[petsc-users] compile petsc with intel compiler
Michael Povolotskyi
mpovolot at purdue.edu
Wed Jul 10 00:00:17 CDT 2013
Hello everybody,
unfortunately building petsc without fortran cannot work for me because
I need MUMPs that requires Scalapack that needs fortran. I played with
the options. As result the configuration runs okay, the build gives an
error that does not seem to be related to fortran:
[ 0%] Building CXX object
CMakeFiles/petscsys.dir/src/sys/totalview/tv_data_display.c.o
Building Fortran object
CMakeFiles/petscsys.dir/src/sys/f90-mod/petscsysmod.F.o
Building CXX object CMakeFiles/petscsys.dir/src/sys/python/pythonsys.c.o
[ 0%] /usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error:
cannot open source file "bits/c++config.h"
#include <bits/c++config.h>
^
/usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error: cannot
open source file "bits/c++config.h"
#include <bits/c++config.h>
^
compilation aborted for
/home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/info/verboseinfo.c
(code 4)
compilation aborted for
/home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/logging/plog.c
(code 4)
I attach here the log files.
Any advise is highly appreciated.
Michael.
On 7/9/2013 4:34 PM, Matthew Knepley wrote:
> On Tue, Jul 9, 2013 at 3:32 PM, Michael Povolotskyi
> <mpovolot at purdue.edu <mailto:mpovolot at purdue.edu>> wrote:
>
> If I do not need to use petsc in fortran programs, can I build
> petsc without fortran and thus avoid this situation?
> Michael.
>
>
> On 07/09/2013 04:31 PM, Satish Balay wrote:
>
> For some reason this issue comes up with mpi.mod provided by intel
> mpi.
>
> We have a configure test for it - but looks like its not
> sufficient to
> catch this issue.
>
> satish
>
>
> On Tue, 9 Jul 2013, Matthew Knepley wrote:
>
> On Tue, Jul 9, 2013 at 3:11 PM, Michael Povolotskyi
> <mpovolot at purdue.edu <mailto:mpovolot at purdue.edu>>wrote:
>
> Dear Petsc users and developers,
> I'm trying to build petsc with Intel compiler.
>
> 1) First, ask yourself whether you really want to build
> with the Intel
> compiler. Then ask again.
>
> 2) Do you need Fortran? If not, turn it off --with-fc=0.
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> Matt
>
> 3) If you want Fortran and Intel (and have a hatred of
> free time), try the
> legacy build
>
> make all-legacy
>
> 4) If this is still broken, send the new make.log
>
> Thanks,
>
> Matt
>
>
> The configuration process runs okay (I attach the log
> here),
> but I get an error when I build it:
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /home/mpovolot/Code_intel/**
> libs/petsc/build-real/linux
> Scanning dependencies of target petscsys
> [ 0%] [ 0%] [ 0%] Building CXX object
> CMakeFiles/petscsys.dir/src/**
> sys/info/verboseinfo.c.o
> Building Fortran object CMakeFiles/petscsys.dir/src/**
> sys/f90-mod/petscsysmod.F.o
> Building CXX object CMakeFiles/petscsys.dir/src/**
> sys/totalview/tv_data_display.**c.o
> Building CXX object
> CMakeFiles/petscsys.dir/src/**sys/python/pythonsys.c.o
> Building CXX object
> CMakeFiles/petscsys.dir/src/**sys/logging/plog.c.o
> /home/mpovolot/Code_intel/**libs/petsc/build-real/src/sys/**
> f90-mod/petscsysmod.F:6.11:
>
> use mpi
> 1
> Fatal Error: File 'mpi.mod' opened at (1) is not a
> GFORTRAN module file
> make[6]: ***
> [CMakeFiles/petscsys.dir/src/**sys/f90-mod/petscsysmod.F.o]
> Error 1
> make[6]: *** Waiting for unfinished jobs....
> make[5]: *** [CMakeFiles/petscsys.dir/all] Error 2
> make[4]: *** [all] Error 2
> make[3]: *** [ccmake] Error 2
> make[2]: *** [cmake] Error 2
> ****************************ERROR**************************************
> Error during compile, check linux/conf/make.log
> Send it and linux/conf/configure.log to
> petsc-maint at mcs.anl.gov <mailto:petsc-maint at mcs.anl.gov>
> ************************************************************************
>
> I attach here the make.log
> What is strange to me that it has something to do with
> Gfortran, while I
> want to build everything with Intel.
