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Code Block
languagebash
titlePseudo Example
#
#$ -N example
#$ -o example.log -cwd -j y
#$ -q uTxlM.rq
#$ -l ssduse=2560G,hm,mres=20G,h_data=20G,h_vmem=20G
#
# pseudo example using a fake package WOW, on the SSD
#
echo $JOB_NAME started `date` on $HOSTNAME in $QUEUE jobID=$JOB_ID
#
module load tools/ssd
module load special/wow
#
# create a wow config file from a generic version, to insert the SSD temp dir value
sed "s=XXXX=$SSD_DIR=" ~/wow/wild-cat.gen > ~/wow/wild-cat.conf
#
# cd to the SSD temp dir and copy the data set to it, using the existing .tgz file
cd $SSD_DIR
tar xf /pool/genomics/smart1/great/project/wild-cat.tgz
#
# create some sub dirs for output and logs
mkdir output
mkdir logs
#
# run the wow analysis (note how some files are not on the SSD)
wow --type=m --params=$HOME/wow/parameters.dat --config=$HOME/wow/wild-cat.conf -o $SSD_DIR/output -l $SSD_DIR/logs
#
# save the output and the logs in a tar compressed file
# (assumes wow did not change current working directory)
# otherwise insert: cd $SSD_DIR
tar -cfz /pool/genomics/smart1/great/project/wild-cat-results.tgz output/ logs/
#
# remove everything (in $SSD_DIR), or remove what you know you can (conservative option)
rm -rf *
#
echo $JOB_NAME done `date`

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Usage Monitoring Tools

  • We have two tools to monitor SSD usage, one on a per-job basis, and one to view usage summary.
  • Both need you to load the gnuplot and tools/local modules

Per Job Basis

Code Block
languagebash
titleplot-qssduse.pl
% module load tools/local
% module load gnuplot
% plot-qssduse.pl -x 7420073

This example plots the SSD usage of job 7420073 to the screen, assuming you have an X-windows capable connection,

  • drop the -x to plot to a file,
  • and use NNNN.TTT, instead of NNNN to show usage for a given task (TTT) of a job array (NNNN).
  • Try plot-qssduse.pl -help or man plot-qssduse.pl for more information.

Usage Summary

Code Block
languagebash
titleplot-qssduse-summary.pl
% module load tools/local
% module load gnuplot
% plot-qssduse-summary.pl -x

As above:

  • drop the -x to plot to a file.
  • Try plot-qssduse-summary.pl -help or man plot-qssduse-summary.pl for more information.


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Last Updated  SGK