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CosmoMC: help with qsub commands and mpirun

Posted: October 13 2005
by Lisa Hall
Has anyone submitted an NxM run using qsub?

I am trying to run CosmoMC on a supercomputer in Sheffield. Sadly, bsub is not available, so I am using qsub. However, I cannot get chains to run on multiple processors.

As an example, I am using N=4, M=2. I have changed "num_threads = 4" in params_wipp.ini, according to the CosmoMC Readme doc.

q1) Should num_threads be left as zero, to set it automatically?

The submission cmd we are using is:

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qsub -cwd -pe mpich-gm 4 -q parallel.q sge_mpirun -np 2 ./cosmomc params_wipp.ini > output.txt
q2) Should I have a qsub option similar to the "-n" for bsub?

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bsub -n {NxM}

Using the naive qsub command above I get an error:

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OMP_NUM_THREADS or NCPUS (2) greater than available cpus (1)
omp_set_num_threads (4) greater than available cpus (1)
q3) Has anyone used qsub before or know of a possible solution?