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pegasus-isi / freesurfer-osg-workflow

A Pegasus workflow for running FreeSurfer on the Open Science Grid
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Unable to submit the workflow using pegasus-run #9

Closed soichih closed 4 years ago

soichih commented 4 years ago

I just tried running this again, and now I am seeing a different error message.

submitting with this this config
+ cat run.yml
output:
    input: ../5ed1a215529ab4221883209e/5e6a9956874067bc9ea3d445/t1.nii.gz
+ ./workflow-generator.py --inputs-def run.yml
{'output': {'input': '../5ed1a215529ab4221883209e/5e6a9956874067bc9ea3d445/t1.nii.gz'}}
+ export PYTHONPATH=:/usr/lib/python2.6/site-packages
+ PYTHONPATH=:/usr/lib/python2.6/site-packages
+ pegasus-plan --conf pegasus.conf --dir /public/hayashis/workdir/5ed1a215529ab491cf83209d/5ed1a215529ab4764b8320a0 --relative-dir work --sites condorpool --output-site local --dax freesurfer-osg.xml --cluster horizontal --submit
2020.05.30 00:00:40.676 GMT:    
2020.05.30 00:00:40.682 GMT:   ----------------------------------------------------------------------- 
2020.05.30 00:00:40.688 GMT:   File for submitting this DAG to HTCondor           : freesurfer-0.dag.condor.sub 
2020.05.30 00:00:40.694 GMT:   Log of DAGMan debugging messages                 : freesurfer-0.dag.dagman.out 
2020.05.30 00:00:40.701 GMT:   Log of HTCondor library output                     : freesurfer-0.dag.lib.out 
2020.05.30 00:00:40.707 GMT:   Log of HTCondor library error messages             : freesurfer-0.dag.lib.err 
2020.05.30 00:00:40.714 GMT:   Log of the life of condor_dagman itself          : freesurfer-0.dag.dagman.log 
2020.05.30 00:00:40.720 GMT:    
2020.05.30 00:00:40.727 GMT:   -no_submit given, not submitting DAG to HTCondor.  You can do this with: 
2020.05.30 00:00:40.738 GMT:   ----------------------------------------------------------------------- 
2020.05.30 00:00:42.582 GMT:   Your database is compatible with Pegasus version: 4.9.3dev 
2020.05.30 00:00:42.691 GMT:   Submitting to condor freesurfer-0.dag.condor.sub 
2020.05.30 00:01:03.444 GMT:   Submitting job(s) 
2020.05.30 00:01:03.451 GMT:   ERROR: store_cred failed! 
2020.05.30 00:01:03.509 GMT: [ERROR]  ERROR: Running condor_submit /usr/local/bin/condor_submit freesurfer-0.dag.condor.sub failed with exit code 1 at /usr/bin/pegasus-run line 327. 
2020.05.30 00:01:03.515 GMT: [FATAL ERROR]  
 [1] java.lang.RuntimeException: Unable to submit the workflow using pegasus-run at edu.isi.pegasus.planner.client.CPlanner.executeCommand(CPlanner.java:697)
rynge commented 4 years ago

The store_cred error was a OSG Connect issue, and should already have been corrected.