Hi All,
I don’t know if this is an MPI or a relion problem, but I have relion running very happily on a 16 core / 32 Gb test machine. However, we are now trying to move across to the university’s substantial and very well established cluster, I am experiencing errors that look like this;
[bmbnar@login2]$ more relion_error16.log
--------------------------------------------------------------------------
A daemon (pid 2493) died unexpectedly with status 137 while attempting
to launch so we are aborting.
There may be more information reported by the environment (see above).
This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
mpirun: clean termination accomplished
[c1s0b4n1:28990] [[9463,0],3] routed:binomial: Connection to lifeline [[9463,0],0] lost
[c1s0b3n0:18602] [[9463,0],1] routed:binomial: Connection to lifeline [[9463,0],0] lost
[c1s0b9n0:26146] [[9463,0],6] routed:binomial: Connection to lifeline [[9463,0],0] lost
[c1s0b8n1:20597] [[9463,0],5] routed:binomial: Connection to lifeline [[9463,0],0] lost
[c1s0b4n0:01028] [[9463,0],2] routed:binomial: Connection to lifeline [[9463,0],0] lost
Does anyone have any ideas? I have obviously asked our cluster sysadmins, but I thought I’d ask for relion-specific advice as well just in case!
KR,
Neil
Neil Ranson PhD
Astbury Centre for Structural Molecular Biology
SMCB
University of Leeds, Leeds, LS2 9JT, UK.
EM Image Processing Suite - Miall 6.02
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