Dear Galaxy devs / support,
I am trying to understand the following snippet from job_conf.xml (I want to use drmaa v1) ------------ <destination id="pbs_drmaa_orion" runner="drmaa" tags="merc"> <param id="destination">galaxy@merc</param> </destination> ------------
Based on someone's configuration above, I am trying to customize to my system.
I'm trying to understand where/how the parameters are associated? - tags? - destination in param id? is this the queue? I also checked the DRMAA specification but cannot find any "destination" as a keyword. - galaxy@merc? is merc pointing to the hostname, and galaxy the queue name? (I know the instution's cluster is called "merc", but I don't know if the "merc" in the tag is for convenience or is being read as the hostname?
I've looked through: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml
but cannot make sense, eg. for "tags" is says "Tags to which this destination belongs." Eg. "tags="longwalltime,bigcluster""
Do you have more detailed documention on configuration?
Thanks Clinton
--
*PBS WorksTM named #1 software product!* HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com
http://pbsworks.com/ *
Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes https://twitter.com/xtechnotes!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore http://platform.twitter.com/widgets.js%27;fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs'); PBSWorks: Facebook https://www.facebook.com/pbsworks| Google+ https://plus.google.com/116621495421190215237| Linkedin http://www.linkedin.com/groups?gid=2112011 | Twitter https://twitter.com/PBSWorks| YouTube http://www.youtube.com/thepbsworks Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
Hi Clinton,
On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee chee@altair.com wrote:
Dear Galaxy devs / support,
I am trying to understand the following snippet from job_conf.xml (I want to use drmaa v1)
<destination id="pbs_drmaa_orion" runner="drmaa" tags="merc"> <param id="destination">galaxy@merc</param> </destination> ------------
Based on someone's configuration above, I am trying to customize to my system.
I'm trying to understand where/how the parameters are associated?
- tags?
Tags are identifiers used to map tools to destinations. You probably do not need to use them, but if you wanted to have a tool (or the default destination) send jobs to more than one destination (selected at random), tags are used for that. They can also be used for setting job concurrency limits.
- destination in param id? is this the queue? I also checked the DRMAA
specification but cannot find any "destination" as a keyword.
I am not sure where this example came from but I don't believe it would work - the "destination" param works with the "pbs" runner, but the pbs runner only works with Torque, as far as I know. The drmaa runner expects params that conform to the DRMAA specification, the most common of which is `nativeSpecification`. If you wanted to set the destination for PBS Pro using the drmaa runner, the param would be:
<param id="nativeSpecification">-q queue@server_name</param>
- galaxy@merc? is merc pointing to the hostname, and galaxy the queue
name? (I know the instution's cluster is called "merc", but I don't know if the "merc" in the tag is for convenience or is being read as the hostname?
That format is a PBS destination identifier, so `galaxy` is the queue on the PBS server `merc`.
Hope this helps, please let us know if this doesn't clear things up.
--nate
I've looked through: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml
but cannot make sense, eg. for "tags" is says "Tags to which this destination belongs." Eg. "tags="longwalltime,bigcluster""
Do you have more detailed documention on configuration?
Thanks Clinton
--
*PBS WorksTM named #1 software product!* HPCwire Reader’s Choice Awards 2014
- For more information on Altair’s award-winning HPC workload management
suite, please visit pbsworks.com http://pbsworks.com/ *
Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes https://twitter.com/xtechnotes!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^ http:/.test(d.location)?'http':'https';if(!d.getElementById(id)) {js=d.createElement(s);js.id=id;js.src=p+':// platform.twitter.com/widgets.js';fjs.parentNode.insertBefore http://platform.twitter.com/widgets.js%27;fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs'); PBSWorks: Facebook https://www.facebook.com/pbsworks| Google+ https://plus.google.com/116621495421190215237| Linkedin http://www.linkedin.com/groups?gid=2112011 | Twitter https://twitter.com/PBSWorks| YouTube http://www.youtube.com/thepbsworks Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
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/
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Hi Nate,
I was trying the Galaxy configuration using the tips you suggested - I think I got one step ahead, but stuck again. Now the job status says "waiting to run"
I got a screenshot attached - focussing on job 42 - which is a Sort job using a dataset I downloaded. Please note, I am setting up Galaxy, but I am not a bioinfomatics person. I'm a PBS person and need to use DRMAA - and I'm not sure how else to debug this.
