From: Pablo C. <pc...@cn...> - 2018-04-05 06:02:20
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Hi Abhisek, did you install relion, through scipion? The installation is exactly the same released by relion, but that way the compilation uses the same MPI libraries. Which MPI are you using and what version? All the best, Pablo. On 05/04/18 07:37, abhisek Mondal wrote: > Hi, > > I'm not being able to run relion of scipion. Despite re building the > scipion from source it keep crashing, however xmipp is working fine > with MPI processes. > > Error report: > > 00368: mpirun -np 2 -bynode `which relion_refine_mpi` --gpu > --tau2_fudge 2 --scale --dont_combine_weights_via_disc --iter 25 > --norm --psi_step 10.0 --ctf --offset_range 5.0 --oversampling 1 > --pool 3 --o Runs/002019_ProtRelionClassify2D/extra/relion --i > Runs/002019_ProtRelionClassify2D/input_particles.star > --particle_diameter 264.6 --K 30 --preread_images --flatten_solvent > --zero_mask --offset_step 2.0 --angpix 1.89 --j 2 > 00369: > -------------------------------------------------------------------------- > 00370: The following command line options and corresponding MCA > parameter have > 00371: been deprecated and replaced as follows: > 00372: > 00373: Command line options: > 00374: Deprecated: --bynode, -bynode > 00375: Replacement: --map-by node > 00376: > 00377: Equivalent MCA parameter: > 00378: Deprecated: rmaps_base_bynode > 00379: Replacement: rmaps_base_mapping_policy=node > 00380: > 00381: The deprecated forms *will* disappear in a future version of > Open MPI. > 00382: Please update to the new syntax. > 00383: > -------------------------------------------------------------------------- > 00384: [localhost.localdomain:12543] PMIX ERROR: BAD-PARAM in file > ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c > at line 1005 > 00385: *** An error occurred in MPI_Init > 00386: *** on a NULL communicator > 00387: *** MPI_ERRORS_ARE_FATAL (processes in this communicator will > now abort, > 00388: *** and potentially your MPI job) > 00389: [localhost.localdomain:12543] 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! > 00390: [localhost.localdomain:12542] PMIX ERROR: BAD-PARAM in file > ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c > at line 1005 > 00391: *** An error occurred in MPI_Init > 00392: *** on a NULL communicator > 00393: *** MPI_ERRORS_ARE_FATAL (processes in this communicator will > now abort, > 00394: *** and potentially your MPI job) > 00395: [localhost.localdomain:12542] 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! > 00396: ------------------------------------------------------- > 00397: Primary job terminated normally, but 1 process returned > 00398: a non-zero exit code.. Per user-direction, the job has been > aborted. > 00399: ------------------------------------------------------- > 00400: > -------------------------------------------------------------------------- > 00401: mpirun detected that one or more processes exited with > non-zero status, thus causing > 00402: the job to be terminated. The first process to do so was: > 00403: > 00404: Process name: [[57465,1],1] > 00405: Exit code: 1 > 00406: > -------------------------------------------------------------------------- > > Please suggest me a fix. > > Thank you. > > -- > Abhisek Mondal > /Senior Research Fellow > / > /Structural Biology and Bioinformatics Division > / > /CSIR-Indian Institute of Chemical Biology/ > /Kolkata 700032 > / > /INDIA > / > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |