{"id":899,"date":"2020-11-08T19:14:27","date_gmt":"2020-11-08T18:14:27","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=899"},"modified":"2022-04-06T14:48:39","modified_gmt":"2022-04-06T12:48:39","slug":"trainings-2019-admin-hpc-module-1-centos7-en","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-1\/trainings-2019-admin-hpc-module-1-centos7-en\/","title":{"rendered":"Trainings 2019 &#8211; Admin HPC &#8211; module 1 &#8211; Centos7 &#8211; EN"},"content":{"rendered":"<h2>Centos 7 installation<\/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-admin-hpc-module-1\/\">HPC Administration Module1<\/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;\">19\/09\/2019<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">19\/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\">RAID configuration for a dell server<\/a><\/li>\n<li><a href=\"#part-2\">Prerequistes<\/a><\/li>\n<li><a href=\"#part-3\">Softwares choice<\/a><\/li>\n<li><a href=\"#part-4\">Disk partitionning<\/a><\/li>\n<li><a href=\"#part-5\">Set Date and time <\/a><\/li>\n<li><a href=\"#part-6\">Begin Installation <\/a><\/li>\n<li><a href=\"#part-7\">Root and user password<\/a><\/li>\n<li><a href=\"#part-8\">Set Date and time <\/a><\/li>\n<li><a href=\"#part-9\">storage configuration<\/a><\/li>\n<li><a href=\"#part-10\">Network configuration<\/a><\/li>\n<li><a href=\"#part-11\">Install packages with yum command<\/a><\/li>\n<li><a href=\"#part-12\">quotas management<\/a><\/li>\n<li><a href=\"#part-13\">Create a local package  repository<\/a><\/li>\n<li><a href=\"#links\">Links<\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<h1>CENTOS 7 INSTALLATION<\/h1>\n<p><a name=\"part-1\"><\/a><\/p>\n<h2>RAID configuration for a dell server<\/h2>\n<h3>modify the boot settings to boot in BIOS mode:<\/h3>\n<p>Boot the server and press <code>F2 system setup<\/code>.<\/p>\n<p>Choose <code>system BIOS<\/code><\/p>\n<p>Choose <code>Boot Settings<\/code><\/p>\n<p>Then on <code>Boot Mode<\/code> choose <code>BIOS<\/code> then press <code>exit<\/code> and finish to go back to the normal boot<\/p>\n<p>When you see that screen, just press <code>CTRL +R<\/code> to go inside the <code>PERC H730P RAID configuration utility<\/code><\/p>\n<p>Choose <code>Create new VD<\/code><\/p>\n<h3>create  The RAID disks<\/h3>\n<p>RAID disk allows you to regroup physical disk into a virtual one.<\/p>\n<p>There are 7 disks available:<\/p>\n<pre><code>*  2 with 300 GB\n*  5 with 4TB<\/code><\/pre>\n<p>We are going to create a RAID1 with the 2 disks of 300Go: they will be used to install the system.<\/p>\n<p>We are going to create a RAID6 with the 5 remaining disk of 4To: they will used to store data.<\/p>\n<h3>create the Virtual disk:<\/h3>\n<p>Underline the <code>PERC H730P Adapter (Bus 0x19, Dev 0x00)<\/code> line and press <code>F2<\/code><\/p>\n<p>Choose <code>create new VD<\/code><\/p>\n<p>In <code>RAID Level<\/code> , choose RAID-1 <\/p>\n<p>Underline the 2 first disks and press enter to select them.<\/p>\n<p>Press <code>OK<\/code> when your are done<\/p>\n<p>Perform the same operation with the 5 remaings disks choosing <code>RAID-6<\/code> <\/p>\n<hr \/>\n<p><a name=\"part-2\"><\/a><\/p>\n<h2>Prerequisites:<\/h2>\n<p>A USB key or a CD is needed<\/p>\n<p>Sources can be found here : <a href=\"https:\/\/www.centos.org\/\">https:\/\/www.centos.org\/<\/a><\/p>\n<h2>Installation:<\/h2>\n<ul>\n<li>Choose <code>\u00ccnstall Centos 7<\/code> on the following screen:<\/li>\n<\/ul>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos1.png\"\/><\/p>\n<ul>\n<li>This screen appears:<\/li>\n<\/ul>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos2.png\"\/><\/p>\n<h2>Language choice:<\/h2>\n<ul>\n<li>Choose your language and click on <code>continue<\/code><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"part-3\"><\/a><\/p>\n<h2>Softwares choice:<\/h2>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos3.png\"\/><\/p>\n<p>In <code>Software selection<\/code>, choose <code>compute node<\/code> with the following softwares:<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos4.png\"\/><\/p>\n<p>Then choose <code>Infrastructure Server<\/code> with the following softwares:<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos5.png\"\/><\/p>\n<hr \/>\n<p><a name=\"part-4\"><\/a><\/p>\n<h2>Disk partitioning:<\/h2>\n<p>We are going to create 4 partitions on the new system:<\/p>\n<pre><code>        \u2022 \/home : hosts users personal data\n        \u2022 \/usr\/local\/bioinfo : hosts bioinformatics software\n        \u2022 \/data : hosts project data\n        \u2022 \/: hosts system configuration files<\/code><\/pre>\n<p>To implement the disk partitioning, choose <code>System<\/code> then <code>\u00ccnstallation Destination<\/code> <\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos6.png\"\/><\/p>\n<p>Select the hard drive on which you want to install Centos7 anc chose <code>I will configure the partitioning<\/code>:<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos7.png\"\/><\/p>\n<p>The partitions are going to be made in LVM.<\/p>\n<p>Click on <code>+<\/code> to add a new partition:<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos8.png\"\/><\/p>\n<p>Create the following partitions with the specified features:<\/p>\n<pre><code>        *  \/boot: 200Mo, mount point: \/boot, type of partition: boot check the <code>Reformat<\/code>box\n\n        *  swap: 4000Mo, mount point: swap, type of partition: swap  check the <code>Reformat<\/code>box\n\n        *  \/home: size to define, mount point: \/home, type of partition: xfs  check the <code>Reformat<\/code>box\n\n        *  \/data: size to define, mount point: \/data, type of partition: xfs  check the <code>Reformat<\/code>box\n\n        *  \/usr\/local: size to define, mount point: \/usr\/local, type of partition: xfs  check the <code>Reformat<\/code>box<\/code><\/pre>\n<p>Once all the partitions are defined click on <code>done<\/code> to continue<\/p>\n<p>A windows appears and click <code>Accept changes<\/code><\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos9.png\"\/><\/p>\n<hr \/>\n<p><a name=\"part-5\"><\/a><\/p>\n<h2>Set Date and Time:<\/h2>\n<p>Click on the clock icon under the localization menu and select a time zone from the map of the world, then click <code>Done<\/code><\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos10.png\"\/><\/p>\n<hr \/>\n<p><a name=\"part-6\"><\/a><\/p>\n<h2>Begin Installation:<\/h2>\n<p>click on the <code>Begin Installation button<\/code>.<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos11.png\"\/><\/p>\n<hr \/>\n<p><a name=\"part-7\"><\/a><\/p>\n<h2>Root and user password:<\/h2>\n<p>The installation begins and you can create a user and choose a root password.