[galaxy-dev] DRMAA Slurm error

2014-09-25 Thread Pardo Diaz, Alfonso
Hi, I have configured a new galaxy-project site with SLURM (version 14). I have one server with a Galaxy-Project instance, one node with SLURM server and two SLURM worker nodes. I have compile SLURM-DRMAA from source codes. When I run “drmaa-run /bin/hostname” it’s work. But, when I try to

Re: [galaxy-dev] DRMAA Slurm error

2014-09-25 Thread Pardo Diaz, Alfonso
Solved! The problem was I have configured the job_conf.xml two plugins entry with DRMAA. I have deleted the entry: plugin id=slurm type=runner load=galaxy.jobs.runners.slurm:SlurmJobRunner And now works! Thanks El 25/09/2014, a las 08:12, Pardo Diaz, Alfonso

[galaxy-dev] drmaa

2014-05-06 Thread Shrum, Donald C
Hi all, I've configured galaxy with the drama python module. This is really more of a drama question... We have no default queue set in moab and I can't seem to find a way to specify a queue in the docs I've been looking at here - http://drmaa-python.readthedocs.org/en/latest/tutorials.html

Re: [galaxy-dev] drmaa

2014-05-06 Thread Nate Coraor
Hi Donny, You should be able to specify the queue using the nativeSpecification field of drmaa requests, e.g. in your job_conf.xml: destination id=batch runner=pbs_drmaa param id=nativeSpecification-q batch/param /destination Documentation on job_conf.xml's syntax by runner can be found

Re: [galaxy-dev] DRMAA configuring issue

2014-04-25 Thread John Chilton
I feel like someone should respond to this but I must admin I don't have a lot of ideas. I assume you are able to use qsub to submit jobs from the Galaxy server? This is worth verifying that before anything else. If that doesn't work - the system configuration needs to be modified. I think there

Re: [galaxy-dev] DRMAA configuring issue

2014-04-22 Thread Hakeem Almabrazi
Does anyone have any tips about this, please :)? Regards From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi Sent: Monday, April 21, 2014 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] DRMAA configuring issue Hi

[galaxy-dev] DRMAA configuring issue

2014-04-21 Thread Hakeem Almabrazi
Hi, I am trying to get DRMAA runner working for my local galaxy cluster. However, I am having hard time configuring it my system. So far, I have installed Torque 2.5.12 and it seems to work as expected. I installed drmaa_1.0.17 and here is DRMAA_LIBRARY_PATH

[galaxy-dev] DRMAA bug in galaxy-central

2014-01-17 Thread Bjoern Gruening
Hi, since a few days there are frequent error messages popping up in my Galaxy log files. galaxy.jobs.runners ERROR 2014-01-17 13:11:17,094 Unhandled exception checking active jobs Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line

Re: [galaxy-dev] DRMAA bug in galaxy-central

2014-01-17 Thread John Chilton
It is hard to test error states... but I assume you have the setup for it :). Any chance you can apply these patches and let me know if they fix the problem? I assume they will. https://bitbucket.org/galaxy/galaxy-central/pull-request/300/potential-drmaa-fixes -John On Fri, Jan 17, 2014 at 6:15

Re: [galaxy-dev] DRMAA bug in galaxy-central

2014-01-17 Thread Björn Grüning
Thanks John, that fixed it for me! Have a nice weekend, Bjoern It is hard to test error states... but I assume you have the setup for it :). Any chance you can apply these patches and let me know if they fix the problem? I assume they will.

[galaxy-dev] DRMAA/SGE job handling regression?

