Re: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
On Fri, Jun 15, 2012 at 4:52 PM, Peter Cock wrote:
> On Fri, Jun 15, 2012 at 4:38 PM, James Taylor wrote:
>> This is exactly what I think we should do (and have for a long time), but I
>> think the variable should be somethin
Hi,
Just add some info about this, I have attempted to do so on SGE cluster.
I found that $NSLOTS works only for MPI jobs as it's part of the MPI
integration in SGE.
Other non MPI jobs won't work. For example:
python parallel_groomer.py input output $NSLOTS, $NSLOTS won't be replaced
by the SGE
On Fri, Jun 15, 2012 at 4:38 PM, James Taylor wrote:
> This is exactly what I think we should do (and have for a long time), but I
> think the variable should be something like:
>
> GALAXY_CPUS
>
> (threads is not accurate, a multithread or multiprocess job might want to use
> this info, something
On Jun 15, 2012, at 11:27 AM, Peter Cock wrote:
> On Fri, Jun 15, 2012 at 4:06 PM, Nate Coraor wrote:
>> On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
>>
>>> On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock
>>> wrote:
Hello all,
I'm wondering if it is sensible to make Galaxy tools
On Fri, Jun 15, 2012 at 4:06 PM, Nate Coraor wrote:
> On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
>
>> On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock
>> wrote:
>>> Hello all,
>>>
>>> I'm wondering if it is sensible to make Galaxy tools automatically use
>>> the environment variable $NSLOTS to a
On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
> On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock
> 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
On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock 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 cluste
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 threa
