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Bug #2894

closed

maximum likelihood jobs won't run

Added by Melody Campbell over 10 years ago. Updated almost 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Anchi Cheng
Category:
-
Target version:
-
Start date:
08/14/2014
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.1.0
Show in known bugs:
No
Workaround:

Description

Both Yong Zi and I have encountered this issue with our most recent maximum likelihood jobs:

Using 32 processors!
... Running on host: guppy-10
Xmipp: /usr/bin/mpirun np 32 /opt/Xmipp/bin/xmipp_mpi_ml_align2d -i /ami/data15/appion/14jul24d/align/maxlike9/partlist.sel -nref 200 -iter 15 -o /ami/data15/appion/14jul24d/align/maxlike9/part14aug14o00 -psi_step 5 -fast -eps 5e-5 -mirror
[guppy-10:22681] plm:tm: failed to spawn daemon, error code = 17000
-------------------------------------------------------------------------
A daemon (pid unknown) died unexpectedly on signal 1 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.
--------------------------------------------------------------------------
... Alignment time: 0.5 sec

self.params['maxlikejobid'] 1
lines= ['\tlibmpi.so.1 => /usr/lib64/libmpi.so.1 (0x000000308f800000)\n', '\tlibmpi_cxx.so.1 => /usr/lib64/libmpi_cxx.so.1 (0x00007f443b752000)\n']
Traceback (most recent call last):
File "/opt/myami-3.0/bin/maxlikeAlignment.py", line 459, in <module>
maxLike.start()
File "/opt/myami-3.0/bin/maxlikeAlignment.py", line 452, in start
self.createReferenceStack()
File "/opt/myami-3.0/bin/maxlikeAlignment.py", line 341, in createReferenceStack
apDisplay.printError("Xmipp did not run")
File "/opt/myami-3.0/lib/appionlib/apDisplay.py", line 62, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
Xmipp did not run

here is the directory:
/ami/data15/appion/14jul24d/align/maxlike9

Please let me know if there is anything I can do to troubleshoot.
Thanks

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