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Re: problem compiling PETSC on MacOS Leopard

To: petsc-maint@xxxxxxxxxxx
Subject: Re: problem compiling PETSC on MacOS Leopard
From: Barry Smith <bsmith@xxxxxxxxxxx>
Date: Sun, 18 Nov 2007 08:54:20 -0600 (CST)
Cc: petsc-users@xxxxxxxxxxx
In-reply-to: <E80B51C8-6448-4E1D-BB95-EF1733CB5389@ulb.ac.be>
References: <E80B51C8-6448-4E1D-BB95-EF1733CB5389@ulb.ac.be>
Reply-to: petsc-users@xxxxxxxxxxx
Sender: owner-petsc-users@xxxxxxxxxxx


   Please direct these problems to petsc-maint instead of petsc-users.

From the log file

Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mpif90...found
           Defined make macro "FC" to "mpif90"
           Pushing language FC
sh: mpif90 -c -o conftest.o   conftest.F
Executing: mpif90 -c -o conftest.o   conftest.F
sh:
Possible ERROR while running compiler: ret =3D 256
error message =3D {ifort: error #10106: Fatal error in /opt/intel/fc/=20
10.0.020/bin/fpp, terminated by segmentation violation
}
Source:
       program main

end

So the mpif90 is crashing on a simple Fortran program with nothing
in it. Can you try compiling exactly as above from the command line?


   Barry


On Sun, 18 Nov 2007, Bernard Knaepen wrote:

Hello,
I would like to compile PETSC on Leopard but I am encountering a problem during configuration. The scripts stops with:

dolfin:petsc-2.3.3-p8 bknaepen$ ./config/configure.py --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx

================================================================================= Configuring PETSc to compile on your system ================================================================================= TESTING: checkFortranCompiler from config.setCompilers(python/BuildSystem/config/setCompilers.py:708) ********************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------- Fortran compiler you provided with --with-fc=mpif90 does not work *********************************************************************************

My MPI installation is mpich2 1.0.6p1 and I have the latest ifort compiler installed (10.0.20). I have test mpif90 and it is working ok. I copy below the configure.log file.
Any help would be appreciated, thanks,
Bernard.
Pushing language C Popping language C Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC sh: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.guess Executing: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.guess sh: i686-apple-darwin9.1.0

sh: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.sub i686-apple-darwin9.1.0

