[mpich-discuss] mpich install error (libstdc++.so)

[Zhifeng Yang]

Hi Min,

Thank you very much for your help. Now I installed MPICH successfully.

However, when I use it for another weather model. It has the following
error.

time mpif90    -w -ffree-form -ffree-line-length-none -fconvert=big-endian
-frecord-marker=4  -fopenmp   -o test_io_idx test_io_idx.f -L. -lwrfio_int

real    0m0.234s
user    0m0.076s
sys     0m0.042s
if [ -f ../../frame/pack_utils.o -a -f ../../frame/clog.o ] ; then \
          time mpif90    -w -ffree-form -ffree-line-length-none
-fconvert=big-endian -frecord-marker=4  -fopenmp   -I../ioapi_share -o
diffwrf diffwrf.f \
                ../../frame/pack_utils.o
../../frame/module_internal_header_util.o
../../frame/module_driver_constants.o ../../frame/module_machine.o
../../frame/module_wrf_error.o ../../frame/wrf_debug.o  libwrfio_int.a ; \
        fi
/umbc/xfs1/zzbatmos/users/vy57456/application/gfortran/mpich-3.2.1/lib/libmpi.so:
undefined reference to `_intel_fast_memset'
/umbc/xfs1/zzbatmos/users/vy57456/application/gfortran/mpich-3.2.1/lib/libmpi.so:
undefined reference to `_intel_fast_memcpy'
/umbc/xfs1/zzbatmos/users/vy57456/application/gfortran/mpich-3.2.1/lib/libmpi.so:
undefined reference to `__intel_sse2_strlen'
/umbc/xfs1/zzbatmos/users/vy57456/application/gfortran/mpich-3.2.1/lib/libmpi.so:
undefined reference to `__intel_sse2_strncmp'
collect2: error: ld returned 1 exit status
0.03user 0.06system 0:00.31elapsed 31%CPU (0avgtext+0avgdata
9716maxresident)k
144inputs+48outputs (0major+10999minor)pagefaults 0swaps
make[3]: [test_io_idx] Error 1 (ignored)
make[3]: Leaving directory
`/umbc/xfs1/zzbatmos/users/vy57456/model/gfortran/wrfchem4_0_c/WRF/external/io_int'

It seems that I used ifort to compile MPICH. But I used gfortran. Any help?

Zhifeng


On Thu, Oct 18, 2018 at 10:19 AM Si, Min <msi at anl.gov> wrote:

> Hi Zhifeng,
>
> It looks like the Intel c++ compiler icpc is used for linking. Maybe you
> did not specify `CXX=g++` at configure time.
>
> Please try this (make sure all compilers are with the same version)
> ./configure <other config options> CC=gcc CXX=g++ FC=gfortran F77=gfortran
>
> If you still see the installation error, please send us the config.log at
> your build directory together with the error message.
>
> Min
> On 2018/10/18 8:28, Zhifeng Yang wrote:
>
> Hi
>
> I tried to install mpich using gcc. However, while make, I got the
> following error message.
>
> libtool: link: icpc -shared  src/binding/cxx/.libs/initcxx.o
> -Wl,-rpath,/home/vy57456/zzbatmos_user/application/gfortran/source_code/mpich-3.2.1/lib/.libs
> -Wl,-rpath,/cm/shared/apps/gcc/4.8.4/lib/../lib
> -Wl,-rpath,/home/vy57456/zzbatmos_user/application/gfortran/mpich-3.2.1/lib
> -Wl,-rpath,/cm/shared/apps/gcc/4.8.4/lib/../lib lib/.libs/libmpi.so
> -lpthread
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/ipp/../compiler/lib/intel64
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/ipp/lib/intel64
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/compiler/lib/intel64
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/mkl/lib/intel64
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/tbb/lib/intel64/gcc4.4
> -L/cm/shared/apps/slurm/14.11.11/lib64/slurm
> -L/cm/shared/apps/slurm/14.11.11/lib64
> -L/usr/cluster/contrib/hdf5/install-1.8.16/lib
> -L/cm/shared/apps/acml/current/ifort64/lib
> -L/cm/shared/apps/slurm/14.11.11/lib64/../lib64
> -L/cm/shared/apps/slurm/14.11.11/lib64/../lib64/
> -L/cm/shared/apps/gcc/4.8.4/lib/gcc/x86_64-unknown-linux-gnu/4.8.4/
> -L/cm/shared/apps/gcc/4.8.4/lib/gcc/x86_64-unknown-linux-gnu/4.8.4/../../../../lib64
> -L/cm/shared/apps/gcc/4.8.4/lib/gcc/x86_64-unknown-linux-gnu/4.8.4/../../../../lib64/
> -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/ipp/../compiler/lib/intel64/
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/ipp/lib/intel64/
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/compiler/lib/intel64/
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/mkl/lib/intel64/
> -L/cm/shared/apps/intel/composer_xe/2015.5.223/tbb/lib/intel64/gcc4.4/
> -L/cm/shared/apps/slurm/14.11.11/lib64/slurm/
> -L/cm/shared/apps/slurm/14.11.11/lib64/
> -L/usr/cluster/contrib/hdf5/install-1.8.16/lib/
> -L/cm/shared/apps/acml/current/ifort64/lib/
> -L/cm/shared/apps/gcc/4.8.4/lib/gcc/x86_64-unknown-linux-gnu/4.8.4/../../../
> -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -limf -lirng -lm -lipgo -ldecimal
> -lcilkrts /cm/shared/apps/gcc/4.8.4/lib/../lib/libstdc++.so -lintlc -lsvml
> -lgcc -lgcc_s -lirc_s -ldl -lc  -O2   -Wl,-soname -Wl,libmpicxx.so.12 -o
> lib/.libs/libmpicxx.so.12.1.1
> /cm/shared/apps/gcc/4.8.4/lib/../lib/libstdc++.so: could not read symbols:
> File in wrong format
> make[2]: *** [lib/libmpicxx.la] Error 1
> make[2]: Leaving directory
> `/umbc/xfs1/zzbatmos/users/vy57456/application/gfortran/source_code/mpich-3.2.1'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory
> `/umbc/xfs1/zzbatmos/users/vy57456/application/gfortran/source_code/mpich-3.2.1'
> make: *** [all] Error 2
>
>
> Do you have any experience on this error? Thank you
>
> Zhifeng
>
>
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