I would actually prefer we use $GALAXY_SLOTS.

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jul 30, 2013 at 11:18 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
>
> Re:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-October/011557.html
>
> Something I raised during the GCC2013, and we talked about
> via Twitter as well was a Galaxy environment variable for use
> within Tool Wrappers setting the number of threads/CPUs to
> use.
>
> The idea is that you can configure a default value, and then
> override this per runner or per tool etc. James Taylor had
> suggested calling this environment variable $GALAXY_CPUS
> which seem fine to me (personally I'd say threads not CPUs
> but I don't really mind). e.g.
>
> <command>my_tool --threads "\$GALAXY_CPUS"
> --input "$input" --output "$output"</command>
>
> Everyone I spoke to about this seemed positive about the idea.
>
> This would/should be integrated into the various cluster back
> ends, for example for SGE/OGE the number of threads is
> already configurable via the DRMAA settings and available
> as the environment variable $NSLOTS for non-MPI jobs, so
> my guess is all Galaxy needs to do is something like this:
>
> $ hg diff
> diff -r ce0d758bb995 lib/galaxy/jobs/runners/drmaa.py
> --- a/lib/galaxy/jobs/runners/drmaa.py  Tue Jul 30 12:30:30 2013 +0100
> +++ b/lib/galaxy/jobs/runners/drmaa.py  Tue Jul 30 16:10:40 2013 +0100
> @@ -43,6 +43,7 @@
>  #  - execute the command
>  #  - take the command's exit code ($?) and write it to a file.
>  drm_template = """#!/bin/sh
> +export GALAXY_CPUS="$NSLOTS"
>  GALAXY_LIB="%s"
>  if [ "$GALAXY_LIB" != "None" ]; then
>      if [ -n "$PYTHONPATH" ]; then
>
> Is there an open Trello card for this?
>
> Thanks,
>
> Peter
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