[mvapich-discuss] Error while compiling mpi4py with MVAPICH

Tue Oct 5 12:22:00 EDT 2010

Hi Jonathan,

Thank you very much for the information. Yes it worked now. I am able to
install mpi4py, after compiling mvapich2 with the mentioned options.

Thanks very much for your support and time.

Senthil

> Hello Senthil,
>
> I just tried building mpi4py using python-pip and it compiled and
> installed successfully for me.  I downloaded mvapich2-1.5.1p1 from
> http://mvapich.cse.ohio-state.edu/download/mvapich2/mvapich2-1.5.1p1.tgz
> and configured using the following options...
>
> --with-prefix=$PWD/install --enable-sharedlibs=gcc
>
> I then used make followed by make install.  In order to use python-pip
> I did the following as root (I tried as a normal user at first but the
> install step fails)...
>
> env MPICC=/home/jonathan/Documents/mvapich2-1.5.1p1/install/bin/mpicc
> python-pip install mpi4py
>
> This completes successfully for me.  When looking at the information
> that you sent in the last email I think the problem that you're facing
> is due to trying to link against the static library and not the
> shared.  Did you use the --enable-sharedlibs=gcc option when building
> mvapich2?  If not I think adding this will resolve the issue for you.
> Please let me know if this helps.
>
> On Thu, Sep 30, 2010 at 7:00 PM,  <senthil.natesan at ndsu.edu> wrote:
>>
>> Hi Jonathan,
>>
>> Thanks for the suggestion. I was running an application using mvapich2,
>> so
>> I didn't want to disturb until it finished now. Today I installed the
>> recommended latest version. But still it is showing the same error when
>> I
>> am trying to compile mpi4py.
>>
>> -----------------------------------------------------------------------
>> [root at craycx1 mpi4py-1.2.1]# python2.7 setup.py build
>> running build
>> running build_py
>> creating build
>> creating build/lib.linux-x86_64-2.7
>> creating build/lib.linux-x86_64-2.7/mpi4py
>> copying src/rc.py -> build/lib.linux-x86_64-2.7/mpi4py
>> copying src/__init__.py -> build/lib.linux-x86_64-2.7/mpi4py
>> creating build/lib.linux-x86_64-2.7/mpi4py/include
>> creating build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.MPI.h ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.h ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.MPI_api.h ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi_c.pxd ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/MPI.pxd ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/__init__.pxd ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/__init__.pyx ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi.pxi ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.i ->
>> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>> running build_ext
>> MPI C compiler:    /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc
>> MPI C++ compiler:  /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicxx
>> MPI linker:        /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc
>> checking for MPI compile and link ...
>> /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc -fPIC -fno-strict-aliasing
>> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>> -I/usr/local/include/python2.7 -c _configtest.c -o _configtest.o
>> /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc _configtest.o -o _configtest
>> success!
>> removing: _configtest.c _configtest.o _configtest
>> checking for MPE availability ...
>> checking for header 'mpe.h' ...
>> /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc -fPIC -fno-strict-aliasing
>> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>> -I/usr/local/include/python2.7 -c _configtest.c -o _configtest.o
>> success!
>> removing: _configtest.c _configtest.o
>> succes!
>> checking for function 'MPE_Init_log' ...
>> /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc -fPIC -fno-strict-aliasing
>> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>> -I/usr/local/include/python2.7 -c _configtest.c -o _configtest.o
>> /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc _configtest.o -lmpe -o
>> _configtest
>> success!
>> removing: _configtest.c _configtest.o _configtest
>> building 'mpi4py.MPI' extension
>> creating build/temp.linux-x86_64-2.7
>> creating build/temp.linux-x86_64-2.7/src
>> /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc -fPIC -fno-strict-aliasing
>> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>> -I/usr/local/include/python2.7 -c src/MPI.c -o
>> build/temp.linux-x86_64-2.7/src/MPI.o
>> /usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc -shared
>> build/temp.linux-x86_64-2.7/src/MPI.o -o
>> build/lib.linux-x86_64-2.7/mpi4py/MPI.so
>> /usr/bin/ld:
>> /usr/mpi/gcc/mvapich2-1.5.1p1/lib/libmpich.a(comm_create_keyval.o):
>> relocation R_X86_64_32 against `MPID_Keyval_mem' can not be used when
>> making a shared object; recompile with -fPIC
>> /usr/mpi/gcc/mvapich2-1.5.1p1/lib/libmpich.a: could not read symbols:
>> Bad
>> value
>> collect2: ld returned 1 exit status
>> error: command '/usr/mpi/gcc/mvapich2-1.5.1p1/bin/mpicc' failed with
>> exit
>> status 1
>>
>> ----------------------------------------------------------------
>>
>> As I mentioned earlier, I was able to compile with MPICH2.
>> It would be great if you can suggest any way out.
>>
>> thanks,
>>
>> Senthil
>>
>>
>> Jonathan wrote:
>>
>>> It looks like you're trying to create a shared library using objects
>>> that were not compiled with -fPIC in the static libmpich.a library.
>>> You may have a bug that was fixed with the mvapich2-1.5.1p1 release.
>>> Please install this version and see if you still encounter this issue.
>>>
>>> For your convenience:
>>> http://mvapich.cse.ohio-state.edu/download/mvapich2/mvapich2-1.5.1p1.tgz
>>>
>>> --
>>> Jonathan Perkins
>>> http://www.cse.ohio-state.edu/~perkinjo
>>>
>>>
>>
>>
>>
>
>
>
> --
> Jonathan Perkins
> http://www.cse.ohio-state.edu/~perkinjo
>
>