[Trilinos-Users] [EXTERNAL] error configuring trilinos

Balakrishnan, Ramesh bramesh at alcf.anl.gov
Mon Oct 26 19:10:10 EDT 2015


All,
I’ve built trilinos-12.2.1 with mvapich2 and Intel C/FORTRAN Composer XE 2015, with the following do-configure.sh script:

=============
#!/bin/sh
TRILINOS_PATH=/gpfs/mira-home/mephistopheles/PUBLIQUE/fen/COOLEY/builds/trilinos-12.2.1-Source
TRILINOS_INSTALL_DIR=/home/mephistopheles/PUBLIQUE/COOLEY/trilinos/trilinos-12.2.1
MPI_HOME=/soft/libraries/mpi/mvapich2/intel/
BOOST_HOME=/home/mephistopheles/PUBLIQUE/COOLEY/boost/boost_1_59_0
MKLROOT=/soft/compilers/intel/composerxe/mkl
EXTRA_ARGS=$@

rm -f CMakeCache.txt

/soft/buildtools/cmake/current/bin/cmake \
  -D CMAKE_INSTALL_PREFIX:PATH="$TRILINOS_INSTALL_DIR" \
  -D CMAKE_BUILD_TYPE:STRING=RELEASE \
  -D TPL_ENABLE_MPI:BOOL=ON \
  -D MPI_BASE_DIR:PATH="$MPI_HOME"\
  -D MPI_BIN_DIR:PATH="$MPI_HOME/bin"\
  -D MPI_INCLUDE_PATH:PATH="$MPI_HOME/include" \
  -D MPI_USE_COMPILER_WRAPPERS:BOOL=ON \
  -D MPI_Fortran_COMPILER:FILEPATH="$MPI_HOME/bin/mpif90" \
  -D MPI_CXX_COMPILER:FILEPATH="$MPI_HOME/bin/mpicxx" \
  -D MPI_C_COMPILER:FILEPATH="$MPI_HOME/bin/mpicc" \
  -D HAVE_GCC_ABI_DEMANGLE:BOOL=ON \
  -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \
  -D Trilinos_ENABLE_DEFAULT_PACKAGES:BOOL=ON \
  -D BLAS_LIBRARY_DIRS:FILEPATH="${MKLROOT}/lib/intel64" \
  -D BLAS_LIBRARY_NAMES:STRING="mkl_rt" \
  -D LAPACK_LIBRARY_DIRS:FILEPATH="${MKLROOT}/lib/intel64" \
  -D LAPACK_LIBRARY_NAMES:STRING="mkl_rt" \
  -D TPL_ENABLE_MKL:BOOL=ON \
  -D MKL_LIBRARY_DIRS:FILEPATH="${MKLROOT}/lib/intel64" \
  -D MKL_LIBRARY_NAMES:STRING="mkl_rt" \
  -D MKL_INCLUDE_DIRS:FILEPATH="${MKLROOT}/include" \
  -D Trilinos_ENABLE_OpenMP:BOOL=ON \
  -D TPL_ENABLE_Pthread:BOOL=ON \
  -D TPL_ENABLE_Boost:BOOL=ON \
  -D Boost_LIBRARY_DIRS:FILEPATH="${BOOST_HOME}/lib" \
  -D Boost_INCLUDE_DIRS:FILEPATH="${BOOST_HOME}/include" \
  -D DART_TESTING_TIMEOUT:STRING=600 \
  -D CMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
  -D Trilinos_ENABLE_CTrilinos:BOOL=ON\
  -D Trilinos_ENABLE_ForTrilinos:BOOL=ON\
  -D Trilinos_ENABLE_Kokkos:BOOL=ON \
  -D Kokkos_ENABLE_TSQR:BOOL=ON \
  -D TSQR_ENABLE_Fortran:BOOL=ON \
  -D ForTrilinos_ENABLE_OBJECT_ORIENTED:BOOL=ON \
  -D ForTrilinos_DISABLE_DEFERRED_LENGTH_CHARACTERS:BOOL=ON \
  -D ForTrilinos_DISABLE_FINAL_SUBROUTINES:BOOL=ON \
  -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
  -D Trilinos_ENABLE_CONFIGURE_TIMING:BOOL=ON \
  -D Trilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON \
$EXTRA_ARGS \
$TRILINOS_PATH
=============

I had no problems building it with the Intel compiler. Two things, however: I had to disable the building of examples and tests. There are two reasons for doing this: a) The ForTrilinos unit tests require header files that can be found _after_ one does gmake install (yes, its strange!). So, it you were to include ForTrilinos example/tests and run into this error message (after 99% of the builds are done), you may want to do the counterintuitive steps of "gmake install" followed by "gmake all”, just to make sure that there are no ForTrilinos UNIT TESTS related errors. b) I disabled the example/tests on the viz cluster here, because it calls to futzing with the do-configure script to go through the tests via the COBALT scheduler (a system dependent, and not a trilinos, problem).

Hope this helps.

Ramesh


On Oct 23, 2015, at 8:47 AM, Thompson, KT <kgt at lanl.gov<mailto:kgt at lanl.gov>> wrote:

Take a look at the Intel flags ‘-gcc-name=name’, ‘-gcc-version’ and related options.  When configuring Trilinos, add the appropriate options. For example,

cmake –DCMAKE_CXX_FLAGS=”-gxx-name=g++-4.7” … /path/to/source

-kt

From: Trilinos-Users [mailto:trilinos-users-bounces at trilinos.org] On Behalf Of Irena Johnson
Sent: Friday, October 23, 2015 6:37 AM
To: Andrey Prokopenko <aprokop at sandia.gov<mailto:aprokop at sandia.gov>>
Cc: trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>
Subject: Re: [Trilinos-Users] [EXTERNAL] error configuring trilinos

Is it possible to build trilinos with Intel compiler 2015, using a non-native gcc-4.9.1 ?

Thank you

Irena

On Fri, Oct 16, 2015 at 11:58 AM, Irena Johnson <ijohnson at pppl.gov<mailto:ijohnson at pppl.gov>> wrote:
Dear Trilinos Support,

I am getting errors (pasted below) while trying to build trilinos with Intel 2015.u1 and using non-native gcc-4.9.1 on a rhel 6 system.
I have attached the configuration script. Please advise. Thank you,
Irena


 [100%] Linking CXX executable VerifyFortranC
    /usr/pppl/cmake/3.4.0-rc1/bin/cmake -E cmake_link_script CMakeFiles/VerifyFortranC.dir/link.txt --verbose=1
    /usr/pppl/intel/2015.u1/bin/icpc   -O2 -std=c++11 -ggdb -Wno-sign-compare -O3 -DNDEBUG   CMakeFiles/VerifyFortranC.dir/main.c.o CMakeFiles/VerifyFortranC.dir/VerifyC.c.o CMakeFiles/VerifyFortranC.dir/VerifyCXX.cxx.o  -o VerifyFortranC libVerifyFortran.a -lifport -lifcore -lpthread
    ld: warning: libimf.so, needed by /usr/pppl/intel/2015.u1/composer_xe_2015.1.133/compiler/lib/intel64/libifport.so.5, not found (try using -rpath or -rpath-link)
    ld: warning: libintlc.so.5, needed by /usr/pppl/intel/2015.u1/composer_xe_2015.1.133/compiler/lib/intel64/libifport.so.5, not found (try using -rpath or -rpath-link)
    CMakeFiles/VerifyFortranC.dir/main.c.o: In function `main':
    /usr/pppl/cmake/3.4.0-rc1/share/cmake-3.4/Modules/FortranCInterface/Verify/main.c:14: undefined reference to `VerifyFortran'
    gmake[2]: *** [VerifyFortranC] Error 1
    gmake[2]: Leaving directory `/pfs/tmp/ijohnson/trilinos-12.2.1-Source/build/CMakeFiles/FortranCInterface/VerifyCXX'
    gmake[1]: *** [CMakeFiles/VerifyFortranC.dir/all] Error 2
    gmake[1]: Leaving directory `/pfs/tmp/ijohnson/trilinos-12.2.1-Source/build/CMakeFiles/FortranCInterface/VerifyCXX'
    gmake: *** [all] Error 2

Call Stack (most recent call first):
  cmake/tribits/core/package_arch/TribitsFortranMangling.cmake:50 (FortranCInterface_VERIFY)
  cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:1713 (INCLUDE)
  cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:188 (TRIBITS_SETUP_ENV)
  cmake/tribits/core/package_arch/TribitsProject.cmake:93 (TRIBITS_PROJECT_IMPL)
  CMakeLists.txt:89 (TRIBITS_PROJECT)


-- Configuring incomplete, errors occurred!


