11:55 a.m.
Hi,
This is my first Galaxy installation setup so apologies for stupid
questions. I am setting up Galaxy on a Cluster running Torque as the
resource manager. I am working through the documentation but I am unclear
on some things:
Firstly I am unable to find : *start_job_runners *within the
universe_wsgi.ini and I dont want to just add this anywhere - any help on
this would be create.
Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
</plugins>
<handlers>
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini.
<handler id="cn01"/>
<handler id="cn02"/>
</handlers>
<destinations>
<destination id="hpc" runner="drmaa"/>
</destinations>
</job_conf>
Does this look meaning full, further more where to I set the additional
server:<id>
in the universe_wsgi.ini.
As background the cluster has 13 compute nodes and a shared storage array
that can be accessed by all nodes in the cluster.
Thanks again
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
1:23 a.m.
Yes,and I also have the same confuse about that.Actually when I set server:<id> in
the universe_wsgi.ini as follows for a try,my Galaxy doesn't work with Cluster,if I
remove server:<id>,it work .
[server:node01]
use = egg:Paste#http
port = 8080
host = 0.0.0.0
use_threadpool = true
threadpool_workers = 5
This is my job_conf.xml :
<?xml version="1.0"?>
<job_conf>
<plugins workers="4">
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
</plugins>
<handlers default="batch">
<handler id="node01" tags="batch"/>
<handler id="node02" tags="batch"/>
</handlers>
<destinations default="regularjobs">
<destination id="local" runner="local"/>
<destination id="regularjobs" runner="pbs"
tags="cluster">
<param
id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
<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>
</destinations>
</job_conf>
Further more when I want to kill my jobs by clicking in galaxy web,the job keeps on
running in my background.I do not know how to fix this.
Any help on this would be grateful.Thank you very much.
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Subject: [galaxy-dev] Help with cluster setup
Hi,
This is my first Galaxy installation setup so apologies for stupid questions. I am setting
up Galaxy on a Cluster running Torque as the resource manager. I am working through the
documentation but I am unclear on some things:
Firstly I am unable to find : start_job_runners within the universe_wsgi.ini and I dont
want to just add this anywhere - any help on this would be create.
Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
</plugins>
<handlers>
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini.
<handler id="cn01"/>
<handler id="cn02"/>
</handlers>
<destinations>
<destination id="hpc" runner="drmaa"/>
</destinations>
</job_conf>
Does this look meaning full, further more where to I set the additional
server:<id>
in the universe_wsgi.ini.
As background the cluster has 13 compute nodes and a shared storage array that can be
accessed by all nodes in the cluster.
Thanks again
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
2:58 p.m.
On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
Yes,and I also have the same confuse about that.Actually when I set
server:<id> in the universe_wsgi.ini as follows for a try,my Galaxy doesn't work
with Cluster,if I remove server:<id>,it work .
Hi Shenwiyn,
Are you starting all of the servers that you have defined in universe_wsgi.ini? If using
run.sh, setting GALAXY_RUN_ALL in the environment will do this for you:
http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
[server:node01]
use = egg:Paste#http
port = 8080
host = 0.0.0.0
use_threadpool = true
threadpool_workers = 5
This is my job_conf.xml :
<?xml version="1.0"?>
<job_conf>
<plugins workers="4">
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
</plugins>
<handlers default="batch">
<handler id="node01" tags="batch"/>
<handler id="node02" tags="batch"/>
</handlers>
<destinations default="regularjobs">
<destination id="local" runner="local"/>
<destination id="regularjobs" runner="pbs"
tags="cluster">
<param
id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
<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>
</destinations>
</job_conf>
The galaxy_external_* options are only supported with the drmaa plugin, and actually only
belong in the univese_wsgi.ini for the moment, they have not been migrated to the
new-style job configuration. They should also only be used if you are attempting to set
up "run jobs as the real user" job running capabilities.
Further more when I want to kill my jobs by clicking
<Catch(08-08-09-12-39).jpg> in galaxy web,the job keeps on running in my
background.I do not know how to fix this.
