Submitting multi-thread jobs to the cluster
Entered On
Type of Procedure
Image processing
Short Description
Adding options to the qsub command when submitting threaded (multi-core) jobs
When submitting to the queuing system a job which will be using more than a single core, add the following options to your qsub command:
-pe multi N
where N is the number of threads your job will be running
Also, assuming your jobs are parallelised using OpenMP, you may want to add the following option to qsub so that the OpenMP is set up properly on the node:
-v OMP_NUM_THREADS=N
where N is the number of threads
