[scipion-users] error with relion

[abhisek M. <abh...@gm...>]

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*