[mvapich-discuss] Error while compiling mpi4py with MVAPICH

[Jonathan Perkins]

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