HTCondor Quick Start Guide
To users, HTCondor is a job scheduler. You give HTCondor a file containing commands that tell it how to run jobs. HTCondor locates a machine that can run each job within the pool of machines, packages up the job and ships it off to this execute machine. The jobs run, and output is returned to the machine that submitted the jobs.
This guide provides enough guidance to submit and observe the successful completion of a first job. It then suggests extensions that you can apply to your individual jobs.
This guide presumes that
- HTCondor is running
- that you have access to a machine within the pool that may submit jobs, termed a submit machine
- that you are logged in to and working on the submit machine
- that your program executable, your submit description file, and any needed input files are all on the file system of the submit machine
- that your job (the program executable) is able to run without any interactive input. Standard input (from the keyboard), standard output (seen on the display), and standard error (seen on the display) may still be used, but their contents will be redirected from/to files.
A First HTCondor Job
For HTCondor to run a job, it must be given details such as the names and location of the executable and all needed input files. These details are specified in a submit description file.
Before presenting the details of the submit description file, consider this first HTCondor job. It is a sleep job that waits for 6 seconds and then exits. While most aspects of HTCondor are identical on Unix and Windows machines, awareness of the platform of the submit machine will lead to a better understanding of jobs and job submission.
This first executable program is a
shell script (Unix) or batch file (Windows).
The file that represents this differs based on operating system;
Unix version is shown on the left
the Windows version is shown on the right
To try this example,
log in to the submit machine,
and use an editor to type in or copy and paste the file contents.
Name the resulting file
sleep.sh if the submit machine
is running a Unix operating system,
and name the resulting file
sleep.bat if the submit machine
is running Windows.
Note that you will need to know whether the operating system on your
submit machine is a Unix operating system or Windows.
a shell script
#!/bin/bash # file name: sleep.sh TIMETOWAIT="6" echo "sleeping for $TIMETOWAIT seconds" /bin/sleep $TIMETOWAIT
a batch file
:: file name: sleep.bat @echo off set TIMETOWAIT=6 echo sleeping for %TIMETOWAIT% seconds choice /D Y /T %TIMETOWAIT% > NUL
For a Unix submit machine only,
sleep.sh file to be executable by running
the Unix command
chmod u+x sleep.sh
The contents of the submit description file
The submit description file describes the job.
To submit this sample job,
again use an editor to create the file
The submit description file contents for this job differs on Unix and Windows
machines only in the name of the script or batch file:
# Unix submit description file # sleep.sub -- simple sleep job executable = sleep.sh log = sleep.log output = outfile.txt error = errors.txt should_transfer_files = Yes when_to_transfer_output = ON_EXIT queue
# Windows submit description file # sleep.sub -- simple sleep job executable = sleep.bat log = sleep.log output = outfile.txt error = errors.txt should_transfer_files = Yes when_to_transfer_output = ON_EXIT queue
The first two lines of this submit description file are comments.
Comments begin with the
Comments do not span lines.
Each line of the submit description file has the form
command name = value
The command name is case insensitive and precedes an equals sign. Values to right of the equals sign are likely to be case sensitive, especially in the case that they specify paths and file names.
Next in this file is a specification of the
It specifies the program that becomes the HTCondor job.
For this example, it is the file name of the Unix script or Windows batch file.
A full path and executable name,
or a path and executable relative to the current working directory
may be specified.
log command causes
a job event log file named
sleep.log to be created
on the submit machine once the job is submitted.
A log is not necessary, but it can be incredibly useful in figuring
out what happened or is happening with a job.
If this script/batch file were to to be invoked from the command line, and outside of HTCondor, its single line of output
sleeping for 6 seconds
would be sent to standard output (the display).
When submitted as an HTCondor job, standard output of the execute
machine is on that execute machine, and thus unavailable.
HTCondor captures standard output in a file
due to the
output command in the submit description file.
This example names the redirected standard output file
and this file is returned to the submit machine when the job completes.
The same structure is specified for standard error,
as specified with the
should_transfer_files = Yes when_to_transfer_output = ON_EXIT
direct HTCondor to explicitly send the needed files, including the executable, to the machine where the job executes. These commands will likely not be necessary for jobs in which the submit machine and the execute machine access a shared file system. However, including these commands will allow this first sample job to work under a large variety of pool configurations.
queue command tells HTCondor to run one instance of this job.
Submitting the job
With this submit description file, all that remains is to hand off
the job to HTCondor. With the current working directory being
the one that contains the
sleep.sub submit description file
and the executable (
this job submission is accomplished with the command line
condor_submit sleep.subIf the submission is successful, the terminal will display a response that identifies the job, of the form
Submitting job(s). 1 job(s) submitted to cluster 6.
Monitoring the job
Once the job has been submitted, command line tools may help follow
along with the progress of the job.
condor_q command prints a listing of all the jobs currently in
a short time after Kris submits the sleep job from a Unix submit machine
on a pool that has no other queued jobs,
output appears as
% condor_q -- Submitter: example.wisc.edu : <126.96.36.199:56550> : example.wisc.edu ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD 6.0 kris 2/13 10:49 0+00:00:03 R 0 97.7 sleep.sh 1 jobs; 0 completed, 0 removed, 0 idle, 1 running, 0 held, 0 suspended
The queue might contain many jobs.
To see only Kris' jobs, add an option to the
that specifies to only print Kris' jobs:
% condor_q -submitter kris
The first column of output from
condor_q identifies the job;
the identifier is composed of two integers separated by a period.
The first integer is known as a cluster number,
and it will be the same for each of the potentially many jobs
submitted by this single invocation of
The second integer in the identifier is known as a process ID,
and it distinguishes between distinct job instances that have
the same cluster number. These values start at 0.
Of interest in this output, the job is running, and it has used 3 seconds of time so far.
At job completion, the log file contains
000 (006.000.000) 02/13 10:49:04 Job submitted from host: <188.8.131.52:46062> ... 001 (006.000.000) 02/13 10:49:24 Job executing on host: <184.108.40.206:43051?PrivNet=cs.wisc.edu> ... 006 (006.000.000) 02/13 10:49:30 Image size of job updated: 100000 0 - MemoryUsage of job (MB) 0 - ResidentSetSize of job (KB) ... 005 (006.000.000) 02/13 10:49:31 Job terminated. (1) Normal termination (return value 0) Usr 0 00:00:00, Sys 0 00:00:00 - Run Remote Usage Usr 0 00:00:00, Sys 0 00:00:00 - Run Local Usage Usr 0 00:00:00, Sys 0 00:00:00 - Total Remote Usage Usr 0 00:00:00, Sys 0 00:00:00 - Total Local Usage 23 - Run Bytes Sent By Job 113 - Run Bytes Received By Job 23 - Total Bytes Sent By Job 113 - Total Bytes Received By Job Partitionable Resources : Usage Request Allocated Cpus : 1 1 Disk (KB) : 100000 100000 2033496 Memory (MB) : 0 98 2001 ...
Each event in the job event log file is separated by a line containing three periods. For each event, the first 3-digit value is an event number.
Removing a job
Successfully submitted jobs will occasionally need to be removed
from the queue.
condor_rm command specifying the job identifier
as a command line argument.
Kris' job may be removed from the queue with
Specification of the cluster number only as with the command
condor_rm 6will cause all jobs within that cluster to be removed.
science Job Example
A second example job illustrates aspects of file specification for the job.
Assume that the program executable is called
This program does not use standard input or output;
the command line to invoke this program
specifies two input files and one output file.
For this example, the command line to invoke
(not as an HTCondor job) will be
science.exe infile-A.txt infile-B.txt outfile.txt
While the name of the executable is specified in the submit description
file with the
the remainder of the command line will be specified with
Here is the submit description file for this job:
# science1.sub -- run one instance of science.exe executable = science.exe arguments = "infile-A.txt infile-B.txt outfile.txt" transfer_input_files = infile-A.txt,infile-B.txt should_transfer_files = IF_NEEDED when_to_transfer_output = ON_EXIT log = science1.log queue
The input files
will need to be available
on the execute machine within the pool where the job runs.
HTCondor cannot interpret command line arguments,
so it cannot know that these command line arguments for this job
specify input and output files.
The submit command
HTCondor to transfer these input files
from the machine where the job is submitted to the machine chosen
to execute the job.
