# Munge Errors submitting job on SGE gridengine Galaxy 18.09 **URL:** \ **Category:** Uncategorized\ **Tags:** devops-administration, cluster\ **Created:** [February 20, 2019, 4:41pm UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655 "2019-02-20T16:41:49Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![bring52405](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bring52405/32/269_2.png) [@bring52405](https://help.galaxyproject.org/u/bring52405)\ **Post date:** [February 20, 2019, 4:41pm UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655/1 "2019-02-20T16:41:49Z")
I have a new install of Galaxy 18.09 and am attempting to run a test job that returns the number of cores on the cluster (same job we ran at galaxy admin training at Penn State in February). The job errors out at the submission with `MUNGE ERROR: INVALID CREDENTIAL FORMAT` Munge and gridengine are configured correctly on the submitting host. I have verified this. I can manually go into the jobs\_directory as the galaxy user and run a qsub with the same commands that galaxy would have run and the sub submits successfully. I will place log output and versioning below: **Logged info with errors:** ```auto galaxy.jobs.runners DEBUG 2019-02-19 16:00:05,795 [p:17958,w:1,m:0] [DRMAARunner.work_thread-0] (16) command is: rm -rf working; mkdir -p working; cd working; /Dedicated/clingalproddata/database/jobs_directory/000/16/tool_script.sh; return_code=$?; cd '/Dedicated/clingalproddata/database/jobs_directory/000/16'; ["$GALAXY_VIRTUAL_ENV" = "None"] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/Dedicated/clingalproddata/database/jobs_directory/000/16/set_metadata_BVKS9G.py" "/Dedicated/clingalproddata/database/jobs_directory/000/16/registry.xml" "/Dedicated/clingalproddata/database/jobs_directory/000/16/working/galaxy.json" "/Dedicated/clingalproddata/database/jobs_directory/000/16/metadata_in_HistoryDatasetAssociation_16_ZwFjOq,/Dedicated/clingalproddata/database/jobs_directory/000/16/metadata_kwds_HistoryDatasetAssociation_16_Vl4XIt,/Dedicated/clingalproddata/database/jobs_directory/000/16/metadata_out_HistoryDatasetAssociation_16_momZ6M,/Dedicated/clingalproddata/database/jobs_directory/000/16/metadata_results_HistoryDatasetAssociation_16_B5Qnpf,/Dedicated/clingalproddata/database/files/000/dataset_16.dat,/Dedicated/clingalproddata/database/jobs_directory/000/16/metadata_override_HistoryDatasetAssociation_16_Kwuloa" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2019-02-19 16:00:05,865 [p:17958,w:1,m:0] [DRMAARunner.work_thread-0] (16) submitting file /Dedicated/clingalproddata/database/jobs_directory/000/16/galaxy_16.sh galaxy.jobs.runners.drmaa DEBUG 2019-02-19 16:00:05,865 [p:17958,w:1,m:0] [DRMAARunner.work_thread-0] (16) native specification is: -V -q IIHG -pe smp 2 error: getting configuration: MUNGE authentication failed: Invalid credential format ``` **manually submitting the galaxy created job as galaxy user** ```auto [svc-clingalprod@clinical-galaxy 16]$ qsub -clear -V -q IIHG -pe smp 2 galaxy_16.sh Your job 2711251 ("galaxy_16.sh") has been submitted ``` **Versioning Info** ```auto [svc-clingalprod@clinical-galaxy 16]$ cat /etc/redhat-release CentOS Linux release 7.5.1804 (Core) [svc-clingalprod@clinical-galaxy 16]$ yum list installed | grep gridengine *Note* Spacewalk repositories are not listed below. You must run this command as root to access Spacewalk repositories. gridengine.x86_64 8.1.9-2.el7 @loveshack-SGE gridengine-devel.noarch 8.1.9-2.el7 @loveshack-SGE [svc-clingalprod@clinical-galaxy 16]$ yum list installed | grep munge *Note* Spacewalk repositories are not listed below. You must run this command as root to access Spacewalk repositories. munge.x86_64 0.5.11-3.el7 @epel-centos-x86_64-7 munge-devel.x86_64 0.5.11-3.el7 @epel-centos-x86_64-7 munge-libs.x86_64 0.5.11-3.el7 @epel-centos-x86_64-7 [svc-clingalprod@clinical-galaxy 16]$ source /Dedicated/clingalaxy/.venv/bin/activate (.venv) [svc-clingalprod@clinical-galaxy 16]$ pip search drmaa drmaa (0.7.9) - a python DRMAA library ``` ---
**Author:** ![mvdbeek](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mvdbeek/32/110_2.png) [@mvdbeek](https://help.galaxyproject.org/u/mvdbeek)\ **Post date:** [February 21, 2019, 10:01am UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655/2 "2019-02-21T10:01:36Z")
At first glance this looks like a drmaa-python problem, similar to [https://github.com/pygridtools/drmaa-python/issues/44](https://github.com/pygridtools/drmaa-python/issues/44). You could try installing python-drmaa according to the instructions in the readme and submit a job via python as in the opening post in [https://github.com/pygridtools/drmaa-python/issues/44](https://github.com/pygridtools/drmaa-python/issues/44). If that doesn’t work you could try submitting without the threadpool, or with just a single thread. If that works we may be able to lock job submission somehow, if it doesn’t we’d need to dig deeper in the drmaa / python-drmaa libraries. ---
**Author:** ![bring52405](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bring52405/32/269_2.png) [@bring52405](https://help.galaxyproject.org/u/bring52405)\ **Post date:** [February 21, 2019, 2:07pm UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655/3 "2019-02-21T14:07:27Z")
I agree. I wrote a single thread and a thread-pool Python script outside of galaxy to test. I posted those results in [drmaa library threads and munge: Invalid Credential Format](https://help.galaxyproject.org/t/drmaa-library-threads-and-munge-invalid-credential-format/617) . Single-thread submission works. My skill-set falls short on digging into the code and creating a wrapper to lock the submission on Galaxy. I thought about spinning up PULSAR and using that to submit the job to the SGE Cluster as a means to bypass the drmaa job runner. Could that act as a work-around? ---
**Author:** ![mvdbeek](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mvdbeek/32/110_2.png) [@mvdbeek](https://help.galaxyproject.org/u/mvdbeek)\ **Post date:** [February 21, 2019, 2:20pm UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655/4 "2019-02-21T14:20:17Z")
No need to open a new post for this, but OK, we can continue in the other thread. ---
**Author:** ![bring52405](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bring52405/32/269_2.png) [@bring52405](https://help.galaxyproject.org/u/bring52405)\ **Post date:** [February 21, 2019, 2:22pm UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655/5 "2019-02-21T14:22:32Z")
Honestly that first post was so all over the place I wanted to delete it and rewrite something a bit more coherent and professional. Apologies. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [February 21, 2019, 5:11pm UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655/6 "2019-02-21T17:11:12Z")
Iinked post > [@drmaa library threads and munge: Invalid Credential Format](https://help.galaxyproject.org/t/drmaa-library-threads-and-munge-invalid-credential-format/617/2): > > So this is interesting and going a bit further than [https://github.com/pygridtools/drmaa-python/issues/44](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 ProcessPool instead of a ThreadPool ? ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 17, 2026, 6:27am UTC](https://help.galaxyproject.org/t/munge-errors-submitting-job-on-sge-gridengine-galaxy-18-09/655/7 "2026-03-17T06:27:44Z")
Closed on March 17, 2026, 6:27am UTC