Re: [scipion-users] Error running Relion-2.0 with MPI

[Jose M. de la R. T. <del...@gm...>]

Hi Abishek,

Have you check that the OpenMPI variables in scipion/config/scipion.conf
points
to the same version/location that the OpenMPI used to compile Relion?

Best,
Jose Miguel


On Wed, Apr 4, 2018 at 10:44 AM, abhisek Mondal <abh...@gm...>
wrote:

> 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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