The default operation of HTCondor is to transfer all files created
by the job on the execute machine back to the submit machine.
Therefore, there is no specification of the
This example submit description file modifies the commands that direct the transfer of files from submit machine to execute machine and back again.
should_transfer_files = IF_NEEDED when_to_transfer_output = ON_EXIT
These values are the HTCondor defaults,
so are not needed in this example.
They are included to direct attention to the capabilities of HTCondor.
should_transfer_files specifies whether HTCondor should assume
the existence of a shared file system by the
submit machine and the execute machine.
Where there is a shared file system, a correctly configured
pool of machines will not need to transfer
the files from one machine to the other, as both can access the
shared file system.
Where there is not a shared file system, HTCondor must transfer
the files from one machine to the other.
IF_NEEDED asks HTCondor to use
a shared file system when one is detected,
but to transfer the files when no shared file system is detected.
When files are to be transferred, HTCondor automatically sends the
executable as well as a file representing standard input;
this file would be specified by the
input submit command,
and it is not relevant to this example.
Other files are specified in a comma separated list
transfer_input_files, as they are in this example.
When the job completes, all files created by the executable as it ran are transferred back to the submit machine.
science Job and the Organization of Files
A further example promotes understanding of how HTCondor makes
the submission of lots of jobs easy.
Assume that the
science.exe job is to be run 40 times.
If the input and output files were exactly the same for each run,
then only the last line of the given submit description file
It is likely that this does not produce the desired outcome,
as the output file created,
outfile.txt, has the same name
for each queued instance of the job,
and thus this file of results for each run conflicts.
Chances are that the input files also must be distinct for each
of the 40 separate instances of the job.
HTCondor offers the use of a macro that can uniquely name
each run's input and output file names.
$(Process) macro causes substitution by the process ID from
the job identifier.
The submit description file for this proposed solution
uniquely names the files:
# science2.sub -- run 40 instances of science.exe executable = science.exe arguments = "infile-$(Process)A.txt infile-$(Process)B.txt outfile$(Process).txt" transfer_input_files = infile-$(Process)A.txt,infile-$(Process)B.txt should_transfer_files = IF_NEEDED when_to_transfer_output = ON_EXIT log = science2.log queue 40
The 40 instances of this job will have process ID values that
run from 0 to 39.
The two input files for process ID 0 are
the ones for process ID 1 will
and so on,
all the way to process ID 39, which will
Using this macro also for the output file naming of each
of the 40 jobs creates
outfile0.txt for process ID 0,
outfile1.txt for process ID 1,
and so on, to
outfile39.txt for process ID 39.
This example does not scale well as the number of jobs increases,
because the number of files in the same directory becomes unwieldy.
Assume now that there will be 100 instances of the
and each instance has distinct input files, and produces an output file.
A recommended organization introduces a unique directory for each
The submit description file facilitates this organization by
specifying the directory with the
The directories for this example are named
all the way to
run99 for the 100 instances of this example,
specified in the submit description file:
# science3.sub -- run 100 instances of science.exe, with # unique directories named by the $(Process) macro executable = science.exe arguments = "infile-A.txt infile-B.txt outfile.txt" should_transfer_files = IF_NEEDED when_to_transfer_output = ON_EXIT initialdir = run$(Process) transfer_input_files = infile-A.txt,infile-B.txt log = science3.log queue 100
The input and output files for each job instance can again
be the initial simple names that do not incorporate
These files are distinct for each run due to their placement
within a uniquely named directory.
This organization also works well for executables that
do not facilitate command line naming of input or output files.
Here is a listing of the files and directories on the
submit machine within this suggested directory structure.
The files and directories that are present before the
jobs are submitted using
condor_submit are shown
in regular text font.
The files created due to submitting and running the jobs
are shown in bold text font.
Only a subset of the 100 directories are shown.
Directories are identified using the Unix convention of appending
the directory name with a slash character (
science.exe science3.sub run0/ infile-A.txt infile-B.txt outfile.txt science3.log run1/ infile-A.txt infile-B.txt outfile.txt science3.log run2/ infile-A.txt infile-B.txt outfile.txt science3.log