Submitting jobs to Condor using the command-line

• Connecting to alatar
• Submitting a job with csubmit
  • Syntax
  • Submitting a normal executable job
  • Submitting a Gaussian job
• Submitting a job with condor_submit
  • Setting up your job directory
  • Creating a job file
  • Running condor_submit
• Job Maintenance
  • Listing the Condor Queue
  • Removing a job

Connecting to alatar

alatar is our condor job submission and master server. You must connect to it using ssh. The address you should connect to is condor.chem.indiana.edu

Submitting a job with csubmit

csubmit is an EasyCondor command line interface to make it really easy to submit new jobs, using the same workflow as the web interface. It will automatically detect the type and platform of your executable, setup a directory under /data/username, and build a job command file for you.

It currently does not support very advanced job commands however.

Syntax

The basic syntax is: csubmit [options] <data files>...

Here are the current options:

• -x - your job id. Automatically assigned if not given.k
• -e - the filename for your executable file
• -g - the filename for your Gaussian input file
• -a - argument to pass your executable file
• -o - output files that your executable may generate

• -n - number of sessions to run

Submitting a normal executable job

This will run uptime.exe on 10 Windows machines:

csubmit -e uptime.exe -n 10

This will create a directory named /data/username/testjob, and queue a job to sort a textfile on the first Linux machine that picks up the job.

csubmit -x testjob -e /usr/bin/sort -a "textfile" textfile

Submitting a Gaussian job

The following creates a job named "molecule" that processes 1HF.gjf.

csubmit -x molecule -g 1HF.gjf

Submitting a job with condor_submit

condor_submit gives you all of the flexibility you need, but requires you to create a command file to run a job.

Setting up your job directory

First you will want to create a directory for your job to run from:

mkdir /data/$USERNAME/testjob

It is recommended that you place all of your input files and executables in this directory.

Creating a job file

In the directory we created above, we will create a job command file. For this example, we will just name it condor.cmd.

universe = Vanilla
Requirements = (OpSys == "LINUX") && (Arch == "x86_64")
executable = /data/tstrombe/uploads/df
output = condor.out
error = condor.err
log = condor.log
rank = kflops

when_to_transfer_output = ON_EXIT_OR_EVICT
should_transfer_files = YES
queue 1

It's beyond the scope of the document to explain what each setting is, as these files can get pretty complex. Please see the Official Condor documentation on Submitting a Job.

Running condor_submit

Once you've setup your job file, you can submit it to the queue.

condor_submit condor.cmd

Job Maintenance

Listing the Condor Queue

This will list all of the jobs currently in queue:

condor_q

Removing a job

You can remove a job at any time with the condor_rm command. If your job cluster # is 89.0, and you would like to kill it, you can type:

condor_rm 89