Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

submit does not work on SGE #57

Open
jdidion opened this issue Nov 17, 2014 · 2 comments
Open

submit does not work on SGE #57

jdidion opened this issue Nov 17, 2014 · 2 comments

Comments

@jdidion
Copy link

jdidion commented Nov 17, 2014

From what I can gather, jip submits jobs to SGE by calling qsub with its arguments and then passing "exec jip exec --db " on stdin. This does not work, at least on the version of SGE installed on our cluster. The job just ends up in the Eqw state. It seems like a much better option is just to call qsub with the -b y option and then pass the jip exec command on the command line. The fix described below works.

Add the following method to db.py/Job:

def get_cluster_command_list(self):
    """Returns the command that should send to the
    cluster to run this job as a list of arguments.

    :returns: list
    """
    if db_in_memory or db_path is None:
        return ["jip", "exec", str(self.id)]
    else:
        return ["jip", "exec", "--db", db_path, str(self.id)]

Then change cluster.py/SGE.submit:

job_cmd = job.get_cluster_command_list()
...
cmd.extend(["-b", "y"])
process = Popen(cmd + job_cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE)

@thasso
Copy link
Owner

thasso commented Jan 2, 2015

@emi80 I don't have a access to a real world SGE implementation :( Can you confirm that you have the -b command line option as well? If its version dependent we might need to add some configuration option.

@emi80
Copy link
Collaborator

emi80 commented Jan 7, 2015

@thasso I also have the -b option in our SGE (univa 8.2 as you can see below):

$ gsub -help
UGE 8.2.0
usage: qsub [options]
   ...
   [-b y[es]|n[o]]                          handle command as binary
   ...

I think that also the Open Grid Scheduler SGE implementation has the -b option even if I cannot check.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants