On Jun 15, 2012, at 9:05 AM, Peter Cock wrote: > On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock <p.j.a.c...@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.
Hi Peter, $NSLOTS is SGE-specific. Torque uses a file whose path is set in $PBS_NODEFILE to list out the nodes you've been allocated (the node name is repeated for each slot you have on it). A couple of DRM-agnostic solutions: A common variable set by the job template before the tool runs. Or, the ability to set tool parameters from the runner URL in universe_wsgi.ini. --nate > >> Would this work in principle on other cluster setups? i.e. Is $NSLOTS >> sufficiently general? > > Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
