Job submission on Duke CI 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 Duke CI Connect. The submitted jobs are executed on the remote worker node(s) and the outputs are transferred 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 Duke CI Connect

First, we log in to Duke CI Connect:

$ ssh username@login.duke.ci-connect.net   # username is your username
password:                                  # enter your password

Let's introduce a command that will be useful throughout your Duke CI Connect usage: connect.

Connect is a single interface to tools that enhance or simplify your use of the Duke CI 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 client [opts] <subcommand> [args]
       connect help [subcommands...]
       connect histogram [-l | --last] [user]
       connect project 
       connect show-projects [-u username] [projectname]
       connect status [-f | --full]
       connect watch 

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:
  * duke-SWC-Duke15

Each time you run a workload on Duke CI Connect, you need a project name to associate with. For your research work later on, we can get you started with a permanent project, but for now you should find the duke-SWC-Duke15 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 Duke CI 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.

We will get our example files for all today's lessons using tutorial.

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. You may 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: duke-login.osgconnect.net

Job running as user: uid=49152(username) gid=1000(users) groups=1000(users),5478(@duke-SWC-Duke15),5532(@connect),5782(@osg),7114(@duke)

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: duke-login.osgconnect.net : <128.135.158.173:43606> : duke-login.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: duke-login.osgconnect.net : <128.135.158.173:43606> : duke-login.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 Duke CI 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.

Job Requirements - A Basic OSG Job

HTCondor job and machines are represented as HTCondor classads. These are sets of key/value attribute pairs. Let's examine a what a machine classad looks like. This is a two step process, first we get a name for one of the machines, and then we ask condor_status to give us the details for that machine (-long).

$ condor_status -pool osg-flock.grid.iu.edu -af Name | head -n 1
[resource name]
$ condor_status -long -pool osg-flock.grid.iu.edu [resource name] | sort
HAS_FILE_usr_lib64_libgfortran_so_3 = true
HAS_MODULES = false
OSGVO_OS_STRING = "RHEL 6"

You can make use any of these attributes to limit where your jobs go. The following is a fairly complete OSG job which you can use when getting started on OSG. Note the Requirements and requests_* lines.

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

# These are good base requirements for your jobs on OSG. It is specific on OS and
# OS version, core cound and memory, and wants to use the software modules. 
Requirements = OSGVO_OS_STRING == "RHEL 6" && HAS_MODULES == True
request_cpus = 1
request_memory = 1 GB

# 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.$(Cluster).$(Process).error
Output = job.$(Cluster).$(Process).output

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

# Send the job to Held state on failure. 
on_exit_hold = (ExitBySignal == True) || (ExitCode != 0)  

# Periodically retry the jobs every 60 seconds, up to a maximum of 5 retries.
periodic_release =  (NumJobStarts < 5) && ((CurrentTime - EnteredCurrentStatus) > 60)

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

You can test this job by submitting and monitoring it as we have just covered:

$ condor_submit osg-template-job.submit
Submitting job(s).
1 job(s) submitted to cluster 830

The filenames for this job includes a job id, which means that if you submit more than one job, they will all have unique outputs.

$ ls *.output
job.830.0.output
job.831.0.output

Challenges

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