{"id":941,"date":"2020-11-09T11:50:39","date_gmt":"2020-11-09T10:50:39","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=941"},"modified":"2022-04-06T14:48:39","modified_gmt":"2022-04-06T12:48:39","slug":"trainings-2019-admin-hpc-module-2-creation-container-en","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-2\/trainings-2019-admin-hpc-module-2-creation-container-en\/","title":{"rendered":"Trainings 2019 &#8211; Admin HPC &#8211; module 2 &#8211; creation container &#8211; EN"},"content":{"rendered":"<h2>Container creation<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Create your own Singularity containers<\/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-admin-hpc-module-2\/\">HPC Administration Module2<\/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;\">24\/09\/2019<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">24\/09\/2019<\/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=\"#part-1\">Install dependencies<\/a><\/li>\n<li><a href=\"#part-2\">Install The programming  language Go<\/a><\/li>\n<li><a href=\"#part-3\">Download and install singularity from repo<\/a><\/li>\n<li><a href=\"#part-4\">Modify Bind path in Singularity<\/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=\"part-1\"><\/a><\/p>\n<h2>Install dependencies<\/h2>\n<pre><code> $ sudo yum update -y &amp;&amp; \\\n      sudo yum groupinstall -y &#039;Development Tools&#039; &amp;&amp; \\\n      sudo yum install -y \\\n      openssl-devel \\\n      libuuid-devel \\\n      libseccomp-devel \\\n      wget \\\n      squashfs-tools \\\n      git<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-2\"><\/a><\/p>\n<h2>Install The programming  language Go:<\/h2>\n<p>Go to the <a href=\"https:\/\/golang.org\/dl\/\">Download Page<\/a> and choose the archive go.1.12.5.linux-amd64.tar.gz<\/p>\n<p>Launch the following commands:<\/p>\n<pre><code># Download the archive\n    wget https:\/\/dl.google.com\/go\/go1.12.5.linux-amd64.tar.gz\n    # Extract the archive into \/usr\/local\n    sudo tar -C \/usr\/local -xzvf go1.12.5.linux-amd64.tar.gz<\/code><\/pre>\n<p>Set up your environment for Go with  the following commands:<\/p>\n<pre><code># Create the GOPATH variable into .bashrc\n    echo &#039;export GOPATH=${HOME}\/go&#039; &gt;&gt; ~\/.bashrc\n    # Set the PATH with Go\n    echo &#039;export PATH=\/usr\/local\/go\/bin:${PATH}:${GOPATH}\/bin&#039; &gt;&gt; ~\/.bashrc\n    # Resource your environment to take the modifications into account\n     source ~\/.bashrc<\/code><\/pre>\n<p>For Singularity &gt; v3.0.0, we also need to install <code>dep<\/code> for dependency resolution<\/p>\n<pre><code>go get -u github.com\/golang\/dep\/<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-3\"><\/a><\/p>\n<h2>Download and install singularity from repo:<\/h2>\n<p>To ensure that the Singularity source code is downloaded to the appropriate directory use these commands.<\/p>\n<pre><code>go get -d github.com\/sylabs\/singularity<\/code><\/pre>\n<p>You will obtain a warning but it will still download Singularity source code to the appropriate directory within the <code>$GOPATH<\/code><\/p>\n<pre><code># move to the singularity folder\n     cd ~\/go\/src\/github.com\/sylabs\/singularity\/ \n     # launch the mconfig command ( you can add the option --prefix=path to custom the installation directory)\n     .\/mconfig --prefix=\/usr\/local\/singularity\n     # Compile into the build directory\n     make -C .\/builddir\n     # Install the binaries into \/usr\/local\/singularity\/bin by default as superuser\n     sudo make -C .\/builddir install<\/code><\/pre>\n<p>Type the following command to  your <code>.bashrc<\/code> file to enable completion in singularity:<\/p>\n<pre><code>. \/usr\/local\/etc\/bash_completion.d\/singularity\n    # resource your .bashrc\n    source ~\/.bashrc<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-4\"><\/a><\/p>\n<h2>Modify Bind path in Singularity<\/h2>\n<p>bind path allows to mount host partitions into the container directly at startup.<\/p>\n<p>Modify the  file <code>\/usr\/local\/singularity\/etc\/singularity\/singularity.conf<\/code><\/p>\n<p>In BIND PATH part<\/p>\n<p>Add the partitions you want to see in the container:<\/p>\n<p>For example:<\/p>\n<pre><code>bind path = \/opt\nbind path = \/scratch\nbind path = \/data<\/code><\/pre>\n<p>Activate the overlay with the line:<\/p>\n<pre><code>enable overlay = yes<\/code><\/pre>\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-hpc\">HPC Trainings<\/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>Container creation Description Create your own Singularity containers Related-course materials HPC Administration Module2 Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 24\/09\/2019&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-2\/trainings-2019-admin-hpc-module-2-creation-container-en\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":928,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-941","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 2019 - Admin HPC - module 2 - creation container - EN - 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\/trainings-fr\/trainings-2019-admin-hpc-module-2\/trainings-2019-admin-hpc-module-2-creation-container-en\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Trainings 2019 - Admin HPC - module 2 - creation container - EN - itrop\" \/>\n<meta property=\"og:description\" content=\"Container creation Description Create your own Singularity containers Related-course materials HPC Administration Module2 Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 24\/09\/2019&hellip; 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