Any help on this would be grateful.Thank you very much.
Job deletion in the pbs runner was recently broken, but a fix for this bug will be part of
the next stable release (on Monday).
--nate
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Subject: [galaxy-dev] Help with cluster setup
Hi,
This is my first Galaxy installation setup so apologies for stupid questions. I am
setting up Galaxy on a Cluster running Torque as the resource manager. I am working
through the documentation but I am unclear on some things:
Firstly I am unable to find : start_job_runners within the universe_wsgi.ini and I dont
want to just add this anywhere - any help on this would be create.
Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
</plugins>
<handlers>
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini.
<handler id="cn01"/>
<handler id="cn02"/>
</handlers>
<destinations>
<destination id="hpc" runner="drmaa"/>
</destinations>
</job_conf>
Does this look meaning full, further more where to I set the additional
server:<id>
in the universe_wsgi.ini.
As background the cluster has 13 compute nodes and a shared storage array that can be
accessed by all nodes in the cluster.
Thanks again
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
___________________________________________________________
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/
2:53 p.m.
I am totally lost on what is happening now, I have Galaxy running but jobs
are not being run:
This is my setup:
torque:
qmgr -c 'p s'
#
# Create queues and set their attributes.
#
#
# Create and define queue batch
#
create queue batch
set queue batch queue_type = Execution
set queue batch resources_default.nodes = 1
set queue batch resources_default.walltime = 01:00:00
set queue batch enabled = True
set queue batch started = True
#
# Set server attributes.
#
set server scheduling = True
set server acl_hosts = manager
set server managers = root@*
set server managers += jurgens@*
set server operators = galaxy@*
set server operators += jurgens@*
set server operators += root@*
set server default_queue = batch
set server log_events = 511
set server mail_from = adm
set server scheduler_iteration = 600
set server node_check_rate = 150
set server tcp_timeout = 300
set server job_stat_rate = 45
set server poll_jobs = True
set server mom_job_sync = True
set server keep_completed = 300
set server next_job_number = 17
set server moab_array_compatible = True
This is my 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="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
-->
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
</plugins>
<handlers default="batch">
<handler id="cn01" tags="batch"/>
<handler id="cn02" tags="batch"/>
</handlers>
<destinations default="batch">
<destination id="batch" runner="drmaa"
tag="cluster,batch">
<param id="nativeSpecfication">-q batch</param>
</destination>
</destinations>
</job_conf>
This is parts of the universe_wsgi.ini
# Configuration of the internal HTTP server.
[server:main]
# The internal HTTP server to use. Currently only Paste is provided. This
# option is required.
use = egg:Paste#http
# The port on which to listen.
port = 8989
# The address on which to listen. By default, only listen to localhost
(Galaxy
# will not be accessible over the network). Use '0.0.0.0' to listen on all
# available network interfaces.
#host = 127.0.0.1
host = 0.0.0.0
# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True
# Number of threads in the web server thread pool.
#threadpool_workers = 10
# Set the number of seconds a thread can work before you should kill it
(assuming it will never finish) to 3 hours.
threadpool_kill_thread_limit = 10800
[server:cn01]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
[server:cn02]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
Where cn01 and cn02 are cluster nodes
echo $DRMAA_LIBRARY_PATH
/usr/local/lib/libdrmaa.so
On 8 August 2013 16:58, Nate Coraor <nate(a)bx.psu.edu <javascript:_e({},
'cvml', 'nate(a)bx.psu.edu');>> wrote:
On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
> Yes,and I also have the same confuse about that.Actually when I set
server:<id> in the universe_wsgi.ini as follows for a try,my Galaxy doesn't
work with Cluster,if I remove server:<id>,it work .
