Hi all - We recently merged in Galaxy 15.10 changes into our staging instance and have noticed jobs are no longer dispatched. There is no obvious problem in the log file. I see in github, commits have recently been made to revert something, but I'm not clear what. Is there something going on with the job runner? Better yet, how can I track down what my issue is?
On Tue, Mar 1, 2016 at 1:19 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi all - We recently merged in Galaxy 15.10 changes into our staging instance and have noticed jobs are no longer dispatched. There is no obvious problem in the log file.
I see in github, commits have recently been made to revert something, but I'm not clear what.
Is there something going on with the job runner? Better yet, how can I track down what my issue is?
Hi Ryan, There aren't any current issues with job running that I'm aware of. Typically the first thing to check is your job_conf.xml and make sure that handlers defined are the same as handlers (with matching server names) that you are starting). The log for your handlers should show them loading the job_conf.xml and setting up job plugins if they are identified as handlers in the config. --nate
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Hi Nate - Thanks. Our galaxy.ini shows: job_config_file = config/job_conf.xml Our job_conf.xml is (which is the same as job_conf.xml.sample_basic) : <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations> <destination id="local" runner="local"/> </destinations> </job_conf> Hmmm, ok weird. We just restart Galaxy for the 5th or 6th time to get a clean log file to send and it works now. Hmmm. I will consider this issue closed. Is there any documention that talks about how the job runner and manager, all work together? I'd like to add some debugging statements in the code so there is more info in the log file. On Wed, Mar 2, 2016 at 12:00 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Tue, Mar 1, 2016 at 1:19 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi all - We recently merged in Galaxy 15.10 changes into our staging instance and have noticed jobs are no longer dispatched. There is no obvious problem in the log file.
I see in github, commits have recently been made to revert something, but I'm not clear what.
Is there something going on with the job runner? Better yet, how can I track down what my issue is?
Hi Ryan,
There aren't any current issues with job running that I'm aware of. Typically the first thing to check is your job_conf.xml and make sure that handlers defined are the same as handlers (with matching server names) that you are starting). The log for your handlers should show them loading the job_conf.xml and setting up job plugins if they are identified as handlers in the config.
--nate
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On Thu, Mar 3, 2016 at 1:09 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi Nate - Thanks. Our galaxy.ini shows:
job_config_file = config/job_conf.xml
Our job_conf.xml is (which is the same as job_conf.xml.sample_basic) : <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations> <destination id="local" runner="local"/> </destinations> </job_conf>
Hmmm, ok weird. We just restart Galaxy for the 5th or 6th time to get a clean log file to send and it works now. Hmmm. I will consider this issue closed. Is there any documention that talks about how the job runner and manager, all work together? I'd like to add some debugging statements in the code so there is more info in the log file.
Hi Ryan, There's no code-level documentation for it. The relevant code is in lib/galaxy/jobs/__init__.py --nate
On Wed, Mar 2, 2016 at 12:00 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Tue, Mar 1, 2016 at 1:19 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi all - We recently merged in Galaxy 15.10 changes into our staging instance and have noticed jobs are no longer dispatched. There is no obvious problem in the log file.
I see in github, commits have recently been made to revert something, but I'm not clear what.
Is there something going on with the job runner? Better yet, how can I track down what my issue is?
Hi Ryan,
There aren't any current issues with job running that I'm aware of. Typically the first thing to check is your job_conf.xml and make sure that handlers defined are the same as handlers (with matching server names) that you are starting). The log for your handlers should show them loading the job_conf.xml and setting up job plugins if they are identified as handlers in the config.
--nate
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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Ryan G