Below is the job_conf.xml - I've also tried the hostname apart from localhost.
<?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no expl icit 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" workers="4"/> </plugins> <handlers default="localhost"> <handler id="localhost"/> </handlers> <destinations default="drmaa"> <destination id="local" runner="local"/> <destination id="drmaa" runner="drmaa"> <param id="nativeSpecification">-q workq@localhost</param> </destination> </destinations> </job_conf>
Thanks Clinton
On 9/09/2015 4:44 AM, Nate Coraor wrote:
Hi Clinton,
On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee <chee@altair.com mailto:chee@altair.com> wrote:
Dear Galaxy devs / support, I am trying to understand the following snippet from job_conf.xml (I want to use drmaa v1) ------------ <destination id="pbs_drmaa_orion" runner="drmaa" tags="merc"> <param id="destination">galaxy@merc</param> </destination> ------------ Based on someone's configuration above, I am trying to customize to my system. I'm trying to understand where/how the parameters are associated? - tags?Tags are identifiers used to map tools to destinations. You probably do not need to use them, but if you wanted to have a tool (or the default destination) send jobs to more than one destination (selected at random), tags are used for that. They can also be used for setting job concurrency limits.
- destination in param id? is this the queue? I also checked the DRMAA specification but cannot find any "destination" as a keyword.I am not sure where this example came from but I don't believe it would work - the "destination" param works with the "pbs" runner, but the pbs runner only works with Torque, as far as I know. The drmaa runner expects params that conform to the DRMAA specification, the most common of which is `nativeSpecification`. If you wanted to set the destination for PBS Pro using the drmaa runner, the param would be:
<param id="nativeSpecification">-q queue@server_name</param> - galaxy@merc? is merc pointing to the hostname, and galaxy the queue name? (I know the instution's cluster is called "merc", but I don't know if the "merc" in the tag is for convenience or is being read as the hostname?That format is a PBS destination identifier, so `galaxy` is the queue on the PBS server `merc`. Hope this helps, please let us know if this doesn't clear things up.
--nate
I've looked through: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml but cannot make sense, eg. for "tags" is says "Tags to which this destination belongs." Eg. "tags="longwalltime,bigcluster"" Do you have more detailed documention on configuration? Thanks Clinton-- ------------------------------------------------------------------------ *PBS WorksTM named #1 software product!* HPCwire Reader’s Choice Awards 2014 * For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com <http://pbsworks.com/> * ------------------------------------------------------------------------ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com <mailto:chee@altair.com> Skype: live:clinton.chee Twitter: @xtechnotes <https://twitter.com/xtechnotes>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)) <http:/.test%28d.location%29?%27http%27:%27https%27;if%28%21d.getElementById%28id%29%29>{js=d.createElement(s);js.id <http://js.id>=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore <http://platform.twitter.com/widgets.js%27;fjs.parentNode.insertBefore>(js,fjs);}}(document, 'script', 'twitter-wjs'); PBSWorks: Facebook <https://www.facebook.com/pbsworks>| Google+ <https://plus.google.com/116621495421190215237>| Linkedin <http://www.linkedin.com/groups?gid=2112011> | Twitter <https://twitter.com/PBSWorks>| YouTube <http://www.youtube.com/thepbsworks> Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com <mailto:pbs-support@india.altair.com>___________________________________________________________ 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/
Hi Nate,
Also, the only configuration I did on my Galaxy installation is the job_conf.xml file. I have not edited any of the other xml files or used other config sample files. Should I also have edited some other XML configuration files.
Also, do I need to have run any of the executbales in the main directory, besides ./run.sh?
