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

Zhifeng Yang yangzf01 at gmail.com
Thu Oct 18 12:30:40 CDT 2018 

Hi Min,

You may want to see my config.log file while configuring MPICH. Here it is.
It seems that there are some intel compiler path. But I am not sure whether
they affect my make.

Thank you
Zhifeng


On Thu, Oct 18, 2018 at 1:23 PM Zhifeng Yang <yangzf01 at gmail.com> wrote:

> 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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