Executing: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.sub i686-apple-darwin9.1.0
sh: i686-apple-darwin9.1.0
================================================================================ ================================================================================ Starting Configure Run at Sun Nov 18 10:29:29 2007 Configure Options: --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx --with-shared=0 --configModules=PETSc.Configure --optionsModule=PETSc.compilerOptions Working directory: /Users/bknaepen/Unix/petsc-2.3.3-p8 Python version: 2.5.1 (r251:54863, Oct 5 2007, 21:08:09) [GCC 4.0.1 (Apple Inc. build 5465)] ================================================================================ Pushing language C Popping language C Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC ================================================================================ TEST configureExternalPackagesDir from config.framework(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/framework.py:807) TESTING: configureExternalPackagesDir from config.framework(python/BuildSystem/config/framework.py:807) ================================================================================ TEST configureLibrary from PETSc.packages.PVODE(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/packages/PVODE.py:10) TESTING: configureLibrary from PETSc.packages.PVODE(python/PETSc/packages/PVODE.py:10) Find a PVODE installation and check if it can work with PETSc ================================================================================ TEST configureLibrary from PETSc.packages.NetCDF(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/packages/NetCDF.py:10) TESTING: configureLibrary from PETSc.packages.NetCDF(python/PETSc/packages/NetCDF.py:10) Find a NetCDF installation and check if it can work with PETSc ================================================================================ TEST configureMercurial from config.sourceControl(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/sourceControl.py:23) TESTING: configureMercurial from config.sourceControl(python/BuildSystem/config/sourceControl.py:23) Find the Mercurial executable Checking for program /opt/intel/fc/10.0.020/bin/hg...not found Checking for program /usr/X11R6/bin/hg...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/hg...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/hg...not found Checking for program /bin/hg...not found Checking for program /sbin/hg...not found Checking for program /usr/bin/hg...not found Checking for program /usr/sbin/hg...not found Checking for program /usr/local/bin/hg...not found Checking for program /usr/texbin/hg...not found Checking for program /Users/bknaepen/hg...not found ================================================================================ TEST configureCVS from config.sourceControl(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/sourceControl.py:30) TESTING: configureCVS from config.sourceControl(python/BuildSystem/config/sourceControl.py:30) Find the CVS executable Checking for program /opt/intel/fc/10.0.020/bin/cvs...not found Checking for program /usr/X11R6/bin/cvs...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/cvs...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/cvs...not found Checking for program /bin/cvs...not found Checking for program /sbin/cvs...not found Checking for program /usr/bin/cvs...found Defined make macro "CVS" to "cvs" ================================================================================ TEST configureSubversion from config.sourceControl(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/sourceControl.py:35) TESTING: configureSubversion from config.sourceControl(python/BuildSystem/config/sourceControl.py:35) Find the Subversion executable Checking for program /opt/intel/fc/10.0.020/bin/svn...not found Checking for program /usr/X11R6/bin/svn...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/svn...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/svn...not found Checking for program /bin/svn...not found Checking for program /sbin/svn...not found Checking for program /usr/bin/svn...found Defined make macro "SVN" to "svn" ================================================================================ TEST configureMkdir from config.programs(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/programs.py:21) TESTING: configureMkdir from config.programs(python/BuildSystem/config/programs.py:21) Make sure we can have mkdir automatically make intermediate directories Checking for program /opt/intel/fc/10.0.020/bin/mkdir...not found Checking for program /usr/X11R6/bin/mkdir...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/mkdir...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mkdir...not found Checking for program /bin/mkdir...found sh: /bin/mkdir -p .conftest/tmp Executing: /bin/mkdir -p .conftest/tmp sh: Adding -p flag to /bin/mkdir -p to automatically create directories Defined make macro "MKDIR" to "/bin/mkdir -p" ================================================================================ TEST configurePrograms from config.programs(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/programs.py:43) TESTING: configurePrograms from config.programs(python/BuildSystem/config/programs.py:43) Check for the programs needed to build and run PETSc Checking for program /opt/intel/fc/10.0.020/bin/sh...not found Checking for program /usr/X11R6/bin/sh...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/sh...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/sh...not found Checking for program /bin/sh...found Defined make macro "SHELL" to "/bin/sh" Checking for program /opt/intel/fc/10.0.020/bin/sed...not found Checking for program /usr/X11R6/bin/sed...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/sed...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/sed...not found Checking for program /bin/sed...not found Checking for program /sbin/sed...not found Checking for program /usr/bin/sed...found Defined make macro "SED" to "/usr/bin/sed" Checking for program /opt/intel/fc/10.0.020/bin/mv...not found Checking for program /usr/X11R6/bin/mv...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/mv...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mv...not found Checking for program /bin/mv...found Defined make macro "MV" to "/bin/mv" Checking for program /opt/intel/fc/10.0.020/bin/cp...not found Checking for program /usr/X11R6/bin/cp...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/cp...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/cp...not found Checking for program /bin/cp...found Defined make macro "CP" to "/bin/cp" Checking for program /opt/intel/fc/10.0.020/bin/grep...not found Checking for program /usr/X11R6/bin/grep...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/grep...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/grep...not found Checking for program /bin/grep...not found Checking for program /sbin/grep...not found Checking for program /usr/bin/grep...found Defined make macro "GREP" to "/usr/bin/grep" Checking for program /opt/intel/fc/10.0.020/bin/rm...not found Checking for program /usr/X11R6/bin/rm...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/rm...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/rm...not found Checking for program /bin/rm...found Defined make macro "RM" to "/bin/rm -f" Checking for program /opt/intel/fc/10.0.020/bin/diff...not found Checking for program /usr/X11R6/bin/diff...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/diff...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/diff...not found Checking for program /bin/diff...not found Checking for program /sbin/diff...not found Checking for program /usr/bin/diff...found sh: /usr/bin/diff -w diff1 diff2 Executing: /usr/bin/diff -w diff1 diff2 sh: Defined make macro "DIFF" to "/usr/bin/diff -w" Checking for program /usr/ucb/ps...not found Checking for program /usr/usb/ps...not found Checking for program /Users/bknaepen/ps...not found Checking for program /opt/intel/fc/10.0.020/bin/gzip...not found Checking for program /usr/X11R6/bin/gzip...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/gzip...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/gzip...not found Checking for program /bin/gzip...not found Checking for program /sbin/gzip...not found Checking for program /usr/bin/gzip...found Defined make macro "GZIP" to "/usr/bin/gzip" Defined "HAVE_GZIP" to "1" ================================================================================ TEST configureMake from PETSc.utilities.Make(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/Make.py:21) TESTING: configureMake from PETSc.utilities.Make(python/PETSc/utilities/Make.py:21) Check various things about make Checking for program /opt/intel/fc/10.0.020/bin/make...not found Checking for program /usr/X11R6/bin/make...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/make...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/make...not found Checking for program /bin/make...not found Checking for program /sbin/make...not found Checking for program /usr/bin/make...found Defined make macro "MAKE" to "/usr/bin/make" sh: strings /usr/bin/make Executing: strings /usr/bin/make sh: attempt to use unsupported feature: `%s' touch: Archive `%s' does not exist touch: `%s' is not a valid archive touch: touch: Member `%s' does not exist in `%s' touch: Bad return code from ar_member_touch on `%s' !<arch> ARFILENAMES/ $(MAKE) ${MAKE} *** [%s] Archive member `%s' may be bogus; not deleted *** Archive member `%s' may be bogus; not deleted *** [%s] Deleting file `%s' *** Deleting file `%s' unlink: kill # commands to execute (built-in): (from `%s', line %lu): %.*s GNUMAKE MAKEFILEPATH $(NEXT_ROOT)/Developer/Makefiles CHECKOUT,v +$(if $(wildcard $@),,$(CO) $(COFLAGS) $< $@) COFL... ... h: can't allocate %ld bytes for hash table: memory exhausted Load=%ld/%ld=%.0f%%, Rehash=%d, Collisions=%ld/%ld=%.0f%% $(VPATH) Can't do VPATH expansion on a null file. =|^();&<>*?[]:$`'"\ Using old-style VPATH substitution. Consider using automatic variable substitution instead. glob next != NULL /SourceCache/gnumake/gnumake-119/make/glob/glob.c alnum alpha blank cntrl digit graph lower print punct space upper xdigit .out .a .ln .o .c .cc .C .cpp .p .f .F .m .r .y .l .ym .lm .s .S .mod .sym .def .h .info .dvi .tex .texinfo .texi .txinfo .w .ch .web .sh .elc .el /bin/sh #;"*?[]&|<>(){}$`^~!

Defined make macro "OMAKE " to "/usr/bin/make --no-print-directory" Defined make rule "libc" with dependencies "${LIBNAME}(${OBJSC} ${SOBJSC})" and code [] Defined make rule "libf" with dependencies "${OBJSF}" and code -${AR} ${AR_FLAGS} ${LIBNAME} ${OBJSF} ================================================================================ TEST configureDebuggers from PETSc.utilities.debuggers(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/debuggers.py:22) TESTING: configureDebuggers from PETSc.utilities.debuggers(python/PETSc/utilities/debuggers.py:22) Find a default debugger and determine its arguments Checking for program /opt/intel/fc/10.0.020/bin/gdb...not found Checking for program /usr/X11R6/bin/gdb...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/gdb...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/gdb...not found Checking for program /bin/gdb...not found Checking for program /sbin/gdb...not found Checking for program /usr/bin/gdb...found Defined make macro "GDB" to "/usr/bin/gdb" Checking for program /opt/intel/fc/10.0.020/bin/dbx...not found Checking for program /usr/X11R6/bin/dbx...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/dbx...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/dbx...not found Checking for program /bin/dbx...not found Checking for program /sbin/dbx...not found Checking for program /usr/bin/dbx...not found Checking for program /usr/sbin/dbx...not found Checking for program /usr/local/bin/dbx...not found Checking for program /usr/texbin/dbx...not found Checking for program /Users/bknaepen/dbx...not found Checking for program /opt/intel/fc/10.0.020/bin/xdb...not found Checking for program /usr/X11R6/bin/xdb...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/xdb...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/xdb...not found Checking for program /bin/xdb...not found Checking for program /sbin/xdb...not found Checking for program /usr/bin/xdb...not found Checking for program /usr/sbin/xdb...not found Checking for program /usr/local/bin/xdb...not found Checking for program /usr/texbin/xdb...not found Checking for program /Users/bknaepen/xdb...not found Defined "USE_GDB_DEBUGGER" to "1" ================================================================================ TEST configureCLanguage from PETSc.utilities.languages(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/languages.py:43) TESTING: configureCLanguage from PETSc.utilities.languages(python/PETSc/utilities/languages.py:43) Choose between C and C++ bindings ================================================================================ TEST configureLanguageSupport from PETSc.utilities.languages(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/languages.py:49) TESTING: configureLanguageSupport from PETSc.utilities.languages(python/PETSc/utilities/languages.py:49) Check c-support c++-support and other misc tests Turning off C++ support Allowing C++ name mangling C language is C Defined "CLANGUAGE_C" to "1" ================================================================================ TEST configureExternC from PETSc.utilities.languages(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/languages.py:66) TESTING: configureExternC from PETSc.utilities.languages(python/PETSc/utilities/languages.py:66) Protect C bindings from C++ mangling Defined "USE_EXTERN_CXX" to " " ================================================================================ TEST configureFortranLanguage from PETSc.utilities.languages(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/languages.py:72) TESTING: configureFortranLanguage from PETSc.utilities.languages(python/PETSc/utilities/languages.py:72) Turn on Fortran bindings Using Fortran ================================================================================ TEST configureDirectories from PETSc.utilities.petscdir(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/petscdir.py:34) TESTING: configureDirectories from PETSc.utilities.petscdir(python/PETSc/utilities/petscdir.py:34) Checks PETSC_DIR and sets if not set Version Information: #define PETSC_VERSION_RELEASE 1 #define PETSC_VERSION_MAJOR 2 #define PETSC_VERSION_MINOR 3 #define PETSC_VERSION_SUBMINOR 3 #define PETSC_VERSION_PATCH 8 #define PETSC_VERSION_DATE "May, 23, 2007" #define PETSC_VERSION_PATCH_DATE "Fri Nov 16 17:03:40 CST 2007" #define PETSC_VERSION_HG "414581156e67e55c761739b0deb119f7590d0f4b" Defined make macro "DIR" to "/Users/bknaepen/Unix/petsc-2.3.3-p8" Defined "DIR" to "/Users/bknaepen/Unix/petsc-2.3.3-p8" sh: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/bin/config/config.guess Executing: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/bin/config/config.guess sh: i686-apple-darwin9.1.0

sh: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/bin/config/config.sub i686-apple-darwin9.1.0

Executing: /bin/sh /Users/bknaepen/Unix/petsc-2.3.3-p8/bin/config/config.sub i686-apple-darwin9.1.0
sh: i686-apple-darwin9.1.0
================================================================================ TEST configureExternalPackagesDir from PETSc.utilities.petscdir(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/petscdir.py:112) TESTING: configureExternalPackagesDir from PETSc.utilities.petscdir(python/PETSc/utilities/petscdir.py:112) ================================================================================ TEST configureInstallationMethod from PETSc.utilities.petscdir(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/petscdir.py:119) TESTING: configureInstallationMethod from PETSc.utilities.petscdir(python/PETSc/utilities/petscdir.py:119) This is a tarball installation ================================================================================ TEST configureETags from PETSc.utilities.Etags(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/Etags.py:27) TESTING: configureETags from PETSc.utilities.Etags(python/PETSc/utilities/Etags.py:27) Determine if etags files exist and try to create otherwise Found etags file ================================================================================ TEST getDatafilespath from PETSc.utilities.dataFilesPath(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/utilities/dataFilesPath.py:29) TESTING: getDatafilespath from PETSc.utilities.dataFilesPath(python/PETSc/utilities/dataFilesPath.py:29) Checks what DATAFILESPATH should be Defined make macro "DATAFILESPATH" to "None" ================================================================================ TEST checkVendor from config.setCompilers(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:262) TESTING: checkVendor from config.setCompilers(python/BuildSystem/config/setCompilers.py:262) Determine the compiler vendor Compiler vendor is "" ================================================================================ TEST checkInitialFlags from config.setCompilers(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:272) TESTING: checkInitialFlags from config.setCompilers(python/BuildSystem/config/setCompilers.py:272) Initialize the compiler and linker flags Pushing language C Initialized CFLAGS to Initialized CFLAGS to Initialized LDFLAGS to Popping language C 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 executableFlags to [] Initialized sharedLibraryFlags to [] Initialized dynamicLibraryFlags to [] ================================================================================ TEST checkCCompiler from config.setCompilers(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:380) TESTING: checkCCompiler from config.setCompilers(python/BuildSystem/config/setCompilers.py:380) Locate a functional C compiler Checking for program /opt/intel/fc/10.0.020/bin/mpicc...not found Checking for program /usr/X11R6/bin/mpicc...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/mpicc...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mpicc...found Defined make macro "CC" to "mpicc" Pushing language C sh: mpicc -c -o conftest.o conftest.c Executing: mpicc -c -o conftest.o conftest.c sh: sh: mpicc -c -o conftest.o conftest.c Executing: mpicc -c -o conftest.o conftest.c sh: Pushing language C Popping language C Pushing language Cxx Popping language Cxx Pushing language FC Popping language FC Pushing language C Popping language C sh: mpicc -o conftest conftest.o Executing: mpicc -o conftest conftest.o sh: sh: mpicc -c -o conftest.o conftest.c Executing: mpicc -c -o conftest.o conftest.c sh: Pushing language C Popping language C sh: mpicc -o conftest conftest.o Executing: mpicc -o conftest conftest.o sh: Executing: ./conftest sh: ./conftest Executing: ./conftest sh: Popping language C ================================================================================ TEST checkCPreprocessor from config.setCompilers(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:437) TESTING: checkCPreprocessor from config.setCompilers(python/BuildSystem/config/setCompilers.py:437) Locate a functional C preprocessor Checking for program /opt/intel/fc/10.0.020/bin/mpicc...not found Checking for program /usr/X11R6/bin/mpicc...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/mpicc...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mpicc...found Defined make macro "CPP" to "mpicc -E" Pushing language C sh: mpicc -E conftest.c Executing: mpicc -E conftest.c sh: # 1 "conftest.c" # 1 "<built-in>" # 1 "<command line>" # 1 "conftest.c" # 1 "confdefs.h" 1 # 2 "conftest.c" 2 # 1 "conffix.h" 1 # 3 "conftest.c" 2 # 1 "/usr/include/stdlib.h" 1 3 4 # 61 "/usr/include/stdlib.h" 3 4 # 1 "/usr/include/available.h" 1 3 4 # 62 "/usr/include/stdlib.h" 2 3 4 # 1 "/usr/include/_types.h" 1 3 4 # 27 "/usr/include/_types.h" 3 4 # 1 "/usr/include/sys/_types.h" 1 3 4 # 32 "/usr/include/sys/_types.h" 3 4 # 1 "/usr/include/sys/cdefs.h" 1 3 4 # 33 "/usr/include/sys/_types.h" 2 3 4 # 1 "/usr/include/machine/_types.h" 1 3 4 # 34 "/usr/include/machine/_types.h" 3 4 # 1 "/usr/inc... ... size_t, size_t, int (*)(const void *, const void *)); void qsort_r(void *, size_t, size_t, void *, int (*)(void *, const void *, const void *)); int radixsort(const unsigned char **, int, const unsigned char *, unsigned); void setprogname(const char *); int sradixsort(const unsigned char **, int, const unsigned char *, unsigned); void sranddev(void); void srandomdev(void); void *reallocf(void *, size_t); long long strtoq(const char *, char **, int); unsigned long long strtouq(const char *, char **, int); extern char *suboptarg; void *valloc(size_t); # 3 "conftest.c" 2

