Python error

[David Hoover]

I am running v2.12 of EMAN2, and get a generic python error:

close failed in file object destructor:
sys.excepthook is missing
lost sys.stderr
close failed in file object destructor:
sys.excepthook is missing
lost sys.stderr
close failed in file object destructor:
sys.excepthook is missing
lost sys.stderr

The EMAN2 command is:

e2refine2d.py \
  --input=sets/jasper.lst \
  --ncls=50 \
  --normproj \
  --fastseed \
  --iter=16 \
  --nbasisfp=12 \
  --naliref=5 \
  --parallel=mpi:8:/lscratch/$SLURM_JOBID \
  --center=xform.center \
  --simalign=rotate_translate_flip \
  --simaligncmp=ccc \
  --simraligncmp=dot \
  --simcmp=ccc \
  --classkeep=0.85 \
  --classiter=5 \
  --classalign=rotate_translate_flip \
  --classaligncmp=ccc \
  --classraligncmp=ccc \
  --classaverager=mean \
  --classcmp=ccc \
  --classnormproc=normalize.edgemean

The scratch space is dynamically allocated as part of the batch system job.  The program continues to run normally past the error, so I'm not sure if it is relevant or not.

David Hoover
HPC @ NIH
CIT/National Institutes of Health

[Steve Ludtke]

Hi David. 

You can ignore this if it isn't related to a fatal error. This message is complaining that a program is executing another program and not retaining the standard error output. It is harmless, unless an actual crash is occurring, in which case there may be some error messages you aren't seeing.

I'd add that unless you are running on a machine where you are getting 8 cores which aren't guaranteed to be on the same physical computer, --parallel thread:8  would be far more efficient. MPI should only be used when you are using more than one node's worth of processors.

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slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

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