Job submission on OSG Connect

Overview

In this section, we will learn the basics of HTCondor in submitting and monitoring workloads, or “jobs”. The jobs are submitted through the login node of OSG Connect. The submitted jobs are executed on the remote worker node(s) and the outputs are transfered back to the login node. In the HTCondor job submit file, we have to describe how to execute the program and transfer the output data.

Login to OSG Connect

First, we log in to OSG Connect:

$ ssh username@login.osgconnect.net  # username is your username
password:                            # enter your password

Let’s introduce two commands that will be useful throughout your OSG Connect usage: connect and tutorial.

Connect is a single interface to tools that enhance or simplify your use of the OSG Connect platform. We occasionally add components to this command to provide new capabilities, or to make common tasks easier. Let’s look at usage:

$ connect
usage: connect <subcommand> [args]
       connect addsite user@hostname sched-type
       connect cclog
       connect debug
       connect histogram [-l | --last] [user]
       connect project
       connect reset
       connect setup
       connect show-projects [-u username] [projectname]
       connect status [-f | --full]
       connect submit
       connect watch [seconds [user]]

Each of these subcommands has a specific role, and we’ll explore some of them during this workshop. Fow now, just take a look at two:

$ connect show-projects
Based on your username (username), here is a list of projects you have
access to:
  * MiniWorkshopUC15

Each time you run a workload on OSG Connect, you need a project name to associate it. For your research work later on, we can get you started with a permanent project, but for now you should find the SWC-OSG-IU15 project available. Some of you might also find the ConnectTrain project listed – that is OK but not necessary.

$ connect project

If you’re a heavy user of OSG Connect, you may end up with multiple projects. connect project is a way both to see your available projects, and to change which project is used for your job submission. Your choice here is saved, so whatever project you selected most recently is used for all future workloads, until you change it again.

A little more about projects

Every user should start out with a reasonable project – it’s not necessary to change your project to get started computing. Once you’re ready to begin research on OSG, there are two routes: join an existing project, or create a new one.
To join a current project, take a look at the current projects list. If your research is represented by one of these existing projects, click its name to open a request to join it.
Otherwise, you can create a new project. Begin with the new project documentation - you may wish to sign on your advisor as a principal investigator.

The second command to learn up front is tutorial. We will get our example files for all today’s lessons using tutorial.

$ tutorial
usage: tutorial list                 - show available tutorials
       tutorial info <tutorial-name> - show details of a tutorial
       tutorial <tutorial-name>      - set up a tutorial

Currently available tutorials:
R ..................... Estimate Pi using the R programming language
cp2k .................. How-to for the electronic structure package CP2K
dagman-namd ........... Launch a series of NAMD simulations via Condor DAG
error101 .............. Use condor_q -better-analyze to analyze stuck jobs
exitcode .............. Use HTCondor's periodic_release to retry failed jobs
htcondor-transfer ..... Transfer data via HTCondor's own mechanisms
namd .................. Run a molecular dynamics simulation using NAMD
oasis-parrot .......... Software access with OASIS and Parrot
octave ................ Matrix manipulation via the Octave programming language
pegasus ............... An introduction to the Pegasus job workflow manager
photodemo ............. A complete analysis workflow using HTTP transfer
quickstart ............ How to run your first OSG job
root .................. Inspect ntuples using the ROOT analysis framework
scaling ............... Learn to steer jobs to particular resources
scaling-up-resources .. A simple multi-job demonstration
software .............. Software access tutorial
stash-chirp ........... Use the chirp I/O protocol for remote data access
stash-http ............ Retrieve job input files from Stash via HTTP
stash-namd ............ Provide input files for NAMD via Stash's HTTP interface
swift ................. Introduction to the SWIFT parallel scripting language

Enter "tutorial name-of-tutorial" to clone and try out a tutorial.

Each of these rows above is a tutorial that you can work through on your own, after the workshop. We add new tutorials from time to time, as well. Each tutorial has a README.md file within that gives teaching material on what the tutorial is trying to illustrate, and you can read them online at the OSG Connectbook.

Note the word clone in that last line of output. There’s no mistake that it’s the same term as we used for copying a git repository. Each tutorial is version-controlled, and actually resides on GitHub. When you use the tutorial command you’re getting content from there.

Let’s get started with the quickstart tutorial:

$ tutorial quickstart       # creates a directory "tutorial-quickstart"
$ cd tutorial-quickstart    # script and input files are inside this directory

We will look at two files in detail: “short.sh” and “tutorial01.submit”

##Job execution script##

Inside the tutorial directory, open up short.sh in an editor.

$ nano short.sh

This is a shell script, quite ordinary and much like the ones we worked with in Unit I.

#!/bin/bash
# short.sh: a short discovery job
printf "Start time: "; /bin/date
printf "Job is running on node: "; /bin/hostname
printf "Job running as user: "; /usr/bin/id
printf "Job is running in directory: "; /bin/pwd
echo
echo "Working hard..."
sleep ${1-15}
echo "Science complete!"

To close nano, hold down Ctrl and press X. Press Y to save, and then Enter Now, make the script executable. Recall that this is not necessary for shell programs that you create and run locally. However, it is extremely important for jobs running on the grid. So is the “shbang” line (#!/bin/sh).

$ chmod +x short.sh

Since we used the tutorial command, all files are already in your workspace. Run the job locally when setting up a new job type – it is important to test your job outside of HTCondor before submitting into the Open Science Grid.

