Hi Yingyi,
Perhaps you compiled relion with a different openMPI installation from
the one you are now using it with?
This command will show you the one you used to compile:
ldd `which relion_ctffind_mpi`
This command will show you which one you're using:
which mpirun
HTH,
Sjors
On 03/28/2017 03:30 PM, Yingyi Zhang wrote:
> Dear All,
>
> I am running a ctf estimation in Relion2, and I had this error coming up.
> Could you please suggest how to fix it?
> Thanks so much for your help.
>
> The error:
> [swift:02436] mca_base_component_repository_open: shmem
> "/usr/lib64/openmpi-1.8.1/lib/openmpi/mca_shmem_mmap" uses an MCA
> interface that is not recognized (component MCA v2.0.0 != supported MCA
> v2.1.0) -- ignored
> [swift:02436] mca_base_component_repository_open: shmem
> "/usr/lib64/openmpi-1.8.1/lib/openmpi/mca_shmem_sysv" uses an MCA
> interface that is not recognized (component MCA v2.0.0 != supported MCA
> v2.1.0) -- ignored
> [swift:02436] mca_base_component_repository_open: shmem
> "/usr/lib64/openmpi-1.8.1/lib/openmpi/mca_shmem_posix" uses an MCA
> interface that is not recognized (component MCA v2.0.0 != supported MCA
> v2.1.0) -- ignored
> --------------------------------------------------------------------------
> 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
>
> The command line:
> ++++ with the following command(s):
> `which relion_run_ctffind_mpi` --i ./Import/job001/micrographs.star --o
> CtfFind/job003/ --CS 2.7 --HT 300 --AmpCnst 0.1 --XMAG 10000 --DStep 0.9
> --Box 512 --ResMin 30 --ResMax 5 --dFMin 5000 --dFMax 50000 --FStep 500
> --dAst 100 --ctffind_exe
> ../../../../../../../usr/local/ctffind-4.1.5/ctffind --ctfWin -1
> --is_ctffind4 --do_movie_thon_rings --avg_movie_frames 4 --movie_rootname
> _movie.mrcs
> ++++
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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