Hi, I have recently upgraded my system to openmpi-3.0. But despite proper installation and gpu integration I keep receiving this error, as I was also receiving in openmpi-1.4:
*$ mpirun -np 10 -bynode `which relion_preprocess_mpi` --i input_micrographs.star --coord_dir "." --coord_suffix .coords.star --part_star extra/output_particles.star --part_dir "." --extract --extract_size 140 --bg_radius 52 --invert_contrast --norm* *00021: --------------------------------------------------------------------------* *00022: The following command line options and corresponding MCA parameter have* *00023: been deprecated and replaced as follows:* *00024: * *00025: Command line options:* *00026: Deprecated: --bynode, -bynode* *00027: Replacement: --map-by node* *00028: * *00029: Equivalent MCA parameter:* *00030: Deprecated: rmaps_base_bynode* *00031: Replacement: rmaps_base_mapping_policy=node* *00032: * *00033: The deprecated forms *will* disappear in a future version of Open MPI.* *00034: Please update to the new syntax.* *00035: --------------------------------------------------------------------------* *00036: [localhost.localdomain:29946] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00037: [localhost.localdomain:29951] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00038: [localhost.localdomain:29948] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00039: [localhost.localdomain:29952] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00040: [localhost.localdomain:29944] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00041: [localhost.localdomain:29950] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00042: [localhost.localdomain:29949] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005* *00043: *** An error occurred in MPI_Init* *00044: *** on a NULL communicator* *00045: *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,* *00046: *** and potentially your MPI job)* *00047: *** An error occurred in MPI_Init* *00048: *** on a NULL communicator* *00049: *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,* *00050: *** and potentially your MPI job)* *00051: *** An error occurred in MPI_Init* *00052: *** on a NULL communicator* *00053: *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,* *00054: *** and potentially your MPI job)* *00055: [localhost.localdomain:29952] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!* I'm not sure what is causing this crash. Please help me out. Thank you *-- * Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*
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