CODEWITHSUNDEEP
qsub
KR_Henninger
KR_Henninger

Reputation: 107

How do I know where my qsub job is running/being written

A silly question, perhaps, about qsub on SGE.

I submit a job via a script 

#PBS -V
#PBS -l select=1:ncpus=20:mpiprocs=20,walltime=01:00:00 
#PBS -o /path/to/out.file
#PBS -e /path/to/errors.txt
#PBS -q smp
#PBS -m ae
#PBS -M myemail@address
#PBS -P Projectname
#PBS -I
#PBS -N Job

 mpirun -np 20 mpiexecutable args input.file

The job of "mpiexecutable" is to act on input.file to minimise its parameters, and then write them to input.file again.

My job runs. But input.file remains unchanged. I think there is either

1) Something missing in my PATH, or

2) Some other reason why the cluster won't write to input.file.

In order to troubleshoot it, I need to know:

1) How do I find out where the job is running (i.e. what the path is wherever the job is running - should be the same as whatever the path is in the working directory, surely?) 2) How do I find out where the job is writing to?

Thanks so much for your help!

Upvotes: 1

Views: 498

Answers (1)

KR_Henninger
KR_Henninger

Reputation: 107

I just made some progress! I think the best way to proceed with a question like this is to be explicit about where the job is being run and written and where to find executables and input etc.

With this in mind, my new submission script is:

 #PBS -V
 #PBS -l select=1:ncpus=20:mpiprocs=20,walltime=01:00:00 
 #PBS -o /path/lfor/out.txt
 #PBS -e /path/for/errors.txt
 #PBS -q smp
 #PBS -m ae
 #PBS -M email@address
 #PBS -P Project-name
 #PBS -I
 #PBS -N Job

 module load importantmodules

 SRCDIR=$SCRATCH/my_project/code

 cp my_input_params.inp $RUNDIR

 RUNDIR=$SCRATCH/my_project/run-${PBS_JOBID/.*}

 mkdir -p $RUNDIR

 mpirun -np 20 $SRCDIR/mpiexecutable args < my_input_file.inp

I haven't tried this yet, but I am crossing my fingers that it works. I got some great directives for improving the submission script like this from this website: https://wikis.nyu.edu/display/NYUHPC/Writing+and+submitting+a+job+-+content

Let's keep going! I feel marginally less lost now

Upvotes: 1

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