I asked this question at meta.stackoverflow.com; they said it was the wrong forum
I am using the FALCON assembler (for genomes by PacBio; https://github.com/PacificBiosciences/pb-assembly) and it's designed for usage on GRID engines with a scheduler (local, sge, lsf, pbs, torque, slurm).
The software installs via CONDA and I've run the test data (locally; within my login node) and the program runs as expected. Now I am trying to run it out on the GRID from my login node using the PBS/TORQUE scheduler.
My question is this: How do I properly specify the maximum number of processors and maximum memory variables?
The script should query the GRID and find out the resources [${NPROC} & ${MB}] at the beginning of the run - but I am unclear as to whether or not the term for the variables ${NPROC} and ${MB} are appropriate (correct) for PBS/TORQUE
For SGE this is how the config was written, and I've begun to modify it for PBS/TORQUE.
#JMout job_type=sge
#JMout pwatcher_type=blocking
job_type=pbs
JOB_QUEUE=batch
MB=32768
NPROC=6
njobs=32
submit = qsub -S /bin/bash -V \
-q ${JOB_QUEUE} \
-N ${JOB_NAME} \
-o "${JOB_STDOUT}" \
-e "${JOB_STDERR}" \
-pe smp ${NPROC} \
-l h_vmem=${MB}M \
"${JOB_SCRIPT}"
Specifically these two lines are the ones that I had concerns about:
-pe smp ${NPROC} \
-l h_vmem=${MB}M \
TIA