Advanced jobscripts

[heatherkellyucl]

Possibly should put these in an advanced jobscripts section?

Useful environment variables that can be used in more complicated scripts

Eg $SGE_O_WORKDIR, $JOB_ID, $SGE_TASK_ID, $NSLOTS, $NHOSTS

The reusable jobscript where the input files are passed in on the command line:

qsub -v infile=`pwd`/myMatlabJob.m,addinfiles=`pwd`/initialise.m:`pwd`/analyse.m run-matlab.sh

where the script does

cp $infile .
Matlab_infile=`basename $infile`
for file in `echo $addinfiles | tr ':' ' '` 
do
  cp $file .
done

matlab -nosplash -nodesktop -nodisplay < $Matlab_infile

Submitting a chain of jobs with dependencies

Getting the job ID at submit time so it can be passed on to the next. qsub -terse