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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