I hope John can give some more input on this,
but if you're really short on time you could try the ssh runner
directly from galaxy without pulsar. I'm very happy with this driving a
Torque 4 cluster.
The relevant part of my job_conf.xml looks like this:
```
<destination id="bicalc" runner="cli">
<param id="shell_plugin">SecureShell</param>
<param id="job_plugin">Torque</param>
<param id="shell_username">myusername</param>
<param id="shell_hostname">submitnode.curie.fr</param>
<param
id="job_Resource_List">walltime=2:00:00,nodes=1:ppn=8,mem=32gb</param>
<param id="remote_metadata">true</param>
<env
file="/bioinfo/guests/mvandenb/galaxy/.venv/bin/activate" />
</destination>
```
You'll only have to be able to do a passwordless ssh login using your
galaxy user.
Best,
Marius
On 01/12/2016 15:35, Philip Blood wrote:
Hi Folks,
I'm working on a time-sensitive project (just a day or two left to
sort it out) that requires I be able to submit jobs from a remote
resource (TACC) to my resources (Pittsburgh Supercomputing Center)
using a shared filesystem for data rather than staging via Pulsar.
I've tried to set it up so that Pulsar does not do any staging, but is
just handling the remote job submission and tool dependencies.
However, Pulsar continues to use a local staging directory for the
data and then copies the data back to the Galaxy directory.
What I'm hoping to do is have all the data stay in the shared
filesystem for the entire course of the job. The quick test below does
not have input data, but just issues commands on the remote compute
node and generates output.
I'm using latest stable releases of Galaxy (16.07, installed on a TACC
VM) and Pulsar (installed via pip at PSC). If anyone can provide some
quick pointers I'd appreciate it.
Here are relevant parts of my configuration and some of the log output:
_Shared filesystem:_ /hopper
*_Local staging dir created by
Pulsar:_* /usr/local/packages/pulsar/etc/files/staging
*_galaxy.ini_*
file_path = /hopper/sy3l67p/blood/galaxy_home/database/files
new_file_path = /hopper/sy3l67p/blood/galaxy_home/database/tmp
job_working_directory =
/hopper/sy3l67p/blood/galaxy_home/database/job_working_directory
tool_dependency_dir =
/hopper/sy3l67p/blood/galaxy_home/database/dependencies
dependency_resolvers_config_file =
/hopper/sy3l67p/blood/galaxy_home/config/dependency_resolvers_conf.xml
*_job_conf.xml
_*
<destination id="pulsar" runner="pulsar_rest">
<param id="url">https://128.182.99.126:8913/</param>
<param id="default_file_action">none</param>
<param
id="file_action_config">/home/tg455546/galaxy/config/file_actions.yaml</param>
<param id="dependency_resolution">remote</param>
<param id="submit_native_specification">-q batch</param>
</destination>
*_file_actions.yml_*
paths:
# If Galaxy, the Pulsar, and the compute nodes all mount the same
directory
# staging can be disabled altogether for given paths.
- path: /hopper/sy3l67p/blood/galaxy_home/database/files
action: none
- path: /hopper/sy3l67p/blood/galaxy_home/database/job_working_directory
action: none
*_app.yml_*
---
manager:
type: queued_drmaa
dependency_resolvers_config_file:
/usr/local/packages/pulsar/etc/dependency_resolvers_conf.xml
tool_dependency_dir: /usr/local/packages/pulsar/dependencies
*_Galaxy paster.log_*
galaxy.jobs <http://galaxy.jobs> DEBUG 2016-12-01 08:07:35,770 (50)
Working directory for job is:
/hopper/sy3l67p/blood/galaxy_home/database/job_working_directory\
/000/50
pulsar.client.staging.down INFO 2016-12-01 08:08:08,305 collecting
output output with action FileAction[action_type=copy]
pulsar.client.client DEBUG 2016-12-01 08:08:08,814 Copying path
[/usr/local/packages/pulsar/etc/files/staging/50/working/output] to
[/hopper/\
sy3l67p/blood/galaxy_home/database/files/000/dataset_50.dat]
*_Pulsar uwsgi.log_*
2016-12-01 09:07:38,174 INFO
[pulsar.managers.base.base_drmaa][[manager=_default_]-[action=preprocess]-[job=50]]
Submitting DRMA\
A job with nativeSpecification [-q batch]
t #78bc [ 539.97] -> drmaa_allocate_job_template
t #78bc [ 539.97] <- drmaa_allocate_job_template =0: jt=0x7f69cc002f80
t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80,
name='drmaa_remote_command', value='/usr/local/packages/pulsar/etc/\
files/staging/50/command.sh')
t #78bc [ 539.97] ->
fsd_template_set_attr(drmaa_remote_command=/usr/local/packages/pulsar/etc/files/staging/50/command.sh)
t #78bc [ 539.97] <- drmaa_set_attribute =0
t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80,
name='drmaa_output_path', value=':/usr/local/packages/pulsar/etc/fi\
les/staging/50/stdout')
t #78bc [ 539.97] ->
fsd_template_set_attr(drmaa_output_path=:/usr/local/packages/pulsar/etc/files/staging/50/stdout)
t #78bc [ 539.97] <- drmaa_set_attribute =0
t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80,
name='drmaa_job_name', value='pulsar_50')
t #78bc [ 539.97] -> fsd_template_set_attr(drmaa_job_name=pulsar_50)
t #78bc [ 539.97] <- drmaa_set_attribute =0
t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80,
name='drmaa_error_path', value=':/usr/local/packages/pulsar/etc/fil\
es/staging/50/stderr')
t #78bc [ 539.97] ->
fsd_template_set_attr(drmaa_error_path=:/usr/local/packages/pulsar/etc/files/staging/50/stderr)
t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80,
name='drmaa_native_specification', value='-q batch')
t #78bc [ 539.97] ->
fsd_template_set_attr(drmaa_native_specification=-q batch)
t #78bc [ 539.97] <- drmaa_set_attribute =0
t #78bc [ 539.97] -> drmaa_run_job(jt=0x7f69cc002f80)
t #78bc [ 539.97] -> pbsdrmaa_session_run_impl(jt=0x7f69cc002f80,
bulk_idx=-1)
t #78bc [ 539.97] -> fsd_template_set_attr(Checkpoint=u)
t #78bc [ 539.97] -> fsd_template_set_attr(Keep_Files=n)
t #78bc [ 539.97] -> fsd_template_set_attr(Priority=0)
t #78bc [ 539.97] -> pbsdrmaa_write_tmpfile
t #78bc [ 539.97] <- pbsdrmaa_write_tmpfile=/tmp/pbs_drmaa.n6VpuR
t #78bc [ 539.97] -> fsd_template_set_attr(Job_Name=pulsar_50)
t #78bc [ 539.97] ->
fsd_template_set_attr(Output_Path=/usr/local/packages/pulsar/etc/files/staging/50/stdout)
t #78bc [ 539.97] ->
fsd_template_set_attr(Error_Path=/usr/local/packages/pulsar/etc/files/staging/50/stderr)
t #78bc [ 539.97] ->
fsd_template_set_attr(Variable_List=PBS_O_WORKDIR=/usr/local/packages/pulsar/etc)
t #78bc [ 539.97] ->
pbsdrmaa_submit_apply_native_specification({native_specification=(null)})
d #78bc [ 539.97] * self->destination_queue = batch
t #78bc [ 539.97] -> fsd_template_set_attr(submit_args=-q batch)
d #78bc [ 539.97] * set attr: submit_args = -q batch
d #78bc [ 539.97] * set attr: Job_Name = pulsar_50
d #78bc [ 539.97] * set attr: Variable_List =
PBS_O_WORKDIR=/usr/local/packages/pulsar/etc
d #78bc [ 539.97] * set attr: Priority = 0
d #78bc [ 539.97] * set attr: Output_Path =
/usr/local/packages/pulsar/etc/files/staging/50/stdout
d #78bc [ 539.97] * set attr: Keep_Files = n
d #78bc [ 539.97] * set attr: Error_Path =
/usr/local/packages/pulsar/etc/files/staging/50/stderr
d #78bc [ 539.97] * set attr: Checkpoint = u
2016-12-01 09:08:06,707 INFO
[pulsar.client.staging.down][[manager=_default_]-[action=postprocess]-[job=50]]
collecting output o\
utput with action FileAction[action_type=copy]
2016-12-01 09:08:06,708 INFO
[pulsar.managers.stateful][[manager=_default_]-[action=postprocess]-[job=50]]
Status of job [50] ch\
anged to [complete]. No callbacks enabled.
--
Philip D. Blood, Ph.D.
Senior Computational Scientist Voice: (412) 268-9329
Pittsburgh Supercomputing Center Fax: (412) 268-5832
Carnegie Mellon University Email: [email protected]
<mailto:[email protected]>
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