Re: [galaxy-dev] Limit number of Jobs to Trinity
Hi Carlos and John Please allow me to pick up this thread. I have been experimenting with this, but I cant get it to work. The default destination is always used. Does it work for you, Carlos? Regards, Hans-Rudolf On 09/23/2013 03:32 AM, John Chilton wrote: As your Galaxy instance becomes more production ready I would definitely recommend installing a job queue such as grid engine, Torque, or SLURM. For this simple use case though, you should be able t define multiple local job runner instances to ensure only one Trinity job runs a time. Your job_conf.xml should look something like this: ?xml version=1.0? job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ plugin id=local2 type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=1/ /plugins handlers handler id=main/ /handlers destinations default=local destination id=local runner=local/ destination id=local2 runner=local2 / /destinations tools tool id=trinity destination=local2/ /tools /job_conf Hope this helps. -John On Sat, Sep 21, 2013 at 10:40 AM, Carlos Canchaya ccanch...@gmail.com wrote: Hi adam, So far we have just a standalone server since we are still setting up our tools (we will scale up to our sge cluster, though). Any clue how to limit jobs per tool basis? Best, Carlos On Saturday, September 21, 2013, Adam Brenner wrote: Carlos, Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being dispatched to your node(s)? More info here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya ccanch...@gmail.com wrote: Hi guys, I have a running local galaxy installation on one of our servers. I've just installed Trinity for de novo assembly of transcripts and it will use up to 32 processors. However i would like to limit the number of concurrent jobs only for this tool. Do you know if it would be possible to limit the number of concurrent jobs per tool basis? Bests, Carlos -- Carlos Canchaya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Carlos A. Canchaya Universidade de Vigo ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Limit number of Jobs to Trinity
well, I was just reading today's commits and I spotted: Nate's commit: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased. - Changeset: 0b955e54451c So I changed: tool id=addValue destination=local2 / to tool id=addvalue destination=local2 / and it seems to work. Regards, Hans-Rudolf On 09/26/2013 05:43 PM, Hans-Rudolf Hotz wrote: Hi Carlos and John Please allow me to pick up this thread. I have been experimenting with this, but I cant get it to work. The default destination is always used. Does it work for you, Carlos? Regards, Hans-Rudolf On 09/23/2013 03:32 AM, John Chilton wrote: As your Galaxy instance becomes more production ready I would definitely recommend installing a job queue such as grid engine, Torque, or SLURM. For this simple use case though, you should be able t define multiple local job runner instances to ensure only one Trinity job runs a time. Your job_conf.xml should look something like this: ?xml version=1.0? job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ plugin id=local2 type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=1/ /plugins handlers handler id=main/ /handlers destinations default=local destination id=local runner=local/ destination id=local2 runner=local2 / /destinations tools tool id=trinity destination=local2/ /tools /job_conf Hope this helps. -John On Sat, Sep 21, 2013 at 10:40 AM, Carlos Canchaya ccanch...@gmail.com wrote: Hi adam, So far we have just a standalone server since we are still setting up our tools (we will scale up to our sge cluster, though). Any clue how to limit jobs per tool basis? Best, Carlos On Saturday, September 21, 2013, Adam Brenner wrote: Carlos, Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being dispatched to your node(s)? More info here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya ccanch...@gmail.com wrote: Hi guys, I have a running local galaxy installation on one of our servers. I've just installed Trinity for de novo assembly of transcripts and it will use up to 32 processors. However i would like to limit the number of concurrent jobs only for this tool. Do you know if it would be possible to limit the number of concurrent jobs per tool basis? Bests, Carlos -- Carlos Canchaya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Carlos A. Canchaya Universidade de Vigo ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Limit number of Jobs to Trinity
As your Galaxy instance becomes more production ready I would definitely recommend installing a job queue such as grid engine, Torque, or SLURM. For this simple use case though, you should be able t define multiple local job runner instances to ensure only one Trinity job runs a time. Your job_conf.xml should look something like this: ?xml version=1.0? job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ plugin id=local2 type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=1/ /plugins handlers handler id=main/ /handlers destinations default=local destination id=local runner=local/ destination id=local2 runner=local2 / /destinations tools tool id=trinity destination=local2/ /tools /job_conf Hope this helps. -John On Sat, Sep 21, 2013 at 10:40 AM, Carlos Canchaya ccanch...@gmail.com wrote: Hi adam, So far we have just a standalone server since we are still setting up our tools (we will scale up to our sge cluster, though). Any clue how to limit jobs per tool basis? Best, Carlos On Saturday, September 21, 2013, Adam Brenner wrote: Carlos, Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being dispatched to your node(s)? More info here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya ccanch...@gmail.com wrote: Hi guys, I have a running local galaxy installation on one of our servers. I've just installed Trinity for de novo assembly of transcripts and it will use up to 32 processors. However i would like to limit the number of concurrent jobs only for this tool. Do you know if it would be possible to limit the number of concurrent jobs per tool basis? Bests, Carlos -- Carlos Canchaya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Carlos A. Canchaya Universidade de Vigo ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Limit number of Jobs to Trinity
Hi guys, I have a running local galaxy installation on one of our servers. I've just installed Trinity for de novo assembly of transcripts and it will use up to 32 processors. However i would like to limit the number of concurrent jobs only for this tool. Do you know if it would be possible to limit the number of concurrent jobs per tool basis? Bests, Carlos -- Carlos Canchaya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Limit number of Jobs to Trinity
Carlos, Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being dispatched to your node(s)? More info here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya ccanch...@gmail.comwrote: Hi guys, I have a running local galaxy installation on one of our servers. I've just installed Trinity for de novo assembly of transcripts and it will use up to 32 processors. However i would like to limit the number of concurrent jobs only for this tool. Do you know if it would be possible to limit the number of concurrent jobs per tool basis? Bests, Carlos -- Carlos Canchaya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Limit number of Jobs to Trinity
Hi adam,
So far we have just a standalone server since we are still setting up our
tools (we will scale up to our sge cluster, though). Any clue how to limit
jobs per tool basis?
Best,
Carlos
On Saturday, September 21, 2013, Adam Brenner wrote:
Carlos,
Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being
dispatched to your node(s)? More info here:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu javascript:_e({}, 'cvml', 'aebre...@uci.edu');
On Sat, Sep 21, 2013 at 4:47 AM, Carlos Canchaya
ccanch...@gmail.comjavascript:_e({}, 'cvml', 'ccanch...@gmail.com');
wrote:
Hi guys,
I have a running local galaxy installation on one of our servers. I've
just installed Trinity for de novo assembly of transcripts and it will use
up to 32 processors. However i would like to limit the number of concurrent
jobs only for this tool. Do you know if it would be possible to limit the
number of concurrent jobs per tool basis?
Bests,
Carlos
--
Carlos Canchaya
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Carlos A. Canchaya
Universidade de Vigo
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
