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  1. Pegasus
  2. PM-696

pegasus-cleanup should delete symlinks

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      Description

      In case the symlinking is turned on , the cleanup jobs generated by the planner have symlink url's


      Currently, the cleanup scripts all run into errors with the symlink files.

      i just pasted the stdout/stderr message here :

          <data>2013-03-20 15:03:55,805 INFO: Reading URL pairs from stdin
      2013-03-20 15:03:55,805 INFO: PATH=/home/globus/gt5.0.4/bin:/u/home/eeskin/polyacti/bin/pegasus/bin:/u/home/eeskin/polyacti/bin:/u/local/apps/R/R-2.12.2-gnu/bin:/u/local/gcc/4.4.4/apps/graphviz/2.28.0/bin:/u/local/apps/lynx/2.8.7/bin:/u/local/python/2.6/bin:/u/home/eeskin/polyacti/bin/globus/bin:/u/home/eeskin/polyacti/bin/globus/sbin:/u/local/intel/11.1/libs/hdf5/1.8.8-shared//bin:/u/home/eeskin/polyacti/bin/condor/sbin:/u/home/eeskin/polyacti/bin/condor/bin:/u/home/eeskin/polyacti/bin/:/u/home/eeskin/polyacti/bin/jdk/bin:/u/systems/UGE8.0.1/bin/lx-amd64:/u/local/compilers/intel/11.1/080/bin/intel64/:/u/local/intel/11.1/openmpi/1.4.5/bin:/u/local/bin:/u/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/u/local/intel/11.1/libs/hdf5/1.8.8-shared//bin
      2013-03-20 15:03:55,805 INFO: LD_LIBRARY_PATH=/home/globus/gt5.0.4/lib:/u/home/eeskin/polyacti/lib:/u/local/apps/R/R-2.12.2-gnu//lib64/R/lib:/u/local/python/2.6//lib:/u/local/intel/11.1/openmpi/1.4.2/lib:/u/local/compilers/intel/11.1/073/mkl/lib/em64t:/u/local/compilers/intel/11.1/073/lib/intel64:/u/local/intel/11.1/libs/hdf5/1.8.8-shared//lib
      2013-03-20 15:03:55,823 INFO: Command &apos;lcg-del&apos; not found in the current environment
      2013-03-20 15:03:55,831 INFO: Command &apos;srm-rm&apos; not found in the current environment
      2013-03-20 15:03:55,839 INFO: Command &apos;irm&apos; not found in the current environment
      2013-03-20 15:03:55,847 INFO: pegasus-gridftp Version: N/A Path: /u/home/eeskin/polyacti/bin/pegasus/bin/pegasus-gridftp
      2013-03-20 15:03:55,853 INFO: pegasus-s3 Version: N/A Path: /u/home/eeskin/polyacti/bin/pegasus/bin/pegasus-s3
      2013-03-20 15:03:55,854 INFO: /bin/rm -f &quot;/u/scratch2/p/polyacti/pegasus/ShortRead2Alignment/ShortRead2AlignmentPipeline_VRCPart5_vs_3280_AlnMethod2_patch.2013.Mar.20T143201/1339_6215_2005056_GA_0_1/33832_30886_1016_5_Index-10_59134071713114522_2_10.sai&quot;
      2013-03-20 15:03:55,860 CRITICAL: Error: This tool does not know how to remove from symlink://


      pegasus-cleanup should be able to handle this.
      In addition, the planner should ensure that the cleanup jobs get mapped to compute site in this case.

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            • Assignee:
              rynge-page Mats Rynge [X] (Inactive)
              Reporter:
              vahi Karan Vahi
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              • Created:
                Updated:
                Resolved: