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<!DOCTYPE html><html><head><meta charset="utf-8"><title>GNU Parallel.md</title><style>@charset "UTF-8";@import 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.9.0-alpha2/katex.min.css';code{color:#c7254e;background-color:#f9f2f4;border-radius:4px}code,kbd{padding:2px 4px}kbd{color:#fff;background-color:#333;border-radius:3px;box-shadow:inset 0 -1px 0 rgba(0,0,0,.25)}kbd kbd{padding:0;font-size:100%;box-shadow:none}pre{display:block;margin:0 0 10px;word-break:break-all;word-wrap:break-word;color:#333;background-color:#f5f5f5;border:1px solid #ccc;border-radius:4px}pre code{padding:0;font-size:inherit;color:inherit;white-space:pre-wrap;background-color:transparent;border-radius:0}.pre-scrollable{max-height:340px;overflow-y:scroll}table{background-color:transparent}th{text-align:left}.table{width:100%;max-width:100%;margin-bottom:20px}.table>thead>tr>th{padding:8px;line-height:1.4285714;border-top:1px solid 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<p>Slurm is a resource manager and job scheduler designed for scheduling and allocating resources as per user job requirements. Slurm is a open source software originally created by the Livermore Computing Center.</p>
<h2><a id="Slurm_Commands_2"></a>Slurm Commands</h2>
<p><code>sinfo</code> provides information regarding resources that are available from server.<br>
Example :</p>
<pre><code>(ceodspsp) taos:~$ sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
normal* up 2-00:00:00 2 mix taos[01,09]
normal* up 2-00:00:00 1 alloc taos02
normal* up 2-00:00:00 6 idle taos[03-08]
</code></pre>
<p>From the above above, we can see one node(taos02) is allocated under normal partition. Similarly 2 nodes from ( 01-09) are in mixed state referring some nodes being used and some being idle.</p>
<p><code>sinfo –N –l</code> provides more information of Node including CPU count, memory, temporary disk and so.</p>
<pre><code>(ceodspsp) taos:~$ sinfo -N -l
Tue Feb 19 19:08:16 2019
NODELIST NODES PARTITION STATE CPUS S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON
taos01 1 normal* mixed 80 2:20:2 386868 690861 10 (null) none
taos02 1 normal* allocated 40 2:10:2 64181 309479 1 (null) none
taos03 1 normal* idle 40 2:10:2 64181 309479 1 (null) none
taos04 1 normal* idle 40 2:10:2 64181 358607 1 (null) none
taos05 1 normal* idle 40 2:10:2 64181 309479 1 (null) none
taos06 1 normal* idle 40 2:10:2 64181 309479 1 (null) none
taos07 1 normal* idle 40 2:10:2 64181 309479 1 (null) none
taos08 1 normal* idle 40 2:10:2 64181 309479 1 (null) none
taos09 1 normal* mixed 40 2:10:2 103198 6864803 20 (null) none
</code></pre>
<p>More information regarding sinfo can be found as <code>man sinfo</code></p>
<p><code>squeue</code> provides information regarding currently allocated resources.</p>
<pre><code>(ceodspsp) taos:~$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
22632 normal BinPacke schultzj PD 0:00 1 (Resources)
22548 normal minia lijing R 1-07:30:18 1 taos09
22562 normal unicycle bishoyh R 22:34:59 1 taos02
22567 normal sspace lijing R 22:00:50 1 taos01
22576 normal megahit lijing R 7:22:53 1 taos09
</code></pre>
<p>To cancel a job, you can use <code>scancel <JOBID></code> . TIME stands for the current running time of the job.</p>
<h2><a id="Slurm_JOB_Submission_43"></a>Slurm JOB Submission</h2>
<p>To create a job in slurm, you need to write a shell script called submission script which comprises of resource requests and job steps. The Resource requests consists details regarding number of CPUs, wall time, RAM and disk requirements. The submission script are usually prefixed with SBATCH which Slurm understands as parameters for resource request and submission.</p>
<p>Example of a Slurm submission script : <code>submission.sh</code></p>
<pre><code>#!/bin/bash
#
#SBATCH --job-name=demo
#SBATCH --output=result.txt
#
#SBATCH --ntasks=4
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
srun hostname
srun sleep
</code></pre>
<p>Above script requests for allocation of 4 CPUs for 10 minutes with 100MB of ram per CPU. AS the job starts to run, the script first execute the <code>srun hostname</code> followed by <code>srun sleep</code>.</p>
<p>Arguments <code>–-job-name</code> and <code>–-output</code> correspond to name of the job and output file name where the results are saved.</p>
<p>To submit the job you need to run</p>
<p><code>sbatch submission.sh</code></p>
<p>Once you execute the above command, the job enters into pending state until the resources are available for execution. If the job completes successfully then it goes to COMPLETED state, otherwise goes to FAILED state.</p>
<p>Once the job is submitted, you can use <code>sstat</code> command to see information about memory usage, CPU usage,etc.</p>
<p>As the job gets successfully completed, you can see the results by executing <code>cat result.txt</code></p>
<p>Example of a Slurm submission script for python program : <code>submission_python.sh</code></p>
<pre><code>#!/bin/bash
#
#SBATCH --job-name=demo
#SBATCH --output=result.txt
#
#SBATCH --ntasks=4
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
module load anaconda3
python demo.py 34
</code></pre>
<p><code>demo.py</code> script</p>
<pre><code># Import Libraries
import numpy
from numpy import linspace
from numpy.random import rand
from numpy.linalg import inv
import timeit
import argparse
# define command line inputs
parser = argparse.ArgumentParser()
parser.add_argument("matrix", type=int, help='provide single integer for matrix')
args = parser.parse_args()
#define our matrix inverse function
def matinv(x):
mat = rand(x, x)
b = inv(mat)
return b
out = matinv(args.matrix)
numpy.savetxt("%d.csv" % args.matrix, out, delimiter=",")
</code></pre>
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