Pushing language C Popping language C Pushing language CUDA Popping language CUDA Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC ================================================================================ ================================================================================ Starting Configure Run at Fri Jun 19 11:32:43 2015 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --download-parmetis=1 --download-metis=1 --with-hdf5-dir=/Users/markadams/Codes/hdf5 --with-x=0 --with-debugging=1 PETSC_ARCH=arch-macosx-gnu-g PETSC_DIR=/Users/markadams/Codes/petsc_fresh Working directory: /Users/markadams/Codes/petsc_fresh Machine platform: ('Darwin', 'MacBook-Pro.local', '14.3.0', 'Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64', 'x86_64', 'i386') Python version: 2.7.8 (default, Oct 5 2014, 14:58:30) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.51)] ================================================================================ Pushing language C Popping language C Pushing language CUDA Popping language CUDA Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC ================================================================================ TEST configureExternalPackagesDir from config.framework(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/framework.py:832) TESTING: configureExternalPackagesDir from config.framework(config/BuildSystem/config/framework.py:832) ================================================================================ TEST configureDebuggers from config.utilities.debuggers(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/utilities/debuggers.py:22) TESTING: configureDebuggers from config.utilities.debuggers(config/BuildSystem/config/utilities/debuggers.py:22) Find a default debugger and determine its arguments Checking for program /Applications/kdiff3.app/Contents/MacOS/gdb...not found Checking for program /Applications/CMake2.8-6.app/Contents/bin/gdb...not found Checking for program /Users/markadams/Codes/git-fat/gdb...not found Checking for program /Users/markadams/homebrew/bin/gdb...not found Checking for program /usr/local/bin/gdb...found Defined make macro "GDB" to "/usr/local/bin/gdb" Checking for program /Applications/kdiff3.app/Contents/MacOS/dbx...not found Checking for program /Applications/CMake2.8-6.app/Contents/bin/dbx...not found Checking for program /Users/markadams/Codes/git-fat/dbx...not found Checking for program /Users/markadams/homebrew/bin/dbx...not found Checking for program /usr/local/bin/dbx...not found Checking for program /Users/markadams/homebrew/bin/dbx...not found Checking for program /usr/local/bin/dbx...not found Checking for program /usr/local/bin/dbx...not found Checking for program /usr/bin/dbx...not found Checking for program /bin/dbx...not found Checking for program /usr/sbin/dbx...not found Checking for program /sbin/dbx...not found Checking for program /opt/X11/bin/dbx...not found Checking for program /usr/texbin/dbx...not found Checking for program /opt/X11/bin/dbx...not found Checking for program /Users/markadams/dbx...not found Checking for program /Applications/kdiff3.app/Contents/MacOS/xdb...not found Checking for program /Applications/CMake2.8-6.app/Contents/bin/xdb...not found Checking for program /Users/markadams/Codes/git-fat/xdb...not found Checking for program /Users/markadams/homebrew/bin/xdb...not found Checking for program /usr/local/bin/xdb...not found Checking for program /Users/markadams/homebrew/bin/xdb...not found Checking for program /usr/local/bin/xdb...not found Checking for program /usr/local/bin/xdb...not found Checking for program /usr/bin/xdb...not found Checking for program /bin/xdb...not found Checking for program /usr/sbin/xdb...not found Checking for program /sbin/xdb...not found Checking for program /opt/X11/bin/xdb...not found Checking for program /usr/texbin/xdb...not found Checking for program /opt/X11/bin/xdb...not found Checking for program /Users/markadams/xdb...not found Checking for program /Applications/kdiff3.app/Contents/MacOS/dsymutil...not found Checking for program /Applications/CMake2.8-6.app/Contents/bin/dsymutil...not found Checking for program /Users/markadams/Codes/git-fat/dsymutil...not found Checking for program /Users/markadams/homebrew/bin/dsymutil...not found Checking for program /usr/local/bin/dsymutil...not found Checking for program /Users/markadams/homebrew/bin/dsymutil...not found Checking for program /usr/local/bin/dsymutil...not found Checking for program /usr/local/bin/dsymutil...not found Checking for program /usr/bin/dsymutil...found Defined make macro "DSYMUTIL" to "/usr/bin/dsymutil" Defined make macro "DSYMUTIL" to "/usr/bin/dsymutil" Defined "USE_GDB_DEBUGGER" to "1" ================================================================================ TEST configureGit from config.sourceControl(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/sourceControl.py:24) TESTING: configureGit from config.sourceControl(config/BuildSystem/config/sourceControl.py:24) Find the Git executable Checking for program /Applications/kdiff3.app/Contents/MacOS/git...not found Checking for program /Applications/CMake2.8-6.app/Contents/bin/git...not found Checking for program /Users/markadams/Codes/git-fat/git...not found Checking for program /Users/markadams/homebrew/bin/git...found Defined make macro "GIT" to "git" Executing: git --version stdout: git version 2.1.2 ================================================================================ TEST configureCLanguage from PETSc.options.languages(/Users/markadams/Codes/petsc_fresh/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" ================================================================================ TEST configureDirectories from PETSc.options.petscdir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/petscdir.py:23) TESTING: configureDirectories from PETSc.options.petscdir(config/PETSc/options/petscdir.py:23) Checks PETSC_DIR and sets if not set Version Information: #define PETSC_VERSION_RELEASE 0 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 6 #define PETSC_VERSION_SUBMINOR 0 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "unknown" #define PETSC_VERSION_GIT "unknown" #define PETSC_VERSION_DATE_GIT "unknown" #define PETSC_VERSION_(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ Defined make macro "DIR" to "/Users/markadams/Codes/petsc_fresh" ================================================================================ TEST configureInstallationMethod from PETSc.options.petscclone(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/petscclone.py:20) TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:20) bin/maint exists. This appears to be a repository clone .git directory exists Executing: cd /Users/markadams/Codes/petsc_fresh && git describe stdout: v3.6-35-g822156d Executing: cd /Users/markadams/Codes/petsc_fresh && git log -1 --pretty=format:%H stdout: 822156d0eaf4278b89172cbf4eec8e9ab5093b24 Executing: cd /Users/markadams/Codes/petsc_fresh && git log -1 --pretty=format:%ci stdout: 2015-06-18 08:53:22 -0500 Executing: cd /Users/markadams/Codes/petsc_fresh && git branch stdout: * master Defined "VERSION_GIT" to ""v3.6-35-g822156d"" Defined "VERSION_DATE_GIT" to ""2015-06-18 08:53:22 -0500"" Defined "VERSION_BRANCH_GIT" to ""master"" ================================================================================ TEST getDatafilespath from PETSc.options.dataFilesPath(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/dataFilesPath.py:29) TESTING: getDatafilespath from PETSc.options.dataFilesPath(config/PETSc/options/dataFilesPath.py:29) Checks what DATAFILESPATH should be ================================================================================ TEST configureArchitecture from PETSc.options.arch(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/arch.py:25) TESTING: configureArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:25) Checks PETSC_ARCH and sets if not set Defined "ARCH" to ""arch-macosx-gnu-g"" ================================================================================ TEST setInstallDir from PETSc.options.installDir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/installDir.py:35) TESTING: setInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:35) setup installDir to either prefix or if that is not set to PETSC_DIR/PETSC_ARCH ================================================================================ TEST saveReconfigure from PETSc.options.installDir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/installDir.py:74) TESTING: saveReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:74) ================================================================================ TEST cleanInstallDir from PETSc.options.installDir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/installDir.py:67) TESTING: cleanInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:67) ================================================================================ TEST configureInstallDir from PETSc.options.installDir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/installDir.py:51) TESTING: configureInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:51) Makes installDir subdirectories if it does not exist for both prefix install location and PETSc work install location Changed persistence directory to /Users/markadams/Codes/petsc_fresh/arch-macosx-gnu-g/lib/petsc/conf ================================================================================ TEST restoreReconfigure from PETSc.options.installDir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/installDir.py:87) TESTING: restoreReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:87) ================================================================================ TEST setExternalPackagesDir from PETSc.options.externalpackagesdir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/externalpackagesdir.py:15) TESTING: setExternalPackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:15) ================================================================================ TEST cleanExternalpackagesDir from PETSc.options.externalpackagesdir(/Users/markadams/Codes/petsc_fresh/config/PETSc/options/externalpackagesdir.py:22) TESTING: cleanExternalpackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:22) ================================================================================ TEST printEnvVariables from config.setCompilers(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:1535) TESTING: printEnvVariables from config.setCompilers(config/BuildSystem/config/setCompilers.py:1535) **** printenv **** GIT_PS1_SHOWDIRTYSTATE=1 XTERM_SHELL=/bin/bash HDF5_DIR=/Users/markadams/Codes/hdf5 BISICLES_HOME=/Users/markadams/Codes