BMI Students

Thursday, May 05, 2005

Using the bioxcluster

Some info on the bioxcluster:

To open the firewall, eg #usernum=152, #sunetid=brian
ssh -p 259
To ssh in there:
ssh -p 1000+#usernum
To scp files to the cluster:
scp -oport=1000+#usernum file
Submitting a job:
Deleting a job:
What jobs are running:
qstat, or showq (slow)

Format of simplest
#PBS -l nodes=1,walltime=24:00:00
#PBS -N my_job

export tempdir=$TMPDIR # temp space on local compute node
export inputdir=$HOME/dir1 # location of input files
export outputdir=$HOME/dir2 # location to put results into
export output=outfile # file for redirected standard output
export error=errfile # file for redirected standard error

cp -r $inputdir/* $tempdir

cd $tempdir

python 1>$output 2>$error

cp outfile errfile $outputdir


  • --oport doesn't work any more, you have to use -P

    By Blogger brian, at 10:04 AM  

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