2013-11-11 Thread Peter Cock
Hello all, On our main Galaxy tracking galaxy-dist using DRMAA/SGE, jobs submitted to the cluster and queued and waiting (qw) are correctly shown in Galaxy as grey pending entries in the history. With my test instance tracking galaxy-central (along with a new visual look and new icons), such

Re: [galaxy-dev] DRMAA Runner URL Specify TORQUE host

2013-07-16 Thread Bart Gottschalk
I've had success using the pbs runner rather than drmaa runner for this case. It's quite straightforward to specify the pbs_server for the pbs runner. Works just as the documentation indicates. - Bart On Tue, Jul 9, 2013 at 1:46 PM, Bart Gottschalk bgott...@umn.edu wrote: I haven't been

Re: [galaxy-dev] DRMAA Runner URL Specify TORQUE host

2013-07-09 Thread Bart Gottschalk
I haven't been able to find a way to make the drmaa runner work in this situation. I'm going to move on to trying this with a pbs runner instead. I will post to this thread if this works for me. - Bart ___ Please keep all replies on the

[galaxy-dev] DRMAA Runner URL Specify TORQUE host

2013-06-26 Thread Bart Gottschalk
Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options

[galaxy-dev] DRMAA Runner URL Specify TORQUE host

2013-06-26 Thread Bart Gottschalk
Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options

Re: [galaxy-dev] DRMAA Runner URL Specify TORQUE host

2013-06-26 Thread Adam Brenner
Bart, I believe drmaa://-q somehost@queue-name will work. However I could be very wrong. It has been a while since I messed with the actual drmaa runners. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support

[galaxy-dev] drmaa and JSV

2013-04-15 Thread jean-François Taly
Hi, Our galaxy instance runs jobs in a SGE cluster using 2 job-handlers. The SGE cluster uses a Job Submission Verifier (JSV) that rejects any job submission that specify core binding strategies. When Galaxy starts, the first jobs we submit works perfectly: First job submission:

Re: [galaxy-dev] DRMAA runner weirdness

2013-01-11 Thread Liisa Koski
. So I am afraid to update our production instance. Thanks in advance, Liisa From: Kyle Ellrott kellr...@soe.ucsc.edu To: Nate Coraor n...@bx.psu.edu Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Date: 10/01/2013 07:44 PM Subject:Re: [galaxy-dev] DRMAA runner

[galaxy-dev] DRMAA runner weirdness

2013-01-08 Thread Kyle Ellrott
I'm running a test Galaxy system on a cluster (merged galaxy-dist on Janurary 4th). And I've noticed some odd behavior from the DRMAA job runner. I'm running a multithread system, one web server, one job_manager, and three job_handlers. DRMAA is the default job runner (the command for tophat2 is

Re: [galaxy-dev] DRMAA job will now be errored - Segmentation fault

2012-11-27 Thread Nate Coraor
On Nov 20, 2012, at 8:15 AM, Peter Cock wrote: On Thu, Nov 15, 2012 at 11:21 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 15, 2012 at 10:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi

Re: [galaxy-dev] DRMAA job will now be errored - Segmentation fault

2012-11-27 Thread Nate Coraor
On Nov 27, 2012, at 12:03 PM, Peter Cock wrote: On Tue, Nov 27, 2012 at 4:50 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 20, 2012, at 8:15 AM, Peter Cock wrote: Is anyone else seeing this? I am wary of applying the update to our production Galaxy until I know how to resolve this (other

Re: [galaxy-dev] DRMAA job will now be errored - Segmentation fault

2012-11-27 Thread Peter Cock
On Tue, Nov 27, 2012 at 5:19 PM, Nate Coraor n...@bx.psu.edu wrote: So a little defensive coding could prevent the segfault then (leaving the separate issue of why the jobs lack this information)? Indeed, I pushed a check for this in 4a95ae9a26d9. Great. That will help. This was a week

Re: [galaxy-dev] DRMAA job will now be errored - Segmentation fault

2012-11-20 Thread Peter Cock
On Thu, Nov 15, 2012 at 11:21 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 15, 2012 at 10:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Something has changed in the job handling, and

[galaxy-dev] DRMAA job will now be errored - Segmentation fault

2012-11-15 Thread Peter Cock
Hi all, Something has changed in the job handling, and in a bad way. On my development machine submitting jobs to the cluster didn't seem to be working anymore (never sent to SGE). I killed Galaxy and restarted: Starting server in PID 12180. serving on http://127.0.0.1:8081

