gridtk 1.1.3

Submitting a simple job

To interact with the Job Manager we use the jman utility. Make sure to have your shell environment setup to reach it w/o requiring to type-in the full path. The first task you may need to pursue is to submit jobs. Here is how:

$ jman -vv submit myscript.py --help
... Added job '<Job: 1> : submitted -- /usr/bin/python myscript.py --help' to the database
... Submitted job '<Job: 6151645> : queued -- /usr/bin/python myscript.py --help' to the SGE grid.

Submitting a parametric job

Parametric or array jobs are jobs that execute the same way, except for the environment variable SGE_TASK_ID, which changes for every job. This way, your program controls, which bit of the full job has to be executed in each (parallel) instance. It is great for forking thousands of jobs into the grid.

The next example sends 10 copies of the myscript.py job to the grid with the same parameters. Only the variable SGE_TASK_ID changes between them:

$ jman -vv submit -t 10 myscript.py --help
... Added job '<Job: 2> : submitted -- /usr/bin/python myscript.py --help' to the database
... Submitted job '<Job: 6151646> : queued -- /usr/bin/python myscript.py --help' to the SGE grid.

The -t option in jman accepts different kinds of job array descriptions. Have a look at the help documentation for details with jman --help.

Probing for jobs

Once the job has been submitted you will noticed a database file (by default called submitted.sql3) has been created in the current working directory. It contains the information for the job you just submitted:

$ jman list

       job-id           queue        status            job-name                 dependencies                      submitted command line
====================  =========  ==============  ====================  ==============================  ===========================================
      6151645           all.q        queued             None                        []                 /usr/bin/python myscript.py --help
  6151646 [1-10:1]      all.q        queued             None                        []                 /usr/bin/python myscript.py --help

From this dump you can see the SGE job identifier including the number of array jobs, the queue the job has been submitted to, the current status of the job in the SGE grid, the dependencies of the job and the command that was executed in the SGE grid. The list command from jman will show the current status of the job, which is updated automatically as soon as the grid job finishes. Several calls to list might end up in

Submitting dependent jobs

Sometimes, the execution of one job might depend on the execution of another job. The JobManager can take care of this, simply by adding the id of the job that we have to wait for:

$ jman -vv submit --dependencies 6151645 -- /usr/bin/python myscript.py --help
... Added job '<Job: 3> : submitted -- /usr/bin/python myscript.py --help' to the database
... Submitted job '<Job: 6151647> : queued -- /usr/bin/python myscript.py --help' to the SGE grid.

Now, the new job will only be run after the first one finished.

Inspecting log files

If jobs finish, the result of the executed job will be shown in the list. In case it is non-zero, might want to inspect the log files as follows:

$ jman report --errors-only
...
<Job: 6151646  - 'jman'> : failure (2) -- /usr/bin/python myscript.py --help
/usr/bin/python: can't open file 'myscript.py': [Errno 2] No such file or directory

Hopefully, that helps in debugging the problem!

Re-submitting the job

If you are convinced the job did not work because of external conditions (e.g. temporary network outage), you may re-submit it, exactly like it was submitted the first time:

$ jman -vv resubmit --job-id 6151645
... Deleting job '6151645'
... Submitted job '<Job: 6151673> : queued -- /usr/bin/python myscript.py --help' to the SGE grid.

By default, the log files of the old job are deleted during re-submission. If for any reason you want to keep the old log files, use the --keep-logs option. Notice the new job identifier has changed as expected.

Stopping a grid job

In case you found an error in the code of a grid job that is currently executing, you might want to kill the job in the grid. For this purpose, you can use the command:

$ jman stop

The job is removed from the grid, but all log files are still available. A common use case is to stop the grid job, fix the bugs, and re-submit it.

Cleaning-up

If the job in question will not work no matter how many times we re-submit it, you may just want to clean it up and do something else. The Job Manager is here for you again:

$ jman -vvv delete
... Deleting job '8258327' from the database.

In case, jobs are still running or queued in the grid, they will be stopped before they are removed from the database. By default, all logs will be deleted with the job. Inspection on the current directory will now show you everything concerning the jobs is gone.

Running jobs on the local machine

The JobManager is designed such that it supports mainly the same infrastructure when submitting jobs locally or in the SGE grid. To submit jobs locally, just add the --local option to the jman command:

$ jman --local -vv submit /usr/bin/python myscript.py --help

One important difference to the grid submission is that the jobs that are submitted to the local machine do not run immediately, but are only collected in the submitted.sql3 database. To run the collected jobs using 4 parallel processes, simply use:

$ jman --local -vv run-scheduler --parallel 4

and all jobs that have not run yet are executed, keeping an eye on the dependencies.

Another difference is that by default, the jobs write their results into the command line and not into log files. If you want the log file behavior back, specify the log directory during the submission:

$ jman --local -vv submit --log-dir logs myscript.py --help

Of course, you can choose a different log directory (also for the SGE submission).

Furthermore, the job identifiers during local submission usually start from 1 and increase. Also, during local re-submission, the job ID does not change.

Using the local machine for debugging

One possible use case for the local job submission is the re-submission of jobs to the local machine. In this case, you might re-submit the grid job locally:

$ jman --local -vv resubmit --job-id 6151646 --keep-logs

(as mentioned above, no new ID is assigned) and run the local scheduler:

$ jman --local -vv run-scheduler --no-log-files --job-ids 6151646

to print the output and the error to console instead of to log files.