On Nov 27, 2012, at 9:37 AM, Peter Cock wrote:
> On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko
> wrote:
>>
>> The "Right Way (TM)" I believe would be to have a universal resource request
>> selector that could be plugged into any wrapper simply by including an
>> appropriate element l
On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko wrote:
>
> The "Right Way (TM)" I believe would be to have a universal resource request
> selector that could be plugged into any wrapper simply by including an
> appropriate element like say .
> Those variables could be exported, so the corres
On Nov 27, 2012, at 6:06 AM, Andreas Kuntzagk
wrote:
> Hi Peter,
>
> thanks for your replies.
>
> On 27.11.2012 11:44, Peter Cock wrote:
>> On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
>> wrote:
>>> Dear Peter,
>>>
As the author of several tool wrappers, I've been asking for a Gal
Hi Peter,
thanks for your replies.
On 27.11.2012 11:44, Peter Cock wrote:
On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
wrote:
Dear Peter,
As the author of several tool wrappers, I've been asking for a Galaxy
wide mechanism for Galaxy to tell the tool how many threads it can
use, for e
On Tue, Nov 27, 2012 at 10:44 AM, Andreas Kuntzagk
wrote:
> Hi Alex,
>
>> I am not sure if you can call these "surprises".
>
> Well at least it surprised me :-)
> Didn't want to sound to negative.
>
>> Some tools (which I highly appreciate) of Peter have been "parallelised"
>> to get the job done
On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
wrote:
> Dear Peter,
>
>> As the author of several tool wrappers, I've been asking for a Galaxy
>> wide mechanism for Galaxy to tell the tool how many threads it can
>> use, for example via an environment variable. The value could then
>> be set w
galaxy-dev-boun...@lists.bx.psu.edu] Namens Andreas Kuntzagk Verzonden:
dinsdag 27
november 2012 9:58 Aan: Bob Harris CC: galaxy-dev@lists.bx.psu.edu Onderwerp:
Re: [galaxy-dev]
multithreaded tools
Hi,
the four processes I saw where all called "lastz" and ran in parallel and
consu
Dear Peter,
As the author of several tool wrappers, I've been asking for a Galaxy
wide mechanism for Galaxy to tell the tool how many threads it can
use, for example via an environment variable. The value could then
be set with a general default, per runner default, or even per tool
using the ex
On Tue, Nov 27, 2012 at 8:58 AM, Andreas Kuntzagk
wrote:
> Hi,
>
> the four processes I saw where all called "lastz" and ran in parallel and
> consumed 100% of a core each.
> My guess is that the lastz_wrapper.py is responsible for this.
> Looking at it I see a some code regarding queuing and in t
x.psu.edu] Namens Andreas Kuntzagk
Verzonden: dinsdag 27 november 2012 9:58
Aan: Bob Harris
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] multithreaded tools
Hi,
the four processes I saw where all called "lastz" and ran in parallel and
consumed 100% of a core each.
My gu
Hi,
the four processes I saw where all called "lastz" and ran in parallel and
consumed 100% of a core each.
My guess is that the lastz_wrapper.py is responsible for this.
Looking at it I see a some code regarding queuing and in the very beginning
this line:
WORKERS = 4
and further one the cla
Howdy, Andreas,
The four processes started for a galaxy lastz job must involve post-
processing the lastz output through some other shell tool. Lastz by
itself doesn't support multiple threads or processes.
Bob H
On Nov 26, 2012, at 3:58 AM, Andreas Kuntzagk wrote:
Hi,
I'm wandering ho
-dev-boun...@lists.bx.psu.edu] Namens Andreas Kuntzagk
Verzonden: maandag 26 november 2012 9:58
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] multithreaded tools
Hi,
I'm wandering how galaxy supports tools that are multithreaded or multi-process.
When working with lastz I noticed th
Hi,
I'm wandering how galaxy supports tools that are multithreaded or multi-process.
When working with lastz I noticed that it starts 4 parallel processes.
Is that always so? Can this be adjusted? What other tools also are
multi-process?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrato
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