Users’ Quick Start Guide
HTCondor is a system for dynamically sharing computational resources between competing computational tasks. As an HTCondor user, you will describe your computational tasks as a series of independent, asynchronous “jobs.” You access computational resources managed by HTCondor by submitting (or “placing”) job descriptions at an HTCondor “access point” (AP), also known as a “submit node.” HTCondor locates an appropriate machine for each job, packages up the job and ships it off to that machine for execution. Machines providing resources to HTCondor are therefore known as execution points (EP).
This guide covers submitting and observing the successful completion of a first, example job. It then suggests extensions that you can apply to your own jobs.
This guide presumes that
HTCondor is running
You have access to a machine within the pool that may submit jobs, termed an Access Point (AP).
You are logged in to and working on the AP. (If you just finished getting HTCondor, the one machine you just installed is this AP.)
Your program executable, your submit description file, and any needed input files are all on the file system of the AP.
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.
What is a Job?
“Job” is a very specific term in HTCondor. A job is the atomic unit of work. A job may use multiple cores on one machine, but one job may not (in general) run across more than one machine. To effectively use HTCondor, you will need to divide your total work (often called a workflow) into a number of jobs. These atomic units of work run asynchronously with respect to each other, but may be connected by input and output files. Each job is described by a Job ClassAd, which is usually created by the system from a submit description file. HTCondor is a High Throughput system, which means it has been designed to effectively manage hundreds of thousands of jobs. Attributes of jobs that must be defined include the executable or script to run, the amount of memory, CPU and other machine resources it needs, and descriptions of the file inputs it need. The set of files used by a job is called the “sandbox”. There is an input sandbox, the input files that exist before a job starts; the output sandbox, the set of files created by the job; and a scratch sandbox, the set of files made as the job runs.
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 Linux (or Mac) and Windows machines, awareness of the AP’s operating system will lead to a better understanding of jobs and job submission.
This first executable program is a shell script (Linux or Mac) or batch file
(Windows). The file that represents this differs based on operating
system; the Linux (or Mac) version is shown first, and
the Windows version is shown second. To try this example,
log in to the AP, and use an editor to type in or copy and paste
the file contents. Name the resulting file
sleep.sh if the AP
is Linux (or Mac) operating system, and name the resulting file
if the AP is running Windows. Note that you will need to
know whether the operating system on your AP is a Linux (or Mac)
operating system or Windows.
#!/bin/bash # file name: sleep.sh TIMETOWAIT="6" echo "sleeping for $TIMETOWAIT seconds" /bin/sleep $TIMETOWAIT
:: file name: sleep.bat @echo off set TIMETOWAIT=6 echo sleeping for %TIMETOWAIT% seconds choice /D Y /T %TIMETOWAIT% > NUL
For a Linux (or Mac) AP only, change the
sleep.sh file to be
executable by running the following 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
sleep.sub. The submit
description file contents for this job differs on Linux (or Mac) and Windows
machines only in the name of the script or batch file:
# sleep.sub -- simple sleep job executable = sleep.sh log = sleep.log output = sleep.out error = sleep.err should_transfer_files = Yes when_to_transfer_output = ON_EXIT request_cpus = 1 request_memory = 512M request_disk = 1G queue
# sleep.sub -- simple sleep job executable = sleep.bat log = sleep.log output = sleep.out error = sleep.err should_transfer_files = Yes when_to_transfer_output = ON_EXIT request_cpus = 1 request_memory = 512M request_disk = 1G queue
The first line of this submit description file is a comment. Comments begin with the # character. 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
executable to run. It
specifies the program that becomes the HTCondor job. For this example, it
is the file name of the Linux (or Mac) 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 AP 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.
