---------- Forwarded message ---------- From: Wenkai Wang (Kevin)<[hidden email]> Date: Thu, May 11, 2017 at 8:01 PM Subject: Galaxy Error while Using PBS
I am an engineer at a National Research and Engineering Center in Shanghai. Recently I am trying the outstanding Galaxy system developed by your team. The Galaxy system is great; however, there are some errors when Galaxy is connected to Torque PBS, about which errors I have to ask for help and advice from you.
When I tried to execute a tool for output like "Hello Galaxy" from within the webpage, it was shown in webpage that "Unable to run this job due to a cluster error, please retry it later" (ref.: line 321 of file galaxy/lib/galaxy/jobs/runners/pbs.py). Meanwhile, the STDOUT of Linux shell displays information including,
galaxy.jobs.runners.pbs ERROR 2017-05-12 11:41:57,473 (25) All attempts to submit job failed
galaxy.model.metadata DEBUG 2017-05-12 11:41:57,574 Cleaning up external metadata files
galaxy.model.metadata DEBUG 2017-05-12 11:41:57,604 Failed to cleanup MetadataTempFile temp files from /data3/wangwk/app/galaxy/database/jobs_directory/000/25/metadata_out_HistoryDatasetAssociation_26_wrVwaf: No JSON object could be decoded
Further information: (1) Linux version: RHEL 6.2, 2.6.32-220.el6.x86_64; (2) Torque PBS 4.2; (3) pbs-python: 220.127.116.11 (pbs-python 18.104.22.168 requires CentOS 7 with PBS Torque 5, and thus was not chosen); (4) glibc 2.12; (5) munge service has been installed, configured, and started on the master node and compute nodes of the cluster; (6) job_conf.xml file is attached with this email.
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