Practice: Submit HTC Jobs using HTCondor

Purpose

This guide discusses how to run jobs on the CHTC using HTCondor.

Workflow Overview

The process of running computational workflows on CHTC resources follows the following outline:

Terminology:

  • Access point is where you login and stage your data, executables/scripts, and software to use in jobs.
  • HTCondor is a job scheduling software that will run your jobs out on the execution points.
  • The Execution Points is the set of resources your job runs on. It is composed of servers, as well as other technologies, that compose the cpus, memory, and disk space that will run the computations of your jobs.

Run Jobs using HTCondor

We are going to run the traditional ‘hello world’ program with a CHTC twist. In order to demonstrate the distributed resource nature of CHTC’s HTC System, we will produce a ‘Hello CHTC’ message 3 times, where each message is produced within is its own ‘job’. Since you will not run execution commands yourself (HTCondor will do it for you), you need to tell HTCondor how to run the jobs for you in the form of a submit file, which describes the set of jobs.

Note: You must be logged into a CHTC Access Point for the following example to work.

🎞️ Demo: Submit HTC Jobs using HTCondor

You can follow along with the job submission tutorial outlined in this guide in video format.

You may notice that the example in the video is slightly different—it uses executable and arguments in the submit file instead of shell. This is reflects an older submit convention, however, either case still works!

Prepare job executable and submit file on an Access Point

  1. First, create the executable script you would like HTCondor to run. For our example, copy the text below and paste it into a file called hello-world.sh (we recommend using a command line text editor) in your home directory.

    #!/bin/bash
#
# hello-world.sh
# My CHTC job
#
# print a 'hello' message to the job's terminal output:
echo "Hello CHTC from Job $1 running on `whoami`@`hostname`"
#
# keep this job running for a few minutes so you'll see it in the queue:
sleep 180

    Let’s test this script locally. First, let’s add executable permissions to the script with the chmod command, which allows us to execute the code.

    chmod +x hello-world.sh

    Test the code by typing the following line:

    ./hello-world.sh 0

    You should see a message printed to the terminal, like so:

    [alice@ap2002 hello-world]$ ./hello-world.sh 0
Hello CHTC from Job 0 running on alice@ap2002

    The terminal will pause for 3 minutes, as specified by sleep 180 in our script. Cancel the pause time by pressing CTRL + C. Now we’ve successfully run the script locally!

    However, to run it on CHTC, we will use our HTCondor submit file to run the hello-world.sh executable and to automatically pass different arguments to our script.

    ⚠️ Do not test your full workload directly on the Access Points!

    Simple scripts, such as this example, which use few compute resources, are safe to test, but any script or executable that requires computing power or excessive memory should be tested inside of a job.

  2. Prepare your HTCondor submit file, which you will use to tell HTCondor what job to run and how to run it. Copy the text below, and paste it into file called hello-world.sub. This is the file you will submit to HTCondor to describe your jobs (known as the submit file).

    # hello-world.sub
   
# Specify your executable (single binary or a script that runs several
#  commands) and arguments to be passed to jobs. 
#  $(Process) will be a integer number for each job, starting with "0"
#  and increasing for the relevant number of jobs.
shell = ./hello-world.sh $(Process)
   		
# Specify the name of the log, standard error, and standard output (or
# "screen output") files. Wherever you see $(Cluster), HTCondor will insert the 
#  queue number assigned to this set of jobs at the time of submission.
log = hello-world_$(Cluster)_$(Process).log
error = hello-world_$(Cluster)_$(Process).err
output = hello-world_$(Cluster)_$(Process).out
   
# Transfer our executable script
transfer_input_files = hello-world.sh
   
# Requirements (e.g., operating system) your job needs, what amount of
# compute resources each job will need on the computer where it runs.
request_cpus = 1
request_memory = 1GB
request_disk = 5GB
   
# Run 3 instances of our job:
queue 3

    By using the “$1” variable in our hello-world.sh executable, we are telling HTCondor to fetch the value of the argument in the first position in the submit file and to insert it in location of “$1” in our executable file.

    Therefore, when HTCondor runs this executable, it will pass the $(Process) value for each job and hello-world.sh will insert that value for “$1” in hello-world.sh.

    More information on special variables like “$1", “$2”, and “$@” can be found here.

  3. Now, submit your job to HTCondor’s queue using condor_submit:

    [alice@ap2002]$ condor_submit hello-world.sub

    The condor_submit command actually submits your jobs to HTCondor. If all goes well, you will see output from the condor_submit command that appears as:

    Submitting job(s)...
3 job(s) submitted to cluster 36062145.

  4. To check on the status of your jobs in the queue, run the following command:

    [alice@ap2002]$ condor_q

    The output of condor_q should look like this:

    -- Schedd: ap2002.chtc.wisc.edu : <128.104.101.92:9618?... @ 04/14/23 15:35:17
OWNER     BATCH_NAME     SUBMITTED   DONE   RUN    IDLE  TOTAL JOB_IDS
Alice ID: 3606214       4/14 12:31      2     1       _      3 36062145.0-2
   
3 jobs; 2 completed, 0 removed, 0 idle, 1 running, 0 held, 0 suspended

    You can run the condor_q command periodically to see the progress of your jobs. By default, condor_q shows jobs grouped into batches by batch name (if provided), or executable name. To show all of your jobs on individual lines, add the -nobatch option.

