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    Details

    • Type: Sub-task
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: master, 4.9.0
    • Fix Version/s: master, 5.0.0, 4.9.1
    • Component/s: pegasus-plan
    • Labels:
      None

      Description

      changes for PM-1321 have broken our test cases, where we are running in nonsharedfs mode on a compute site, but the staging site is set to be the shared filesystem on the compute site.

      for e.g. 044-singularity-nonsharedfs-shared

      ******************************Failed jobs' details******************************
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 ==============================preprocess_ID0000001==============================
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 last state: POST_SCRIPT_FAILED
      06-Nov-2018 20:39:33 site: condorpool
      06-Nov-2018 20:39:33 submit file: 00/00/preprocess_ID0000001.sub
      06-Nov-2018 20:39:33 output file: 00/00/preprocess_ID0000001.out.001
      06-Nov-2018 20:39:33 error file: 00/00/preprocess_ID0000001.err.001
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 -------------------------------Task #1 - Summary--------------------------------
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 site : condorpool
      06-Nov-2018 20:39:33 hostname : -
      06-Nov-2018 20:39:33 executable : /lfs1/software/bamboo/data/xml-data/build-dir/PEGASUS-WT49-T044D/test/core/044-singularity-nonsharedfs-shared/dags/bamboo/pegasus/diamond/run0001/00/00/preprocess_ID0000001.sh
      06-Nov-2018 20:39:33 arguments : -
      06-Nov-2018 20:39:33 exitcode : -1
      06-Nov-2018 20:39:33 working dir : /lfs1/software/bamboo/data/xml-data/build-dir/PEGASUS-WT49-T044D/test/core/044-singularity-nonsharedfs-shared/dags/bamboo/pegasus/diamond/run0001
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 --------------Job stderr file - 00/00/preprocess_ID0000001.err.001--------------
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 2018-11-06 20:31:27: PegasusLite: version 4.9.1dev
      06-Nov-2018 20:39:33 2018-11-06 20:31:27: Executing on host compute-6.isi.edu
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 ########################[Pegasus Lite] Setting up workdir ########################
      06-Nov-2018 20:39:33 2018-11-06 20:31:27: Checking /var/lib/condor/execute/dir_48143 for potential use as work space...
      06-Nov-2018 20:39:33 2018-11-06 20:31:27: Workdir is /var/lib/condor/execute/dir_48143/pegasus.llFa69RwM - 2.8T available
      06-Nov-2018 20:39:33 2018-11-06 20:31:27: Changing cwd to /var/lib/condor/execute/dir_48143/pegasus.llFa69RwM
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 ##############[Pegasus Lite] Figuring out the worker package to use ##############
      06-Nov-2018 20:39:33 2018-11-06 20:31:27: The job contained a Pegasus worker package
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 #######################[Pegasus Lite] Staging in container #######################
      06-Nov-2018 20:39:33 2018-11-06 20:31:27,796 INFO: Reading URL pairs from stdin
      06-Nov-2018 20:39:33 2018-11-06 20:31:27,797 INFO: 1 transfers loaded
      06-Nov-2018 20:39:33 2018-11-06 20:31:27,797 INFO: PATH=/var/lib/condor/execute/dir_48143/pegasus.llFa69RwM/pegasus-4.9.1dev/bin:/usr/local/bin:/usr/bin:/bin
      06-Nov-2018 20:39:33 2018-11-06 20:31:27,797 INFO: LD_LIBRARY_PATH=
      06-Nov-2018 20:39:33 2018-11-06 20:31:27,857 INFO: --------------------------------------------------------------------------------
      06-Nov-2018 20:39:33 2018-11-06 20:31:27,857 INFO: Starting transfers - attempt 1
      06-Nov-2018 20:39:33 2018-11-06 20:31:29,874 INFO: ln -f -s '/lizard/scratch-90-days/044-singularity-nonsharedfs-shared/bamboo/pegasus/diamond/run0001/00/00/centos-base.img' '/var/lib/condor/execute/dir_48143/pegasus.llFa69RwM/centos-base.img'
      06-Nov-2018 20:39:33 2018-11-06 20:31:29,894 INFO: --------------------------------------------------------------------------------
