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
++++
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