[mvapich-discuss] MPI4PY with mvapich2

[Xing Wang]

Hi All,

Thanks for reading the email.
We have been using mvapich2-1.8.1 since last Oct. and it's working very well. Recently we need to install MPI4PY but met with following error messages. 

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ld: /usr/local/mvapich2/intel/1.8.1/lib/liblmpe.a(log_mpi_util.o): relocation R_X86_64_32 against `.rodata.str1.4' can not be used when making a shared object; recompile with -fPIC
/usr/local/mvapich2/intel/1.8.1/lib/liblmpe.a(log_mpi_util.o): could not read symbols: Bad value
warning: build_clib: building library "mpe" failed

warning: build_clib: command '/usr/local/mvapich2/intel/1.8.1/bin/mpicc' failed with exit status 1
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Did anyone have a similar error before? Any help/hint is really appreciated!


Here is the full log of during the installation
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[root at turnbull mpi4py-1.3]# ../bin/python setup.py build
running build
running build_src
running build_py
running build_clib
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpicc
MPI C++ compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpicxx
MPI F77 compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpif77
MPI F90 compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpif90
checking for library 'mpe' ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -c _configtest.c -o _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc _configtest.o -lmpe -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for library 'lmpe' ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -c _configtest.c -o _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc _configtest.o -llmpe -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for library 'pthread' ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -c _configtest.c -o _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc _configtest.o -lpthread -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpe' dylib library
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -c src/pmpi-mpe.c -o build/temp.linux-x86_64-2.7/src/pmpi-mpe.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -shared -g build/temp.linux-x86_64-2.7/src/pmpi-mpe.o -o build/lib.linux-x86_64-2.7/mpi4py/lib-pmpi/libmpe.so -Wl,-whole-archive -llmpe -Wl,-no-whole-archive -lmpe -lpthread
ld: /usr/local/mvapich2/intel/1.8.1/lib/liblmpe.a(log_mpi_util.o): relocation R_X86_64_32 against `.rodata.str1.4' can not be used when making a shared object; recompile with -fPIC
/usr/local/mvapich2/intel/1.8.1/lib/liblmpe.a(log_mpi_util.o): could not read symbols: Bad value
warning: build_clib: building library "mpe" failed

warning: build_clib: command '/usr/local/mvapich2/intel/1.8.1/bin/mpicc' failed with exit status 1

running build_ext
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpicc
MPI C++ compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpicxx
MPI F77 compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpif77
MPI F90 compiler: /usr/local/mvapich2/intel/1.8.1/bin/mpif90
checking for MPI compile and link ...
checking for header 'mpi.h' ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c _configtest.c -o _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc _configtest.o -L//share/apps/EPD_64bit/lib -Lbuild/temp.linux-x86_64-2.7 -Wl,-R//share/apps/EPD_64bit/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for missing MPI functions/symbols ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
checking for function 'MPI_Type_create_f90_integer' ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c _configtest.c -o _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc _configtest.o -L//share/apps/EPD_64bit/lib -Lbuild/temp.linux-x86_64-2.7 -Wl,-R//share/apps/EPD_64bit/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_real' ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c _configtest.c -o _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc _configtest.o -L//share/apps/EPD_64bit/lib -Lbuild/temp.linux-x86_64-2.7 -Wl,-R//share/apps/EPD_64bit/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_complex' ...
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c _configtest.c -o _configtest.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc _configtest.o -L//share/apps/EPD_64bit/lib -Lbuild/temp.linux-x86_64-2.7 -Wl,-R//share/apps/EPD_64bit/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.MPI' extension
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -O2 -I/share/apps/EPD_64bit/include/python2.7 -c src/MPI.c -o build/temp.linux-x86_64-2.7/src/MPI.o
/usr/local/mvapich2/intel/1.8.1/bin/mpicc -shared -g build/temp.linux-x86_64-2.7/src/MPI.o -L//share/apps/EPD_64bit/lib -Lbuild/temp.linux-x86_64-2.7 -Wl,-R//share/apps/EPD_64bit/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/mpi4py/MPI.so
ld: /usr/local/mvapich2/intel/1.8.1/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/local/mvapich2/intel/1.8.1/lib/libmpich.a: could not read symbols: Bad value
error: command '/usr/local/mvapich2/intel/1.8.1/bin/mpicc' failed with exit status 1

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--
Sincerely, 
WANG, Xing

Graduate Student 
Department of Engineering Physics & 
Nuclear Engineering, UW-Madison
Room 137, 1509 University Ave.
Madison, WI, 53706 
(Cell)608-320-7086