submitting a job to a SGE 8.1.9 Cluster from an application called galaxy logged the following error: galaxy.jobs.runners.drmaa WARNING 2019-02-13 13:20:43,111 (427) drmaa.Session.runJob() failed, will retry: code 17: MUNGE authentication failed: Invalid credential format I have verified UIDs and…

Yes, but that’s more complicated than necessary. If you can use qsub on the host where Galaxy runs your best bet is probably to use the command line interface runner with the PBS backend. I’m using this in production (though ssh), this should be a viable option.

So this is interesting and going a bit further than https://github.com/pygridtools/drmaa-python/issues/44 , as this is failing also with just a single thread. Maybe we can come up with a patch for drmaa-python, which would probably be the best solution. Can you check that this works with a ProcessPoo…

Also, does it work if you initialize the session within the thread: import drmaa from multiprocessing.pool import ThreadPool import tempfile import os import stat pool = ThreadPool(1) def pTask(n): session = drmaa.Session() session.initialize() smt = "ls . > test.out" script_file …

That will take me a little while to work through. Parallel processes and threads are new to me. I will let you know. In the meantime is Pulsar a viable option for my situation? I need to provide some options for solutions.

linked post/discussion [image] Munge Errors submitting job on SGE gridengine Galaxy 18.09 No need to open a new post for this, but OK, we can continue in the other thread.

FYI – drmaa python no longer has an active package maintainer to go to for issues. Where can I get some documentation that covers the CLI job runner? I need to figure out how to translate the Torque information to SGE. Using the drmaa queue with pulsar suffers from the same munge auth issue as Ga…

@mvdbeek Initializing the session from within the threadpool does work. Does this have any bearing on how Galaxy is submitting jobs using python-drmaa?

Yes, we probably need to move the session initialization around to accommodate this. Alternatively it might be necessary to make the drmaa session global. I’ll try to find some time to look into this and to setup a test case. What did you try for the CLI runner ? It might just work with the torque o…

I had hoped it would work with the LocalShell in conjunction with the Torque Job. I have submitted a request to get ssh or rsh access for my default galaxy user configured on the head-node for submissions so i can test that. I appreciate you looking into it.

Yes, they use the same interface. If on the Galaxy node you can submit jobs you don’t need to use the remote shell, you can use the local shell interface.

@mvdbeek Running a basic job using local shell threw an error. Error is same as LocalShell runner fails on "No such file or directory" · Issue #7269 · galaxyproject/galaxy · GitHub . job conf: <destination id="LocalShell" runner="cli"> <param id="shell_plugin">LocalShell</param> <param i…

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drmaa library threads and munge: Invalid Credential Format

jennaj February 21, 2019, 5:11pm 6

linked post/discussion