The list of files in config/ is: [galaxy_user@bio config]$ ls -latrF total 312 -rw-rw-r-- 1 galaxy_user galaxy_user 416 Sep 3 10:42 disposable_email_blacklist.conf.sample -rw-rw-r-- 1 galaxy_user galaxy_user 44878 Sep 3 10:42 datatypes_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4444 Sep 3 10:42 auth_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 234 Sep 3 10:42 external_service_types_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 48599 Sep 3 10:42 galaxy.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 463 Sep 3 10:42 job_conf.xml.sample_basic -rw-rw-r-- 1 galaxy_user galaxy_user 30390 Sep 3 10:42 job_conf.xml.sample_advanced -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:42 migrated_tools_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 725 Sep 3 10:42 job_resource_params_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 6728 Sep 3 10:42 job_metrics_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 220 Sep 3 10:42 openid_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 2165 Sep 3 10:42 object_store_conf.xml.sample drwxrwxr-x 4 galaxy_user galaxy_user 4096 Sep 3 10:42 plugins/ -rw-rw-r-- 1 galaxy_user galaxy_user 69 Sep 3 10:42 shed_tool_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 shed_data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3139 Sep 3 10:42 reports_wsgi.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 288 Sep 3 10:42 tool_sheds_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 5552 Sep 3 10:42 tool_shed.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3273 Sep 3 10:42 tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4925 Sep 3 10:42 tool_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 5840 Sep 3 10:42 tool_conf.xml.main -rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:42 shed_tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 548 Sep 3 10:42 workflow_schedulers_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:52 migrated_tools_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 69 Sep 3 10:52 shed_tool_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:52 shed_tool_data_table_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:52 shed_data_manager_conf.xml -rw------- 1 root root 0 Sep 4 17:12 STDIN.o2 -rw------- 1 root root 0 Sep 4 17:12 STDIN.e2 -rw-rw-r-- 1 galaxy_user galaxy_user 512 Sep 4 22:11 job_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 48599 Sep 4 22:42 galaxy.ini -rw-rw-r-- 1 galaxy_user galaxy_user 631 Sep 7 14:48 job_conf.xmlDRA -rw-r--r-- 1 galaxy_user galaxy_user 909 Sep 14 16:20 job_conf.xml drwxrwxr-x 3 galaxy_user galaxy_user 4096 Sep 14 16:23 ./ drwxrwxr-x 24 galaxy_user galaxy_user 4096 Sep 14 16:27 ../
On 14/09/2015 4:22 PM, Clinton Chee wrote:
Hi Nate,
I was trying the Galaxy configuration using the tips you suggested - I think I got one step ahead, but stuck again. Now the job status says "waiting to run"
I got a screenshot attached - focussing on job 42 - which is a Sort job using a dataset I downloaded. Please note, I am setting up Galaxy, but I am not a bioinfomatics person. I'm a PBS person and need to use DRMAA - and I'm not sure how else to debug this.
Below is the job_conf.xml - I've also tried the hostname apart from localhost.
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no expl icit 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" workers="4"/> </plugins> <handlers default="localhost"> <handler id="localhost"/> </handlers> <destinations default="drmaa"> <destination id="local" runner="local"/> <destination id="drmaa" runner="drmaa"> <param id="nativeSpecification">-q workq@localhost</param> </destination> </destinations> </job_conf>
Thanks Clinton
On 9/09/2015 4:44 AM, Nate Coraor wrote:
Hi Clinton,
On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee <chee@altair.com mailto:chee@altair.com> wrote:
Dear Galaxy devs / support, I am trying to understand the following snippet from job_conf.xml (I want to use drmaa v1) ------------ <destination id="pbs_drmaa_orion" runner="drmaa" tags="merc"> <param id="destination">galaxy@merc</param> </destination> ------------ Based on someone's configuration above, I am trying to customize to my system. I'm trying to understand where/how the parameters are associated? - tags?Tags are identifiers used to map tools to destinations. You probably do not need to use them, but if you wanted to have a tool (or the default destination) send jobs to more than one destination (selected at random), tags are used for that. They can also be used for setting job concurrency limits.
- destination in param id? is this the queue? I also checked the DRMAA specification but cannot find any "destination" as a keyword.I am not sure where this example came from but I don't believe it would work - the "destination" param works with the "pbs" runner, but the pbs runner only works with Torque, as far as I know. The drmaa runner expects params that conform to the DRMAA specification, the most common of which is `nativeSpecification`. If you wanted to set the destination for PBS Pro using the drmaa runner, the param would be:
<param id="nativeSpecification">-q queue@server_name</param> - galaxy@merc? is merc pointing to the hostname, and galaxy the queue name? (I know the instution's cluster is called "merc", but I don't know if the "merc" in the tag is for convenience or is being read as the hostname?That format is a PBS destination identifier, so `galaxy` is the queue on the PBS server `merc`. Hope this helps, please let us know if this doesn't clear things up.
