.a /tmp/petsc-uw1fxxf1/config.setCompilers/conf1.o Executing: /usr/bin/ranlib -c /tmp/petsc-uw1fxxf1/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. 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. 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" Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /home/kongf/workhome/rod/miniconda3/bin/ar...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/ar...not found Checking for program /home/kongf/workhome/rod/miniconda3/condabin/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/kongf/workhome/rod/miniconda3/bin/ranlib...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/ranlib...not found Checking for program /home/kongf/workhome/rod/miniconda3/condabin/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" Executing: /usr/bin/ar cr /tmp/petsc-uw1fxxf1/config.setCompilers/libconf1.a /tmp/petsc-uw1fxxf1/config.setCompilers/conf1.o Executing: /usr/bin/ranlib /tmp/petsc-uw1fxxf1/config.setCompilers/libconf1.a Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/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; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -L/tmp/petsc-uw1fxxf1/config.setCompilers -lconf1 Defined make macro "AR_FLAGS" to "cr" Defined make macro "AR_LIB_SUFFIX" to "a" ================================================================================ TEST checkSharedLinker from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1369) TESTING: checkSharedLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1369) Check that the linker can produce shared libraries Executing: uname -s stdout: Linux Checking shared linker mpicc using flags ['-shared'] Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpicc...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpicc...found Defined make macro "LD_SHARED" to "mpicc" Trying C compiler flag Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -shared /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Valid C linker flag -shared Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/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();} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/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 /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/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'] Executing: mpicc --help | head -n 20 stdout: Usage: x86_64-conda_cos6-linux-gnu-cc [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 Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fPIC Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Valid C linker flag -shared Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/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();} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/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; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -L/tmp/petsc-uw1fxxf1/config.setCompilers -lconftest Using shared linker mpicc with flags ['-shared'] and library extension so Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux ================================================================================ TEST checkPIC from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1103) TESTING: checkPIC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1103) Determine the PIC option for each compiler Trying Cxx for PIC code without any compiler flag Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/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();} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/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 /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status Rejected Cxx compiler flag because shared linker cannot handle it Executing: mpicxx --help | head -n 20 stdout: Usage: x86_64-conda_cos6-linux-gnu-c++ [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 Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fPIC Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/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();} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Accepted Cxx compiler flag -fPIC for PIC code Trying FC for PIC code without any compiler flag Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `xx_' can not be used when making a shared object; recompile with -fPIC /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status Rejected FC compiler flag because shared linker cannot handle it Executing: mpif90 --help | head -n 20 stdout: Usage: x86_64-conda_cos6-linux-gnu-gfortran.bin [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 Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -fPIC Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Accepted FC compiler flag -fPIC for PIC code ================================================================================ TEST checkSharedLinkerPaths from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1481) TESTING: checkSharedLinkerPaths from config.setCompilers(config/BuildSystem/config/setCompilers.py:1481) Determine the shared linker path options - IRIX: -rpath - Linux, OSF: -Wl,-rpath, - Solaris: -R - FreeBSD: -Wl,-R, Executing: uname -s stdout: Linux Executing: mpicc -V Trying C linker flag -Wl,-rpath, Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -Wl,-rpath,/home/kongf/workhome/rod/moose/petsc -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Valid C linker flag -Wl,-rpath,/home/kongf/workhome/rod/moose/petsc Executing: uname -s stdout: Linux Executing: mpicc -V Trying Cxx linker flag -Wl,-rpath, Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -Wl,-rpath,/home/kongf/workhome/rod/moose/petsc /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Valid Cxx linker flag -Wl,-rpath,/home/kongf/workhome/rod/moose/petsc Executing: uname -s stdout: Linux Executing: mpicc -V Trying FC linker flag -Wl,-rpath, Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -Wl,-rpath,/home/kongf/workhome/rod/moose/petsc -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Valid FC linker flag -Wl,-rpath,/home/kongf/workhome/rod/moose/petsc ================================================================================ TEST checkLibC from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1516) TESTING: checkLibC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1516) Test whether we need to explicitly include libc in shared linking - Mac OSX requires an explicit reference to libc for shared linking Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/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;} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o Shared linking does not require an explicit libc reference ================================================================================ TEST checkDynamicLinker from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1562) TESTING: checkDynamicLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1562) Check that the linker can dynamicaly load shared libraries Checking for header: dlfcn.h All intermediate test results are stored in /tmp/petsc-uw1fxxf1/config.headers Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.headers /tmp/petsc-uw1fxxf1/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-uw1fxxf1/config.libraries Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.libraries/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.libraries -fPIC /tmp/petsc-uw1fxxf1/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; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.libraries/conftest -fPIC /tmp/petsc-uw1fxxf1/config.libraries/conftest.o -ldl Defined "HAVE_LIBDL" to "1" Adding ['dl'] to LIBS Executing: uname -s stdout: Linux Checking dynamic linker mpicc using flags ['-shared'] Checking for program /home/kongf/workhome/rod/miniconda3/bin/mpicc...not found Checking for program /home/kongf/workhome/rod/miniconda3/envs/moose/bin/mpicc...found Defined make macro "DYNAMICLINKER" to "mpicc" Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -ldl Valid C linker flag -shared Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {printf("test");return 0;} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -ldl Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { void *handle = dlopen("/tmp/petsc-uw1fxxf1/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; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -ldl Using dynamic linker mpicc with flags ['-shared'] and library extension so ================================================================================ TEST output from config.setCompilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py:1611) TESTING: output from config.setCompilers(config/BuildSystem/config/setCompilers.py:1611) 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 4.921483 ================================================================================ TEST checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(/home/kongf/workhome/rod/moose/petsc/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/kongf/workhome/rod/moose/petsc/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 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/kongf/workhome/rod/moose/petsc/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/kongf/workhome/rod/moose/petsc/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 0.007979 ================================================================================ TEST configureIndexSize from PETSc.options.indexTypes(/home/kongf/workhome/rod/moose/petsc/config/PETSc/options/indexTypes.py:30) TESTING: configureIndexSize from PETSc.options.indexTypes(config/PETSc/options/indexTypes.py:30) Defined make macro "PETSC_INDEX_SIZE" to "32" child PETSc.options.indexTypes 0.000896 ================================================================================ TEST configureCompilerFlags from config.compilerFlags(/home/kongf/workhome/rod/moose/petsc/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 "x86_64-conda_cos6-linux-gnu-cc (crosstool-NG 1.23.0.450-d54ae) 7.3.0" Defined make macro "MPICC_SHOW" to "x86_64-conda_cos6-linux-gnu-cc -march=nocona -mtune=haswell -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,--enable-new-dtags -lmpi" Trying C compiler flag -Wall Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall /tmp/petsc-uw1fxxf1/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 Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings /tmp/petsc-uw1fxxf1/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 Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing /tmp/petsc-uw1fxxf1/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 Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas /tmp/petsc-uw1fxxf1/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 Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector /tmp/petsc-uw1fxxf1/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 Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -mfp16-format=ieee /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: x86_64-conda_cos6-linux-gnu-cc: 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 x86_64-conda_cos6-linux-gnu-cc: 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 Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fvisibility=hidden Defined make macro "MPICC_SHOW" to "x86_64-conda_cos6-linux-gnu-cc -march=nocona -mtune=haswell -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,--enable-new-dtags -lmpi" Trying C compiler flag -g Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -g Trying C compiler flag -O Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -O Defined make macro "Cxx_VERSION" to "x86_64-conda_cos6-linux-gnu-c++ (crosstool-NG 1.23.0.450-d54ae) 7.3.0" Defined make macro "MPICXX_SHOW" to "x86_64-conda_cos6-linux-gnu-c++ -march=nocona -mtune=haswell -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -lmpicxx -Wl,-rpath -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,--enable-new-dtags -lmpi" Trying Cxx compiler flag -Wall Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -fPIC /tmp/petsc-uw1fxxf1/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 Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -fPIC /tmp/petsc-uw1fxxf1/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 Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -fPIC /tmp/petsc-uw1fxxf1/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 Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fPIC /tmp/petsc-uw1fxxf1/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 Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fPIC /tmp/petsc-uw1fxxf1/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 Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fvisibility=hidden Defined make macro "MPICXX_SHOW" to "x86_64-conda_cos6-linux-gnu-c++ -march=nocona -mtune=haswell -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -lmpicxx -Wl,-rpath -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,--enable-new-dtags -lmpi" Trying Cxx compiler flag -g Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -g Trying Cxx compiler flag -O Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -O Defined make macro "FC_VERSION" to "GNU Fortran (crosstool-NG 1.23.0.450-d54ae) 7.3.0" Defined make macro "MPIFC_SHOW" to "x86_64-conda_cos6-linux-gnu-gfortran -march=nocona -mtune=haswell -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -lmpifort -Wl,-rpath -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,--enable-new-dtags -lmpi" Trying FC compiler flag -Wall Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wall Trying FC compiler flag -ffree-line-length-0 Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -ffree-line-length-0 /tmp/petsc-uw1fxxf1/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 Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wno-unused-dummy-argument Defined make macro "MPIFC_SHOW" to "x86_64-conda_cos6-linux-gnu-gfortran -march=nocona -mtune=haswell -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -lmpifort -Wl,-rpath -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,--enable-new-dtags -lmpi" Trying FC compiler flag -g Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -g Trying FC compiler flag -O Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -O child config.compilerFlags 2.079137 Executing: mpicc --help | head -n 20 stdout: Usage: x86_64-conda_cos6-linux-gnu-cc [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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: mpicc -V All intermediate test results are stored in /tmp/petsc-uw1fxxf1/config.compilers Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-uw1fxxf1/config.compilers/conftest.c: In function 'main': /tmp/petsc-uw1fxxf1/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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:391) TESTING: checkCFormatting from config.compilers(config/BuildSystem/config/compilers.py:391) Activate format string checking if using the GNU compilers ================================================================================ TEST checkCInline from config.compilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:108) TESTING: checkCInline from config.compilers(config/BuildSystem/config/compilers.py:108) Check for C inline keyword Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:402) TESTING: checkDynamicLoadFlag from config.compilers(config/BuildSystem/config/compilers.py:402) Checks that dlopen() takes RTLD_XXX, and defines PETSC_HAVE_RTLD_XXX if it does Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/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; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:202) TESTING: checkCLibraries from config.compilers(config/BuildSystem/config/compilers.py:202) Determines the libraries needed to link with C compiled code Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -ldl C libraries are not needed when using Fortran linker Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicxx -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -ldl C libraries are not needed when using C++ linker ================================================================================ TEST checkDependencyGenerationFlag from config.compilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:1343) TESTING: checkDependencyGenerationFlag from config.compilers(config/BuildSystem/config/compilers.py:1343) 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" Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -MMD -MP /tmp/petsc-uw1fxxf1/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" Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.compilers -I/tmp/petsc-uw1fxxf1/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC -MMD -MP /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ================================================================================ TEST checkC99Flag from config.compilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:1388) TESTING: checkC99Flag from config.compilers(config/BuildSystem/config/compilers.py:1388) Check for -std=c99 or equivalent flag Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.c: In function 'main': /tmp/petsc-uw1fxxf1/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" Executing: mpicxx --help | head -n 20 stdout: Usage: x86_64-conda_cos6-linux-gnu-c++ [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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: mpicc -V Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc Possible ERROR while running compiler: stderr: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc: In function 'int main()': /tmp/petsc-uw1fxxf1/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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:421) TESTING: checkCxxOptionalExtensions from config.compilers(config/BuildSystem/config/compilers.py:421) Check whether the C++ compiler (IBM xlC, OSF5) need special flag for .c files which contain C++ Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:123) TESTING: checkCxxInline from config.compilers(config/BuildSystem/config/compilers.py:123) Check for C++ inline keyword Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:533) TESTING: checkCxxLibraries from config.compilers(config/BuildSystem/config/compilers.py:533) Determines the libraries needed to link with C++ from C and Fortran Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/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"; }} Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -ldl Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/confc.o: in function `asub()': /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `__cxa_allocate_exception' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `typeinfo for int' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `__cxa_throw' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `__cxa_begin_catch' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `std::cout' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `__cxa_end_catch' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.cc:7: undefined reference to `__cxa_end_catch' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/confc.o: in function `__static_initialization_and_destruction_0': /home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iostream:74: undefined reference to `std::ios_base::Init::Init()' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iostream:74: undefined reference to `std::ios_base::Init::~Init()' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/confc.o:(.data.DW.ref._ZTIi[DW.ref._ZTIi]+0x0): undefined reference to `typeinfo for int' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/confc.o:(.data.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0' collect2: error: ld returned 1 exit status Executing: uname -s stdout: Linux Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/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"; }} Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -lstdc++ -ldl compilers: C++ requires -lstdc++ to link with C compiler Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/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"; }} Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -lstdc++ -ldl C++ libraries are not needed when using FC linker ================================================================================ TEST checkCxxDialect from config.compilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:449) TESTING: checkCxxDialect from config.compilers(config/BuildSystem/config/compilers.py:449) 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 CXX11 with flag: Defined "HAVE_CXX_DIALECT_CXX11" to "1" Executing: mpicxx -c -o /tmp/petsc-uw1fxxf1/config.setCompilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /tmp/petsc-uw1fxxf1/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; ; return 0; } Executing: mpicxx -V ================================================================================ TEST checkFortranNameMangling from config.compilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:838) TESTING: checkFortranNameMangling from config.compilers(config/BuildSystem/config/compilers.py:838) 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;} Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1chk_(void){return;} Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran name mangling is underscore Defined "HAVE_FORTRAN_UNDERSCORE" to "1" Executing: mpif90 --version stdout: GNU Fortran (crosstool-NG 1.23.0.450-d54ae) 7.3.0 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/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:876) TESTING: checkFortranNameManglingDouble from config.compilers(config/BuildSystem/config/compilers.py:876) Checks if symbols containing an underscore append an extra underscore, and defines HAVE_FORTRAN_UNDERSCORE_UNDERSCORE if necessary Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1_chk__(void){return;} Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90 Successful compile: Source: program main call d1_chk() end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.o: in function `MAIN__': /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90:2: undefined reference to `d1_chk_' collect2: error: ld returned 1 exit status ================================================================================ TEST checkFortranLibraries from config.compilers(/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py:886) TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:886) 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. Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90 Successful compile: Source: program main #include call MPI_Allreduce() end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -lstdc++ -ldl Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90 Successful compile: Source: subroutine asub() print*,'testing' call MPI_Allreduce() return end Executing: mpicc -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.libraries -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/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; } Executing: mpicc -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o /tmp/petsc-uw1fxxf1/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/confc.o: in function `asub_': /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90:2: undefined reference to `_gfortran_st_write' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90:2: undefined reference to `_gfortran_transfer_character_write' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90:2: undefined reference to `_gfortran_st_write_done' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90:3: 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 Executing: mpif90 -c -o /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -I/tmp/petsc-uw1fxxf1/config.setCompilers -I/tmp/petsc-uw1fxxf1/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -lstdc++ -ldl stdout: mpifort for MPICH version 3.3.2 Possible ERROR while running linker: stdout: mpifort for MPICH version 3.3.2stderr: Driving: /home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gfortran.bin -specs=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs -march=nocona -mtune=haswell -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -o /tmp/petsc-uw1fxxf1/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -lstdc++ -ldl -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -I/home/kongf/workhome/rod/miniconda3/envs/moose/include -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -lmpifort -Wl,-rpath -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib -Wl,--enable-new-dtags -lmpi -l gfortran -l m -shared-libgcc Reading specs from /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs Reading specs from /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs COLLECT_GCC=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gfortran.bin COLLECT_LTO_WRAPPER=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/lto-wrapper Target: x86_64-conda_cos6-linux-gnu Configured with: /home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/src/gcc/configure --build=x86_64-build_pc-linux-gnu --host=x86_64-build_pc-linux-gnu --target=x86_64-conda_cos6-linux-gnu --prefix=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built --with-sysroot=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-languages=c,c++,fortran,objc,obj-c++ --with-pkgversion='crosstool-NG 1.23.0.450-d54ae' --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-libsanitizer --enable-libmpx --with-gmp=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpfr=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpc=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-isl=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --enable-lto --with-host-libstdcxx='-static-libgcc -Wl,-Bstatic,-lstdc++,-Bdynamic -lm' --enable-threads=posix --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-multilib --with-local-prefix=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-long-long --enable-default-pie Thread model: posix gcc version 7.3.0 (crosstool-NG 1.23.0.450-d54ae) Reading specs from /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/libgfortran.spec rename spec lib to liborig COLLECT_GCC_OPTIONS='-specs=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs' '-march=nocona' '-mtune=haswell' '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib' '-o' '/tmp/petsc-uw1fxxf1/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-g' '-O' '-I' '/home/kongf/workhome/rod/miniconda3/envs/moose/include' '-I' '/home/kongf/workhome/rod/miniconda3/envs/moose/include' '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib' '-shared-libgcc' COMPILER_PATH=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ LIBRARY_PATH=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/ COLLECT_GCC_OPTIONS='-specs=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs' '-march=nocona' '-mtune=haswell' '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib' '-o' '/tmp/petsc-uw1fxxf1/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-g' '-O' '-I' '/home/kongf/workhome/rod/miniconda3/envs/moose/include' '-I' '/home/kongf/workhome/rod/miniconda3/envs/moose/include' '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib' '-shared-libgcc' /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/collect2 -plugin /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/liblto_plugin.so -plugin-opt=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccHZcJx3.