On Wed, Oct 14, 2015 at 11:35 AM, Irena Johnson <ijohnson at pppl.gov<mailto:ijohnson at pppl.gov>> wrote:
Hi Andrey,

Our users need trilinos to be built under Intel 2015.u1. I understand that in order to build trilinos, you need at least gcc/4.7.2 , and  on RHEL 6, the native gcc compiler is 4.4.7.

I have attached the confiugration script to this email.



$ module li
Currently Loaded Modulefiles:
  1) slurm/14.11.1        3) bbcp/10.08.29.00.0   5) gcc4/4.9.1
  2) ppplcluster/1.2      4) cmake/3.4.0-rc1

echo $INCLUDE_PATH
/usr/pppl/gcc/4.9.1/include:/usr/pppl/slurm/14.03.5/include

echo $LD_LIBRARY_PATH
/usr/pppl/gcc/4.9.1/lib64:/usr/pppl/mpc/1.0.2/lib:/usr/pppl/mpfr/3.1.2/lib:/usr/pppl/gmp/6.0.0a/lib:/usr/pppl/slurm/14.11.1/lib


Thanks,
--
Irena

On Wed, Oct 14, 2015 at 10:47 AM, Andrey Prokopenko <aprokop at sandia.gov<mailto:aprokop at sandia.gov>> wrote:
Hi Irena,

If you are building with gcc, why does it use intel (icpc) to compile the code? It's hard to say what's going on without more details. Could you please attach your configuration script and environment?

-Andrey

On 10/14/2015 08:20 AM, Irena Johnson wrote:
Hello,

I am building trilinos-12.2.1 on a RHEL 6 system, with non-native gcc4/4.9.1

Could you advise what I am missing from the configuration. I have attached the configuration script.

The error I am getting is:


    [100%] Linking CXX executable VerifyFortranC
    /usr/pppl/cmake/3.4.0-rc1/bin/cmake -E cmake_link_script CMakeFiles/VerifyFortranC.dir/link.txt --verbose=1
    /usr/pppl/intel/2015.u1/bin/icpc   -O2 -std=c++11 -ggdb -Wno-sign-compare -O3 -DNDEBUG   CMakeFiles/VerifyFortranC.dir/main.c.o CMakeFiles/VerifyFortranC.dir/VerifyC.c.o CMakeFiles/VerifyFortranC.dir/VerifyCXX.cxx.o  -o VerifyFortranC libVerifyFortran.a -lifport -lifcore -lpthread
    ld: warning: libimf.so, needed by /usr/pppl/intel/2015.u1/composer_xe_2015.1.133/compiler/lib/intel64/libifport.so.5, not found (try using -rpath or -rpath-link)
    ld: warning: libintlc.so.5, needed by /usr/pppl/intel/2015.u1/composer_xe_2015.1.133/compiler/lib/intel64/libifport.so.5, not found (try using -rpath or -rpath-link)
    CMakeFiles/VerifyFortranC.dir/main.c.o: In function `main':
    /usr/pppl/cmake/3.4.0-rc1/share/cmake-3.4/Modules/FortranCInterface/Verify/main.c:14: undefined reference to `VerifyFortran'
    gmake[2]: *** [VerifyFortranC] Error 1
    gmake[2]: Leaving directory `/pfs/tmp/ijohnson/trilinos-12.2.1-Source/build/CMakeFiles/FortranCInterface/VerifyCXX'
    gmake[1]: *** [CMakeFiles/VerifyFortranC.dir/all] Error 2
    gmake[1]: Leaving directory `/pfs/tmp/ijohnson/trilinos-12.2.1-Source/build/CMakeFiles/FortranCInterface/VerifyCXX'
    gmake: *** [all] Error 2

Call Stack (most recent call first):
  cmake/tribits/core/package_arch/TribitsFortranMangling.cmake:50 (FortranCInterface_VERIFY)
  cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:1713 (INCLUDE)
  cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:188 (TRIBITS_SETUP_ENV)
  cmake/tribits/core/package_arch/TribitsProject.cmake:93 (TRIBITS_PROJECT_IMPL)
  CMakeLists.txt:89 (TRIBITS_PROJECT)


-- Configuring incomplete, errors occurred!





--
Irena


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--
Irena

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