Hi Shenwiyn,
Are you starting all of the servers that you have defined in
universe_wsgi.ini? If using run.sh, setting GALAXY_RUN_ALL in the
environment will do this for you:
http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> [server:node01]
> use = egg:Paste#http
> port = 8080
> host = 0.0.0.0
> use_threadpool = true
> threadpool_workers = 5
> This is my job_conf.xml :
> <?xml version="1.0"?>
> <job_conf>
> <plugins workers="4">
> <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> <plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
> </plugins>
> <handlers default="batch">
> <handler id="node01" tags="batch"/>
> <handler id="node02" tags="batch"/>
> </handlers>
> <destinations default="regularjobs">
> <destination id="local" runner="local"/>
> <destination id="regularjobs" runner="pbs"
tags="cluster">
> <param
id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
> <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>
> </destinations>
> </job_conf>
The galaxy_external_* options are only supported with the drmaa plugin,
and actually only belong in the univese_wsgi.ini for the moment, they have
not been migrated to the new-style job configuration. They should also
only be used if you are attempting to set up "run jobs as the real user"
job running capabilities.
> Further more when I want to kill my jobs by clicking
<Catch(08-08-09-12-39).jpg> in galaxy web,the job keeps on running in my
background.I do not know how to fix this.
> Any help on this would be grateful.Thank you very much.
Job deletion in the pbs runner was recently broken, but a fix for this bug
will be part of the next stable release (on Monday).
--nate
>
> shenwiyn
>
> From: Jurgens de Bruin
> Date: 2013-08-07 19:55
> To: galaxy-dev
> Subject: [galaxy-dev] Help with cluster setup
> Hi,
>
> This is my first Galaxy installation setup so apologies for stupid
questions. I am setting up Galaxy on a Cluster running Torque as the
resource manager. I am working through the documentation but I am unclear
on some things:
>
> Firstly I am unable to find : start_job_runners within the
universe_wsgi.ini and I dont want to just add this anywhere - any help on
this would be create.
>
> Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
> </plugins>
> <handlers>
> <!-- Additional job handlers - the id should match the name of a
> [server:<id>] in universe_wsgi.ini.
> <handler id="cn01"/>
> <handler id="cn02"/>
> </handlers>
> <destinations>
> <destination id="hpc" runner="drmaa"/>
> </destinations>
> </job_conf>
>
>
> Does this look meaning full, further more where to I set the additional
server:<id>
> in the universe_wsgi.ini.
>
> As background the cluster has 13 compute nodes and a shared storage
array that can be accessed by all nodes in the cluster.
>
>
> Thanks again
>
>
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
> ___________________________________________________________
> 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/
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
11:48 a.m.
Hi
just to keep things up to date I have the the cluster up and running jobs
are being submitted. Last problem I am facing is:
21: UCSC Main on Pig: refGene (chr18:1-61220071)
error
An error occurred with this dataset: *The remote data source application
may be off line, please try again later. Error: [Errno socket error] [Errno
101] Network is unreachable*
On 13 August 2013 16:53, Jurgens de Bruin <debruinjj(a)gmail.com> wrote:
I am totally lost on what is happening now, I have Galaxy running but
jobs
are not being run:
This is my setup:
torque:
qmgr -c 'p s'
#
# Create queues and set their attributes.
#
#
# Create and define queue batch
#
create queue batch
set queue batch queue_type = Execution
set queue batch resources_default.nodes = 1
set queue batch resources_default.walltime = 01:00:00
set queue batch enabled = True
set queue batch started = True
#
# Set server attributes.
#
set server scheduling = True
set server acl_hosts = manager
set server managers = root@*
set server managers += jurgens@*
set server operators = galaxy@*
set server operators += jurgens@*
set server operators += root@*
set server default_queue = batch
set server log_events = 511
set server mail_from = adm
set server scheduler_iteration = 600
set server node_check_rate = 150
set server tcp_timeout = 300
set server job_stat_rate = 45
set server poll_jobs = True
set server mom_job_sync = True
set server keep_completed = 300
set server next_job_number = 17
set server moab_array_compatible = True
This is my 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="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
-->
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
</plugins>
<handlers default="batch">
<handler id="cn01" tags="batch"/>
<handler id="cn02" tags="batch"/>
</handlers>
<destinations default="batch">
<destination id="batch" runner="drmaa"
