Re: [galaxy-dev] galaxy-dev Digest, Vol 61, Issue 10 - Handling runner-specific (SLURM) DRMAA settings (Roman Valls)
The general config file allows us to set a fixed project:
default_cluster_job_runner = drmaa://-A a2010002 -p core
And even set per-tool job settings. But we would like each user to have the ability to change those settings.
What is the least intrusive way to set per-user native (site-specific) job manager settings ?
you may try to use an user's local DRMAA configuration file: ~/.slurm_drmaa.conf ". If multiple configuration sources are present then all configurations are merged with values from user-defined files taking precedence (in following order: $SLURM_DRMAA_CONF, ~/.slurm_drmaa.conf, /etc/slurm_drmaa.conf)" there you can put any user's specific settings, e.g.: job_categories: { default: "-A a2010002 -p core", } Cheers, -- Mariusz
Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful ! I wonder how this approach will work out when one runs galaxy as advised in a production setting: http://usegalaxy.org/production Together with the gordon patch to run drmaa as different users: http://wiki.g2.bx.psu.edu/Events/GCC2011?action=AttachFile&do=get&target=RunningGalaxyDRMAAJobsAsDifferentUsers.pdf My concern is that probably the SUID code will end up clearing up all the environment variables and/or ignoring the user's ~/.slurm_drmaa.conf as happened to me before with "screen": http://superuser.com/questions/235760/ld-library-path-unset-by-screen I'll jump in that Gordon patch/code eventually, but for now your insight/fixes have been very helpful from a galaxy developer instance perspective, thanks much again ! /Roman On 2011-07-19 19:53, Mariusz Mamoński wrote:
The general config file allows us to set a fixed project:
default_cluster_job_runner = drmaa://-A a2010002 -p core
And even set per-tool job settings. But we would like each user to have the ability to change those settings.
What is the least intrusive way to set per-user native (site-specific) job manager settings ?
you may try to use an user's local DRMAA configuration file:
~/.slurm_drmaa.conf
". If multiple configuration sources are present then all configurations are merged with values from user-defined files taking precedence (in following order: $SLURM_DRMAA_CONF, ~/.slurm_drmaa.conf, /etc/slurm_drmaa.conf)"
there you can put any user's specific settings, e.g.:
job_categories: { default: "-A a2010002 -p core", }
Cheers,
Roman Valls wrote:
Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
I wonder how this approach will work out when one runs galaxy as advised in a production setting:
http://usegalaxy.org/production
Together with the gordon patch to run drmaa as different users:
My concern is that probably the SUID code will end up clearing up all the environment variables and/or ignoring the user's ~/.slurm_drmaa.conf as happened to me before with "screen":
http://superuser.com/questions/235760/ld-library-path-unset-by-screen
I'll jump in that Gordon patch/code eventually, but for now your insight/fixes have been very helpful from a galaxy developer instance perspective, thanks much again !
From the Galaxy side of things, you could add a new section to universe_wsgi.ini as we do with tool_runners, and specify, perhaps, user_runners. This is parsed in lib/galaxy/config.py and implemented in
Hi Roman, lib/galaxy/tools/__init__.py. The correct place to do the per-user code might be in lib/galaxy/jobs/__init__.py itself, but I'm not sure how you'd resolve overlapping tool and user runners. I'd also been working on more complex configuration of job parameters that would probably make what you want to do easier, but that work is stalled. --nate
/Roman
On 2011-07-19 19:53, Mariusz Mamoński wrote:
The general config file allows us to set a fixed project:
default_cluster_job_runner = drmaa://-A a2010002 -p core
And even set per-tool job settings. But we would like each user to have the ability to change those settings.
What is the least intrusive way to set per-user native (site-specific) job manager settings ?
you may try to use an user's local DRMAA configuration file:
~/.slurm_drmaa.conf
". If multiple configuration sources are present then all configurations are merged with values from user-defined files taking precedence (in following order: $SLURM_DRMAA_CONF, ~/.slurm_drmaa.conf, /etc/slurm_drmaa.conf)"
there you can put any user's specific settings, e.g.:
job_categories: { default: "-A a2010002 -p core", }
Cheers,
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:
Hey Nate, On 2011-08-16 20:21, Nate Coraor wrote:
Roman Valls wrote:
Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
I wonder how this approach will work out when one runs galaxy as advised in a production setting:
http://usegalaxy.org/production
Together with the gordon patch to run drmaa as different users:
My concern is that probably the SUID code will end up clearing up all the environment variables and/or ignoring the user's ~/.slurm_drmaa.conf as happened to me before with "screen":
http://superuser.com/questions/235760/ld-library-path-unset-by-screen
I'll jump in that Gordon patch/code eventually, but for now your insight/fixes have been very helpful from a galaxy developer instance perspective, thanks much again !
Hi Roman,
From the Galaxy side of things, you could add a new section to universe_wsgi.ini as we do with tool_runners, and specify, perhaps, user_runners. This is parsed in lib/galaxy/config.py and implemented in lib/galaxy/tools/__init__.py. The correct place to do the per-user code might be in lib/galaxy/jobs/__init__.py itself, but I'm not sure how you'd resolve overlapping tool and user runners.
I got it up&running in Vienna, thanks to Jeremy. I didn't want to put it as a universe_wsgi.ini since users don't have access to it and thus tweak the parameters when their needs change (different time limits, projects, etc...). The overlapping of parameters still needs to be solved indeed :-S
I'd also been working on more complex configuration of job parameters that would probably make what you want to do easier, but that work is stalled.
Let me know where this partial work is ! My changeset on this issue is: https://bitbucket.org/brainstorm/galaxy-central/changeset/ec53f3a4d37a PD: Btw, the per-user UNIXy ~/.slurm_drmaa.conf works, but lacks some native flags (job title, time limit, etc...)... for now (I'm in contact with the slurm-drmaa dev). PD2: (TODO as well) I think the drm_template should be removed altogether from the drmaa.py runner, it defeats the whole purpose of the DRMAA abstraction.
--nate
/Roman
On 2011-07-19 19:53, Mariusz Mamoński wrote:
The general config file allows us to set a fixed project:
default_cluster_job_runner = drmaa://-A a2010002 -p core
And even set per-tool job settings. But we would like each user to have the ability to change those settings.
What is the least intrusive way to set per-user native (site-specific) job manager settings ?
you may try to use an user's local DRMAA configuration file:
~/.slurm_drmaa.conf
". If multiple configuration sources are present then all configurations are merged with values from user-defined files taking precedence (in following order: $SLURM_DRMAA_CONF, ~/.slurm_drmaa.conf, /etc/slurm_drmaa.conf)"
there you can put any user's specific settings, e.g.:
job_categories: { default: "-A a2010002 -p core", }
Cheers,
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:
Roman Valls wrote:
Hey Nate,
On 2011-08-16 20:21, Nate Coraor wrote:
Roman Valls wrote:
Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
I wonder how this approach will work out when one runs galaxy as advised in a production setting:
http://usegalaxy.org/production
Together with the gordon patch to run drmaa as different users:
My concern is that probably the SUID code will end up clearing up all the environment variables and/or ignoring the user's ~/.slurm_drmaa.conf as happened to me before with "screen":
http://superuser.com/questions/235760/ld-library-path-unset-by-screen
I'll jump in that Gordon patch/code eventually, but for now your insight/fixes have been very helpful from a galaxy developer instance perspective, thanks much again !
Hi Roman,
From the Galaxy side of things, you could add a new section to universe_wsgi.ini as we do with tool_runners, and specify, perhaps, user_runners. This is parsed in lib/galaxy/config.py and implemented in lib/galaxy/tools/__init__.py. The correct place to do the per-user code might be in lib/galaxy/jobs/__init__.py itself, but I'm not sure how you'd resolve overlapping tool and user runners.
I got it up&running in Vienna, thanks to Jeremy. I didn't want to put it as a universe_wsgi.ini since users don't have access to it and thus tweak the parameters when their needs change (different time limits, projects, etc...).
The overlapping of parameters still needs to be solved indeed :-S
I'd also been working on more complex configuration of job parameters that would probably make what you want to do easier, but that work is stalled.
Let me know where this partial work is ! My changeset on this issue is:
I was still trying to hash out the XML language for it, here's what I did so far: https://bitbucket.org/natefoo/galaxy-jobcontrol/changeset/tip This isn't fine-grained enough because it doesn't allow for multiple clusters of the same runner type, etc. --nate
https://bitbucket.org/brainstorm/galaxy-central/changeset/ec53f3a4d37a
PD: Btw, the per-user UNIXy ~/.slurm_drmaa.conf works, but lacks some native flags (job title, time limit, etc...)... for now (I'm in contact with the slurm-drmaa dev).
PD2: (TODO as well) I think the drm_template should be removed altogether from the drmaa.py runner, it defeats the whole purpose of the DRMAA abstraction.
--nate
/Roman
On 2011-07-19 19:53, Mariusz Mamoński wrote:
The general config file allows us to set a fixed project:
default_cluster_job_runner = drmaa://-A a2010002 -p core
And even set per-tool job settings. But we would like each user to have the ability to change those settings.
What is the least intrusive way to set per-user native (site-specific) job manager settings ?
you may try to use an user's local DRMAA configuration file:
~/.slurm_drmaa.conf
". If multiple configuration sources are present then all configurations are merged with values from user-defined files taking precedence (in following order: $SLURM_DRMAA_CONF, ~/.slurm_drmaa.conf, /etc/slurm_drmaa.conf)"
there you can put any user's specific settings, e.g.:
job_categories: { default: "-A a2010002 -p core", }
Cheers,
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:
participants (3)
-
Mariusz Mamoński -
Nate Coraor -
Roman Valls