PCIC PBS Job Queueing Tool

Purpose

The PCIC PBS Job Queueing tool (hereafter, JQ) is a command-line tool for managing and recording the submission of jobs to the PCIC compute nodes via PBS.

PBS (qsub et al.) is a third-party tool that manages queueing and running of jobs on the PCIC compute nodes. Even alone, PBS is very useful, but we have some additional requirements that are not directly met by it:

• Submit similar jobs (scripts) repeatedly with varying parameters (e.g, files to be processed).
• Record the fact and outcome of each such job permanently.

The solution is centered on a database that manages and records submissions to the PBS queue. Since adding something to the database does not have to cause it to be submitted immediately (nor is that necessarily desirable), JQ is effectively a "queue for a queue" in addition to its function as a record-keeping service.

Installation

Easy

Create and activate a Python virtual environment:

$ python3 -m venv venv
$ venv/bin/activate
(venv) $ pip install --upgrade pip

Install JQ from our pypi:

(venv) $ pip install -i https://pypi.pacificclimate.org/simple/ jobqueueing

Geeky

Clone the project repository from github:

$ git clone git@github.com:pacificclimate/jobqueueing.git

As usual, it is best to install JQ in a Python virtual environment:

$ cd jobqueueing
$ python3 -m venv venv
$ venv/bin/activate
(venv) $ pip install --upgrade pip
(venv) $ pip install .

Verify

This installs the jq command-line script. Verify installation by running:

(venv) $ jq --help

Configuration

There's little to configure in JQ, just a couple of environment variables and those all optional:

• JQ_DATABASE: The Job Queueing database to run against. There are at present two standard databases set up on the gluster storage nodes. The location of these databases may change in future (but will remain on gluster).

  • /storage/data/projects/comp_support/climate_exporer_data_prep/climatological_means/jobqueue-prod.sqlite
  • /storage/data/projects/comp_support/climate_exporer_data_prep/climatological_means/jobqueue-climdex.sqlite
  • /storage/data/projects/comp_support/climate_exporer_data_prep/climatological_means/jobqueue-test.sqlite

  The test database (jobqueue-test.sqlite) is exclusively for testing JQ, and should not be used for normal operations.

• JQ_PY_VENV: The Python virtual environment in which to run the script submitted to PBS.

  This variable, if set, determines the default value for the jq add option -P / --py-venv.

  (This is not necessarily the same as the virtual environment you are running JQ from! You can run JQ from the predefined environments below, because for convenience they have JQ installed as well as generate_climos.)

There are a predefined environments suitable for JQ jobs at

• /storage/data/projects/comp_support/climate_exporer_data_prep/climatological_means/venv
• /storage/data/projects/comp_support/climate_exporer_data_prep/climatological_means/venv_climdex

which should be used in most cases.

In short, your JQ configuration should normally be:

$ export JQ_DATABASE=/storage/data/projects/comp_support/climate_explorer_data_prep/climatological_means/jobqueue-prod.sqlite
$ export JQ_PY_VENV=/storage/data/projects/comp_support/climate_explorer_data_prep/climatological_means/venv

Usage

JQ commands are all of the form:

jq [<global options>] <action> [<action options>]

To find out what the options and actions are, run:

(venv) $ jq -h

To find out the options for specific actions, run:

(venv) $ jq <action> -h

Actions overview

The actions available are, in alphabetical order:

Action	Effect
add	Add a file to the queue for processing with generate_climos
alter-params	Update entries with generate_climos params and PBS params (but not status). Updated entry must be in status NEW. WARNING: ANY entry that partially matches the input filename is updated.
hold	Set entries in generate_climos queue from NEW to HOLD status
unhold	Set entries in generate_climos queue from HOLD to NEW status
list	List entries in generate_climos queue
reset	Reset the status of a queue entry
script	Write to stdout the script that will be or was submitted by jq submit for a specified queue entry.
submit	Dequeue one or more generate_climos queue entries with NEW status, and submit a PBS job for each, updating the queue entries accordingly.
summarize	Summarize entries in generate_climos queue (generate statistics)
update-qstat	Update generate_climos queue using PBS qstat

JQ workflow

States

A JQ job is always in one of the following states (see "States and actions" for details):

• NEW
• HOLD
• SUBMITTED
• RUNNING
• SUCCESS
• ERROR

Happy path workflow

The typical, no-errors workflow is as follows:

State	Action	Note
no queue entry	jq add
NEW	jq submit
SUBMITTED	jq update-qstat
RUNNING	jq update-qstat	This state entered only if update done while job actually running
SUCCESS		Job completed, data available

States and actions

This section describes the workflow for JQ. It describes the various states defined for JQ entries, and the actions that cause transitions from one state to another. The general format is

<JQ STATE>

description

Action: Something that causes transition to another state

jq <action>

--> <NEXT JQ STATE>

The JQ workflow is:

[no queue entry]

Action: Add to queue

jq add

--> new JQ entry with status NEW

NEW

Job exists in JQ but has not been submitted to PBS.