tag="cluster,batch">
<param id="nativeSpecfication">-q batch</param>
</destination>
</destinations>
</job_conf>
This is parts of the universe_wsgi.ini
# Configuration of the internal HTTP server.
[server:main]
# The internal HTTP server to use. Currently only Paste is provided. This
# option is required.
use = egg:Paste#http
# The port on which to listen.
port = 8989
# The address on which to listen. By default, only listen to localhost
(Galaxy
# will not be accessible over the network). Use '0.0.0.0' to listen on all
# available network interfaces.
#host = 127.0.0.1
host = 0.0.0.0
# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True
# Number of threads in the web server thread pool.
#threadpool_workers = 10
# Set the number of seconds a thread can work before you should kill it
(assuming it will never finish) to 3 hours.
threadpool_kill_thread_limit = 10800
[server:cn01]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
[server:cn02]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
Where cn01 and cn02 are cluster nodes
echo $DRMAA_LIBRARY_PATH
/usr/local/lib/libdrmaa.so
On 8 August 2013 16:58, Nate Coraor <nate(a)bx.psu.edu> wrote:
> On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
>
> > Yes,and I also have the same confuse about that.Actually when I set
> server:<id> in the universe_wsgi.ini as follows for a try,my Galaxy
doesn't
> work with Cluster,if I remove server:<id>,it work .
>
> Hi Shenwiyn,
>
> Are you starting all of the servers that you have defined in
> universe_wsgi.ini? If using run.sh, setting GALAXY_RUN_ALL in the
> environment will do this for you:
>
> http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
>
> > [server:node01]
> > use = egg:Paste#http
> > port = 8080
> > host = 0.0.0.0
> > use_threadpool = true
> > threadpool_workers = 5
> > This is my job_conf.xml :
> > <?xml version="1.0"?>
> > <job_conf>
> > <plugins workers="4">
> > <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> > <plugin id="pbs" type="runner"
> load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
> > </plugins>
> > <handlers default="batch">
> > <handler id="node01" tags="batch"/>
> > <handler id="node02" tags="batch"/>
> > </handlers>
> > <destinations default="regularjobs">
> > <destination id="local" runner="local"/>
> > <destination id="regularjobs" runner="pbs"
tags="cluster">
> > <param
>
id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
> > <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>
> > </destinations>
> > </job_conf>
>
> The galaxy_external_* options are only supported with the drmaa plugin,
> and actually only belong in the univese_wsgi.ini for the moment, they have
> not been migrated to the new-style job configuration. They should also
> only be used if you are attempting to set up "run jobs as the real user"
> job running capabilities.
>
> > Further more when I want to kill my jobs by clicking
> <Catch(08-08-09-12-39).jpg> in galaxy web,the job keeps on running in my
> background.I do not know how to fix this.
> > Any help on this would be grateful.Thank you very much.
>
> Job deletion in the pbs runner was recently broken, but a fix for this
> bug will be part of the next stable release (on Monday).
>
> --nate
>
> >
> > shenwiyn
> >
> > From: Jurgens de Bruin
> > Date: 2013-08-07 19:55
> > To: galaxy-dev
> > Subject: [galaxy-dev] Help with cluster setup
> > Hi,
> >
> > This is my first Galaxy installation setup so apologies for stupid
> questions. I am setting up Galaxy on a Cluster running Torque as the
> resource manager. I am working through the documentation but I am unclear
> on some things:
> >
> > Firstly I am unable to find : start_job_runners within the
> universe_wsgi.ini and I dont want to just add this anywhere - any help on
> this would be create.
> >
> > Further more this is my 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="hpc" type="runner"
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
> > </plugins>
> > <handlers>
> > <!-- Additional job handlers - the id should match the name of a
> > [server:<id>] in universe_wsgi.ini.
> > <handler id="cn01"/>
> > <handler id="cn02"/>
> > </handlers>
> > <destinations>
> > <destination id="hpc" runner="drmaa"/>
> > </destinations>
> > </job_conf>
> >
> >
> > Does this look meaning full, further more where to I set the additional
> server:<id>
> > in the universe_wsgi.ini.
