{"id":882,"date":"2020-11-06T10:56:13","date_gmt":"2020-11-06T09:56:13","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=882"},"modified":"2025-05-20T11:47:32","modified_gmt":"2025-05-20T09:47:32","slug":"trainings-2019-hpc-practice-slurm","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/en\/trainings-2019-hpc-practice-slurm\/","title":{"rendered":"Trainings- HPC &#8211; Practice SLURM"},"content":{"rendered":"<h2>HPC Practice SLURM<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Hands On Lab Exercises for HPC<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Related-course materials<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-hpc\/\">HPC<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">Ndomassi TANDO (ndomassi.tando@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">25\/11\/2019<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">20\/05\/2025<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>Summary<\/h3>\n<p><!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 --><\/p>\n<ul>\n<li><a href=\"#preambule\">Preambule: Softwares to install before connecting to a distant linux server <\/a><\/li>\n<li><a href=\"#practice-1\">Practice 1: Get connecting on a linux server by <code>ssh<\/code><\/a><\/li>\n<li><a href=\"#practice-2\">Practice 2: Reserve one core of a node using qrsh and create your working folder<\/a><\/li>\n<li><a href=\"#practice-3\">Practice 3: Transfering files with filezilla <code>sftp<\/code> and install your ssh keys<\/a><\/li>\n<li><a href=\"#practice-4\">Practice 4: Transfering data to the node <code>scp<\/code><\/a><\/li>\n<li><a href=\"#practice-5\">Practice 5: Use module environment to  load your tool<\/a><\/li>\n<li><a href=\"#practice-6\">Practice 6: Launch analyses <\/a><\/li>\n<li><a href=\"#practice-7\">Practice 7: Transfering data to the san server <code>scp<\/code> <\/a><\/li>\n<li><a href=\"#practice-8\">Practice 8: Deleting your temporary folder <\/a><\/li>\n<li><a href=\"#practice-9\">Practice 9: Launch a job via sbatch<\/a><\/li>\n<li><a href=\"#links\">Links<\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"preambule\"><\/a><\/p>\n<h3>Preambule<\/h3>\n<h5>Getting connected to a Linux servers from Windows with SSH (Secure Shell) protocol<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Platform<\/th>\n<th style=\"text-align: left;\">Software<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"20%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osWin.png\"\/><\/td>\n<td style=\"text-align: left;\">mobaXterm<\/td>\n<td style=\"text-align: left;\">an enhanced terminal for Windows with an X11 server and a tabbed SSH client<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/mobaxterm.mobatek.net\/\">more<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"20%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osWin.png\"\/><\/td>\n<td style=\"text-align: left;\">putty<\/td>\n<td style=\"text-align: left;\">Putty allows to  connect to a Linux server from a Windows workstation.<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.chiark.greenend.org.uk\/~sgtatham\/putty\/latest.html\">Download<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>Transferring and copying files from your computer to a Linux servers with SFTP (SSH File Transfer Protocol) protocol<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Platform<\/th>\n<th style=\"text-align: left;\">Software<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"10%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osApple.png\"\/> <img decoding=\"async\" width=\"10%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osLinux.png\"\/> <img decoding=\"async\" width=\"10%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osWin.png\"\/><\/td>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"10%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/filezilla.png\"\/> filezilla<\/td>\n<td style=\"text-align: left;\">FTP and SFTP client<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/filezilla-project.org\/\">Download<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>Viewing and editing files on your computer before transferring on the linux server or directly on the distant server<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Type<\/th>\n<th style=\"text-align: left;\">Software<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Distant, consol mode<\/td>\n<td style=\"text-align: left;\">nano<\/td>\n<td style=\"text-align: left;\"><a href=\"http:\/\/www.howtogeek.com\/howto\/42980\/\">Tutorial<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Distant, consol mode<\/td>\n<td style=\"text-align: left;\">vi<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.washington.edu\/computing\/unix\/vi.html\">Tutorial<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Distant, graphic mode<\/td>\n<td style=\"text-align: left;\">komodo