Set number of threads

[ddomman]

First off, the pyani package looks great. I was wondering if it was possible to limit the number of threads used in the multiprocessing mode to a set number? I'm trying to run the script on a non-SGE server and I'm concerned that the script as is, will try and use all available threads on the node... which is not so good.

Thanks!

[widdowquinn]

Not yet, @ddomman - but it should be a fairly straightforward change. I'll make it in the v0.2 branch, when I do.

FWIW, I think using all the threads available to you is generally a good thing ;)

[widdowquinn]

That should be the appropriate option enabled in the v0.2 branch with commit 5d50a. If this doesn't do the trick, I'll reopen the issue.

To use the new option, add the --workers n argument to the command-line. This will default to the maximum available number of threads if not specified, and cannot use more than the available number of cores if the specified value is too high. For example:

./average_nucleotide_identity.py -v -f \
  -i tests/test_ani_data/ \
  -o tests/test_ANIm_output/ \
  -g --gformat png,pdf,eps \
  --classes tests/test_ani_data/classes.tab --labels tests/test_ani_data/labels.tab \
  --workers 1

should use a single core.

[sarah872]

Although I specify --workers, mummer/nucmer is still running on the maximum number of cores. How can I limit the number of cores for nucmer?