<\/p>\n<h3>Choose a root password:<\/h3>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos12.png\"\/><\/p>\n<p>Then click <code>Done<\/code><\/p>\n<h3>Create a user:<\/h3>\n<p>If you want this user to have admin rights tick <code> Make this user administrator<\/code>:<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/centos13.png\"\/><\/p>\n<hr \/>\n<p><a name=\"part-8\"><\/a><\/p>\n<h2>Name configuration:<\/h2>\n<p>To modify the name, launch the following command:<\/p>\n<pre><code>    $ hostnamectl set-hostname name-server<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-9\"><\/a><\/p>\n<h2>storage configuration:<\/h2>\n<p>We have to configure the RAID-6 disk to be able to mount them in the \/data partition.<\/p>\n<h3>check the name of your device:<\/h3>\n<pre><code>    $ fdisk -l<\/code><\/pre>\n<p>Shows you the list of the hardrives and their names<\/p>\n<p>On this server, it is <code>\/dev\/sdb<\/code><\/p>\n<h3>Format the disk in GPT:<\/h3>\n<pre><code>   $ parted \/dev\/sdb mklabel gpt\n   $ parted \/dev\/sdb\n   $ mkpart primary xfs 1 -1\n   $ quit<\/code><\/pre>\n<p>\/dev\/sdb1 partition has been created.<\/p>\n<h3>Format partition in xfs:<\/h3>\n<pre><code>   $ mkfs.xfs -L data \/dev\/sdb1<\/code><\/pre>\n<h3>Mount the content of the device \/dev\/sdb1 into \/data and enable the quota<\/h3>\n<p>Create the folder <code>\/data<\/code>:<\/p>\n<pre><code>   $ mkdir \/data<\/code><\/pre>\n<p>Modify the file <code>\/etc\/fstab<\/code> with:<\/p>\n<pre><code>   \/dev\/sdb1          \/data  xfs     pquota        1 2<\/code><\/pre>\n<p>launch the following command to take into account the modifications:<\/p>\n<pre><code>    $ mount -a<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-10\"><\/a><\/p>\n<h2>Network configuration:<\/h2>\n<h3>Deactivate selinux:<\/h3>\n<p>The security system selinux has to be deactivated to prevent essentials port to be blocked.<\/p>\n<p>In a console, open the configuration file <code>\/etc\/selinux\/config<\/code> and  set <code>SELINUX<\/code>to  <code>disabled<\/code><\/p>\n<p>Reboot the server to make the change permanent.<\/p>\n<h3>Disable firewalld:<\/h3>\n<pre><code> $ systemctl stop firewalld\n $ systemctl disable firewalld<\/code><\/pre>\n<h3>Set the IP address:<\/h3>\n<p>Determine the name of the network interfaces with the command:<\/p>\n<pre><code> $ ifconfig -a<\/code><\/pre>\n<p>In the following example, the interface to  configure is <code>enp0s3<\/code><\/p>\n<p><img decoding=\"async\" src=\"\/uploads\/1e908d297ede2f72eea59d5b6fb06644\/image.png\" alt=\"image\" \/><\/p>\n<p>The configuration files for the network interfaces are located in : <code>\/etc\/sysconfig\/network-scripts\/<\/code><\/p>\n<p>Usually a network file is named : <code>ifcfg-interface-name<\/code> for example here it will be: <code>\u00ecfcfg-em1<\/code><\/p>\n<p>Open the configuration file corresponding to the interface you want to configure and modify it like this:<\/p>\n<pre><code> TYPE=Ethernet\n BOOTPROTO=static\n DEFROUTE=yes\n NAME=enp0s3\n ONBOOT=yes\n IPADDR0= * IP_Adress *\n PREFIX0= * netmask *\n GATEWAY0= * gateway_ip *\n DNS1=* DNS_Ip_server * <\/code><\/pre>\n<p>Launch the following command to  implement the new configuration:<\/p>\n<pre><code>$ service network restart <\/code><\/pre>\n<h3>Add default route:<\/h3>\n<pre><code>$ route add default gw GATEWAY_IP_ADDRESS INTERFACE_NAME<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-11\"><\/a><\/p>\n<h2>Install packages with yum command<\/h2>\n<p>yum allows you to install packages on Centos from multiple repositories available on the Internet or locally.<\/p>\n<p>To search for a particular package:<\/p>\n<pre><code>$ yum search package <\/code><\/pre>\n<p>To install a particular package:<\/p>\n<pre><code>$ yum install package<\/code><\/pre>\n<p>To list the version of a package:<\/p>\n<pre><code>$ yum list package<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-12\"><\/a><\/p>\n<h2>quotas management<\/h2>\n<h3><strong>Set up quotas on a  XFS partition <\/strong><\/h3>\n<p>1.in the <code>\/etc\/fstab<\/code> file for each xfs partition add uquota and pquota option:<\/p>\n<ul>\n<li>uquota: quota per user on the xfs partition <\/li>\n<li>pquota: quota per project on the xfs partition <\/li>\n<\/ul>\n<pre><code>\/dev\/sdb1       \/data   xfs     uquota,pquota        1 2\n<\/code><\/pre>\n<p>2.Save the file, then type this command to validate modifications:<\/p>\n<pre><code>$ mount -a<\/code><\/pre>\n<h3><strong>Project creation<\/strong><\/h3>\n<p>1.Complete the files:<\/p>\n<ul>\n<li>\/etc\/projects with id_project:\/path\/project_name<\/li>\n<li>\/etc\/projid with project_name:id<\/li>\n<\/ul>\n<p>_with id: the project number to increment each time<br \/>\navec project_name: the project<em>name<\/em><\/p>\n<p>2.Set up the quota with the following commands:<\/p>\n<pre><code>$ xfs_quota -x -c \"project -s project_name\" \n$ xfs_quota -x -c \"limit -p bsoft=199g bhard=200g project_name\" \/partition<\/code><\/pre>\n<ul>\n<li>with bsoft being the limit when the user is going to receive a warning. User has 7 days to remove data<\/li>\n<li>bhard: effective limit<\/li>\n<\/ul>\n<h3><strong>Monitor quotas project<\/strong><\/h3>\n<pre><code>   $ xfs_quota -xc \"report -hp\" \/partition\n   $ xfs_quota -xc \"report -hp\" \/data<\/code><\/pre>\n<h3><strong>User quota creation<\/strong><\/h3>\n<pre><code>  $ xfs_quota -x -c \"limit -u bsoft=99g bhard=100g user\" \/home  <\/code><\/pre>\n<h3><strong>Monitor quota user<\/strong><\/h3>\n<p>{% highlight bash %}$ xfs_quota -xc 'report -hu' \/partition<br \/>\n$ xfs_quota -xc 'report -hu' \/home {% endhighlight %}<\/p>\n<h3><strong>Delete a quota<\/strong><\/h3>\n<p>Set the limits to 0<\/p>\n<p>{% highlight bash %}$ xfs_quota -x -c &quot;limit -p bsoft=0g bhard=0g projet&quot;<br \/>\n$ xfs_quota -x -c &quot;limit -u bsoft=0g bhard=0g user&quot; \/home {% endhighlight %}<\/p>\n<hr \/>\n<p><a name=\"part-13\"><\/a><\/p>\n<h2>Create a local package  repository<\/h2>\n<p>When a server is not connected to the Internet, it is sometimes convenient to be able to install packages from a local repository. <\/p>\n<pre><code>  ### copy the USB key or DVD:<\/code><\/pre>\n<p>launch the following command:<\/p>\n<p>{% highlight bash %}$ mkdir \/opt\/Centos7<br \/>\n$ mount \/dev\/sdc \/mnt  # \/dev\/sdc being the DVDROM or USB key device path<br \/>\n$ cp -r \/mnt\/* \/opt\/Centos7{% endhighlight %}<\/p>\n<h3>Modify the file <code>\/etc\/yum\/repos.d\/Centos-Base.repo<\/code><\/h3>\n<p>In the <code>[base]<\/code>section, comment the  ligne  <code>mirrolist<\/code>and replace <code>baseurl<\/code> line with:<\/p>\n<pre><code>        baseurl=file:\/opt\/Centos7<\/code><\/pre>\n<p>In the sections <code>[updates]<\/code>, <code>[extras]<\/code> and <code>[centosplus]<\/code> add the follwing line:<\/p>\n<pre><code>         enabled=0<\/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>Centos 7 installation Description Hands On Lab Exercises for HPC Related-course materials HPC Administration Module1 Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation&hellip; 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