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
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 guess is that the lastz_wrapper.py is responsible
On Tue, Nov 27, 2012 at 8:58 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de 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
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
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 guess
On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de 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
On Tue, Nov 27, 2012 at 10:44 AM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de 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
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
andreas.kuntz...@mdc-berlin.de 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
On Nov 27, 2012, at 6:06 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de
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
andreas.kuntz...@mdc-berlin.de wrote:
Dear Peter,
As the author of several
On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko o...@hpc.ufl.edu 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 resources proc=x pmem=y walltime=z /.
On Nov 27, 2012, at 9:37 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko o...@hpc.ufl.edu
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
Andreas,
Yes this is possible. You can also have a look at the ncbi blast+ tools written
by Peter. The same is true.
Usually the tool wrappers (xml) have an option preconfigured how many threads
can be used... You can adjust these directly in the xml OR as we did we added
the option to be
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
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