Running Your First HTC Jobs
So, you have an account on a submit node, and you are ready to run your first job in the CHTC. As we described in Our Approach, the CHTC is a collection of distributed resources. The magic that enables you to run jobs on these resources is software, called HTCondor, developed at the UW-Madison.
Table of Contents
1. Let's first do, and then ask why
We recommend that you also check out the HTCondor Job Submission Intro (video), but this example let’s you just run some jobs so you can see what happens, with some additional discussion along the way.
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 an HTCondor submit machine for the following example to work. See the Connecting to CHTC guide for more information on how to log in.
1. Copy the highlighted text below, and paste it into file called
hello-chtc.sub (we recommend using a command line text editor) in your home directory on the submit
machine. This is the file you will submit to HTCondor to describe your jobs (known as the submit file).
# hello-chtc.sub # My very first HTCondor submit file # # Specify the HTCondor Universe (vanilla is the default and is used # for almost all jobs) and your desired name of the HTCondor log file, # which is where HTCondor will describe what steps it takes to run # your job. Wherever you see $(Cluster), HTCondor will insert the # queue number assigned to this set of jobs at the time of submission. universe = vanilla log = hello-chtc_$(Cluster).log # # Specify your executable (single binary or a script that runs several # commands), arguments, and a files for HTCondor to store standard # output (or "screen output"). # $(Process) will be a integer number for each job, starting with "0" # and increasing for the relevant number of jobs. executable = hello-chtc.sh arguments = $(Process) output = hello-chtc_$(Cluster)_$(Process).out error = hello-chtc_$(Cluster)_$(Process).err # # Specify that HTCondor should transfer files to and from the # computer where each job runs. The last of these lines *would* be # used if there were any other files needed for the executable to use. should_transfer_files = YES when_to_transfer_output = ON_EXIT # transfer_input_files = file1,/absolute/pathto/file2,etc # # Tell HTCondor what amount of compute resources # each job will need on the computer where it runs. request_cpus = 1 request_memory = 1GB request_disk = 1MB # # Tell HTCondor to run 3 instances of our job: queue 3
For a "template" version of this submit file without the comments, click here.
2. Now, create the executable that we specified above: copy the text
below and paste it into a file called
#!/bin/bash # # hello-chtc.sh # My very first 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
By using the "$1" variable in our executable, we are telling HTCondor to fetch the value of the agrument 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-chtc.sh will insert that value for "$1",
More information on special variables like "$1", "$2", and "$@" can be found here.
3. Now, submit your job to the queue using
[alice@submit]$ condor_submit hello-chtc.sub
condor_submit command actually submits your jobs to HTCondor. If
all goes well, you will see output from the
condor_submit command that
Submitting job(s)..... 3 job(s) submitted to cluster 436950.
4. To check on the status of your jobs, run the following command:
The output of
condor_q should look like this:
-- Schedd: submit-2.chtc.wisc.edu : <184.108.40.206:9618?... @ 04/05/19 15:35:17 OWNER BATCH_NAME SUBMITTED DONE RUN IDLE TOTAL JOB_IDS alice ID: 436950 4/5 15:34 _ _ 3 3 436950.0-2 3 jobs; 0 completed, 0 removed, 3 idle, 0 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. For more details on this
option, and other options to
condor_q, see our condor_q
Alternately, you can run the
condor_watch_q command to display the
status of your jobs in the queue along with color-coded progress bars.
The display is updated automatically every couple seconds, allowing you
to monitor the status of your jobs in real time. To exit the view,
use the keyboard shortcut
If your jobs go on hold and you usually use a Windows laptop or desktop, please see this page for a potential diagnosis and solution.
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 5 15:37 hello-chtc_436950_0.err -rw-r--r-- 1 alice alice 60 Apr 5 15:37 hello-chtc_436950_0.out -rw-r--r-- 1 alice alice 0 Apr 5 15:37 hello-chtc_436950_1.err -rw-r--r-- 1 alice alice 60 Apr 5 15:37 hello-chtc_436950_1.out -rw-r--r-- 1 alice alice 0 Apr 5 15:37 hello-chtc_436950_2.err -rw-r--r-- 1 alice alice 60 Apr 5 15:37 hello-chtc_436950_2.out -rw-r--r-- 1 alice alice 5111 Apr 5 15:37 hello-chtc_436950.log -rw-rw-r-- 1 alice alice 241 Apr 5 15:33 hello-chtc.sh -rw-rw-r-- 1 alice alice 1387 Apr 5 15:33 hello-chtc.sub
Useful information is provided in the user log and the 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. An excerpt from
hello-chtc_845638.log produced due the
submission of the 3 jobs will look something like this:
000 (436950.000.000) 04/05 15:34:33 Job submitted from host: <220.127.116.11:9618?addrs=128.104...> ... 040 (436950.000.000) 04/05 15:34:50 Started transferring input files Transferring to host: <18.104.22.168:9618?addrs=128.104....> ... 040 (436950.000.000) 04/05 15:34:50 Finished transferring input files ... 001 (436950.000.000) 04/05 15:34:51 Job executing on host: <22.214.171.124:9618?addrs=128.104...> ... 006 (436950.000.000) 04/05 15:35:00 Image size of job updated: 368 1 - MemoryUsage of job (MB) 292 - ResidentSetSize of job (KB) ... 040 (436950.000.000) 04/05 15:37:51 Started transferring output files ... 040 (436950.000.000) 04/05 15:37:51 Finished transferring output files ... 005 (436950.000.000) 04/05 15:37:51 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 60 - Run Bytes Sent By Job 241 - Run Bytes Received By Job 60 - Total Bytes Sent By Job 241 - Total Bytes Received By Job Partitionable Resources : Usage Request Allocated Cpus : 0 1 1 Disk (KB) : 24 1024 908236 Ioheavy : 0 Memory (MB) : 1 1024 1024 ...
And, if you look at one of the output files, you should see something like this:
Hello CHTC from Job 0 running on email@example.com
Congratulations. You've run your first jobs in the CHTC!
2. What Else?
A. Removing Jobs
To remove a specific job, specify the job ID number from the queue (format: Cluster.Process). Example:
[alice@submit]$ condor_rm 845638.0
You can even remove all of the jobs of the same cluster by specifying only the Cluster value for that batch. To remove all of your jobs:
[alice@submit]$ condor_rm $USER
B. The Importance of Testing
1. Examining 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. 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
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 in that case as well.
3. Determining Run Time. Depending on how long each of your jobs are (determined by examining when the job began executing and when it completed), you can send your jobs to even more computers than are in the CHTC Pool (where your jobs will run, by default). Refer to the table below for tips on how to send your jobs to the rest of the UW Grid and to the national OS Pool.
C. Getting the Right Resources
Be sure to always add or modify the following lines in your submit files, as appropriate, and after running a few tests.
|Submit file entry||Resources your jobs will run on|
||Matches each job to a computer "slot" with at least this many CPU cores.|
||Matches each job to a slot with at least this much disk space, in units of KB.|
||Matches each job to a slot with at least this much memory (RAM), in units of MB.|
||Also send jobs to other HTCondor Pools on campus (UW Grid)
Good for jobs that are less than ~8 hours, or checkpoint at least that frequently.
||Also send jobs to the OS Pool.
Good for jobs that are less than ~8 hours (or checkpoint at least that frequently), and have been tested for portability. (Contact Us for more details).
Learn more about sending jobs to the UW Grid and OS pool in our Scaling Beyond Local HTC Capacity guide.
D. Run Your OWN Jobs
If you didn’t check it out already, NOW is a great time to check out the HTCondor Job Submission Intro (video), which introduces various ways to specify differences between jobs (e.g. parameters, different input filenames, etc.), ways to organize your data, etc. You’ll notice that it’s part of a playlist of videos with topics for HTCondor users.
Our full set of CHTC online guides is available here, and includes some specific examples for how to use various software within a job, or a Research Computing Facilitation can help you get your software going. Remember to Get Help whenever you have questions or issues. That's what CHTC staff are here for.
The full HTCondor manual is comprehensive and lengthy, and Googling "HTCondor examples" may lead you to examples that really only work on another campus's HTCondor system. You can always dig into more details as you become more experienced, but the below pages of the manual may be a good place to start, if you like manuals:
- Road-map for Running Jobs
- Submitting a Job
- Managing a Job
- Matchmaking with ClassAds
Now you are ready for some real work
Ok, you have the basics! This should be enough background to get you started using the CHTC for the real problems you came to us for. Remember, we are here to help. Don't hesitate to contact us at firstname.lastname@example.org with questions.