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 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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 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
    language bash title wow.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
    language bash title wow.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
    language bash
    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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