> Thank you for help,
> Michael.
>
> --
> Michael Povolotskyi, PhD
> Research Assistant Professor
> Network for Computational Nanotechnology
> 207 S Martin Jischke Drive
> Purdue University, DLR, room 441-10
> West Lafayette, Indiana 47907
>
> phone: +1-765-494-9396 <tel:%2B1-765-494-9396>
> fax: +1-765-496-6026 <tel:%2B1-765-496-6026>
>
>
>
>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which
> their experiments lead.
> -- Norbert Wiener
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==========================================
See documentation/faq.html and documentation/bugreporting.html
for help with installation problems. Please send EVERYTHING
printed out below when reporting problems
To subscribe to the PETSc announcement list, send mail to
majordomo at mcs.anl.gov with the message:
subscribe petsc-announce
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==========================================
On Wed Jul 10 00:47:31 EDT 2013 on ncnlnx15
Machine characteristics: Linux ncnlnx15 3.8.0-19-generic #29-Ubuntu SMP Wed Apr 17 18:16:28 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
-----------------------------------------
Using PETSc directory: /home/mpovolot/Code_intel/libs/petsc/build-real
Using PETSc arch: linux
-----------------------------------------
PETSC_VERSION_RELEASE 1
PETSC_VERSION_MAJOR 3
PETSC_VERSION_MINOR 4
PETSC_VERSION_SUBMINOR 0
PETSC_VERSION_PATCH 0
PETSC_VERSION_DATE "May, 13, 2013"
PETSC_VERSION_GIT "0f0f11e432ef0f042adf57ab89328b3ebb184576"
PETSC_VERSION_DATE "May, 13, 2013"
PETSC_VERSION_(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \
-----------------------------------------
Using configure Options: --with-x=0 --with-hdf5 --download-hdf5=1 --with-scalar-type=real --with-single-library=0 --with-pic=1 --with-shared-libraries=0 --with-clanguage=C++ --with-fortran=1 --with-debugging=1 --with-cc=/opt/intel/impi/4.1.0/intel64/bin/mpiicc --with-fc=/opt/intel/impi/4.1.0/intel64/bin/mpiifort --with-cxx="/opt/intel/impi/4.1.0/intel64/bin/mpiicpc " COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --LDFLAGS="-Wl,-rpath,/opt/intel/mkl//lib/intel64 -L/opt/intel/mkl//lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -L/opt/intel/lib/intel64 -Wl,-rpath=/opt/intel/lib/intel64 -lintlc" --download-metis=1 --download-parmetis=1 --download-scalapack=/home/mpovolot/Code_intel/libs/petsc/scalapack-2.0.2.tgz --download-mumps=1 --with-fortran-kernels=0 --with-blas-lapack-dir=/opt/intel/mkl/ --download-blacs=1
Using configuration flags:
#define INCLUDED_PETSCCONF_H
#define IS_COLORING_MAX 65535
#define STDC_HEADERS 1
#define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT
#define PETSC_UINTPTR_T uintptr_t
#define PETSC_HAVE_PTHREAD 1
#define PETSC_DEPRECATED(why) __attribute((deprecated(why)))
#define PETSC_STATIC_INLINE static inline
#define PETSC_REPLACE_DIR_SEPARATOR '\\'
#define PETSC_HAVE_HDF5 1
#define PETSC_RESTRICT __restrict__
#define PETSC_HAVE_SO_REUSEADDR 1
#define PETSC_HAVE_MPI 1
#define PETSC_PREFETCH_HINT_T2 _MM_HINT_T2
#define PETSC_PREFETCH_HINT_T0 _MM_HINT_T0
#define PETSC_PREFETCH_HINT_T1 _MM_HINT_T1
#define PETSC__GNU_SOURCE 1
#define PETSC_HAVE_FORTRAN 1
#define PETSC_LIB_DIR "/home/mpovolot/Code_intel/libs/petsc/build-real/linux/lib"
#define PETSC_HAVE_PARMETIS 1
#define PETSC_USE_SOCKET_VIEWER 1
#define PETSC_SLSUFFIX "so"
#define PETSC_FUNCTION_NAME_CXX __func__
#define PETSC_HAVE_FLUSH 1
#define PETSC_HAVE_MUMPS 1
#define PETSC_HAVE_ATOLL 1
#define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1
#define PETSC_UNUSED __attribute((unused))
#define PETSC_FUNCTION_NAME_C __func__
#define PETSC_HAVE_VALGRIND 1
#define PETSC_HAVE_BUILTIN_EXPECT 1
#define PETSC_HAVE_METIS 1
#define PETSC_DIR_SEPARATOR '/'
#define PETSC_PATH_SEPARATOR ':'
#define PETSC__BSD_SOURCE 1
#define PETSC_HAVE_XMMINTRIN_H 1
#define PETSC_PREFETCH_HINT_NTA _MM_HINT_NTA
#define PETSC_Prefetch(a,b,c) _mm_prefetch((const char*)(a),(c))
#define PETSC_HAVE_BLASLAPACK 1
#define PETSC_HAVE_FLOAT_H 1
#define PETSC_HAVE_STRING_H 1
#define PETSC_HAVE_SYS_TIMES_H 1
#define PETSC_HAVE_SYS_TYPES_H 1
#define PETSC_HAVE_ENDIAN_H 1
#define PETSC_HAVE_SYS_PROCFS_H 1
#define PETSC_HAVE_DLFCN_H 1
#define PETSC_HAVE_SCHED_H 1
#define PETSC_HAVE_STDINT_H 1
#define PETSC_HAVE_LINUX_KERNEL_H 1
#define PETSC_HAVE_TIME_H 1
#define PETSC_HAVE_MATH_H 1
#define PETSC_HAVE_STDLIB_H 1
#define PETSC_HAVE_SYS_PARAM_H 1
#define PETSC_HAVE_PTHREAD_H 1
#define PETSC_HAVE_UNISTD_H 1
#define PETSC_HAVE_SYS_WAIT_H 1
#define PETSC_HAVE_SETJMP_H 1
#define PETSC_HAVE_LIMITS_H 1
#define PETSC_HAVE_SYS_UTSNAME_H 1
#define PETSC_HAVE_NETINET_IN_H 1
#define PETSC_HAVE_FENV_H 1
#define PETSC_HAVE_SYS_SOCKET_H 1
#define PETSC_HAVE_MEMORY_H 1
#define PETSC_HAVE_SEARCH_H 1
#define PETSC_HAVE_SYS_RESOURCE_H 1
#define PETSC_TIME_WITH_SYS_TIME 1
#define PETSC_HAVE_NETDB_H 1
#define PETSC_HAVE_MALLOC_H 1
#define PETSC_HAVE_PWD_H 1
#define PETSC_HAVE_FCNTL_H 1
#define PETSC_HAVE_STRINGS_H 1
#define PETSC_HAVE_SYS_SYSINFO_H 1
#define PETSC_HAVE_SYS_TIME_H 1
#define PETSC_USING_F90 1
#define PETSC_USING_F2003 1
#define PETSC_HAVE_RTLD_NOW 1
#define PETSC_HAVE_RTLD_LOCAL 1
#define PETSC_HAVE_RTLD_LAZY 1
#define PETSC_C_STATIC_INLINE static inline
#define PETSC_HAVE_FORTRAN_UNDERSCORE 1
#define PETSC_HAVE_CXX_NAMESPACE 1
#define PETSC_HAVE_RTLD_GLOBAL 1
#define PETSC_C_RESTRICT __restrict__
#define PETSC_CXX_RESTRICT __restrict__
#define PETSC_CXX_STATIC_INLINE static inline
#define PETSC_HAVE_LIBZ 1
#define PETSC_HAVE_LIBDL 1
#define PETSC_HAVE_LIBSCALAPACK 1
#define PETSC_HAVE_LIBMETIS 1
#define PETSC_HAVE_LIBLAPACK 1
#define PETSC_HAVE_LIBM 1
#define PETSC_HAVE_LIBIFCORE 1
#define PETSC_HAVE_LIBMKL_INTEL_LP64 1
#define PETSC_HAVE_LIBIFPORT 1
#define PETSC_HAVE_LIBDMUMPS 1
#define PETSC_HAVE_LIBMUMPS_COMMON 1
#define PETSC_HAVE_LIBPTHREAD 1
#define PETSC_HAVE_LIBHDF5 1
#define PETSC_HAVE_LIBPARMETIS 1
#define PETSC_HAVE_LIBMKL_SEQUENTIAL 1
#define PETSC_HAVE_LIBZMUMPS 1
#define PETSC_HAVE_LIBHDF5_HL 1
#define PETSC_HAVE_LIBMKL_CORE 1
#define PETSC_HAVE_LIBSMUMPS 1
#define PETSC_HAVE_LIBCMUMPS 1
#define PETSC_HAVE_LIBPORD 1
#define PETSC_HAVE_ERF 1
#define PETSC_HAVE_LIBHDF5_FORTRAN 1
#define PETSC_HAVE_TGAMMA 1
#define PETSC_ARCH "linux"
#define PETSC_DIR "/home/mpovolot/Code_intel/libs/petsc/build-real"
#define HAVE_GZIP 1
#define PETSC_CLANGUAGE_CXX 1
#define PETSC_USE_ERRORCHECKING 1
#define PETSC_MISSING_DREAL 1
#define PETSC_SIZEOF_MPI_COMM 4
#define PETSC_BITS_PER_BYTE 8
#define PETSC_SIZEOF_MPI_FINT 4
#define PETSC_SIZEOF_VOID_P 8
#define PETSC_RETSIGTYPE void
#define PETSC_HAVE___INT64 1
#define PETSC_SIZEOF_LONG 8
#define PETSC_USE_FORTRANKIND 1
#define PETSC_SIZEOF_SIZE_T 8
#define PETSC_HAVE_SIGINFO_T 1
#define PETSC_SIZEOF_CHAR 1
#define PETSC_SIZEOF_DOUBLE 8
#define PETSC_SIZEOF_FLOAT 4
#define PETSC_HAVE_C99_COMPLEX 1
#define PETSC_SIZEOF_INT 4
#define PETSC_SIZEOF_LONG_LONG 8
#define PETSC_SIZEOF_SHORT 2
#define PETSC_HAVE_STRCASECMP 1
#define PETSC_HAVE_GET_NPROCS 1
#define PETSC_HAVE_POPEN 1
#define PETSC_HAVE_SIGSET 1
#define PETSC_HAVE_GETWD 1
#define PETSC_HAVE_VSNPRINTF 1
#define PETSC_HAVE_TIMES 1
#define PETSC_HAVE_DLSYM 1
#define PETSC_HAVE_SNPRINTF 1
#define PETSC_HAVE_GETPWUID 1
#define PETSC_HAVE_IPXFARGC_ 1
#define PETSC_HAVE_GETHOSTBYNAME 1
#define PETSC_HAVE_GETCWD 1
#define PETSC_HAVE_DLERROR 1
#define PETSC_HAVE_FORK 1
#define PETSC_HAVE_RAND 1
#define PETSC_HAVE_GETTIMEOFDAY 1
#define PETSC_HAVE_DLCLOSE 1
#define PETSC_HAVE_UNAME 1
#define PETSC_HAVE_GETHOSTNAME 1
#define PETSC_HAVE_MKSTEMP 1
#define PETSC_HAVE_SIGACTION 1
#define PETSC_HAVE_DRAND48 1
#define PETSC_HAVE_MEMALIGN 1
#define PETSC_HAVE_VA_COPY 1
#define PETSC_HAVE_CLOCK 1
#define PETSC_HAVE_ACCESS 1
#define PETSC_HAVE_SIGNAL 1
#define PETSC_HAVE_USLEEP 1
#define PETSC_HAVE_GETRUSAGE 1
#define PETSC_HAVE_VFPRINTF 1
#define PETSC_HAVE_NANOSLEEP 1
#define PETSC_HAVE_GETDOMAINNAME 1
#define PETSC_HAVE__INTEL_FAST_MEMSET 1
#define PETSC_HAVE_TIME 1
#define PETSC_HAVE__INTEL_FAST_MEMCPY 1
#define PETSC_HAVE_LSEEK 1
#define PETSC_HAVE_SOCKET 1
#define PETSC_HAVE_SYSINFO 1
#define PETSC_HAVE_READLINK 1
#define PETSC_HAVE_REALPATH 1
#define PETSC_HAVE_DLOPEN 1
#define PETSC_HAVE_MEMMOVE 1
#define PETSC_HAVE_GETPAGESIZE 1
#define PETSC_HAVE_SLEEP 1
#define PETSC_HAVE_VPRINTF 1
#define PETSC_HAVE_BZERO 1
#define PETSC_SIGNAL_CAST
#define PETSC_WRITE_MEMORY_BARRIER() asm volatile("sfence":::"memory")
