ELOG How-To

Updates and Results Talks and Posters Advice Ideas Important Figures Write-Ups Outreach How-To Funding Opportunities GENETIS

Place to document instructions for how to do things

Fields marked with * are required
Entry time:	Tue Feb 3 10:53:35 2026
Author*:
Subject:
Project:
<p>To analyze data, we sometimes need to run over many thousands of runs at once. To do this in parallel, we can submit a job for every run we want to do. This will proceed in several steps:</p> <ol> <li>We need to prepare an analysis program. <ol> </ol> <ol> <li>This is demo.cxx.</li> <li>The program will take an input data file and an output location.</li> <li>The program will do some analysis on each events, and then write the result of that analysis to an output file labeled by the same number as the input file.</li> </ol> </li> <li>We need to prepare a job script for PBS. <ol> <li>This is "run.sh"; this is the set of instructions to be submitted to the cluster.</li> <li>The instructions say to: <ol> <li>Source a a shell environment</li> <li>To run the executable</li> <li>Move the output root file to the output location.</li> </ol> </li> <li>Note that we're telling the program we wrote in step 1 to write to the node-local $TMPDIR, and then moving the result to our final output directory at the end. This is better for cluster performance.</li> </ol> </li> <li>We need to make a list of data files to run over <ol> <li>We can do this on OSC by running <code>ls -d -1 /fs/scratch/PAS0654/ara/10pct/RawData/A3/2013/sym_links/event.root > run_list.txt</code></li> <li>This places the full path to the ROOT files in that folder into a list called run_list.txt that we can loop over.</li> </ol> </li> <li>Third, we need to script that will submit all of the jobs to the cluster. <ol> <li>This is "submit_jobs.sh".</li> <li>This loops over all the files in our run_list.txt and submits a run.sh job for each of them.</li> <li>This is also where we define the $RUNDIR (where the code is to be exeucted) and the $OUTPUTDIR (where the output products are to be stored)</li> </ol> </li> </ol> <p>Once you've generated all of these output files, you can run over the output files only to make plots and such.</p> <p> </p> Encoding*: HTML ELCode plain Suppress Email notification

Attachment 1:
Drop attachments here...

ELOG V3.1.5-fc6679b