Re: [galaxy-dev] DRMAA job will now be errored - Segmentation fault

2012-11-15 Thread Peter Cock
On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Something has changed in the job handling, and in a bad way. On my development machine submitting jobs to the cluster didn't seem to be working anymore (never sent to SGE). I killed Galaxy and restarted:

Re: [galaxy-dev] DRMAA job will now be errored - Segmentation fault

2012-11-15 Thread Peter Cock
On Thu, Nov 15, 2012 at 10:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Something has changed in the job handling, and in a bad way. On my development machine submitting jobs to the cluster didn't

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-19 Thread Peter Cock
On Tue, Sep 18, 2012 at 7:11 PM, Scott McManus scottmcma...@gatech.edu wrote: Sorry - that's changeset 7714:3f12146d6d81 -Scott Hi Scott, The good news is this error does seem to be fixed as of that commit: TypeError: check_tool_output() takes exactly 5 arguments (4 given) The bad news is

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-19 Thread Jorrit Boekel
Odd, it works for me on EC2/Cloudman. jorrit On 09/19/2012 03:29 PM, Peter Cock wrote: On Tue, Sep 18, 2012 at 7:11 PM, Scott McManus scottmcma...@gatech.edu wrote: Sorry - that's changeset 7714:3f12146d6d81 -Scott Hi Scott, The good news is this error does seem to be fixed as of that

[galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Peter Cock
Hi all (and in particular, Scott), I've just updated my development server and found the following error when running jobs on our SGE cluster via DRMMA: galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper finish method failed Traceback (most recent call last): File

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
I'll check it out. Thanks. - Original Message - Hi all (and in particular, Scott), I've just updated my development server and found the following error when running jobs on our SGE cluster via DRMMA: galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper finish

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
I have to admit that I'm a little confused as to why you would be getting this error at all - the job variable is introduced at line 298 in the same file, and it's used as the last variable to check_tool_output in the changeset you pointed to. (Also, thanks for pointing to it - that made

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Jorrit Boekel
Is it possible that you are looking at different classes? TaskWrapper's finish method does not use the job variable in my recently merged code either (line ~1045), while JobWrapper's does around line 315. cheers, jorrit On 09/18/2012 03:55 PM, Scott McManus wrote: I have to admit that I'm

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
Thanks, Jorrit! That was a good catch. Yes, it's a problem with the TaskWrapper. I'll see what I can do about it. -Scott - Original Message - Is it possible that you are looking at different classes? TaskWrapper's finish method does not use the job variable in my recently merged

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Peter Cock
On Tue, Sep 18, 2012 at 3:09 PM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Is it possible that you are looking at different classes? TaskWrapper's finish method does not use the job variable in my recently merged code either (line ~1045), while JobWrapper's does around line 315.

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
Ok - that change was made. The difference is that the change is applied to the task instead of the job. It's in changeset 7713:bfd10aa67c78, and it ran successfully in my environments on local, pbs, and drmaa runners. Let me know if there are any problems. Thanks again for your patience.

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
Sorry - that's changeset 7714:3f12146d6d81 -Scott - Original Message - Ok - that change was made. The difference is that the change is applied to the task instead of the job. It's in changeset 7713:bfd10aa67c78, and it ran successfully in my environments on local, pbs, and drmaa

Re: [galaxy-dev] drmaa module does not load

2012-03-27 Thread Louise-Amélie Schmitt
Le 27/03/2012 11:03, Louise-Amélie Schmitt a écrit : Le 26/03/2012 16:13, Nate Coraor a écrit : On Mar 26, 2012, at 5:11 AM, Louise-Amélie Schmitt wrote: Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I

[galaxy-dev] drmaa module does not load

2012-03-26 Thread Louise-Amélie Schmitt
Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I start Galaxy: galaxy.jobs ERROR 2012-03-23 15:28:49,845 Job runner is not loadable: galaxy.jobs.runners. drmaa Traceback (most recent call last): File

