On Jun 15, 2012, at 11:27 AM, Peter Cock wrote:

> 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?

Yes, exactly.

> 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?.

You could, but I think it'd be easier to read the $PBS_NODEFILE than attempt to 
parse PBS arguments.

> In the case of SGE,
> all the DRMAA wrapper needs to do is:
> 
> export THREADS="$NSLOTS"
> 
>>  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.
> 
> Peter
> 


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