Re: Cluster jobs running as real user

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Re: Cluster jobs running as real user

Linda Cham

Follow the Galaxy wiki https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User  setup permission instructions.

Follow these 2 steps to get Galaxy to run as real users with IBM Platform LSF:

Step 1) Download the latest LSF DRMAA 1.1.1 from github.


Step 2) LSF needs to disable message being printed out via the LSF environment variable "BSUB_QUIET". This can be done either in in Galaxy drmaa_external_runner.py file or in the galaxy admin environment profile
  • Edit the drmaa_external_runner.py file to add in the LSF environment variable  "BSUB_QUIET" to disable message print out.  Line in blue below.

        scripts/drmaa_external_runner.py:
    def main():
        userid, json_filename, assign_all_groups = validate_paramters()
        set_user(userid, assign_all_groups)
        json_file_exists(json_filename)
        os.environ['BSUB_QUIET'] = 'Y'
        s = drmaa.Session()
        s.initialize()
        jt = s.createJobTemplate()
        load_job_template_from_file(jt, json_filename)

OR
  • Disable LSF message in the galaxy admin profile

    e.g.
     export BSUB_QUIET=Y in .bash_profile


Regards,
Linda

___________________________________________________________
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/