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: bl...@psc.edu
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