On Fri, Jun 15, 2012 at 4:06 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> 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.

That is a shame, it is working nicely for the tools I have tried it on -
You just put "\$NSLOTS" (with a slash to escape the dollar) in
the <command> tag.

> 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.

By that do you mean Galaxy could do some magic in the shell scripts
it generates and submits to the cluster?

i.e. Setup an environment variable, e.g. $THREADS. In the case of
Torque/PBS, it could parse the $PBS_NODEFILE which sounds nasty
- or can you get this from the PBS runner URL?. In the case of SGE,
all the DRMAA wrapper needs to do is:


> Or, the ability to set tool  parameters from the runner URL in
> universe_wsgi.ini.

Setting things via the runner URL in universe_wsgi.ini seems better,
especially as it could be used for "local" runners too.


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