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=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o /tmp/petsc-uw1fxxf1/config.compilers/conftest /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/crti.o /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/crtbeginS.o -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib -rpath /home/kongf/workhome/rod/miniconda3/envs/moose/lib -O2 --sort-common --as-needed -z relro -z now --disable-new-dtags --gc-sections -rpath /home/kongf/workhome/rod/miniconda3/envs/moose/lib -rpath-link /home/kongf/workhome/rod/miniconda3/envs/moose/lib /tmp/petsc-uw1fxxf1/config.compilers/conftest.o -lstdc++ -ldl -lmpifort -rpath /home/kongf/workhome/rod/miniconda3/envs/moose/lib --enable-new-dtags -lmpi -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/crtendS.o /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/crtn.o COLLECT_GCC_OPTIONS='-specs=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs' '-march=nocona' '-mtune=haswell' '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib' '-o' '/tmp/petsc-uw1fxxf1/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-g' '-O' '-I' '/home/kongf/workhome/rod/miniconda3/envs/moose/include' '-I' '/home/kongf/workhome/rod/miniconda3/envs/moose/include' '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib' '-shared-libgcc' compilers: Checking arg mpifort compilers: Unknown arg mpifort compilers: Checking arg for compilers: Unknown arg for compilers: Checking arg MPICH compilers: Unknown arg MPICH compilers: Checking arg version compilers: Unknown arg version compilers: Checking arg 3.3.2 compilers: Unknown arg 3.3.2 compilers: Checking arg Driving: compilers: Unknown arg Driving: compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gfortran.bin compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gfortran.bin compilers: Checking arg -specs=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs compilers: Unknown arg -specs=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs compilers: Checking arg -march=nocona compilers: Unknown arg -march=nocona compilers: Checking arg -mtune=haswell compilers: Unknown arg -mtune=haswell compilers: Checking arg -Wl,-O2 compilers: Unknown arg -Wl,-O2 compilers: Checking arg -Wl,--sort-common compilers: Unknown arg -Wl,--sort-common compilers: Checking arg -Wl,--as-needed compilers: Unknown arg -Wl,--as-needed compilers: Checking arg -Wl,-z,relro compilers: Unknown arg -Wl,-z,relro compilers: Checking arg -Wl,-z,now compilers: Unknown arg -Wl,-z,now compilers: Checking arg -Wl,--disable-new-dtags compilers: Unknown arg -Wl,--disable-new-dtags compilers: Checking arg -Wl,--gc-sections compilers: Unknown arg -Wl,--gc-sections compilers: Checking arg -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Unknown arg -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Unknown arg -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Found library directory: -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-uw1fxxf1/config.compilers/conftest compilers: Unknown arg /tmp/petsc-uw1fxxf1/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 -g compilers: Unknown arg -g compilers: Checking arg -O compilers: Unknown arg -O compilers: Checking arg /tmp/petsc-uw1fxxf1/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-uw1fxxf1/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Found library: -lstdc++ compilers: Checking arg -ldl compilers: Found library: -ldl compilers: Checking arg -I/home/kongf/workhome/rod/miniconda3/envs/moose/include compilers: Found include directory: /home/kongf/workhome/rod/miniconda3/envs/moose/include compilers: Checking arg -I/home/kongf/workhome/rod/miniconda3/envs/moose/include compilers: Found include directory: /home/kongf/workhome/rod/miniconda3/envs/moose/include compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Already in lflags so skipping: -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -lmpifort compilers: Found library: -lmpifort compilers: Checking arg -Wl,-rpath compilers: Unknown arg -Wl,-rpath compilers: Checking arg -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Unknown arg -Wl,/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -Wl,--enable-new-dtags compilers: Unknown arg -Wl,--enable-new-dtags 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 Reading compilers: Unknown arg Reading compilers: Checking arg specs compilers: Unknown arg specs compilers: Checking arg from compilers: Unknown arg from compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs 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 /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs compilers: Checking arg COLLECT_GCC=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gfortran.bin compilers: Unknown arg COLLECT_GCC=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/x86_64-conda_cos6-linux-gnu-gfortran.bin compilers: Checking arg COLLECT_LTO_WRAPPER=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/lto-wrapper compilers: Unknown arg COLLECT_LTO_WRAPPER=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/lto-wrapper compilers: Checking arg Target: compilers: Unknown arg Target: compilers: Checking arg x86_64-conda_cos6-linux-gnu compilers: Unknown arg x86_64-conda_cos6-linux-gnu compilers: Checking arg Configured compilers: Unknown arg Configured compilers: Checking arg with: compilers: Unknown arg with: compilers: Checking arg /home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/src/gcc/configure compilers: Unknown arg /home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/src/gcc/configure compilers: Checking arg --build=x86_64-build_pc-linux-gnu compilers: Unknown arg --build=x86_64-build_pc-linux-gnu compilers: Checking arg --host=x86_64-build_pc-linux-gnu compilers: Unknown arg --host=x86_64-build_pc-linux-gnu compilers: Checking arg --target=x86_64-conda_cos6-linux-gnu compilers: Unknown arg --target=x86_64-conda_cos6-linux-gnu compilers: Checking arg --prefix=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built compilers: Unknown arg --prefix=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built compilers: Checking arg --with-sysroot=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot compilers: Unknown arg --with-sysroot=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot compilers: Checking arg --enable-languages=c,c++,fortran,objc,obj-c++ compilers: Unknown arg --enable-languages=c,c++,fortran,objc,obj-c++ compilers: Checking arg --with-pkgversion= compilers: Unknown arg --with-pkgversion= compilers: Checking arg --enable-__cxa_atexit compilers: Unknown arg --enable-__cxa_atexit compilers: Checking arg --disable-libmudflap compilers: Unknown arg --disable-libmudflap compilers: Checking arg --enable-libgomp compilers: Unknown arg --enable-libgomp compilers: Checking arg --disable-libssp compilers: Unknown arg --disable-libssp compilers: Checking arg --enable-libquadmath compilers: Unknown arg --enable-libquadmath compilers: Checking arg --enable-libquadmath-support compilers: Unknown arg --enable-libquadmath-support compilers: Checking arg --enable-libsanitizer compilers: Unknown arg --enable-libsanitizer compilers: Checking arg --enable-libmpx compilers: Unknown arg --enable-libmpx compilers: Checking arg --with-gmp=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Unknown arg --with-gmp=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Checking arg --with-mpfr=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Unknown arg --with-mpfr=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Checking arg --with-mpc=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Unknown arg --with-mpc=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Checking arg --with-isl=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Unknown arg --with-isl=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/.build/x86_64-conda_cos6-linux-gnu/buildtools compilers: Checking arg --enable-lto compilers: Unknown arg --enable-lto compilers: Checking arg --with-host-libstdcxx= compilers: Unknown arg --with-host-libstdcxx= compilers: Checking arg --enable-threads=posix compilers: Unknown arg --enable-threads=posix compilers: Checking arg --enable-target-optspace compilers: Unknown arg --enable-target-optspace compilers: Checking arg --enable-plugin compilers: Unknown arg --enable-plugin compilers: Checking arg --enable-gold compilers: Unknown arg --enable-gold compilers: Checking arg --disable-nls compilers: Unknown arg --disable-nls compilers: Checking arg --disable-multilib compilers: Unknown arg --disable-multilib compilers: Checking arg --with-local-prefix=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot compilers: Unknown arg --with-local-prefix=/home/conda/feedstock_root/build_artifacts/ctng-compilers_1580517382604/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot compilers: Checking arg --enable-long-long compilers: Unknown arg --enable-long-long compilers: Checking arg --enable-default-pie compilers: Unknown arg --enable-default-pie 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 7.3.0 compilers: Unknown arg 7.3.0 compilers: Checking arg (crosstool-NG compilers: Unknown arg (crosstool-NG compilers: Checking arg 1.23.0.450-d54ae) compilers: Unknown arg 1.23.0.450-d54ae) 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 /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/libgfortran.spec compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/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=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ compilers: Skipping arg COMPILER_PATH=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ compilers: Checking arg LIBRARY_PATH=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/ compilers: Skipping arg LIBRARY_PATH=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/:/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/ compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/collect2 compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/collect2 compilers: Checking arg -plugin compilers: Unknown arg -plugin compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/liblto_plugin.so compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/liblto_plugin.so compilers: Checking arg -plugin-opt=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/lto-wrapper compilers: Unknown arg -plugin-opt=/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/lto-wrapper compilers: Checking arg -plugin-opt=-fresolution=/tmp/ccHZcJx3.res compilers: Unknown arg -plugin-opt=-fresolution=/tmp/ccHZcJx3.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=-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 --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 -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 -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-uw1fxxf1/config.compilers/conftest compilers: Unknown arg /tmp/petsc-uw1fxxf1/config.compilers/conftest compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/crti.o compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/crti.o compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/crtbeginS.o compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/crtbeginS.o compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Already in lflags so skipping: -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Already in lflags so skipping: -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 compilers: Found library directory: -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc compilers: Found library directory: -L/home/kongf/workhome/rod/miniconda3/envs/moose/lib/gcc compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib compilers: Found library directory: -L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib compilers: Found library directory: -L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib compilers: Found library directory: -L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib compilers: Already in lflags so skipping: -L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib compilers: Already in lflags so skipping: -L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/lib compilers: Checking arg -L/home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib compilers: Already in lflags so skipping: -L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib compilers: Checking arg -rpath compilers: Found -rpath library: /home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg -O2 compilers: Unknown arg -O2 compilers: Checking arg --sort-common compilers: Unknown arg --sort-common compilers: Checking arg --as-needed compilers: Unknown arg --as-needed compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg relro compilers: Unknown arg relro compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg now compilers: Unknown arg now compilers: Checking arg --disable-new-dtags compilers: Unknown arg --disable-new-dtags compilers: Checking arg --gc-sections compilers: Unknown arg --gc-sections compilers: Checking arg -rpath compilers: Already in rpathflags so skipping: -rpath compilers: Checking arg -rpath-link compilers: Unknown arg -rpath-link compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/lib compilers: Checking arg /tmp/petsc-uw1fxxf1/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-uw1fxxf1/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 -lmpifort compilers: Already in lflags: -lmpifort compilers: Checking arg -rpath compilers: Already in rpathflags so skipping: -rpath compilers: Checking arg --enable-new-dtags compilers: Unknown arg --enable-new-dtags 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 -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 /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/crtendS.o compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/crtendS.o compilers: Checking arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/crtn.o compilers: Unknown arg /home/kongf/workhome/rod/miniconda3/envs/moose/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/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: ['-Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib', '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib', '-lstdc++', '-ldl', '-lmpifort', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0', '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0', '-Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib/gcc', '-L/home/kongf/workhome/rod/miniconda3/envs/moose/lib/gcc', '-Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/lib', '-L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/lib', '-Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/lib', '-L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/lib', '-Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib', '-L/home/kongf/workhome/rod/miniconda3/envs/moose/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib', '-Wl,-rpath,/home/kongf/workhome/rod/miniconda3/envs/moose/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath'] compilers: Libraries needed to link Fortran main with the C linker: [] compilers: Check that Fortran libraries can be used with C as the linker **** Configure header /tmp/petsc-uw1fxxf1/confdefs.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #define PETSC_CLANGUAGE_C 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_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_DYNAMIC_LIBRARIES 1 #define PETSC_USE_SHARED_LIBRARIES 1 #define PETSC_USE_DEBUGGER "gdb" #define PETSC_VERSION_BRANCH_GIT "maint" #define PETSC_VERSION_DATE_GIT "2020-03-11 17:29:20 +0000" #define PETSC_VERSION_GIT "v3.12.4-96-gf413fdba98" #endif **** C specific Configure header /tmp/petsc-uw1fxxf1/conffix.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #if defined(__cplusplus) extern "C" { } #else #endif #endif ******************************************************************************* OSError while running ./configure ------------------------------------------------------------------------------- Cannot run executables created with C. If this machine uses a batch system to submit jobs you will need to configure using ./configure with the additional option --with-batch. Otherwise there is problem with the compilers. Can you compile and run code with your compiler 'mpicc'? ******************************************************************************* File "/home/kongf/workhome/rod/moose/petsc/config/configure.py", line 447, in petsc_configure framework.configure(out = sys.stdout) File "/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/framework.py", line 1195, in configure self.processChildren() File "/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/framework.py", line 1184, in processChildren self.serialEvaluation(self.childGraph) File "/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/framework.py", line 1159, in serialEvaluation child.configure() File "/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py", line 1447, in configure self.executeTest(self.checkFortranLibraries) File "/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/base.py", line 139, in executeTest ret = test(*args,**kargs) File "/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/compilers.py", line 1245, in checkFortranLibraries self.setCompilers.checkCompiler('C') File "/home/kongf/workhome/rod/moose/petsc/config/BuildSystem/config/setCompilers.py", line 484, in checkCompiler raise OSError(msg) ================================================================================ Finishing configure run at Thu, 12 Mar 2020 16:38:50 -0600 ================================================================================