When i run this command sh run.sh, jobs start as expected using job_conf.xml.
<?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"/>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
</plugins>
<destinations default="local">
<destination id="local" runner="local"/>
<destination id="big_jobs" runner="drmaa">
<param id="nativeSpecification">-q cassava.q -pe snode 35</param>
</destination>
</destinations>
<tools>
<tool id="maker" destination="big_jobs" />
<tool id="metaspades" destination="big_jobs" />
</tools>
</job_conf>
when i run sh run.sh --daemon , jobs don’t go in the queue:
Do i need something more the config ?
[pid: 43975|app: 0|req: 60/66] 127.0.0.1 () {46 vars in 1134 bytes} [Fri Apr 24 17:41:18 2020] GET /api/histories/33b43b4e7093c91f/contents?order=hid&v=dev&q=update_time-
ge&q=deleted&q=purged&qv=1970-01-01T00%3A00%3A00.000Z&qv=False&qv=False => generated 4572 bytes in 258 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 3)
galaxy.jobs.runners.drmaa ERROR 2020-04-24 17:41:19,971 [p:43975,w:1,m:0] [DRMAARunner.work_thread-0] (17) drmaa.Session.runJob() failed unconditionally
Traceback (most recent call last):
File "lib/galaxy/jobs/runners/drmaa.py", line 188, in queue_job
external_job_id = self.ds.run_job(**jt)
File "/media/vol2/home/galaxy/galaxy/.venv/lib/python3.6/site-packages/pulsar/managers/util/drmaa/__init__.py", line 67, in run_job
return DrmaaSession.session.runJob(template)
File "/media/vol2/home/galaxy/galaxy/.venv/lib/python3.6/site-packages/drmaa/session.py", line 314, in runJob
c(drmaa_run_job, jid, sizeof(jid), jobTemplate)
File "/media/vol2/home/galaxy/galaxy/.venv/lib/python3.6/site-packages/drmaa/helpers.py", line 302, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File "/media/vol2/home/galaxy/galaxy/.venv/lib/python3.6/site-packages/drmaa/errors.py", line 151, in error_check
raise _ERRORS[code - 1](error_string)
drmaa.errors.DrmCommunicationException: code 2: unable to send message to qmaster using port 6444 on host "node01": got send timeout
galaxy.jobs.runners.drmaa ERROR 2020-04-24 17:41:20,025 [p:43975,w:1,m:0] [DRMAARunner.work_thread-0] (17) All attempts to submit job failed
galaxy.tools.error_reports DEBUG 2020-04-24 17:41:20,864 [p:43975,w:1,m:0] [DRMAARunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fb824231470> generated response None
galaxy.tools.error_reports DEBUG 2020-04-24 17:41:20,865 [p:43975,w:1,m:0] [DRMAARunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fb824231470> generated response None
galaxy.tools.error_reports DEBUG 2020-04-24 17:41:20,865 [p:43975,w:1,m:0] [DRMAARunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fb824231470> generated response None
127.0.0.1 - - [24/Apr/2020:17:41:23 +0200] "GET /api/histories/33b43b4e7093c91f/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=1970-01-01T00%3A00%3A00.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://127.0.0.1:8081/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.92 Safari/537.36"