On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hello all,
I'm wondering if it is sensible to make Galaxy tools automatically use the environment variable $NSLOTS to automatically adjust their number of threads?
Using $NSLOTS works on SGE, but is it generally used on other clusters?
The idea here is rather than hard coding the number of threads in a tool or its XML file, which may need to be altered for different local setups, and it can be specified in universe_wsgi.ini under [galaxy:tool_runners]
Actually thinking about this over lunch, you wouldn't want to evaluate the $NSLOTS variable when the XML <command> is processed, as that would be done on the server not the cluster node. In some cases then embedding $NSLOTS in the command string (suitably escaped) should work, otherwise doing it in a wrapper script seems best.
Would this work in principle on other cluster setups? i.e. Is $NSLOTS sufficiently general?
Peter