[GE users] qsub -wd usage

Reuti reuti at staff.uni-marburg.de
Sat Oct 25 23:58:40 BST 2008


Hi Bart,

when you want to run in a scratch directory on a node, you only need  
the -wd option to locate the source files. This is the directory to  
which SGE will "cd" when the job starts (default is every user's  
home, unless you use the -cwd or -wd option). On the node you can use  
the $TMPDIR which is already created be SGE and is unique for every  
job (it's location is defined in the queue configuration, where you  
can replace /tmp with /scratch for your parth):

#!/bin/sh
#$ -wd /storage/bart/code/
cp helloworld $TMPDIR
cd $TMPDIR
./helloworld

-- Reuti


Am 26.10.2008 um 00:42 schrieb Bart Willems:

> Hi All,
>
> I am trying to make our cluster users make use of local scratch space
> instead of NFS storage while running their jobs. What I would like  
> to do
> is something along the lines of the following job submission script:
>
> #!/bin/bash
>
> # This script should be submitted to the batch scheduler with the qsub
> # command as "qsub <scriptname>".
>
> # Lines that begin with "#$" are interpreted by the batch scheduler  
> (SGE)
> # as scheduling commands.
>
> # Use this shell as the default shell
> #$ -S /bin/bash
>
> # Combine stdout and stderr of job
> #$ -j y
>
> # Specify the requested cpu time
> #$ -l h_cpu=00:10:00
>
> # Define source and working directories
> SRCDIR=/storage/bart/code/
> WRKDIR=/scratch/`whoami`/test
>
> # Create working directory
> mkdir -p $WRKDIR
>
> # Change to working directory
> cd $WRKDIR
>
> # Copy needed files to working directory.
> cp $SRCDIR/helloworld .
>
> # run job from working directory
> #$ -wd $WRKDIR
>
> # computational command to run
> ./helloworld
>
>
> At the end, I would evidently copy back all files from $WRKDIR to  
> $SRCDIR,
> but I 'm not even getting that far. The two problems I seem to be  
> facing
> are
>
> (1) the -wd option does not like to be followed by a variable
> (2) the -wd option must be followed by a directory that already exists
>
> Eventually, I would like the working directory name WRKDIR to be  
> based on
> the job_id to make sure that it 's unique, so I cannot make the
> directories in advance.
>
> Does anyone have any suggestions on how to tackle this?
>
> Thanks,
> Bart
>
>
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