Submitting Jobs Using the ChtcRun Package
To facilitate the submission of large batches of jobs, especially
batches for Matlab, Python, and R, the CHTC has created the ChtcRun
package of scripts, files, and directories that will allow you to easily
construct your own HTCondor workflow (or "DAG" batch). By following the ordered
set of directions given here, you'll be able to easily set up and run
a set of high-throughput computing jobs on CHTC-available resources,
including those outside of the CHTC HTCondor Pool in the UW Grid and
national Open Science Grid.
- From within your home directory on the submit node, in a directory of your choice,
download the ChtcRun package:
Unpack the ChtcRun package.
This will create a
tar xzf ChtcRun.tar.gz
After unpacking the package,
ChtcRun directory will be:
Matlabin/ (example Matlab setup)
Rin/ (example R setup)
- other directories and files
You do not need to download a separate copy of
ChtcRun for every
batch of jobs you submit - each project will be submitted from its own directory
ChtcRun. However, the operations of downloading and unpacking
may be repeated to
obtain updated versions of the scripts and supporting files.
Doing so will overwrite existing, but updated material,
without harming other files and directories already in place.
Stage files specific to your set of jobs into correctly-named directories
For Matlab, Python, and R jobs, it is first essential to have completed
the steps to compile your code dependencies, according to our
"Compiling Matlab, Python and R Code" page.
Make a directory
to house the project's input files and executables.
For purposes of this example, assume that the directory has been named
proj1data, which is otherwise equivalent to the example
proj1data, create one directory
for each job to be run.
Within each of these run-specific directories,
place the input files used for that specific job.
If the work does not require any per-job input files,
then nothing will be in these directories.
The files might include input files and parameter files.
These directories can be given any name,
but the file names may not contain whitespace characters, notably spaces,
in their name.
And, the file name
shared is already
used for the files shared among job submissions.
Each of these directories will create an individual job within
the single DAG.
When the job starts,
its current working directory on the machine where the job executes
will contain copies of all files placed in the run-specific directory
on the submit machine,
as well as copies of all files placed in the
shared directory on the submit machine.
Input files, shared libraries, and all executables shared by
all jobs go into a directory with the name
Create the directory
Place the executable and any input files common to the
set of jobs that will be submitted into directory
shared directory will not become an individual job.
For example, you might want to run several jobs on data you have for
several midwestern states, where there is one job per state.
Each state has its own input data file,
There is also a shared input data file of US-wide averages for comparison,
as well as a single executable (program).
For each job submission, assume this program
will compare contents of
Given this, a portion of the directory hierarchy might look like this:
process.template (a template submit file) in
with respect to the following lines:
request_cpus = 1 (or other integer)
request_disk = (insert KB value)
request_memory = (insert MB value)
+WantFlocking = true (to send jobs shorter than 4 hours to the UW Grid)
+WantGlidein = true (to send jobs shorter than 2 hours to the OSG)
If you are not aware of how much disk or memory your jobs need,
it is ESSENTIAL to first test 5-10 jobs, and then look at the resulting
process.log file for each test job to determine the
amounts that should be requested for your jobs.
For more information on testing, Flocking, and Glidein, please see the
bottom of our "Run Your First HTC Jobs" guide.
With a current working directory of
with a job-specific set of command line arguments.
The output from from running
will be a directory to hold eventual output from running
the project's job(s),
as well as control files:
a DAG input file for describing the DAG
and an HTCondor job submit description files for each of the node jobs within
One of the command line arguments to
will specify the name of this directory.
The command line arguments to
mkdag are viewable by running the
following command, which includes full
mkdag commands for the
examples that come within
This required argument identifies which file within the
directory should be executed.
It should be only the base name of the file
do not include directory information.
This required argument identifies the relative path to and
name of the directory that contains the
The path is specified as relative to the directory containing the
The string used instead of
for this presented example would be
This required argument identifies where the output from your
jobs will be placed.
This is the relative path to and
specifies a name for the directory within
that will be created, and within which the directories and files
produced by the
mkdag script will go.
Do not create this directory before running
The directory will be created by
and it will contain one subdirectory for each of the jobs within the DAG.
This required argument helps identify if a job ran successfully.
For a variety of reasons,
we cannot necessarily trust the return code from MATLAB or R
to tell us if the job was successful.
We determine if a job was successful by checking if at least one
file was created that includes the pattern "SubString" in it's
filename, for each HTCondor job submitted.
This check is identical to running
in a job's output folder after the job completes to see that at least one file is returned.
This optional argument identifies a command line argument that
is to be passed to each invocation (as an HTCondor job) of the executable.
This argument will be listed multiple times to define more than one
command line argument. Optionally, you can use "--parg=unique" to
pass the name of the job directory as an argument to your code for each job.
--type argument is required,
and must be set to one of 3 values.
For MATLAB jobs.
It ensures that necessary MATLAB supporting libraries are made
available to the job.
For R jobs.
It ensures that the R runtime environment is made available to the job.
For jobs that are neither MATLAB or R. "Other" should
be specified for Python jobs.
This argument is required for R and some Matlab jobs.
It specifies the version of R needed.
Possible values are listed below:
(version R-2.10.1 on Scientific Linux)
(version R-2.13.1 on Scientific Linux)
(version R-2.14.1 on Scientific Linux)
(version R-2.15.1 on Scientific Linux)
(version R-2.15.2 on Scientific Linux)
(version R-2.15.3 on Scientific Linux)
(version R-3.0.1 on Scientific Linux)
(version R-3.1.0 on Scientific Linux)
(Matlab version R2011b on Scientific Linux)
(Matlab version R2013b on Scientific Linux)
For example, assume that the
is a compiled MATLAB program that takes two arguments:
the files to compare.
It produces a file called
The command line for
./mkdag --cmdtorun=compare-states --data=proj1data \
--outputdir=proj1output --pattern=output.dat --parg=us.dat \
(The backslashes above are used to break a long command across three lines. You can omit the backslashes and enter your command as a single line.)
outputdir directory created by the
mkdag command, run
This submits and runs the batch of job(s) you setup in the
data" directory (
proj1data in this example).
Output, log, and error files for each job will also be placed
within newly created folders for each job, within the "