There will be new firewall rules applied to Confluence starting at 7am. Weds 11 Sept. If you have any issues please contact me immediately at davisda at si dot edu.
Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

(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.

...

(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,

...

  • 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

...