HTCondor must be told how many resources your job needs on an Execution Point in order to run. This allows HTCondor to run as many jobs as possible on each EP without overloading them. Jobs must declare the number of CPUs, the amount of memory and disk they need. Special jobs may need to request other resources, such as GPUs or licenses. Ask your administrator if your jobs requires such things. The amount of cpus is unit less, but memory and disk requires can have a “M” for megabyte, “G” for Gigabyte suffix for legibility. Without the suffix, memory units are megabytes and disk kilobytes.
request_cpus = 1 request_memory = 512M request_disk = 1G
If this script/batch file were 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 job is on that EP, 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
sleep.out, and this file is returned to the AP 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 AP and the EP (the Execution Point, or worker node) 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. Note that the
queue command should be the last command in the
file. Commands after the
queue are ignored. Otherwise, the order of
commands with the file does not matter. Assuming the current working directory
sleep.sub submit description file and the executable
sleep.bat), the command line
submits the job to the AP. If 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 you follow along
with the progress of the job. The
condor_q command prints a listing of
all your jobs currently in the queue. For example, a short time after Kris
submits the sleep job from a Linux (or Mac) AP on a pool that has
no other queued jobs, the output may appear as
$ condor_q -- Submitter: example.wisc.edu : <188.8.131.52:56550> : 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 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 a single invocation of
condor_submit. 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: <184.108.40.206:46062> ... 001 (006.000.000) 02/13 10:49:24 Job executing on host: <220.127.116.11:43051?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
condor_rm command with the job identifier as a command line
argument removes jobs. Kris’ job may be removed from the queue with
Specification of the cluster number only as with the command
will cause all jobs within that cluster to be removed.
The science Job Example
A second example job illustrates aspects of file specification for the
job. Assume that the program executable is called
program does not use standard input or output; instead, the command line
to invoke this program specifies two input files and one output file. For
this example, the command line to invoke
science.exe (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
executable command, the remainder of the command line will be
specified with the
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 request_cpus = 1 request_memory = 512M request_disk = 1G num_retries = 2 log = science1.log queue
The input files
infile-B.txt will need to be
available on the Execution Point 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
transfer_input_files instructs 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 EP back to the
AP. Therefore, there is no specification of the
This example submit description file modifies the commands that direct the transfer of files from AP to EP 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. The
should_transfer_files command specifies whether HTCondor should assume the
existence of a file system shared by the AP and the EP. 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. The specification
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
submit command, and it is not relevant to this example. Other files are
specified in a comma separated list with
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 AP.
HTCondor assumes that if the job exits of its own accord, with an exit code of zero, that indicates success, and any non-zero exit code is a failure. By default, when the job exits, it will leave the queue. If you would like a job that exits with a non-zero exit code to be restarted some number of times until it does, set num_retries in the submit file like so:
num_retries = 2
Expanding the 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
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 changes: from
It is likely that this does not produce the desired outcome, as the output
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. The
$(Process) macro causes
substitution by the process ID from the job identifier. The submit
description file for this proposed solution uniquely names the files:
# science2.sub -- run 40 instances of science.exe executable = science.exe arguments = "infile-$(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 request_cpus = 1 request_memory = 512M request_disk = 1G num_retries = 2 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
infile-0B.txt, the ones for process ID 1 will be
infile-1B.txt, and so on, all the way to process ID 39, which will be
infile-39B.txt. Using this macro for
the output file naming of each of the 40 jobs creates
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
science.exe job, and each
instance has distinct input files, and produces a distinct output file. A
recommended organization introduces a unique directory for each job
instance. The following submit description file facilitates this organization
by specifying the directory with the
initialdir command. The directories
for this example are named
run1, etc. all the way to
for the 100 instances of the following example submit 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 request_cpus = 1 request_memory = 512M request_disk = 1G num_retries = 2 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 the
$(Process) macro. 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 AP within this suggested directory structure. The files created due to submitting and running the jobs are shown preceded by an asterisk (*). Only a subset of the 100 directories are shown. Directories are identified using the Linux (and Mac) 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
Where to Go from Here
Consider watching our video tutorial for new users.
Slides from past HTCondor Weeks – our annual conference – include the tutorials given there.
The Users’ Manual is a good reference.
If you like what you’ve seen but want to run more jobs simultaneously, the administrator’s quick start guide will help you make more of your machines available to run jobs.