CVS_RSH=ssh LOGNAME=markadams USER=markadams HOME=/Users/markadams PATH=/Applications/kdiff3.app/Contents/MacOS:/Applications/CMake2.8-6.app/Contents/bin:/Users/markadams/Codes/git-fat:/Users/markadams/homebrew/bin:/usr/local/bin:/Users/markadams/homebrew/bin:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin:/opt/X11/bin DISPLAY=/private/tmp/com.apple.launchd.l1jEISNiK8/org.macosforge.xquartz:0 sysname=Darwin TERM=xterm-color SHELL=/bin/bash CHOMBO_HOME=/Users/markadams/Codes/Chombo/lib SHLVL=2 PWD=/Users/markadams/Codes/petsc_fresh XPC_FLAGS=0x0 CH_OUTPUT_INTERVAL=1000 GIT_PS1_SHOWUPSTREAM=auto WINDOWID=12582925 PETSC_DIR=/Users/markadams/Codes/petsc _=../arch-macosx-gnu-g.py SVN_EDITOR=vi ARCHFLAGS=-arch x86_64 XPC_SERVICE_NAME=0 NETCDF_DIR=/Users/markadams/SFE/NETCDF_INSTALL XTERM_VERSION=XTerm(309) SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.M2fW3PO5Ce/Listeners XP_LICENSE_INTERFACE=en0 Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.ws05TbfXYV/Render XTERM_LOCALE=C CH_TIMER=FALSE TMPDIR=/var/folders/sw/67cq0mmx43g93vrb5xkf1j7c0000gn/T/ MACHINE=Darwin BOXLIB_HOME=/Users/markadams/Codes/BoxLib/ OLDPWD=/Users/markadams/Codes CH_TIMER_SAMPLE=60000 SYSTEM=Darwin __CF_USER_TEXT_ENCODING=0x1F5:0x0:0x0 PETSC_ARCH=arch-macosx-gnu-g PIP_DOWNLOAD_CACHE=/Users/markadams/.pip/cache X11_PREFS_DOMAIN=org.macosforge.xquartz.X11 ================================================================================ TEST resetEnvCompilers from config.setCompilers(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:1542) TESTING: resetEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1542) ================================================================================ TEST checkEnvCompilers from config.setCompilers(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:1572) TESTING: checkEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1572) ================================================================================ TEST checkMPICompilerOverride from config.setCompilers(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:1507) TESTING: checkMPICompilerOverride from config.setCompilers(config/BuildSystem/config/setCompilers.py:1507) 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(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:1526) TESTING: requireMpiLdPath from config.setCompilers(config/BuildSystem/config/setCompilers.py:1526) OpenMPI wrappers require LD_LIBRARY_PATH set ================================================================================ TEST checkVendor from config.setCompilers(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:399) TESTING: checkVendor from config.setCompilers(config/BuildSystem/config/setCompilers.py:399) Determine the compiler vendor Compiler vendor is "" ================================================================================ TEST checkInitialFlags from config.setCompilers(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:409) TESTING: checkInitialFlags from config.setCompilers(config/BuildSystem/config/setCompilers.py:409) Initialize the compiler and linker flags Pushing language C Initialized CFLAGS to Initialized CFLAGS to Initialized LDFLAGS to Popping language C Pushing language CUDA Initialized CUDAFLAGS to Initialized CUDAFLAGS to Initialized LDFLAGS to Popping language CUDA Pushing language Cxx Initialized CXXFLAGS to Initialized CXX_CXXFLAGS to Initialized LDFLAGS to Popping language Cxx Pushing language FC Initialized FFLAGS to Initialized FFLAGS to Initialized LDFLAGS to Popping language FC Initialized CPPFLAGS to Initialized CUDAPPFLAGS to Initialized CXXCPPFLAGS 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(/Users/markadams/Codes/petsc_fresh/config/BuildSystem/config/setCompilers.py:535) TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:535) Locate a functional C compiler Executing: mpicc --help stdout: OVERVIEW: clang LLVM compiler USAGE: clang [options] OPTIONS: -### Print (but do not run) the commands to run for this compilation --analyze Run the static analyzer -arcmt-migrate-emit-errors Emit ARC errors even if the migrator can fix them -arcmt-migrate-report-output Output path for the plist report -cxx-isystem Add directory to the C++ SYSTEM include search path -c Only run preprocess, compile, and assemble steps -dD Print macro definitions in -E mode in addition to normal output -dependency-dot Filename to write DOT-formatted header dependencies to -dependency-file Filename (or -) to write dependency output to -dM Print macro definitions in -E mode instead of normal output -emit-ast Emit Clang AST files for source inputs -emit-llvm Use the LLVM representation for assembler and object files -E Only run the preprocessor -faltivec Enable AltiVec vector initializer syntax -fansi-escape-codes Use ANSI escape codes for diagnostics -fapinotes-cache-path= Specify the API notes cache path -fapinotes Enable external API notes support -fapple-kext Use Apple's kernel extensions ABI -fapple-pragma-pack Enable Apple gcc-compatible #pragma pack handling -fapplication-extension Restrict code to those available for App Extensions -fblocks Enable the 'blocks' language feature -fborland-extensions Accept non-standard constructs supported by the Borland compiler -fbuild-session-file= Use the last modification time of as the build session timestamp -fbuild-session-timestamp=