job can't be submitted inside sge file

Question

I want to submit a sge job via sge file.

For example, I have run.sge file as follows:

## SGE options
#$ -cwd
#$ -l mem_free=2G
##$ -q [email protected]
#$ -pe mpich 4
#$ -S /bin/bash

SCRATCH_DIR=/state/partition1/$USER-$JOB_ID
mkdir $SCRATCH_DIR

qsub run_inp.sge

rmdir $SCRATCH_DIR

And run_inp.sge file as follows:

## SGE options
#$ -cwd
#$ -l mem_free=2G
##$ -q [email protected]
#$ -pe mpich 4
#$ -S /bin/bash

INPUTFILE="main.inp"
JOB="main"

SCRATCH_DIR=/state/partition1/$USER-$JOB_ID
mkdir $SCRATCH_DIR

/share/apps/simula/Commands/abaqus double inp=$INPUTFILE scratch=$SCRATCH_DIR job=$JOB mp_mode=mpi interactive

rmdir $SCRATCH_DIR

Whenever I submit job via

qsub run.sge

I got this error:

Unable to run job: denied: host "compute-2-9.local" is no submit host.
Exiting.

But if I submit run_inp.sge directly, it works fine:

qsub run_inp.sge

My question is that can I submit sge jobs inside a sge job? If not, is there alternative way to do such thing?

Answer 1

The normal approach is to submit all jobs from one host where you login, submit your jobs, and check job status. The submitted jobs are scheduled to execute on compute nodes in the cluster. If you have multiple jobs and dependencies between the jobs, you can declare the dependencies to the job scheduler. For example, you can tell the scheduler to wait for job A to finish before starting job B.