Hi again
Oh I see... Not the best way to deal with the resources indeed but
better than nothing though.
I do run Java tools via Galaxy but I haven't paid attention to this
issue, so I can't really help. It's a homemade tool that only has one
class so I guess it's not worth the effort in my case. But if you find
the answer, I'd be interested too.
Good luck,
L-A
On 05/19/2011 04:28 PM, Leandro Hermida wrote:
Hi Louise,
I see thank you for the response, maybe there was some confusion, the
feature I was trying to explain with LSF is that you *don't* need to
tell it the required resources for a job and it will still be able to
run all the submitted jobs on a node without crashing even if the jobs
submitted need e.g. 10 more cores are available (that is 10 more cores
than LSF thought it needed). LSF will just temporarily suspend jobs
in mid-run on a node to keep the load down, but nothing will ever
crash even if you are running jobs that require 20 CPUs and you only
have 2. Thought maybe there was a way to do this with TORQUE. If LSF
or TORQUE are explcitly passed the resources needed then they will
never need to temporarily suspend because they will pick a node with
those resources free. That being said, your method is more efficient
for this reason as it will pick the right node with the cores
available instead of picking a node with maybe just one core available
and then running the multithreaded job slower because it has to
periodically suspend it as it is running.
Also I wonder do you run any Java command-line tools via Galaxy? I
can't seem to find with the JVM exactly how many cores it needs during
execution or how to limit it to a certain max, it just jumps around in
CPU usage from 50% to over 400%
regards,
Leandro
2011/5/19 Louise-Amélie Schmitt <louise-amelie.schm...@embl.de
<mailto:louise-amelie.schm...@embl.de>>
Hi again Leandro
Well I might not have been really clear, perhaps I should have
re-read the mail before posting it :)
The thing is, it was not an issue of Torque starting jobs when
there were not enough resources available, but rather it believing
the needed resources for each job being fewer that they were (e.g.
always assuming the jobs were single-threaded even if the actual
tools needed more tan one core). if Torque is properly notified of
the needed resources, it will dispatch them or make them wait
accordingly (since it knows the nodes' limits and load), like your
LSF does.
This hack is not very sexy but it just notifies Torque of the
cores needed by every multithreaded tool, so it doesn't run a
multithreaded job when there's only one core available in the
chosen node.
Hope that helps :)
Regards,
L-A
On 05/19/2011 03:05 PM, Leandro Hermida wrote:
Hi Louise-Amelie,
Thank you for the post reference, this is exactly what I was
looking for. For us for for example when I want to execute a
tool that is a Java command the JVM typically will typically use
multiple cores as it's running. You said with TORQUE it will
crash when there aren't enough resources when the job is
submitted. I wonder if you can do the same thing we have done
here with LSF? With LSF you can configure a maximum server load
for each node and if the submitted jobs push the node load above
this threshold (e.g. more cores requested than available) LSF
will temporarily suspend jobs (using some kind of heuristics) so
that the load stays below the threshold and unsuspend as
resources become available. So for us things just will run
slower when we cannot pass the requested number of cores to LSF.
I would think maybe there is a way with TORQUE to have it achieve
the same thing so jobs don't crash when resources requested are
more than available?
regards,
Leandro
2011/5/19 Louise-Amélie Schmitt <louise-amelie.schm...@embl.de
<mailto:louise-amelie.schm...@embl.de>>
Hi,
In a previous message, I explained how I did to multithreads
certain jobs, perhaps you can modify the corresponding files
for drmaa in a similar way:
On 04/26/2011 11:26 AM, Louise-Amélie Schmitt wrote:
Just one little fix on line 261:
261 if ( len(l)> 1 and l[0] ==job_wrapper.tool.id
<http://job_wrapper.tool.id> ):
Otherwise it pathetically crashes when non-multithreaded jobs are
submitted. Sorry about that.
Regards,
L-A
Le mardi 19 avril 2011 à 14:33 +0200, Louise-Amélie Schmitt a écrit :
Hello everyone,
I'm using TORQUE with Galaxy, and we noticed that if a tool is
multithreaded, the number of needed cores is not communicated to pbs,
leading to job crashes if the required resources are not available when
the job is submitted.
Therefore I modified a little the code as follows in
lib/galaxy/jobs/runners/pbs.py
256 # define PBS job options
257 attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_%
s" % ( job_wrapper.job_id,job_wrapper.tool.id
<http://job_wrapper.tool.id>, job_wrapper.user ) ) ) )
258 mt_file = open('tool-data/multithreading.csv', 'r')
259 for l in mt_file:
260 l = string.split(l)
261 if ( l[0] ==job_wrapper.tool.id
<http://job_wrapper.tool.id> ):
262 attrs.append( dict( name = pbs.ATTR_l,
resource = 'nodes', value = '1:ppn='+str(l[1]) ) )
263 attrs.append( dict( name = pbs.ATTR_l,
resource = 'mem', value = str(l[2]) ) )
264 break
265 mt_file.close()
266 job_attrs = pbs.new_attropl( len( attrs ) +
len( pbs_options ) )
(sorry it didn't come out very well due to line breaking)
The csv file contains a list of the multithreaded tools, each line
containing:
<tool id>\t<number of threads>\t<memory needed>\n
And it works fine, the jobs wait for their turn properly, but
information is duplicated. Perhaps there would be a way to include
something similar in galaxy's original code (if it is not already the
case, I may not be up-to-date) without duplicating data.
I hope that helps :)
Best regards,
L-A
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
atusegalaxy.org <http://usegalaxy.org>. Please keep all replies on
the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
On 05/19/2011 12:03 PM, Leandro Hermida wrote:
Hi,
When Galaxy is configured to use the DRMAA job runner is
there a way for a tool to tell DRMAA the number of cores it
would like to request? The equivalent of bsub -n X in LSF
where X is min number of cores to have available on node.
best,
leandro
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