edit<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.activestate.com\/komodo-ide\/downloads\/edit\">Download<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Linux &amp; windows based editor<\/td>\n<td style=\"text-align: left;\">Notepad++<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/notepad-plus-plus.org\/download\/v7.5.5.html\">Download<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<p><a name=\"practice-1\"><\/a><\/p>\n<h3>Install your ssh keys on your computer<\/h3>\n<p>Follow the instructions here according to your OS:<\/p>\n<p><a href=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-add-ssh-keys\/\">https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-add-ssh-keys\/<\/a><\/p>\n<h3>Practice 1: Get Connecting on a linux server by <code>ssh<\/code><\/h3>\n<p>In mobaXterm:<\/p>\n<ol>\n<li>Click the session button, then click SSH.\n<ul>\n<li>In the remote host text box, type: bioinfo-master1.ird.fr<\/li>\n<li>Check the specify username box and enter your user name<\/li>\n<\/ul>\n<\/li>\n<li>In the console, enter the password when prompted.<br \/>\nOnce you are successfully logged in, you will be use this console for the rest of the lecture. <\/li>\n<li>Type the command <code>sinfo<\/code> and comment the result<\/li>\n<li>type the command <code>sinfo -N nodes --long<\/code> and noticed what have been added<\/li>\n<li>Type the command <code>scontrol show nodes<\/code><\/li>\n<\/ol>\n<hr \/>\n<p><a name=\"practice-2\"><\/a><\/p>\n<h3>Practice 2: Reserve one core of a node using srun and create your working folder<\/h3>\n<ol>\n<li>Type the command <code>squeue<\/code> and noticed the result<\/li>\n<li>Type the command <code>squeue -u your_login<\/code> with your_login to change with your  account and noticed the difference<\/li>\n<li>More details with the command: <code>squeue -O &quot;username,name:40,partition,nodelist,NumCPUs,state,timeused,timelimit&quot;<\/code><\/li>\n<li>Type the command <code>srun -p short --pty bash -i <\/code> then <code>squeue<\/code> again <\/li>\n<li>Create your own working folder in the \/scratch of your node:<\/li>\n<\/ol>\n<pre><code>cd \/scratch\n mkdir login\n with login : the name of your choice<\/code><\/pre>\n<hr \/>\n<p><a name=\"practice-3\"><\/a><\/p>\n<h3>Practice 3 : Transferring files with filezilla <code>sftp<\/code> and install your ssh keys<\/h3>\n<h5>Download and install FileZilla<\/h5>\n<h5>Open FileZilla and save the IRD cluster into the site manager<\/h5>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-filezilla1.png\"\/><\/p>\n<p>In the FileZilla menu, go to <em>File &gt; Site Manager<\/em>. Then go through these 5 steps:<\/p>\n<ol>\n<li>Click <em>New Site<\/em>.<\/li>\n<li>Add a custom name for this site.<\/li>\n<li>Add the hostname bioinfo-san.ird.fr to have access to \/home<\/li>\n<li>Set the Logon Type to &quot;Normal&quot; and insert your username and password used to connect on the IRD cluster<\/li>\n<li>Press the &quot;Connect&quot; button.<\/li>\n<\/ol>\n<h5>Transferring files<\/h5>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-filezilla2.png\"\/><\/p>\n<ol>\n<li>From your computer to the cluster : click and drag an text file item from the left local colum to the right remote column <\/li>\n<li>From the cluster to your computer : click and drag an text file item from he right remote column to the left local column<\/li>\n<li>Retrieve the file ssh-login.zip from the right window into your folder \/home\/login<\/li>\n<\/ol>\n<hr \/>\n<p><a name=\"practice-4\"><\/a><\/p>\n<h3>Practice 4: Transfer your data from the san server to the node<\/h3>\n<ol>\n<li>Using scp, transfer the folder <code>Ebola<\/code> located in <code>\/share\/formation\/Slurm\/TPassembly<\/code> into your working directory<\/li>\n<li>Check your result with ls<\/li>\n<\/ol>\n<hr \/>\n<p><a name=\"practice-5\"><\/a><\/p>\n<h3>Practice 5: Use module environment to  load your tools<\/h3>\n<ol>\n<li>Load abyss 2.2.5 module<\/li>\n<li>Check if the tool are loaded<\/li>\n<\/ol>\n<hr \/>\n<p><a name=\"practice-6\"><\/a><\/p>\n<h3>Practice 6 : Launch analyses<\/h3>\n<h4>Perform an assembly with abyss-pe<\/h4>\n<p>With abyss software, we reassembly the sequences using the 2 fastq.gz files ebola_R1.fastq.gz and ebola_R2.fastq.gz<\/p>\n<p>Launch the command<\/p>\n<pre><code>abyss-pe k=35 in=&#039;ebola_R1.fastq.gz ebola_R2.fastq.gz&#039; name=k35<\/code><\/pre>\n<p>NB: you can do the same thing using srun directly from the master assuming that the data have been transfer to the \/scratch of your node and that you know the nodename:<\/p>\n<p>From the master, type the following commands:<\/p>\n<pre><code>module load abyss\/2.2.5\nsrun -p partitionname --nodelist=nodename --chdir=\/scratch\/login\/TPassembly\/Ebola abyss-pe k=35 -j1 np=1  in=&#039;ebola1.fastq ebola2.fastq&#039; name=k35<\/code><\/pre>\n<p>the -p allows to indicate the partition to use , replace <code>partitionname<\/code>parameter<br \/>\nthe --nodelist allows to indicate the node to use , replace <code>nodename<\/code>parameter<br \/>\nthe <code>--chdir<\/code> allows to change the working directory and to precise in which directory the analysis will be done directly into the node.<\/p>\n<hr \/>\n<p><a name=\"practice-7\"><\/a><\/p>\n<h3>Practice 7: Transfering data to the san server<\/h3>\n<ol>\n<li>Using scp, transfer your results from your <code>\/scratch\/login<\/code> to your <code>\/home\/login<\/code> <\/li>\n<li>Check if the transfer is OK with ls<\/li>\n<\/ol>\n<hr \/>\n<p><a name=\"practice-8\"><\/a><\/p>\n<h3>Practice 8: Deleting your temporary folder<\/h3>\n<pre><code>cd \/scratch\nrm -r login<\/code><\/pre>\n<pre><code>exit<\/code><\/pre>\n<hr \/>\n<p><a name=\"practice-9\"><\/a><\/p>\n<h3>Practice 9: Launch a job with sbatch<\/h3>\n<p>Following the several steps performed during the practice, create a script to launch the analyses made in practice6:<\/p>\n<p>1er step: create the Slurm section in your script <\/p>\n<p>1) Set  a name for your job<\/p>\n<p>2) Precise your email<\/p>\n<p>3) Choose the short partition<\/p>\n<p>2nd step: type  the commands you want the script to launch:<\/p>\n<p>1) create a personal folder in \/scratch with <code>mkdir<\/code><\/p>\n<p>2) Using scp, transfer the folder <code>Ebola<\/code> located in <code>\/share\/formation\/Slurm\/TPassembly<\/code> into your working directory<\/p>\n<p>3) Launch abyss version 2.2.5 with module load<\/p>\n<p>4) Into the the folder <code>Ebola<\/code>, launch the following command:<\/p>\n<pre><code>abyss-pe k=35 in=&#039;ebola1.fastq ebola2.fastq&#039; name=k35<\/code><\/pre>\n<p>5) Using scp, transfer your results from your <code>\/scratch\/login<\/code> to your <code>\/home\/login<\/code> <\/p>\n<p>6) Delete the personal folder in the  <code>\/scratch<\/code><\/p>\n<p>Launch the following commands to obtain info on the finished job:<\/p>\n<pre><code>seff &lt;JOB_ID&gt;\nsacct --format=JobID,elapsed,ncpus,ntasks,state,node -j &lt;JOB_ID&gt;<\/code><\/pre>\n<h2>Bonus:<\/h2>\n<p>We are  going to launch a 4 steps analysis:<\/p>\n<p>1) Perform a multiple alignment with the nucmer  tool<\/p>\n<p>2) Filter these alignments with the delta-filter  tool<\/p>\n<p>3) Generate a tab file easy to parse the with show-coords tools<\/p>\n<p>4) Generate a png image with mummerplot<\/p>\n<ul>\n<li>\n<p>Retrieve the script \/projects\/medium\/formation\/Slurm\/scripts\/alignment_slurm.sh into your \/home\/login<\/p>\n<\/li>\n<li>\n<p>modify the Slurm section and the variables<\/p>\n<\/li>\n<li>\n<p>launch the script with sbatch:<\/p>\n<\/li>\n<\/ul>\n<pre><code>sbatch alignment.sh<\/code><\/pre>\n<ul>\n<li>\n<p>Do a <code>ls -altr<\/code> in your <code>\/home\/login<\/code>. What do you notice?<\/p>\n<\/li>\n<li>\n<p>Launch the following commands to obtain info on the finished job:<\/p>\n<\/li>\n<\/ul>\n<pre><code>seff &lt;JOB_ID&gt;\nsacct --format=JobID,elapsed,ncpus,ntasks,state,node -j &lt;JOB_ID&gt;<\/code><\/pre>\n<ul>\n<li>\n<p>Open filezilla and retrieve the png image to your computer<\/p>\n<\/li>\n<li>\n<p>Launch the following commande to clear the \/scratch of the node<\/p>\n<\/li>\n<\/ul>\n<pre><code>sh \/opt\/scripts\/scratch-scripts\/scratch_use.sh<\/code><\/pre>\n<p>and choose the number of the node used<\/p>\n<hr \/>\n<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li>Related courses : <a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-linux-for-dummies\/\">Linux for Dummies<\/a><\/li>\n<li>Tutorials : <a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/linux-tutorial\/\">Linux Command-Line Cheat Sheet<\/a><\/li>\n<\/ul>\n<hr \/>\n<h3>License<\/h3>\n<p><a name=\"license\"><\/a><\/p>\n<div>\nThe resource material is licensed under the Creative Commons Attribution 4.0 International License (<a href=\"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">here<\/a>).<br \/>\n<center><img decoding=\"async\" width=\"25%\" class=\"img-responsive\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\"\/><br \/>\n<\/center>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>HPC Practice SLURM Description Hands On Lab Exercises for HPC Related-course materials HPC Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 25\/11\/2019&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/trainings-2019-hpc-practice-slurm\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-882","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Trainings- HPC - Practice SLURM - itrop<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/trainings-2019-hpc-practice-slurm\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Trainings- HPC - Practice SLURM - itrop\" \/>\n<meta property=\"og:description\" content=\"HPC Practice SLURM Description Hands On Lab Exercises for HPC Related-course materials HPC Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 25\/11\/2019&hellip; 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