Action: Submit job to PBS

jq submit

--> SUBMITTED

Action: Hold job (place in HOLD status)

jq hold

--> HOLD

HOLD

Job is not elegible for submission. Use this status to segregate jobs that for some reason you do not want to submit. (Submission is usually bulk and/or non-job-specific, in order of jq add -ing.)

Action: Unhold (place in NEW status)

jq unhold or jq reset

--> NEW

SUBMITTED

Job has been submitted to PBS. Actual state of PBS job is unknown. The JQ state can be updated to reflect the PBS state by manual actions, see below.

Now there is also a PBS status for the job, but it is not updated dynamically in JQ.

Action: Update status while PBS job is running

jq update-qstat

--> RUNNING

Action: Update status after PBS job has terminated with success

jq update-qstat

--> SUCCESS

Action: Update status after PBS job has terminated with error

jq update-qstat

--> ERROR

Action: Reset (place job in NEW status).

Note: This makes the job elegible for submission again, but it removes any information about past submits.

jq reset

--> NEW

RUNNING

Job has been submitted to PBS, and PBS job is known to be running.

Action: Update status after PBS job has terminated with success

jq update-qstat

--> SUCCESS

Action: Update status after PBS job has terminated with error

jq update-qstat

--> ERROR

SUCCESS

Job has been submitted to PBS, and PBS job completed normally.

Action: Reset (place job in NEW status).

Note: This makes the job elegible for submission again, but it removes any information about past submits.

jq reset

--> NEW

ERROR

Job has been submitted to PBS, and PBS job errored.

Action: Reset (place job in NEW status).

Note: This makes the job elegible for submission again, but it removes any information about past submits.

jq reset

--> NEW

jq submit and the work script

Most of JQ is just scaffolding to support what jq submit does, which is to submit a script that causes the real work (generating climatological means) to be done on a compute node.

TL;DR

Here's where the data ends up:

• logs: <output dir>/logs/
• output files: <output dir>/<pbs job num>/
• temporary input files: $TMPDIR/climo/input
• temporary output files: $TMPDIR/climo/output/<pbs job num>/

Details

The script submitted does the following things:

1. Set PBS options based on queue entry values:
   • processes per node (ppn)
   • virtual memory allocation (automatically computed from ppn)
   • walltime
   • stdout and stderr logs directed to logs/ subdirectory of specified output directory
   • email notification
   • name generate_climos:<input filename>
2. Set up the execution environment.
   • Load modules netcdf-bin, cdo-bin.
   • Activate the Python virtual environment specified for this queue entry.
3. Copy the input NetCDF file to $TMPDIR/climo/input.
4. Set up the output directory structure in $TMPDIR.
   • Base output directory for all outputs from this type of job is $TMPDIR/climo/output.
   • Files containing climatological means generated in this particular PBS job are placed in $TMPDIR/climo/output/$pbs_job_num, where pbs_job_num is the job number (e.g., 1234) extracted from the PBS job id for this job.
5. Generate climatological means.
   • Invoke generate_climos with the appropriate options and arguments.
6. Copy result file to final destination and remove temporary input file
   • Use rsync to update the final destination directory (specified for this queue entry) with the files created in the temporary directory. This causes the job id subdirectories to be replicated in the final destination directory, as well as the output files they contain.
   • Remove the temporary input file from $TMPDIR/climo/input.
   • Since the output files are relatively small, we don't remove them from the temporary output directory, so that we have a fallback if something goes wrong with the rsync.

Releasing

To create a versioned release:

1. Increment __version__ in setup.py

2. Summarize the changes from the last release in NEWS.md

3. Commit these changes, then tag the release:

   git add setup.py NEWS.md
   git commit -m"Bump to version x.x.x"
   git tag -a -m"x.x.x" x.x.x
   git push --follow-tags