#define PETSC_MEMORY_BARRIER() asm volatile("mfence":::"memory")
#define PETSC_READ_MEMORY_BARRIER() asm volatile("lfence":::"memory")
#define PETSC_CPU_RELAX() asm volatile("rep; nop" ::: "memory")
#define PETSC_BLASLAPACK_UNDERSCORE 1
#define PETSC_HAVE_MPI_COMM_C2F 1
#define PETSC_HAVE_MPI_EXSCAN 1
#define PETSC_HAVE_MPI_LONG_DOUBLE 1
#define PETSC_HAVE_MPI_COMM_F2C 1
#define PETSC_HAVE_MPI_FINT 1
#define PETSC_HAVE_MPI_F90MODULE 1
#define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1
#define PETSC_HAVE_MPI_FINALIZED 1
#define PETSC_HAVE_MPI_COMM_SPAWN 1
#define PETSC_HAVE_MPI_TYPE_GET_EXTENT 1
#define PETSC_HAVE_MPI_COMBINER_DUP 1
#define PETSC_HAVE_MPI_WIN_CREATE 1
#define PETSC_HAVE_MPI_REPLACE 1
#define PETSC_HAVE_MPI_TYPE_DUP 1
#define PETSC_HAVE_MPIIO 1
#define PETSC_HAVE_MPI_INIT_THREAD 1
#define PETSC_HAVE_MPI_ALLTOALLW 1
#define PETSC_HAVE_MPI_IN_PLACE 1
#define PETSC_LEVEL1_DCACHE_LINESIZE 64
#define PETSC_LEVEL1_DCACHE_SIZE 32768
#define PETSC_LEVEL1_DCACHE_ASSOC 8
#define PETSC_HAVE_DYNAMIC_LIBRARIES 1
#define PETSC_HAVE_SHARED_LIBRARIES 1
#define PETSC_USE_GDB_DEBUGGER 1
#define PETSC_MEMALIGN 16
#define PETSC_USE_INFO 1
#define PETSC_Alignx(a,b)
#define PETSC_USE_BACKWARD_LOOP 1
#define PETSC_USE_DEBUG 1
#define PETSC_USE_LOG 1
#define PETSC_IS_COLOR_VALUE_TYPE short
#define PETSC_USE_CTABLE 1
#define PETSC_USE_SCALAR_REAL 1
#define PETSC_HAVE_ISINF 1
#define PETSC_HAVE_ISNAN 1
#define PETSC_USE_REAL_DOUBLE 1
#define PETSC_HAVE_PXFGETARG_NEW 1
#define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1
#define PETSC_HAVE_GETARG 1
#define PETSC_USE_PROC_FOR_SIZE 1
#define PETSC_HAVE_SCHED_CPU_SET_T 1
#define PETSC_HAVE_PTHREAD_BARRIER_T 1
#define PETSC_HAVE_SYS_SYSCTL_H 1
#define PETSC_HAVE_H5PSET_FAPL_MPIO 1
-----------------------------------------
Using C/C++ compile: /opt/intel/impi/4.1.0/intel64/bin/mpiicpc -c -wd1572 -O3 -fPIC -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include -D__INSDIR__=./
Using Fortran compile: /opt/intel/impi/4.1.0/intel64/bin/mpiifort -c -fPIC -O3 -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include
-----------------------------------------
Using C/C++ linker: /opt/intel/impi/4.1.0/intel64/bin/mpiicpc
Using C/C++ flags: -Wl,-rpath,/opt/intel/mkl//lib/intel64 -L/opt/intel/mkl//lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -L/opt/intel/lib/intel64 -Wl,-rpath=/opt/intel/lib/intel64 -lintlc -wd1572 -O3
Using Fortran linker: /opt/intel/impi/4.1.0/intel64/bin/mpiifort
Using Fortran flags: -Wl,-rpath,/opt/intel/mkl//lib/intel64 -L/opt/intel/mkl//lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -L/opt/intel/lib/intel64 -Wl,-rpath=/opt/intel/lib/intel64 -lintlc -fPIC -O3
-----------------------------------------
Using libraries: -Wl,-rpath,/home/mpovolot/Code_intel/libs/petsc/build-real/linux/lib -L/home/mpovolot/Code_intel/libs/petsc/build-real/linux/lib -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys -Wl,-rpath,/home/mpovolot/Code_intel/libs/petsc/build-real/linux/lib -L/home/mpovolot/Code_intel/libs/petsc/build-real/linux/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -Wl,-rpath,/opt/intel/mkl/lib/intel64 -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -lpthread -lparmetis -lmetis -lhdf5_fortran -lhdf5_hl -lhdf5 -lz -Wl,-rpath,/opt/intel/lib/intel64 -L/opt/intel/lib/intel64 -Wl,-rpath,/opt/intel/impi/4.1.0.024/intel64/lib -L/opt/intel/impi/4.1.0.024/intel64/lib -Wl,-rpath,/opt/intel/composer_xe_2013.1.117/compiler/lib/intel64 -L/opt/intel/composer_xe_2013.1.117/compiler/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.7 -L/usr/lib/gcc/x86_64-linux-gnu/4.7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -Wl,-rpath,/home/mpovolot/Code_intel/libs/petsc/build-real/-Xlinker -Wl,-rpath,/opt/intel/mpi-rt/4.1 -lifport -lifcore -lm -lm -lmpigc4 -ldl -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lintlc -lmpi -lmpigf -lmpigi -lrt -lpthread -limf -lsvml -lirng -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lirc_s -ldl
------------------------------------------
Using mpiexec: /opt/intel/impi/4.1.0.024/intel64/bin/mpiexec
==========================================
Building PETSc using CMake with 5 build threads
==========================================
/usr/bin/cmake -H/home/mpovolot/Code_intel/libs/petsc/build-real -B/home/mpovolot/Code_intel/libs/petsc/build-real/linux --check-build-system CMakeFiles/Makefile.cmake 0
Re-run cmake file: Makefile older than: ../CMakeLists.txt
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mpovolot/Code_intel/libs/petsc/build-real/linux
/usr/bin/cmake -E cmake_progress_start /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/usr/bin/make -f CMakeFiles/petscsys.dir/build.make CMakeFiles/petscsys.dir/depend
cd /home/mpovolot/Code_intel/libs/petsc/build-real/linux && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/mpovolot/Code_intel/libs/petsc/build-real /home/mpovolot/Code_intel/libs/petsc/build-real /home/mpovolot/Code_intel/libs/petsc/build-real/linux /home/mpovolot/Code_intel/libs/petsc/build-real/linux /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles/petscsys.dir/DependInfo.cmake --color=
Dependee "/home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles/petscsys.dir/DependInfo.cmake" is newer than depender "/home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles/petscsys.dir/depend.internal".
Dependee "/home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles/petscsys.dir/depend.internal".
Scanning dependencies of target petscsys
/usr/bin/make -f CMakeFiles/petscsys.dir/build.make CMakeFiles/petscsys.dir/requires
make[6]: Nothing to be done for `CMakeFiles/petscsys.dir/requires'.
/usr/bin/make -f CMakeFiles/petscsys.dir/build.make CMakeFiles/petscsys.dir/build
/usr/bin/cmake -E cmake_progress_report /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles
[ 0%] [ 0%] [ 0%] [ 0%] Building CXX object CMakeFiles/petscsys.dir/src/sys/info/verboseinfo.c.o
Building CXX object CMakeFiles/petscsys.dir/src/sys/logging/plog.c.o
[ 0%] Building CXX object CMakeFiles/petscsys.dir/src/sys/totalview/tv_data_display.c.o
/opt/intel/impi/4.1.0/intel64/bin/mpiicpc -D__INSDIR__="" -wd1572 -O3 -fPIC -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include -o CMakeFiles/petscsys.dir/src/sys/info/verboseinfo.c.o -c /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/info/verboseinfo.c
/opt/intel/impi/4.1.0/intel64/bin/mpiicpc -D__INSDIR__="" -wd1572 -O3 -fPIC -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include -o CMakeFiles/petscsys.dir/src/sys/logging/plog.c.o -c /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/logging/plog.c
Building Fortran object CMakeFiles/petscsys.dir/src/sys/f90-mod/petscsysmod.F.o
/opt/intel/impi/4.1.0/intel64/bin/mpiicpc -D__INSDIR__="" -wd1572 -O3 -fPIC -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include -o CMakeFiles/petscsys.dir/src/sys/totalview/tv_data_display.c.o -c /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/totalview/tv_data_display.c
/opt/intel/impi/4.1.0/intel64/bin/mpiifort -D__INSDIR__="" -fPIC -O3 -module include -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include -c /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/f90-mod/petscsysmod.F -o CMakeFiles/petscsys.dir/src/sys/f90-mod/petscsysmod.F.o
Building CXX object CMakeFiles/petscsys.dir/src/sys/python/pythonsys.c.o
/opt/intel/impi/4.1.0/intel64/bin/mpiicpc -D__INSDIR__="" -wd1572 -O3 -fPIC -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include -o CMakeFiles/petscsys.dir/src/sys/python/pythonsys.c.o -c /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/python/pythonsys.c
/usr/bin/cmake -E cmake_progress_report /home/mpovolot/Code_intel/libs/petsc/build-real/linux/CMakeFiles
[ 0%] /usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error: cannot open source file "bits/c++config.h"
#include <bits/c++config.h>
^
/usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error: cannot open source file "bits/c++config.h"
#include <bits/c++config.h>
^
compilation aborted for /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/info/verboseinfo.c (code 4)
compilation aborted for /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/logging/plog.c (code 4)
make[6]: *** [CMakeFiles/petscsys.dir/src/sys/info/verboseinfo.c.o] Error 4
make[6]: *** Waiting for unfinished jobs....
make[6]: *** [CMakeFiles/petscsys.dir/src/sys/logging/plog.c.o] Error 4
Building CXX object CMakeFiles/petscsys.dir/src/sys/utils/arch.c.o
/opt/intel/impi/4.1.0/intel64/bin/mpiicpc -D__INSDIR__="" -wd1572 -O3 -fPIC -I/home/mpovolot/Code_intel/libs/petsc/build-real/include -I/home/mpovolot/Code_intel/libs/petsc/build-real/linux/include -I/opt/intel/impi/4.1.0.024/intel64/include -o CMakeFiles/petscsys.dir/src/sys/utils/arch.c.o -c /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/utils/arch.c
/usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error: cannot open source file "bits/c++config.h"
#include <bits/c++config.h>
^
compilation aborted for /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/python/pythonsys.c (code 4)
make[6]: *** [CMakeFiles/petscsys.dir/src/sys/python/pythonsys.c.o] Error 4
/usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error: cannot open source file "bits/c++config.h"
#include <bits/c++config.h>
^
compilation aborted for /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/utils/arch.c (code 4)
make[6]: *** [CMakeFiles/petscsys.dir/src/sys/utils/arch.c.o] Error 4
make[5]: *** [CMakeFiles/petscsys.dir/all] Error 2
make[4]: *** [all] Error 2
make[3]: *** [ccmake] Error 2
make[2]: *** [cmake] Error 2
[1;31m**************************ERROR************************************
Error during compile, check linux/conf/make.log
Send it and linux/conf/configure.log to petsc-maint at mcs.anl.gov
********************************************************************[0;39m[0;49m
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