On Dec 6, 2012, at 2:34 PM, Matthew Shirley wrote:
I am fairly new to PBS management, so I can't rule out some misconfiguration, but I have a strange issue when running Galaxy with the PBS job runner. It seems that munge spawns a bunch of defunct processes after running Galaxy on my cluster:
`ps axjf`:
1 25992 25991 25991 ? -1 Sl 77777 8:48 python ./scripts/paster.py serve universe_wsgi.ini --daemon 25992 26032 25991 25991 ? -1 Z 77777 0:00 \_ [munge] <defunct> 25992 26034 25991 25991 ? -1 Z 77777 0:00 \_ [munge] <defunct> 25992 26036 25991 25991 ? -1 Z 77777 0:00 \_ [munge] <defunct>
Now, these processes are being spawned by Galaxy, and I can't figure out why. Can anyone provide some insight or clues about where to start debugging this? Thanks,
Hi Matt, I'm not sure what munge is, it's not something provided with Galaxy. Googling suggests it might be an authentication tool used in some HPC environments. Without having any familiarity with it, I can't say what process in Galaxy would be interacting with it, especially since that interaction must occur implicitly somewhere down the chain of normal Galaxy operations. --nate
Matt
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