--nate
I've looked through: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml but cannot make sense, eg. for "tags" is says "Tags to which this destination belongs." Eg. "tags="longwalltime,bigcluster"" Do you have more detailed documention on configuration? Thanks Clinton-- ------------------------------------------------------------------------ *PBS WorksTM named #1 software product!* HPCwire Reader’s Choice Awards 2014 * For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com <http://pbsworks.com/> * ------------------------------------------------------------------------ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com <mailto:chee@altair.com> Skype: live:clinton.chee Twitter: @xtechnotes <https://twitter.com/xtechnotes>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)) <http:/.test%28d.location%29?%27http%27:%27https%27;if%28%21d.getElementById%28id%29%29>{js=d.createElement(s);js.id <http://js.id>=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore <http://platform.twitter.com/widgets.js%27;fjs.parentNode.insertBefore>(js,fjs);}}(document, 'script', 'twitter-wjs'); PBSWorks: Facebook <https://www.facebook.com/pbsworks>| Google+ <https://plus.google.com/116621495421190215237>| Linkedin <http://www.linkedin.com/groups?gid=2112011> | Twitter <https://twitter.com/PBSWorks>| YouTube <http://www.youtube.com/thepbsworks> Australia Toll Free: 1800 174 396 Urgent / Emergency: <mailto:pbs-support@india.altair.com>pbs-support@india.altair.com___________________________________________________________ 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/--
*PBS WorksTM named #1 software product!* HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com
http://pbsworks.com *
Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes https://twitter.com/xtechnotes PBSWorks: Facebook https://www.facebook.com/pbsworks | Google+ https://plus.google.com/116621495421190215237 | Linkedin http://www.linkedin.com/groups?gid=2112011 | Twitter https://twitter.com/PBSWorks | YouTube http://www.youtube.com/thepbsworks Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
This means the job has probably been queued in PBS, do you want to run qstat as the Galaxy user on the command line and see if you can see the Galaxy job - it may just be sitting there waiting for resources to run. The PBS logs might have more information at this point.
-John
On Mon, Sep 14, 2015 at 7:35 AM, Clinton Chee chee@altair.com wrote:
Hi Nate,
Also, the only configuration I did on my Galaxy installation is the job_conf.xml file. I have not edited any of the other xml files or used other config sample files. Should I also have edited some other XML configuration files.
Also, do I need to have run any of the executbales in the main directory, besides ./run.sh?
The list of files in config/ is: [galaxy_user@bio config]$ ls -latrF total 312 -rw-rw-r-- 1 galaxy_user galaxy_user 416 Sep 3 10:42 disposable_email_blacklist.conf.sample -rw-rw-r-- 1 galaxy_user galaxy_user 44878 Sep 3 10:42 datatypes_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4444 Sep 3 10:42 auth_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 234 Sep 3 10:42 external_service_types_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 48599 Sep 3 10:42 galaxy.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 463 Sep 3 10:42 job_conf.xml.sample_basic -rw-rw-r-- 1 galaxy_user galaxy_user 30390 Sep 3 10:42 job_conf.xml.sample_advanced -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:42 migrated_tools_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 725 Sep 3 10:42 job_resource_params_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 6728 Sep 3 10:42 job_metrics_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 220 Sep 3 10:42 openid_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 2165 Sep 3 10:42 object_store_conf.xml.sample drwxrwxr-x 4 galaxy_user galaxy_user 4096 Sep 3 10:42 plugins/ -rw-rw-r-- 1 galaxy_user galaxy_user 69 Sep 3 10:42 shed_tool_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 shed_data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3139 Sep 3 10:42 reports_wsgi.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 288 Sep 3 10:42 tool_sheds_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 5552 Sep 3 10:42 tool_shed.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3273 Sep 3 10:42 tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4925 Sep 3 10:42 tool_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 5840 Sep 3 10:42 tool_conf.xml.main -rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:42 shed_tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 548 Sep 3 10:42 workflow_schedulers_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:52 migrated_tools_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 69 Sep 3 10:52 shed_tool_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:52 shed_tool_data_table_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:52 shed_data_manager_conf.xml -rw------- 1 root root 0 Sep 4 17:12 STDIN.o2 -rw------- 1 root root 0 Sep 4 17:12 STDIN.e2 -rw-rw-r-- 1 galaxy_user galaxy_user 512 Sep 4 22:11 job_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 48599 Sep 4 22:42 galaxy.ini -rw-rw-r-- 1 galaxy_user galaxy_user 631 Sep 7 14:48 job_conf.xmlDRA -rw-r--r-- 1 galaxy_user galaxy_user 909 Sep 14 16:20 job_conf.xml drwxrwxr-x 3 galaxy_user galaxy_user 4096 Sep 14 16:23 ./ drwxrwxr-x 24 galaxy_user galaxy_user 4096 Sep 14 16:27 ../