> >
> > As background the cluster has 13 compute nodes and a shared storage
> array that can be accessed by all nodes in the cluster.
> >
> >
> > Thanks again
> >
> >
> >
> > --
> > Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> > distinti saluti/siong/duì yú/привет
> >
> > Jurgens de Bruin
> > ___________________________________________________________
> > 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/
>
>
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
2:06 p.m.
On Aug 14, 2013, at 7:48 AM, Jurgens de Bruin wrote:
Hi
just to keep things up to date I have the the cluster up and running jobs are being
submitted. Last problem I am facing is:
21: UCSC Main on Pig: refGene (chr18:1-61220071)
error
An error occurred with this dataset: The remote data source application may be off line,
please try again later. Error: [Errno socket error] [Errno 101] Network is unreachable
Hi Jurgens,
Your cluster node will need the ability to connect to the Internet to connect to external
data sources. Many clusters use private IP space and therefore must rely on NAT for a
connection to the greater Internet.
--nate
On 13 August 2013 16:53, Jurgens de Bruin <debruinjj(a)gmail.com> wrote:
I am totally lost on what is happening now, I have Galaxy running but jobs are not being
run:
This is my setup:
torque:
qmgr -c 'p s'
#
# Create queues and set their attributes.
#
#
# Create and define queue batch
#
create queue batch
set queue batch queue_type = Execution
set queue batch resources_default.nodes = 1
set queue batch resources_default.walltime = 01:00:00
set queue batch enabled = True
set queue batch started = True
#
# Set server attributes.
#
set server scheduling = True
set server acl_hosts = manager
set server managers = root@*
set server managers += jurgens@*
set server operators = galaxy@*
set server operators += jurgens@*
set server operators += root@*
set server default_queue = batch
set server log_events = 511
set server mail_from = adm
set server scheduler_iteration = 600
set server node_check_rate = 150
set server tcp_timeout = 300
set server job_stat_rate = 45
set server poll_jobs = True
set server mom_job_sync = True
set server keep_completed = 300
set server next_job_number = 17
set server moab_array_compatible = True
This is my 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="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
-->
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
</plugins>
<handlers default="batch">
<handler id="cn01" tags="batch"/>
<handler id="cn02" tags="batch"/>
</handlers>
<destinations default="batch">
<destination id="batch" runner="drmaa"
tag="cluster,batch">
<param id="nativeSpecfication">-q batch</param>
</destination>
</destinations>
</job_conf>
This is parts of the universe_wsgi.ini
# Configuration of the internal HTTP server.
[server:main]
# The internal HTTP server to use. Currently only Paste is provided. This
# option is required.
use = egg:Paste#http
# The port on which to listen.
port = 8989
# The address on which to listen. By default, only listen to localhost (Galaxy
# will not be accessible over the network). Use '0.0.0.0' to listen on all
# available network interfaces.
#host = 127.0.0.1
host = 0.0.0.0
# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True
# Number of threads in the web server thread pool.
#threadpool_workers = 10
# Set the number of seconds a thread can work before you should kill it (assuming it will
never finish) to 3 hours.
threadpool_kill_thread_limit = 10800
[server:cn01]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
[server:cn02]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
Where cn01 and cn02 are cluster nodes
echo $DRMAA_LIBRARY_PATH
/usr/local/lib/libdrmaa.so
On 8 August 2013 16:58, Nate Coraor <nate(a)bx.psu.edu> wrote:
On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
> Yes,and I also have the same confuse about that.Actually when I set
server:<id> in the universe_wsgi.ini as follows for a try,my Galaxy doesn't work
with Cluster,if I remove server:<id>,it work .
Hi Shenwiyn,
Are you starting all of the servers that you have defined in universe_wsgi.ini? If using
run.sh, setting GALAXY_RUN_ALL in the environment will do this for you:
http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> [server:node01]
> use = egg:Paste#http
> port = 8080
> host = 0.0.0.0
> use_threadpool = true
> threadpool_workers = 5
> This is my job_conf.xml :
> <?xml version="1.0"?>
> <job_conf>
> <plugins workers="4">
> <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> <plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
> </plugins>
> <handlers default="batch">
> <handler id="node01" tags="batch"/>
> <handler id="node02" tags="batch"/>
> </handlers>
> <destinations default="regularjobs">
> <destination id="local" runner="local"/>
> <destination id="regularjobs" runner="pbs"
tags="cluster">
> <param
id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
> <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>
> </destinations>
> </job_conf>
The galaxy_external_* options are only supported with the drmaa plugin, and actually only
belong in the univese_wsgi.ini for the moment, they have not been migrated to the
new-style job configuration. They should also only be used if you are attempting to set
up "run jobs as the real user" job running capabilities.
> Further more when I want to kill my jobs by clicking
<Catch(08-08-09-12-39).jpg> in galaxy web,the job keeps on running in my
background.I do not know how to fix this.
> Any help on this would be grateful.Thank you very much.
Job deletion in the pbs runner was recently broken, but a fix for this bug will be part
of the next stable release (on Monday).
--nate
>
> shenwiyn
>
> From: Jurgens de Bruin
> Date: 2013-08-07 19:55
> To: galaxy-dev
> Subject: [galaxy-dev] Help with cluster setup
> Hi,
>
> This is my first Galaxy installation setup so apologies for stupid questions. I am
setting up Galaxy on a Cluster running Torque as the resource manager. I am working
through the documentation but I am unclear on some things:
>
> Firstly I am unable to find : start_job_runners within the universe_wsgi.ini and I
dont want to just add this anywhere - any help on this would be create.
>
> Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
> </plugins>
> <handlers>
> <!-- Additional job handlers - the id should match the name of a
> [server:<id>] in universe_wsgi.ini.
> <handler id="cn01"/>
> <handler id="cn02"/>
> </handlers>
> <destinations>
> <destination id="hpc" runner="drmaa"/>
> </destinations>
> </job_conf>
>
>
> Does this look meaning full, further more where to I set the additional
server:<id>
> in the universe_wsgi.ini.
>
> As background the cluster has 13 compute nodes and a shared storage array that can
be accessed by all nodes in the cluster.
>
>
> Thanks again
>
>
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
> ___________________________________________________________
> 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/
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
___________________________________________________________
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/
8:20 a.m.
Hi Nate,
From your previous email,Job deletion in the pbs runner will be fixed
in
the next stable release Galaxy.So whether this bug has been fixed in the
version of Galaxy(
https://bitbucket.org/galaxy/galaxy-dist/get/3b3365a39194.zip)?Thank you
very much for your help.
Regards,weiyan
2013-08-08 22:58 GMT+08:00 Nate Coraor <nate(a)bx.psu.edu>:
On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
> Yes,and I also have the same confuse about that.Actually when I set
server:<id> in the universe_wsgi.ini as follows for a try,my Galaxy doesn't
work with Cluster,if I remove server:<id>,it work .
Hi Shenwiyn,
Are you starting all of the servers that you have defined in
universe_wsgi.ini? If using run.sh, setting GALAXY_RUN_ALL in the
environment will do this for you:
http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> [server:node01]
> use = egg:Paste#http
> port = 8080
> host = 0.0.0.0
> use_threadpool = true
> threadpool_workers = 5
> This is my job_conf.xml :
> <?xml version="1.0"?>
> <job_conf>
> <plugins workers="4">
> <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> <plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
> </plugins>
> <handlers default="batch">
> <handler id="node01" tags="batch"/>
> <handler id="node02" tags="batch"/>
> </handlers>
> <destinations default="regularjobs">
> <destination id="local" runner="local"/>
> <destination id="regularjobs" runner="pbs"
tags="cluster">
> <param
id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
> <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>
> </destinations>
> </job_conf>
The galaxy_external_* options are only supported with the drmaa plugin,
and actually only belong in the univese_wsgi.ini for the moment, they have
not been migrated to the new-style job configuration. They should also
only be used if you are attempting to set up "run jobs as the real user"
job running capabilities.