$ ./short.sh

Start time: Wed Aug 21 09:21:35 CDT 2013

Job is running on node: login01.osgconnect.net

Job running as user: uid=54161(username) gid=1000(users) groups=1000(users),0(root),1001(osg-connect),1002(osg-staff),1003(osg-connect-test),9948(staff),19012(osgconnect)

Job is running in directory: /home/username/tutorial-quickstart

Working hard...

Science complete!

##Job submission file## So far, so good! Next we will create a simple (if verbose) HTCondor submit file. A submit file tells the grid software how to run your workload, with what properties and arguments, and how to collect and return output to you.

$ nano tutorial01.submit

# The UNIVERSE defines an execution environment. You will almost always use VANILLA.
Universe = vanilla

# EXECUTABLE is the program your job will run It's often useful
# to create a shell script to "wrap" your actual work.
Executable = short.sh

# ERROR and OUTPUT are the error and output channels from your job
# that HTCondor returns from the remote host.
Error = job.error
Output = job.output

# The LOG file is where HTCondor places information about your
# job's status, success, and resource consumption.
Log = job.log

# QUEUE is the "start button" - it launches any jobs that have been
# specified thus far.
Queue 1

Job submission

Submit the job using condor_submit.

$ condor_submit tutorial01.submit
Submitting job(s).
1 job(s) submitted to cluster 823.

##Job status##

Your first job is on the grid! The condor_q command tells the status of currently running jobs. Generally you will want to limit it to your own jobs by adding your own username to the command.

$ condor_q username
-- Submitter: login01.osgconnect.net : <128.135.158.173:43606> : login01.osgconnect.net
 ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD
 823.0   username           8/21 09:46   0+00:00:06 R  0   0.0  short.sh
1 jobs; 0 completed, 0 removed, 0 idle, 1 running, 0 held, 0 suspended

If you want to see all jobs running on the system, use condor_q without any extra parameters. You can also get status on a specific job cluster – the number that condor_submit gave you.

$ condor_q 823
-- Submitter: login01.osgconnect.net : <128.135.158.173:43606> : login01.osgconnect.net
 ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD
 823.0   username           8/21 09:46   0+00:00:10 R  0   0.0  short.sh
1 jobs; 0 completed, 0 removed, 0 idle, 1 running, 0 held, 0 suspended

A job cluster identifies one batch of jobs. The batch could have one job or ten thousand in it – what matters is that each time a submit file says “Queue”, you get a cluster. The individual jobs within a job cluster are identified by the numbers after the dot in the job ID – so in this example, 823 is the job cluster, and 823.0 is the job ID (or jobid) of job 0 in that cluster.

Note the ST (state) column. Your job will be in the I state (idle) if it hasn’t started yet. If it’s currently scheduled and running, it will have state R (running). If it has completed already, it will not appear in condor_q.

You may sometimes see jobs in H state. These are held jobs. Held jobs are stalled, usually for a specific reason, and won’t progress until released. Until you gain savvy with diagnosing why a job is held and solving it on your own, you may contact the OSG Connect support team for help with held jobs.

Let’s wait for your job to finish – that is, for condor_q not to show the job in its output.

$ condor_q username | tail -1
1 jobs; 0 completed, 0 removed, 0 idle, 1 running, 0 held, 0 suspended

You could run this over and over to watch for the job to complete – but connect watch can make this simpler. Let’s submit the job again, and watch condor_q output at five-second intervals (the default). Your first job has probably already completed by now, so submit a new one first:

$ condor_submit tutorial01.submit
Submitting job(s).
1 job(s) submitted to cluster 823
$ connect watch

When your job has completed, it will disappear from the list. To close connect watch, press control-C – hold down Control and press C.

##Job history## Once your job has finished, you can get information about its execution from the condor_history command:

$ condor_history 823
 ID      OWNER            SUBMITTED     RUN_TIME ST   COMPLETED CMD
 823.0   username            8/21 09:46   0+00:00:12 C   8/21 09:46 /home/username/

You can see much more information about your job’s final status using the -long option.

##Job output##

Once your job has finished, you can look at the files that HTCondor has returned to the working directory. If everything was successful, it should have returned:

• a log file from Condor for the job cluster: job.log
• an output file for each job’s output: job.output
• an error file for each job’s errors: job.error

Read the output file. It should be something like this:

$ cat job.output
19 Feb 15:11:43| connect_wrapper  | 
Start time: Thu Feb 19 15:11:43 EST 2015
Job is running on node: VPA-WH505-01-S4-its-u12-nfs-20141003
Job running as user: uid=1066(osgconnect) gid=502(condoruser) groups=502(condoruser),108(fuse)
Job is running in directory: /tmp/rcc_syracuse/rcc.9jiqjUmxeB/execute.10.5.30.6-1128/dir_1380

Working hard...
Science complete!

Unscheduling jobs

Once you know how to create files, you want to know how to delete them. And once you can schedule workloads across thousands of computers simultaneously, you need to know how to remove them. The command for that is condor_rm, and it takes only one argument: the job cluster or job ID.

$ condor_submit tutorial01.submit
Submitting job(s).
1 job(s) submitted to cluster 829
$ condor_rm 829
Cluster 829 has been marked for removal.

Or alternately:

$ condor_submit tutorial01.submit
Submitting job(s).
1 job(s) submitted to cluster 829
$ condor_rm 829.0
Job 829.0 has been marked for removal.

Challenges

$ condor_history -long ######.0