GATK2 Unified Genotyper creates too many threads

[nsoranzo]

My colleague Paolo Uva noticed that the gatk2_unified_genotyper tool creates a number of threads which is 6 times the number of cores it has been assigned in job_conf.xml (i.e. $GALAXY_SLOTS). This is due to the options "--num_threads ${GALAXY_SLOTS:-4}" (specified by the macro @threads@) and "--num_cpu_threads_per_data_thread 6".

When this job runs on a machine where it is supposed to occupy only a part of the available CPU cores, it harms the performances of other jobs.

The easiest solution is obviously to change the second option to "--num_cpu_threads_per_data_thread 1".

[bgruening]

I will read again the documentation and make the changes, I think it also applies for the other tools as well.

[nsoranzo]

I think it also applies for the other tools as well.

No, unified_genotyper is the only wrapper having both threading mechanisms enabled:

$ grep -l THREADS *.xml|xargs grep num_cpu_threads_per_data_thread
realigner_target_creator.xml:    --num_cpu_threads_per_data_thread 1
unified_genotyper.xml:    --num_cpu_threads_per_data_thread 6

[bgruening]

Fixed and package updated.
Thanks!