Hello: I try to submit Gromacs job with command:
mpirun -np 2 mdrun_mpi -s md.tpr -g -v but it failed with messages: -------------------------------------------------------------------------- It looks like opal_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during opal_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): opal_shmem_base_select failed --> Returned value -1 instead of OPAL_SUCCESS -------------------------------------------------------------------------- *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [cudaA:5978] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! -------------------------------------------------------------------------- I first compiled openmpi with command: ./configure --prefix=/soft/openmpi-1.7.5_intel CC=icc F77=ifort FC=ifort CXX=icpc then gromacs-4.6.5 was compiled with command: env CC=icc F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/soft/gromacs-4.6.5 -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda thank you very much. ALbert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
