issue with openmpi ?

PICCA Frédéric-Emmanuel frederic-emmanuel.picca at synchrotron-soleil.fr
Mon Aug 19 16:08:56 UTC 2013


Hello, I am using openmpi | 1.6.5-1 to rebuild python-scientific

but Now it FTBFS with this error message.

cd Src/MPI && PYTHONPATH=$(echo /tmp/buildd/python-scientific-2.9.2/build/lib.*-2.7) USE_OPENMPI=yes /usr/bin/python  compile.py
In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1728:0,
                 from /usr/include/python2.7/numpy/ndarrayobject.h:17,
                 from /usr/include/python2.7/numpy/arrayobject.h:15,
                 from /usr/include/python2.7/numpy/oldnumeric.h:1,
                 from ../../Include/Scientific/arrayobject.h:2,
                 from ../../Include/Scientific/mpimodule.h:88,
                 from Scientific_mpi.c:15:
/usr/include/python2.7/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
 [-Wcpp]
/tmp/ccsEpa7s.o: In function `main':
mpipython.c:(.text+0x1f): undefined reference to `ompi_mpi_errors_return'
mpipython.c:(.text+0x26): undefined reference to `ompi_mpi_comm_world'
/tmp/ccrXtLFs.o: In function `mpi_type':
Scientific_mpi.c:(.text+0x25b): undefined reference to `ompi_mpi_char'
Scientific_mpi.c:(.text+0x262): undefined reference to `ompi_mpi_byte'
Scientific_mpi.c:(.text+0x269): undefined reference to `ompi_mpi_short'
Scientific_mpi.c:(.text+0x270): undefined reference to `ompi_mpi_int'
Scientific_mpi.c:(.text+0x277): undefined reference to `ompi_mpi_long'
Scientific_mpi.c:(.text+0x27e): undefined reference to `ompi_mpi_float'
Scientific_mpi.c:(.text+0x285): undefined reference to `ompi_mpi_double'
/tmp/ccrXtLFs.o: In function `PyMPICommunicator_dealloc':
Scientific_mpi.c:(.text+0x466): undefined reference to `ompi_mpi_comm_world'
/tmp/ccrXtLFs.o: In function `PyMPI_SubsetCommunicator':
Scientific_mpi.c:(.text+0x6f0): undefined reference to `ompi_mpi_comm_null'
/tmp/ccrXtLFs.o: In function `PyMPI_ReceiveString':
Scientific_mpi.c:(.text+0x11d5): undefined reference to `ompi_mpi_char'
/tmp/ccrXtLFs.o: In function `initScientific_mpi':
Scientific_mpi.c:(.text+0x30ed): undefined reference to `ompi_mpi_comm_world'
Scientific_mpi.c:(.text+0x311e): undefined reference to `ompi_mpi_op_max'
Scientific_mpi.c:(.text+0x314f): undefined reference to `ompi_mpi_op_min'
Scientific_mpi.c:(.text+0x3180): undefined reference to `ompi_mpi_op_sum'
Scientific_mpi.c:(.text+0x31b1): undefined reference to `ompi_mpi_op_prod'
Scientific_mpi.c:(.text+0x31e2): undefined reference to `ompi_mpi_op_land'
Scientific_mpi.c:(.text+0x3213): undefined reference to `ompi_mpi_op_band'
Scientific_mpi.c:(.text+0x3244): undefined reference to `ompi_mpi_op_lor'
Scientific_mpi.c:(.text+0x3275): undefined reference to `ompi_mpi_op_bor'
Scientific_mpi.c:(.text+0x32a6): undefined reference to `ompi_mpi_op_lxor'
Scientific_mpi.c:(.text+0x32d7): undefined reference to `ompi_mpi_op_bxor'
Scientific_mpi.c:(.text+0x3308): undefined reference to `ompi_mpi_op_maxloc'
Scientific_mpi.c:(.text+0x3339): undefined reference to `ompi_mpi_op_minloc'
Scientific_mpi.c:(.text+0x336a): undefined reference to `ompi_mpi_op_replace'
collect2: error: ld returned 1 exit status
cmd =  mpicc.openmpi -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions -o mpipython.openmpi -I../../Include -I/usr/include/openmpi -I/usr/include/python2.7 -DNUMPY=1 -I/usr/lib/python2.7/dist-packages/numpy/core/include mpipython.c Scientific_mpi.c -L/usr/lib/python2.7/config-i386-linux-gnu -lpython2.7 -lpthread -ldl  -lutil -lm

Indeed the executed command is the cmd one.

So My question to the openmpi expert, is should I change something in my cmd line or is it a problem with 
mpicc.opnempi ?


Cheers

Frederic


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