Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA
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
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 ):
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, 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 ):
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\tnumber of threads\tmemory 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
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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
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Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA
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\tnumber of threads\tmemory 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
Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA
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
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
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 ):
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, 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 ):
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
Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA
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
