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 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: blood@psc.edu

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