Re: [galaxy-dev] DRMAA error with latest update 26920e20157f

2012-01-30 Thread Shantanu Pavgi
Figured it out. It was an error introduced while resolving version control conflicts. -- Shantanu On Jan 29, 2012, at 9:12 PM, Shantanu Pavgi wrote: I am getting following error with the latest galaxy-dist revision '26920e20157f' update. The Python version is 2.6.6. {{{

[galaxy-dev] DRMAA error with latest update 26920e20157f

2012-01-29 Thread Shantanu Pavgi
I am getting following error with the latest galaxy-dist revision '26920e20157f' update. The Python version is 2.6.6. {{{ galaxy.jobs.runners.drmaa ERROR 2012-01-29 21:00:28,577 Uncaught exception queueing job Traceback (most recent call last): File

Re: [galaxy-dev] DRMAA broken following SGE update. How to fix?

2011-08-23 Thread Chris Cole
BUMP Does anyone have any idea on this? Our Galaxy is currently out of action until this is sorted. Thanks, Chris On 22/08/11 10:08, Chris Cole wrote: Hi, Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change

Re: [galaxy-dev] DRMAA broken following SGE update. How to fix?

2011-08-23 Thread remy d1
Hi Chris, Take a look at this file : lib/galaxy/jobs/runners/drmaa.py in your galaxy directory. You can export a path for binaries here. For example : export PATH=$PATH:/opt/bin/ before export PYTHONPATH Moreover, do not forget other path values in your service script or in your galaxy user

[galaxy-dev] DRMAA broken following SGE update. How to fix?

2011-08-22 Thread Chris Cole
Hi, Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change the path for galaxy to find the libdrmaa module? Cheers, Chris -- Dr Chris Cole Senior Research Associate (Bioinformatics) College of Life Sciences

Re: [galaxy-dev] DRMAA options for SGE

2011-07-28 Thread Ka Ming Nip
From: ambarish biswas [ambarishbis...@gmail.com] Sent: July 27, 2011 4:18 PM To: Ka Ming Nip Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] DRMAA options for SGE Hi Ming, just an idea, -w n might be hiding the error reporting. Is your jobs getting

Re: [galaxy-dev] DRMAA options for SGE

2011-07-28 Thread ambarish biswas
@lists.bx.psu.edu Subject: Re: [galaxy-dev] DRMAA options for SGE Hi Ming, just an idea, -w n might be hiding the error reporting. Is your jobs getting submitted and executed correctly? For the queuing , you can add galaxy at the end, makes it drmaa://-w n -l mem_free=1G -l mem_token=1G -l

Re: [galaxy-dev] DRMAA options for SGE

2011-07-27 Thread Ka Ming Nip
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ka Ming Nip [km...@bcgsc.ca] Sent: July 26, 2011 10:39 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] DRMAA options for SGE Hi, I am trying to configure the proper memory resource

[galaxy-dev] DRMAA options for SGE

2011-07-26 Thread Ka Ming Nip
Hi, I am trying to configure the proper memory resource requests for my Galaxy tool. This is what I have under the tool_runners section of universe_wsgi.ini [galaxy:tool_runners] ... mytoolname = drmaa://-l mem_free=1G -l mem_token=1G -l h_vmem=1G/ ... When I execute my tool on Galaxy, I get

[galaxy-dev] drmaa://native/ : native options are ignored

2011-06-20 Thread Geert Vandeweyer
Hi, I'm working on an local installation of galaxy using torque with drmaa (the pbs-torque scramble failed). The torque-drmaa works fine so far, except for one issue. I'd like to specify some tool-dependent requirements from the tool_runners section in universe.wsgi.ini. For now I've been

Re: [galaxy-dev] drmaa://native/ : native options are ignored

2011-06-20 Thread Marina Gourtovaia
Hi default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/ works for me on LSF, so your syntax seems to be correct. Assuming that -l mem=4gb:nodes=1:ppn=6 works teh way you expect when you start the jobs on your cluster from the shell, read on... Bearing in mind the the value of the