      06-Nov-2018 20:39:33 2018-11-06 20:31:29,895 INFO: Stats: Total 1 transfers, 768.0 MB transferred in 2 seconds. Rate: 365.8 MB/s (2.9 Gb/s)
      06-Nov-2018 20:39:33 2018-11-06 20:31:29,895 INFO: Between sites condorpool->condorpool : 1 transfers, 768.0 MB transferred in 2 seconds. Rate: 365.8 MB/s (2.9 Gb/s)
      06-Nov-2018 20:39:33 2018-11-06 20:31:29,895 INFO: All transfers completed successfully.
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 ########[Pegasus Lite] Writing out script to launch user task in container ########
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 #################[Container] Now in pegasus lite container script #################
      06-Nov-2018 20:39:33 /srv
      06-Nov-2018 20:39:33 2018-11-06 20:31:30: PegasusLite: version 4.9.1dev
      06-Nov-2018 20:39:33 2018-11-06 20:31:30: Executing on host compute-6.isi.edu
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 ##############[Container] Figuring out Pegasus worker package to use ##############
      06-Nov-2018 20:39:33 2018-11-06 20:31:30: Downloading Pegasus worker package from http://download.pegasus.isi.edu/pegasus/4.9.1dev/pegasus-worker-4.9.1dev-x86_64_rhel_7.tar.gz
      06-Nov-2018 20:39:33 PATH in container is set to is set to /srv/pegasus-4.9.1dev/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
      06-Nov-2018 20:39:33
      06-Nov-2018 20:39:33 ###################### Staging in input data and executables ######################
      06-Nov-2018 20:39:33 2018-11-06 20:31:30,978 INFO: Reading URL pairs from stdin
      06-Nov-2018 20:39:33 2018-11-06 20:31:30,979 INFO: 2 transfers loaded
      06-Nov-2018 20:39:33 2018-11-06 20:31:30,979 INFO: PATH=/srv/pegasus-4.9.1dev/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
      06-Nov-2018 20:39:33 2018-11-06 20:31:30,979 INFO: LD_LIBRARY_PATH=
      06-Nov-2018 20:39:33 2018-11-06 20:31:31,044 INFO: --------------------------------------------------------------------------------
      06-Nov-2018 20:39:33 2018-11-06 20:31:31,044 INFO: Starting transfers - attempt 1
      06-Nov-2018 20:39:33 2018-11-06 20:31:33,047 ERROR: Expected local file does not exist: /lizard/scratch-90-days/044-singularity-nonsharedfs-shared/bamboo/pegasus/diamond/run0001/00/00/diamond-preprocess-4_0
      06-Nov-2018 20:39:33 2018-11-06 20:31:33,048 ERROR: Expected local file does not exist: /lizard/scratch-90-days/044-singularity-nonsharedfs-shared/bamboo/pegasus/diamond/run0001/00/00/f.a
      06-Nov-2018 20:39:33 2018-11-06 20:33:44,073 INFO: --------------------------------------------------------------------------------
      06-Nov-2018 20:39:33 2018-11-06 20:33:44,076 INFO: Starting transfers - attempt 2
      06-Nov-2018 20:39:33 2018-11-06 20:33:46,089 ERROR: Expected local file does not exist: /lizard/scratch-90-days/044-singularity-nonsharedfs-shared/bamboo/pegasus/diamond/run0001/00/00/diamond-preprocess-4_0
      06-Nov-2018 20:39:33 2018-11-06 20:33:46,090 ERROR: Expected local file does not exist: /lizard/scratch-90-days/044-singularity-nonsharedfs-shared/bamboo/pegasus/diamond/run0001/00/00/f.a
      06-Nov-2018 20:39:33 2018-11-06 20:38:46,147 INFO: --------------------------------------------------------------------------------
      06-Nov-2018 20:39:33 2018-11-06 20:38:46,150 INFO: Starting transfers - attempt 3
      06-Nov-2018 20:39:33 2018-11-06 20:38:48,159 ERROR: Expected local file does not exist: /lizard/scratch-90-days/044-singularity-nonsharedfs-shared/bamboo/pegasus/diamond/run0001/00/00/diamond-preprocess-4_0
      06-Nov-2018 20:39:33 2018-11-06 20:38:48,165 ERROR: Expected local file does not exist: /lizard/scratch-90-days/044-singularity-nonsharedfs-shared/bamboo/pegasus/diamond/run0001/00/00/f.a
      06-Nov-2018 20:39:33 2018-11-06 20:38:48,169 INFO: -----------------------------------------------------------------------------

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            • Assignee:
              vahi Karan Vahi
              Reporter:
              vahi Karan Vahi
            • Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: