On Jul 31, 2013, at 8:52 AM, shenwiyn shenwiyn@gmail.com wrote:
Hi Thon Deboer , I am a newer in Galaxy.I installed my Galaxy with Torque2.5.0 ,and Galaxy uses the pbs_modoule to interface with TORQUE.But I have some question of the job_conf.xml : 1.)In your job_conf.xml ,you use regularjobs,longjobs,shortjobs...to run different jobs ,how our Galaxy know which tool belongs to regularjobs or longjobs.And what is the meaning of "nativeSpecification"?
by specifying, as Thon did, in tools the id of the tool and its "destination" which are the settings. the nativeSpecification allows you to set additional parameters that are passed with the call. e.g. -pe smp 4 tells the grid engine to use the parallel environment smp with 4 cores.
2.)Shall us use <tools>collection of <tool id="bwa_wrapper" destination="multicorejobs4"/>to specify bwa ?Does it mean the bwa belong to multicorejobs4,and run in cluster?
exactly
3.)Does every tool need us to specify which job it belong to? I saw http://wiki.galaxyproject.org/Admin/Config/Jobs about this,but I am not sure above.Could you help me please?
fortunately there is a default
shenwiyn
From: Thon Deboer Date: 2013-07-18 14:31 To: galaxy-dev Subject: [galaxy-dev] Jobs remain in queue until restart Hi,
I have noticed that from time to time, the job queue seems to be “stuck” and can only be unstuck by restarting galaxy. The jobs seem to be in the queue state and the python job handler processes are hardly ticking over and the cluster is empty.
When I restart, the startup procedure realizes all jobs are in the a “new state” and it then assigns a jobhandler after which the jobs start fine….
Any ideas? Torque
Thon
P.S I am using the june version of galaxy and I DO set limits on my users in job_conf.xml as so: (Maybe it is related? Before it went into dormant mode, this user had started lots of jobs and may have hit the limit, but I assumed this limit was the number of running jobs at one time, right?)
<?xml version="1.0"?>
<job_conf> <plugins workers="4"> <!-- "workers" is the number of threads for the runner's work queue. The default from <plugins> is used if not defined for a <plugin>. --> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="8"/> <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" workers="2"/> </plugins> <handlers default="handlers"> <!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini. --> <handler id="handler0" tags="handlers"/> <handler id="handler1" tags="handlers"/> <handler id="handler2" tags="handlers"/> <handler id="handler3" tags="handlers"/> <!-- <handler id="handler10" tags="handlers"/> <handler id="handler11" tags="handlers"/> <handler id="handler12" tags="handlers"/> <handler id="handler13" tags="handlers"/> --> </handlers> <destinations default="regularjobs"> <!-- Destinations define details about remote resources and how jobs should be executed on those remote resources. --> <destination id="local" runner="local"/> <destination id="regularjobs" runner="drmaa" tags="cluster"> <!-- These are the parameters for qsub, such as queue etc. --> <param id="nativeSpecification">-V -q long.q -pe smp 1</param> </destination> <destination id="longjobs" runner="drmaa" tags="cluster,long_jobs"> <!-- These are the parameters for qsub, such as queue etc. --> <param id="nativeSpecification">-V -q long.q -pe smp 1</param> </destination> <destination id="shortjobs" runner="drmaa" tags="cluster,short_jobs"> <!-- These are the parameters for qsub, such as queue etc. --> <param id="nativeSpecification">-V -q short.q -pe smp 1</param> </destination> <destination id="multicorejobs4" runner="drmaa" tags="cluster,multicore_jobs"> <!-- These are the parameters for qsub, such as queue etc. --> <param id="nativeSpecification">-V -q long.q -pe smp 4</param> </destination>
<!-- <destination id="real_user_cluster" runner="drmaa"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> --> <destination id="dynamic" runner="dynamic"> <!-- A destination that represents a method in the dynamic runner. --> <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> <tools> <!-- Tools can be configured to use specific destinations or handlers, identified by either the "id" or "tags" attribute. If assigned to a tag, a handler or destination that matches that tag will be chosen at random. --> <tool id="bwa_wrapper" destination="multicorejobs4"/> </tools> <limits> <!-- Certain limits can be defined. <limit type="registered_user_concurrent_jobs">500</limit> <limit type="unregistered_user_concurrent_jobs">1</limit> <limit type="concurrent_jobs" id="local">1</limit> <limit type="concurrent_jobs" tag="cluster">200</limit> <limit type="concurrent_jobs" tag="long_jobs">200</limit> <limit type="concurrent_jobs" tag="short_jobs">200</limit> <limit type="concurrent_jobs" tag="multicore_jobs">100</limit> --> </limits></job_conf> ___________________________________________________________ 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/
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