Popping language C ================================================================================ TEST checkCxxCompiler from config.setCompilers(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:541) TESTING: checkCxxCompiler from config.setCompilers(python/BuildSystem/config/setCompilers.py:541) Locate a functional Cxx compiler ================================================================================ TEST checkFortranCompiler from config.setCompilers(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:708) TESTING: checkFortranCompiler from config.setCompilers(python/BuildSystem/config/setCompilers.py:708) Locate a functional Fortran compiler Checking for program /opt/intel/fc/10.0.020/bin/mpif90...not found Checking for program /usr/X11R6/bin/mpif90...not found Checking for program /opt/toolworks/totalview.8.3.0-0/bin/mpif90...not found Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mpif90...found Defined make macro "FC" to "mpif90" Pushing language FC sh: mpif90 -c -o conftest.o conftest.F Executing: mpif90 -c -o conftest.o conftest.F sh: Possible ERROR while running compiler: ret = 256 error message = {ifort: error #10106: Fatal error in /opt/intel/fc/10.0.020/bin/fpp, terminated by segmentation violation } Source: program main

end Popping language FC Error testing Fortran compiler: Cannot compile FC with mpicc. MPI installation mpif90 is likely incorrect. Use --with-mpi-dir to indicate an alternate MPI. ********************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------- Fortran compiler you provided with --with-fc=mpif90 does not work ********************************************************************************* File "./config/configure.py", line 190, in petsc_configure framework.configure(out = sys.stdout) File "/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/framework.py", line 878, in configure child.configure() File "/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py", line 1267, in configure self.executeTest(self.checkFortranCompiler) File "/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/base.py", line 93, in executeTest return apply(test, args,kargs) File "/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py", line 714, in checkFortranCompiler for compiler in self.generateFortranCompilerGuesses(): File "/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py", line 631, in generateFortranCompilerGuesses raise RuntimeError('Fortran compiler you provided with --with-fc='+self.framework.argDB['with-fc']+' does not work')

References:
- problem compiling PETSC on MacOS Leopard
  - From: Bernard Knaepen

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