Xinran Miao

CHTC Examples

Posted on March 13, 2023 by Xinran Miao

This post prepares a few examples on running jobs on the Center for High Throughout Computing (CHTC) at UW-Madison.

I. Getting Started

  1. Request an account.
  2. Log in.
ssh username@ap2002.chtc.wisc.edu
  1. Write two files: a submit file including submit information and a bash script to execuate your job.
# r_example.submit
universe=docker
docker_image=xinranmiao/r_example:20221006
log=r_example.log
error=r_example.err
output=r_example.out
executable=r_example.sh
request_disk=1GB
queue
# r_example.sh
#!/bin/bash
R -e "installed.packages()"
  1. Submit your job.
condor_submit r_example.submit
  1. (Optional) Check your job and/or edit it.
# query your jobs
condor_q
# you'll find your job_id, say it's 9644580 

# query jobs on hold
condor_q -hold

# analyze a job (e.g., why a job keeps idle)
condor_q -better-analyze 9644580 

# log into a job
condor_ssh_to_job -auto-retry 9644580 

# change requested resources
# use it when a job is held due to insufficient resources
condor_qedit 9644580 RequestMemory 2200

# remove a job
condor_rm 9644580

II. Parallel Jobs

Example 1: Run Multiple Jobs

Suppose you wish to run 20 jobs, you may change the queue in r_example.submit to be queue 20.

# r_example.submit
universe=docker
docker_image=xinranmiao/r_example:20221006

log=r_example$(Process).log
error=r_example$(Process).err
output=r_example$(Process).out

executable=r_example.sh

request_disk=1GB
queue 20

Example 2: Read Arguments from File

Suppose one wishes to read arguments from args.txt in order to run an R file run.R taking several input arguments.

# run.R
opts <- commandArgs(trailingOnly=TRUE)
print(opts)
# args.txt
1,3,100
2,3,200

Then we can modify the last line of the submit file so that it reads from the args.txt. Remember to transfer both args.txt and run.R by setting transfer_input_files.

# parallel_example.submit
universe=docker
docker_image=xinranmiao/r_example:20221006
log=parallel_example$(job_id).log
error=parallel_example$(job_id).err
output=parallel_example$(job_id).out

executable=parallel_example.sh
arguments=$(job_id) $(n) $(d)

transfer_input_files=args.txt, run.R

request_cpus=1
request_memory=1GB
request_disk=2GB
requirements=(has_avx == true)

queue job_id, d, n from args.txt

We may also update the bash script so that it runs the run.R file.

# parallel_example.sh
#!/bin/bash
Rscript run.R $2 $3

III. Environment

Docker Images

The CHTC supports using pulling docker images; see their documentation. In fact, all the examples above used a toy docker image I made from this dockerfile. You may find some toy examples for R and python from my earlier repo.

Installing Packages

There are official tutorials on running R, Julia, Python, and others on CHTC.

IV. Resources

CHTC User Guide
Prof. Kris Sankaran’s blog on using CHTC