On 14/09/2015 4:22 PM, Clinton Chee wrote:
Hi Nate,
I was trying the Galaxy configuration using the tips you suggested - I think I got one step ahead, but stuck again. Now the job status says "waiting to run"
I got a screenshot attached - focussing on job 42 - which is a Sort job using a dataset I downloaded. Please note, I am setting up Galaxy, but I am not a bioinfomatics person. I'm a PBS person and need to use DRMAA - and I'm not sure how else to debug this.
Below is the job_conf.xml - I've also tried the hostname apart from localhost.
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no expl icit 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" workers="4"/> </plugins> <handlers default="localhost"> <handler id="localhost"/> </handlers> <destinations default="drmaa"> <destination id="local" runner="local"/> <destination id="drmaa" runner="drmaa"> <param id="nativeSpecification">-q workq@localhost</param> </destination> </destinations> </job_conf>
Thanks Clinton
On 9/09/2015 4:44 AM, Nate Coraor wrote:
Hi Clinton,
On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee chee@altair.com wrote:
Dear Galaxy devs / support,
I am trying to understand the following snippet from job_conf.xml (I want to use drmaa v1)
<destination id="pbs_drmaa_orion" runner="drmaa" tags="merc"> <param id="destination">galaxy@merc</param> </destination> ------------
Based on someone's configuration above, I am trying to customize to my system.
I'm trying to understand where/how the parameters are associated?
- tags?
Tags are identifiers used to map tools to destinations. You probably do not need to use them, but if you wanted to have a tool (or the default destination) send jobs to more than one destination (selected at random), tags are used for that. They can also be used for setting job concurrency limits.
- destination in param id? is this the queue? I also checked the DRMAA
specification but cannot find any "destination" as a keyword.
I am not sure where this example came from but I don't believe it would work
- the "destination" param works with the "pbs" runner, but the pbs runner
only works with Torque, as far as I know. The drmaa runner expects params that conform to the DRMAA specification, the most common of which is `nativeSpecification`. If you wanted to set the destination for PBS Pro using the drmaa runner, the param would be:
<param id="nativeSpecification">-q queue@server_name</param>
- galaxy@merc? is merc pointing to the hostname, and galaxy the queue
name? (I know the instution's cluster is called "merc", but I don't know if the "merc" in the tag is for convenience or is being read as the hostname?
That format is a PBS destination identifier, so `galaxy` is the queue on the PBS server `merc`.
Hope this helps, please let us know if this doesn't clear things up.
--nate
I've looked through: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml
but cannot make sense, eg. for "tags" is says "Tags to which this destination belongs." Eg. "tags="longwalltime,bigcluster""
Do you have more detailed documention on configuration?
Thanks Clinton
-- ________________________________ PBS WorksTM named #1 software product! HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com ________________________________ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs'); PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
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-- ________________________________ PBS WorksTM named #1 software product! HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com ________________________________ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
-- ________________________________ PBS WorksTM named #1 software product! HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com ________________________________ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
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Hi John,
Thanks for your reply, the qstat printout is below. It just shows the last job on this machine occurred last Wed 9 Sep. Checked the PBS logs - there is no activity at all.
Note - this is a VM, single node, everything is installed on this one-node-VM pretending to be a cluster.
I'm using PBSPro 12, with Centos 6.4, DRMAA plugin (libdrmaa.so). I'm quite experienced with HPC and PBSpro, but almost zero experience in setting up drmaa to connect with Galaxy.
I can't help but feeling there is some step in setting up the DRMAA <-> Galaxy connection that I have missed. Seems like Galaxy can talk to DRMAA, but PBSpro has not receieved any info at all.
Do you have any other suggestions? Is there a recipe to setup Galaxy for DRMAA with PBSPro?
I've gone through these sites many times and cannot see what I missed. https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml http://dev.list.galaxyproject.org/ - galaxy-dev@lists.galaxyproject.org
[galaxy_user@bio galaxy-dist]$ qstat -x Job id Name User Time Use S Queue ---------------- ---------------- ---------------- -------- - ----- 0.bio STDIN root 00:00:00 F workq 1.bio STDIN chee 00:00:00 F workq 2.bio STDIN root 00:00:00 F workq 4.bio dummy chee 00:00:00 F normal 5.bio dummy chee 00:00:00 F normal 6.bio dummy chee 00:00:00 F normal 7.bio STDIN root 00:00:00 F workq 9.bio STDIN root 00:00:00 F workq 10.bio STDIN galaxy_user 00:00:00 F workq 11.bio STDIN root 00:00:00 F workq
[galaxy_user@bio galaxy-dist]$ qstat -xansw 11 bio.centos64: Req'd Req'd Elap Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time ------------------------------ --------------- --------------- --------------- -------- ---- ----- ------ ----- - ----- 11.bio.centos64 root workq STDIN 14321 -- -- -- -- F 00:00: 05 bio/0 Job run at Wed Sep 09 at 19:27 on (bio:ncpus=1) and finished
On 14/09/2015 10:55 PM, John Chilton wrote:
This means the job has probably been queued in PBS, do you want to run qstat as the Galaxy user on the command line and see if you can see the Galaxy job - it may just be sitting there waiting for resources to run. The PBS logs might have more information at this point.
-John
On Mon, Sep 14, 2015 at 7:35 AM, Clinton Chee chee@altair.com wrote:
Hi Nate,
Also, the only configuration I did on my Galaxy installation is the job_conf.xml file. I have not edited any of the other xml files or used other config sample files. Should I also have edited some other XML configuration files.
Also, do I need to have run any of the executbales in the main directory, besides ./run.sh?
The list of files in config/ is: [galaxy_user@bio config]$ ls -latrF total 312 -rw-rw-r-- 1 galaxy_user galaxy_user 416 Sep 3 10:42 disposable_email_blacklist.conf.sample -rw-rw-r-- 1 galaxy_user galaxy_user 44878 Sep 3 10:42 datatypes_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4444 Sep 3 10:42 auth_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 234 Sep 3 10:42 external_service_types_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 48599 Sep 3 10:42 galaxy.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 463 Sep 3 10:42 job_conf.xml.sample_basic -rw-rw-r-- 1 galaxy_user galaxy_user 30390 Sep 3 10:42 job_conf.xml.sample_advanced -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:42 migrated_tools_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 725 Sep 3 10:42 job_resource_params_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 6728 Sep 3 10:42 job_metrics_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 220 Sep 3 10:42 openid_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 2165 Sep 3 10:42 object_store_conf.xml.sample drwxrwxr-x 4 galaxy_user galaxy_user 4096 Sep 3 10:42 plugins/ -rw-rw-r-- 1 galaxy_user galaxy_user 69 Sep 3 10:42 shed_tool_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 shed_data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3139 Sep 3 10:42 reports_wsgi.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 288 Sep 3 10:42 tool_sheds_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 5552 Sep 3 10:42 tool_shed.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3273 Sep 3 10:42 tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4925 Sep 3 10:42 tool_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 5840 Sep 3 10:42 tool_conf.xml.main -rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:42 shed_tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 548 Sep 3 10:42 workflow_schedulers_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:52 migrated_tools_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 69 Sep 3 10:52 shed_tool_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:52 shed_tool_data_table_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:52 shed_data_manager_conf.xml -rw------- 1 root root 0 Sep 4 17:12 STDIN.o2 -rw------- 1 root root 0 Sep 4 17:12 STDIN.e2 -rw-rw-r-- 1 galaxy_user galaxy_user 512 Sep 4 22:11 job_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 48599 Sep 4 22:42 galaxy.ini -rw-rw-r-- 1 galaxy_user galaxy_user 631 Sep 7 14:48 job_conf.xmlDRA -rw-r--r-- 1 galaxy_user galaxy_user 909 Sep 14 16:20 job_conf.xml drwxrwxr-x 3 galaxy_user galaxy_user 4096 Sep 14 16:23 ./ drwxrwxr-x 24 galaxy_user galaxy_user 4096 Sep 14 16:27 ../
On 14/09/2015 4:22 PM, Clinton Chee wrote:
Hi Nate,
I was trying the Galaxy configuration using the tips you suggested - I think I got one step ahead, but stuck again. Now the job status says "waiting to run"
I got a screenshot attached - focussing on job 42 - which is a Sort job using a dataset I downloaded. Please note, I am setting up Galaxy, but I am not a bioinfomatics person. I'm a PBS person and need to use DRMAA - and I'm not sure how else to debug this.
Below is the job_conf.xml - I've also tried the hostname apart from localhost.
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no expl icit 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" workers="4"/> </plugins> <handlers default="localhost"> <handler id="localhost"/> </handlers> <destinations default="drmaa"> <destination id="local" runner="local"/> <destination id="drmaa" runner="drmaa"> <param id="nativeSpecification">-q workq@localhost</param> </destination> </destinations> </job_conf>
Thanks Clinton
On 9/09/2015 4:44 AM, Nate Coraor wrote:
Hi Clinton,
On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee chee@altair.com wrote:
Dear Galaxy devs / support,
I am trying to understand the following snippet from job_conf.xml (I want to use drmaa v1)
<destination id="pbs_drmaa_orion" runner="drmaa" tags="merc"> <param id="destination">galaxy@merc</param> </destination> ------------
Based on someone's configuration above, I am trying to customize to my system.
I'm trying to understand where/how the parameters are associated?
- tags?
Tags are identifiers used to map tools to destinations. You probably do not need to use them, but if you wanted to have a tool (or the default destination) send jobs to more than one destination (selected at random), tags are used for that. They can also be used for setting job concurrency limits.
- destination in param id? is this the queue? I also checked the DRMAA
specification but cannot find any "destination" as a keyword.
I am not sure where this example came from but I don't believe it would work
- the "destination" param works with the "pbs" runner, but the pbs runner
only works with Torque, as far as I know. The drmaa runner expects params that conform to the DRMAA specification, the most common of which is `nativeSpecification`. If you wanted to set the destination for PBS Pro using the drmaa runner, the param would be:
<param id="nativeSpecification">-q queue@server_name</param>
- galaxy@merc? is merc pointing to the hostname, and galaxy the queue
name? (I know the instution's cluster is called "merc", but I don't know if the "merc" in the tag is for convenience or is being read as the hostname?
That format is a PBS destination identifier, so `galaxy` is the queue on the PBS server `merc`.
Hope this helps, please let us know if this doesn't clear things up.
--nate
I've looked through: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml
but cannot make sense, eg. for "tags" is says "Tags to which this destination belongs." Eg. "tags="longwalltime,bigcluster""
Do you have more detailed documention on configuration?
Thanks Clinton
-- ________________________________ PBS WorksTM named #1 software product! HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com ________________________________ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs'); PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
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/
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-- ________________________________ PBS WorksTM named #1 software product! HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com ________________________________ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
-- ________________________________ PBS WorksTM named #1 software product! HPCwire Reader’s Choice Awards 2014
For more information on Altair’s award-winning HPC workload management suite, please visit pbsworks.com ________________________________ Clinton Chee (PhD) PBS Application Engineer Altair - Innovation Intelligence Mob: 61 (0)402 058 983 Email: chee@altair.com Skype: live:clinton.chee Twitter: @xtechnotes PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube Australia Toll Free: 1800 174 396 Urgent / Emergency: pbs-support@india.altair.com
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/
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galaxy-dev@lists.galaxyproject.org
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John Chilton -
Nate Coraor