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(lightbulb) The SSDs are currently only available for the uTxlMuTSSD.rqq queue, a restricted queue. Contact Paul Sylvain or Sylvain Rebecca if you want to be authorized to use it.

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(lightbulb) Remember, your job will still be able to access the /home, /data, /pool, and /scratch disks, hence you don't have to copy everything on the SSD,

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  • You need to replace all references to /pool/genomics/smart1/great/project/wild-cat by $SSD_DIR,
  • this can be easily done at the shell script level, but not in a configuration file, i.e., for flags/options
      execute -o /pool/genomics/smart1/great/project/wild-cat/result.dat
    is replaced by
      execute -o $SSD_DIR/result.dat

  • Here is a simple trick to modify a configuration file:
    • Let's assume that your analysis uses a file wow.conf, where for instance the full path of some files must be listed, like:


      Code Block
      languagebash
      titlewow.conf
      # this is the configuration file of the fabulous WOW package
      input=/pool/genomics/smart1/great/project/wild-cat/wiskers.dat
      output=/pool/genomics/smart1/great/project/wild-cat/tail.dat
      paws=4
      eyes=2


    • Replace the wow.conf file by a wow.gen file as follows:


      Code Block
      languagebash
      titlewow.gen
      # this is the configuration file of the fabulous WOW package
      input=XXXX/wiskers.dat
      output=XXXX/wild-cat/tail.dat
      paws=4
      eyes=2


    • And create thethe wow.confconf file from thethe wow.gengen at run-time by adding the following in the job script:

      Code Block
      languagebash
      sed"s=XXXX=$SSD_DIR="wow.gen > wow.conf

      As long as XXXXXXXX is not used for anything else, this will replace every occurrence of XXXXXXXX by the value of the environment variablevariable SSD_DIR.

3 Run the Analysis

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