> Further more when I want to kill my jobs by clicking
<Catch(08-08-09-12-39).jpg> in galaxy web,the job keeps on running in my
background.I do not know how to fix this.
> Any help on this would be grateful.Thank you very much.
Job deletion in the pbs runner was recently broken, but a fix for this bug
will be part of the next stable release (on Monday).
--nate
>
> shenwiyn
>
> From: Jurgens de Bruin
> Date: 2013-08-07 19:55
> To: galaxy-dev
> Subject: [galaxy-dev] Help with cluster setup
> Hi,
>
> This is my first Galaxy installation setup so apologies for stupid
questions. I am setting up Galaxy on a Cluster running Torque as the
resource manager. I am working through the documentation but I am unclear
on some things:
>
> Firstly I am unable to find : start_job_runners within the
universe_wsgi.ini and I dont want to just add this anywhere - any help on
this would be create.
>
> Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
> </plugins>
> <handlers>
> <!-- Additional job handlers - the id should match the name of a
> [server:<id>] in universe_wsgi.ini.
> <handler id="cn01"/>
> <handler id="cn02"/>
> </handlers>
> <destinations>
> <destination id="hpc" runner="drmaa"/>
> </destinations>
> </job_conf>
>
>
> Does this look meaning full, further more where to I set the additional
server:<id>
> in the universe_wsgi.ini.
>
> As background the cluster has 13 compute nodes and a shared storage
array that can be accessed by all nodes in the cluster.
>
>
> Thanks again
>
>
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
> ___________________________________________________________
> 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/
7:28 p.m.
On Wed, Apr 30, 2014 at 4:20 AM, 沈维燕 <shenwiyn(a)gmail.com> wrote:
Hi Nate,
From your previous email,Job deletion in the pbs runner will be fixed in
the next
stable release Galaxy.So whether this bug has been fixed in the
version of Galaxy(
https://bitbucket.org/galaxy/galaxy-dist/get/3b3365a39194.zip)?Thank you
very much for your help.
Regards,weiyan
Hi Weiyan,
Yes, this fix is included in the April, 2014 stable release. However, I
would strongly encourage you to use `hg clone` rather than downloading a
static tarball. There have been a number of patches to the stable branch
since its April release. In addition, the tarball linked would pull from
the "default" branch of Galaxy, which includes unstable changesets.
--nate
2013-08-08 22:58 GMT+08:00 Nate Coraor <nate(a)bx.psu.edu>:
>
> On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
>
> > Yes,and I also have the same confuse about that.Actually when I set
server:<id> in the universe_wsgi.ini as follows for a try,my Galaxy
doesn't
work with Cluster,if I remove server:<id>,it work .
>
> Hi Shenwiyn,
>
> Are you starting all of the servers that you have defined in
universe_wsgi.ini?
If using run.sh, setting GALAXY_RUN_ALL in the
environment will do this for you:
>
> http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
>
> > [server:node01]
> > use = egg:Paste#http
> > port = 8080
> > host = 0.0.0.0
> > use_threadpool = true
> > threadpool_workers = 5
> > This is my job_conf.xml :
> > <?xml version="1.0"?>
> > <job_conf>
> > <plugins workers="4">
> > <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner"
workers="4"/>
> > <plugin id="pbs"
type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner"
workers="8"/>
> > </plugins>
> > <handlers default="batch">
> > <handler id="node01" tags="batch"/>
> > <handler id="node02" tags="batch"/>
> > </handlers>
> > <destinations default="regularjobs">
> > <destination id="local" runner="local"/>
> > <destination id="regularjobs" runner="pbs"
tags="cluster">
> > <param
id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
> > <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>
> > </destinations>
> > </job_conf>
>
> The galaxy_external_* options are only supported with the drmaa plugin,
and
actually only belong in the univese_wsgi.ini for the moment, they have
not been migrated to the new-style job configuration. They should also
only be used if you are attempting to set up "run jobs as the real user"
job running capabilities.
>
> > Further more when I want to kill my jobs by clicking
<Catch(08-08-09-12-39).jpg> in galaxy web,the job keeps on running in my
background.I do not know how to fix this.
> > Any help on this would be grateful.Thank you very much.
>
> Job deletion in the pbs runner was recently broken, but a fix for this
bug will
be part of the next stable release (on Monday).
>
> --nate
>
> >
> > shenwiyn
> >
> > From: Jurgens de Bruin
> > Date: 2013-08-07 19:55
> > To: galaxy-dev
> > Subject: [galaxy-dev] Help with cluster setup
> > Hi,
> >
> > This is my first Galaxy installation setup so apologies for stupid
questions. I am setting up Galaxy on a Cluster running Torque as the
resource manager. I am working through the documentation but I am unclear
on some things:
> >
> > Firstly I am unable to find : start_job_runners within the
universe_wsgi.ini and I dont want to just add this anywhere - any help on
this would be create.
> >
> > Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"
workers="4"/>
> > </plugins>
> > <handlers>
> > <!-- Additional job handlers - the id should match the name of a
> > [server:<id>] in universe_wsgi.ini.
> > <handler id="cn01"/>
> > <handler id="cn02"/>
> > </handlers>
> > <destinations>
> > <destination id="hpc" runner="drmaa"/>
> > </destinations>
> > </job_conf>
> >
> >
> > Does this look meaning full, further more where to I set the
additional
server:<id>
> > in the universe_wsgi.ini.
> >
> > As background the cluster has 13 compute nodes and a shared storage
array
that can be accessed by all nodes in the cluster.
> >
> >
> > Thanks again
> >
> >
> >
> > --
> > Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures
salutations/
> > distinti saluti/siong/duì yú/привет
> >
> > Jurgens de Bruin
> > ___________________________________________________________
> > 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/
>
2:53 p.m.
On Aug 7, 2013, at 7:55 AM, Jurgens de Bruin wrote:
Hi,
This is my first Galaxy installation setup so apologies for stupid questions. I am
setting up Galaxy on a Cluster running Torque as the resource manager. I am working
through the documentation but I am unclear on some things:
Firstly I am unable to find : start_job_runners within the universe_wsgi.ini and I dont
want to just add this anywhere - any help on this would be create.
Hi Jurgens,
This option was removed from universe_wsgi.ini, the job handler definitions are done via
the job_conf.xml file now. The following page explains that syntax:
http://wiki.galaxyproject.org/Admin/Config/Jobs
However, the scaling page was still for the old style of configuration, so I have just
updated it for the new style:
http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
Further more this is my 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="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
</plugins>
<handlers>
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini.
<handler id="cn01"/>
<handler id="cn02"/>
</handlers>
<destinations>
<destination id="hpc" runner="drmaa"/>
</destinations>
</job_conf>
You'll need to set a default handler. Try the following config:
<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="hpc" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
</plugins>
<handlers default="handlers">
<handler id="cn01" tags="handlers"/>
<handler id="cn02" tags="handlers"/>
</handlers>
<destinations>
<destination id="hpc" runner="drmaa"/>
</destinations>
</job_conf>
Does this look meaning full, further more where to I set the
additional server:<id>
in the universe_wsgi.ini.
You can add them anywhere between existing sections, although I'd do it near the top
of the file, above the [app:main] section. Assuming you leave [server:main] in, you could
add the following definitions just above [app:main]:
[server:cn01]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
[server:cn02]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
Web requests would still be handled by the server configured with the host:port in
[server:main].
--nate
As background the cluster has 13 compute nodes and a shared storage array that can be
accessed by all nodes in the cluster.
Thanks again
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
___________________________________________________________
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/
3203
days inactive
3470
days old
galaxy-dev@lists.galaxyproject.org
8 comments
4 participants
participants (4)
-
Jurgens de Bruin -
Nate Coraor -
shenwiyn -
沈维燕