  5. When your jobs complete after a few minutes, they’ll leave the queue. If you do a listing of your /home directory with the command ls -l, you should see something like:

    [alice@submit]$ ls -l
total 28
-rw-r--r-- 1 alice alice    0 Apr  14 15:37 hello-world_36062145_0.err
-rw-r--r-- 1 alice alice   60 Apr  14 15:37 hello-world_36062145_0.out
-rw-r--r-- 1 alice alice    0 Apr  14 15:37 hello-world_36062145_0.log
-rw-r--r-- 1 alice alice    0 Apr  14 15:37 hello-world_36062145_1.err
-rw-r--r-- 1 alice alice   60 Apr  14 15:37 hello-world_36062145_1.out
-rw-r--r-- 1 alice alice    0 Apr  14 15:37 hello-world_36062145_1.log
-rw-r--r-- 1 alice alice    0 Apr  14 15:37 hello-world_36062145_2.err
-rw-r--r-- 1 alice alice   60 Apr  14 15:37 hello-world_36062145_2.out
-rw-r--r-- 1 alice alice    0 Apr  14 15:37 hello-world_36062145_2.log
-rw-rw-r-- 1 alice alice  241 Apr  14 15:33 hello-world.sh
-rw-rw-r-- 1 alice alice 1387 Apr  14 15:33 hello-world.sub

    Useful information is provided in the user log, standard error, and standard output files.

    HTCondor creates a transaction log of everything that happens to your jobs. Looking at the log file is very useful for debugging problems that may arise. Additionally, at the completion of a job, the .log file will print a table describing the amount of compute resources requested in the submit file compared to the amount the job actually used. An excerpt from hello-world_36062145_0.log produced due the submission of the 3 jobs will looks like this:

    …
005 (36062145.000.000) 2023-04-14 12:36:09 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
	72  -  Run Bytes Sent By Job
	265  -  Run Bytes Received By Job
	72  -  Total Bytes Sent By Job
	265  -  Total Bytes Received By Job
	Partitionable Resources :    Usage  Request  Allocated 
	   Cpus                 :        0        1          1 
	   Disk (KB)            :      118     1024 1810509281 
	   Memory (MB)          :       54     1024       1024 
   
	Job terminated of its own accord at 2023-04-14T17:36:09Z with exit-code 0.

    And, if you look at one of the output files, you should see something like this: Hello CHTC from Job 0 running on alice@e389.chtc.wisc.edu.

Congratulations. You’ve run an HTCondor job!

Important Workflow Elements

Removing Jobs

To remove a specific job, use condor_rm <JobID, ClusterID, Username>. Example:

[alice@ap2002]$ condor_rm 845638.0

Test and Optimize Resources

  1. Examine Job Success. Within the log file, you can see information about the completion of each job, including a system error code (as seen in “return value 0”). You can use this code, as well as information in your “.err” file and other output files, to determine what issues your job(s) may have had, if any.

  2. Improve Efficiency. Researchers with input and output files greater than 1GB, should store them in their /staging directory instead of /home to improve file transfer efficiency. See our data transfer guides to learn more.

  3. Get the Right Resource Requests Be sure to always add or modify the following lines in your submit files, as appropriate, and after running a few tests.

                                                   
    Submit file entryResources your jobs will run on
    request_cpus = cpusMatches each job to a computer "slot" with at least this many CPU cores.
    request_disk = kilobytesMatches each job to a slot with at least this much disk space, in units of KB.
    request_memory = megabytesMatches each job to a slot with at least this much memory (RAM), in units of MB.

  4. Determining Memory and Disk Requirements. The log file also indicates how much memory and disk each job used, so that you can first test a few jobs before submitting many more with more accurate request values. When you request too little, your jobs will be terminated by HTCondor and set to “hold” status to flag that job as requiring your attention. To learn more about why a job as gone on hold, use condor_q -hold. When you request too much, your jobs may not match to as many available “slots” as they could otherwise, and your overall throughput will suffer.

Use shell or executable/arguments in your submit file

You can either use shell or executable and arguments in your submit file to specify how to run your jobs.

Option 1: Submit with shell

You can use shell to specify the whole command you want to run.

shell = ./hello-world.sh $(Process)
transfer_input_files = hello-world.sh

When using shell, consider:

  • Do you need to transfer your executable? You may need to add your executable script (i.e., hello-world.sh) in the transfer_input_files line, as HTCondor does not have the ability to autodetect scripts to be transferred.
  • If you are using ./ to execute your code, as in the example above, ensure your shell script has executable permissions with the chmod +x <script> command.
  • Alternatively, you may use a shell like bash to execute your code, (i.e., shell = bash hello-world.sh 0). When you use this option, you do not have to give your shell script executable permissions.
  • Keep your shell script simple; quoting and special characters may throw errors. If you need complex scripting, we recommend writing a wrapper script.

Option 2: executable and arguments

In this convention, you break your command into two parts—the executable and the arguments.

executable = hello-world.sh
arguments = $(Process)

When using this option:

  • HTCondor will transfer your executable by default. You do not need to list your executable in transfer_input_files.
  • You do not have to add a ./ or /bin/bash to the beginning of your executable line.
  • You do not have to give your executable script executable permissions.
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