<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Michael answered your question but since I completed my response
just as it came through I guess I will still send it. The only
thing I would reiterate over Michael's response is you can set the
slurm array id's as desired so you don't necessarily have to do
the subtract 1 add 1 to determine array limits. <br>
</p>
<p>The situation you are describing is an excellent use for array
jobs. You can create a list of the non-numerical values you want
to use and then call the specific one you want using the built in
jobid environment vairables. The list can be created as a bash
list in your submission script directly or an input file based on
what is easiest to make.</p>
<p>Example: Assume I have 4 different input values I want to run for
the same script. I would create a submission script as such:</p>
<tt>#!/bin/bash</tt><br>
<tt>#SBATCH --array=0-3</tt><br>
<tt>inputs=('in1' 'in2' 'in3' 'in4')</tt><br>
<tt>script.py ${inputs[$SLURM_ARRAY_TASK_ID]}</tt>
<p>This will submit 4 separate jobs running different inputs for
your python script.</p>
<p>If you have 500 individual jobs that you want to run putting all
you inputs in your submission script is probably a lot of
unnecessary work and would make changing your inputs difficult. In
that case you can make a file where each input is on it's own line
and create a submission script similar to:</p>
<tt>#!/bin/bash</tt><br>
<tt>#SBATCH --array=1-4</tt><br>
<tt>file='inputfile'</tt><br>
<tt>input=$(sed -n -e ${SLURM_ARRAY_TASK_ID}p $file</tt><br>
<tt>script.py $input</tt>
<p>Be aware that bash lists start indexing at 0 so your array would
likely start at 0 and sed line numbers will start at 1 so you want
to start at 1. You can also make the array index to be anything
you want so if you know you only want to run lines 100-200 you can
set array=100-200.</p>
<p>Regards,</p>
<div class="moz-signature">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<title></title>
<table cellspacing="0" cellpadding="0" border="0">
<tbody>
<tr>
<td width="150" valign="top" height="30" align="left">
<p style="font-size:14px;">Willy Markuske</p>
</td>
</tr>
<tr>
<td style="border-right: 1px solid #000;" align="left">
<p style="font-size:12px;">HPC Systems Engineer</p>
</td>
<td rowspan="3" width="180" valign="center" height="42"
align="center"><tt><img moz-do-not-send="false"
src="cid:part1.467F9548.0B7434D5@sdsc.edu" alt=""
width="168" height="48"></tt> </td>
</tr>
<tr>
<td style="border-right: 1px solid #000;" align="left">
<p style="font-size:12px;">Research Data Services</p>
</td>
</tr>
<tr>
<td style="border-right: 1px solid #000;" align="left">
<p style="font-size:12px;">P: (858) 246-5593</p>
</td>
</tr>
</tbody>
</table>
<p> </p>
</div>
<div class="moz-cite-prefix">On 7/15/20 1:45 PM, Renfro, Michael
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:3061F8F0-9BF7-4D9D-BCCA-B96B63817818@tntech.edu">
<pre class="moz-quote-pre" wrap="">If the 500 parameters happened to be filenames, you could do adapt like (appropriated from somewhere else, but I can’t find the reference quickly:
=====
#!/bin/bash
# get count of files in this directory
NUMFILES=$(ls -1 *.inp | wc -l)
# subtract 1 as we have to use zero-based indexing (first element is 0)
ZBNUMFILES=$(($NUMFILES - 1))
# submit array of jobs to SLURM
if [ $ZBNUMFILES -ge 0 ]; then
sbatch --array=0-$ZBNUMFILES array_job.sh
else
echo "No jobs to submit, since no input files in this directory.”
fi
=====
with:
=====
#!/bin/bash
#SBATCH --nodes=1 --ntasks-per-node=1 --cpus-per-task=1
#SBATCH --time=00:01:00
#SBATCH --job-name array_demo_2
echo "All jobs in this array have:"
echo "- SLURM_ARRAY_JOB_ID=${SLURM_ARRAY_JOB_ID}"
echo "- SLURM_ARRAY_TASK_COUNT=${SLURM_ARRAY_TASK_COUNT}"
echo "- SLURM_ARRAY_TASK_MIN=${SLURM_ARRAY_TASK_MIN}"
echo "- SLURM_ARRAY_TASK_MAX=${SLURM_ARRAY_TASK_MAX}"
echo "This job in the array has:"
echo "- SLURM_JOB_ID=${SLURM_JOB_ID}"
echo "- SLURM_ARRAY_TASK_ID=${SLURM_ARRAY_TASK_ID}"
# grab our filename from a directory listing
FILES=($(ls -1 *.inp))
FILENAME=${FILES[$SLURM_ARRAY_TASK_ID]}
echo "My input file is ${FILENAME}”
# make new directory, change into it, and run
mkdir ${FILENAME}_out
cd ${FILENAME}_out
echo "First 10 lines of ../${FILENAME} are:" > ${FILENAME}_results.out
head ../${FILENAME} >> ${FILENAME}_results.out
=====
If the 500 parameters were lines in a file, the same logic would apply:
- subtract 1 from the number of lines in the file to determine the array limit
- add 1 to ${SLURM_ARRAY_TASK_ID} to get a line number for a specific parameter
- something like "sed -n ‘${TASK_ID_PLUS_ONE}p’ filename” to retrieve that parameter
- run the Python script with that value
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">On Jul 15, 2020, at 3:13 PM, c b <a class="moz-txt-link-rfc2396E" href="mailto:breedthoughts.www@gmail.com"><breedthoughts.www@gmail.com></a> wrote:
External Email Warning
This email originated from outside the university. Please use caution when opening attachments, clicking links, or responding to requests.
I'm trying to run an embarrassingly parallel experiment, with 500+ tasks that all differ in one parameter. e.g.:
job 1 - script.py foo
job 2 - script.py bar
job 3 - script.py baz
and so on.
This seems like a case where having a slurm array hold all of these jobs would help, so I could just submit one job to my cluster instead of 500 individual jobs. It seems like sarray is only set up for varying an integer index parameter. How would i do this for non-numeric values (say, if the parameter I'm varying is a string in a given list) ?
</pre>
</blockquote>
<pre class="moz-quote-pre" wrap="">
</pre>
</blockquote>
</body>
</html>