{"id":39,"date":"2018-01-16T19:12:17","date_gmt":"2018-01-16T19:12:17","guid":{"rendered":"https:\/\/in.nau.edu\/hpc\/?page_id=39"},"modified":"2026-10-29T17:15:24","modified_gmt":"2026-10-29T17:15:24","slug":"faqs","status":"publish","type":"page","link":"https:\/\/in.nau.edu\/arc\/faqs\/","title":{"rendered":"FAQs"},"content":{"rendered":"<!-- shortcode-right-column -->\n<div class=\"shortcode-right-column\" >\n    <div class=\"shortcode-right-column__container\"><\/p>\n<p><!-- shortcode-contact -->\n<div class=\"shortcode-contact\">\n    <div class=\"contact-header\">\n        <h3>Contact Advanced Research Computing<\/h3>\n    <\/div>\n    <div class=\"contact-body\">\n                <a href=\"mailto:ask-arc@nau.edu\" aria-label=\"Contact Advanced Research Computing: Email Address\" title=\"Email Address\">\n            <div class=\"contact-icon-container\">\n                <i class=\"fas fa-envelope\" aria-hidden=\"true\"><\/i>\n                <span class=\"sr-only\">Email:<\/span>\n            <\/div>\n            <div class=\"contact-email\">ask-arc&#8203;@nau.edu<\/div>\n        <\/a>\n                    <\/div>\n<\/div>\n\n<\/p>\n<hr \/>\n<h2>Quick Links<\/h2>\n<ul>\n<li><a href=\"https:\/\/in.nau.edu\/arc\/documentation-page\/\">Monsoon Documentation<\/a><\/li>\n<li><a href=\"https:\/\/in.nau.edu\/hpc\/overview\/submitting-your-first-job\/\">Submitting your first job<\/a><\/li>\n<li><a href=\"https:\/\/in.nau.edu\/hpc\/request-storage\/\">Request storage<\/a><\/li>\n<li><a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-introduction\/\">Using the cluster: introduction<\/a><\/li>\n<li><a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-advanced\/\">Using the cluster: advanced<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><\/div>\n<\/div>\n\n<h1>FAQs<\/h1>\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"pending\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Why is my job pending?_0\" id=\"shortcode-accordion-1-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-1-panel\">\n            Why is my job pending?\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-1-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-1-trigger\" inert>\n        <html><body>\n<p>Most of the time, questions that we get about the cluster related to why jobs are not starting(in the pending or \u201cPD\u201d state). There are often many different contributing factors to this.<\/p>\n<p>When jobs remain pending for long periods of time, you can see why by running the \u201csqueue\u201d command. The reason slurm has declared your job to be \u201cpending\u201d will be listed in parentheses under the (REASON) column. For example, if user abc123 wanting to see all jobs that were pending, he would enter<\/p>\n<p style=\"padding-left: 30px;\">squeue -u abc123 -s PD<\/p>\n<p>The following questions on this page explain what these different reasons are and how you can avoid them in the future.<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"dependency\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Dependency_0\" id=\"shortcode-accordion-2-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-2-panel\">\n            Dependency\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-2-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-2-trigger\" inert>\n        <html><body>\n<p>This occurs when a job \u201cdepends on\u201d another being completed before it is allowed to start. This will only happen if a dependency is specified inside the job script using the \u2013\u2013 <a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-advanced\/dependent-jobs\/\">dependency<\/a> option.<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"dependency-not-satisfied\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"DependencyNeverSatisfied_0\" id=\"shortcode-accordion-3-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-3-panel\">\n            DependencyNeverSatisfied\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-3-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-3-trigger\" inert>\n        <html><body>\n<p>This occurs when a job that must run first in a dependency fails. This usually means that there was an error of some kind that caused SLURM to cancel the job. When this happens, any jobs that depend on the failed job will never be allowed to run.<br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"node-unavailable\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"ReqNodeNotAvail_0\" id=\"shortcode-accordion-4-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-4-panel\">\n            ReqNodeNotAvail\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-4-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-4-trigger\" inert>\n        <html><body>\n<p>This occurs when a requested node is either down, or there is currently a reservation in place for it. If you have requested a specific node in your job script using the \u201c\u2013\u2013nodelist\u201d command, try removing this option in order to speed your job along. Slurm is very good at allocating resources, so it is often best to let it decide which nodes and processors to use in order to run your job.<\/p>\n<p>To see if the node you requested is down, run<\/p>\n<p style=\"padding-left: 30px;\">sinfo -N -l<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"assoc-grp-cpu-run-mins\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"AssocGrpCPURunMinsLimit\/AssocGrpMemRunMinsLimit_0\" id=\"shortcode-accordion-5-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-5-panel\">\n            AssocGrpCPURunMinsLimit\/AssocGrpMemRunMinsLimit\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-5-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-5-trigger\" inert>\n        <html><body>\n<p>This occurs when either the associated account or QOS that you belong to is currently using all available CPU minutes or MEM minutes it has been allotted. Read more about <a href=\"https:\/\/in.nau.edu\/hpc\/overview\/\">Monsoon\u2019s GrpCPURunMinsLimit<\/a>.<br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"resources\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Resources_0\" id=\"shortcode-accordion-6-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-6-panel\">\n            Resources\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-6-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-6-trigger\" inert>\n        <html><body>\n<p><span id=\"resources1\">This<\/span> occurs when any resources that you have requested are not currently available. This could refer to memory, processors, gpus, or nodes. For example, if you have requested the use of 20 processors and 10 nodes, and there is currently a high volume of jobs being run, it is likely that your job will remain in the pending state due to \u201cResources\u201d for a long time.<\/p>\n<h5 id=\"resources2\"><\/h5>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"priority\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Priority_0\" id=\"shortcode-accordion-7-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-7-panel\">\n            Priority\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-7-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-7-trigger\" inert>\n        <html><body>\n<p>This occurs when there are jobs ahead of yours that have a higher priority. Not to worry, you can help alleviate this issue by updating your job time limit to a lower estimate (See the man page for the \u201cscontrol\u201d command). For example, if you have put \u201c\u2013\u2013time=1-00:00:00\u201d in your script, Slurm will set your time limit to one day. If you know your job will not take longer than four hours, you can set this number accordingly and Slurm will give you a higher priority due to the lower time limit. This is because we have the backfill option turned on in Slurm which will enable small jobs (lower time limit) to fill the unused small time windows.<br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"jobheld\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"JobHeld\/admin_0\" id=\"shortcode-accordion-8-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-8-panel\">\n            JobHeld\/admin\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-8-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-8-trigger\" inert>\n        <html><body>\n<p>This occurs when your job is being held by the administrator for some reason. Email <a href=\"mailto:hpcsupport@nau.edu\">hpcsupport@nau.edu<\/a> to find out why.<br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"expedite-jobs\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Expedite your job\u2019s start time_0\" id=\"shortcode-accordion-9-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-9-panel\">\n            Expedite your job\u2019s start time\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-9-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-9-trigger\" inert>\n        <html><body>\n<p>Sometimes jobs will remain in the pending state indefinitely due to certain settings in the job script. Here is a list of things you can do to ensure that your job gets going:<\/p>\n<ul>\n<li>Give your script a lower time limit (if at all possible).<\/li>\n<li>If you know the job will take a long time, try breaking it up into several different scripts that can be run separately and with shorter time limits. Consider <a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-advanced\/job-arrays\/\">job arrays<\/a> for this. Also, the <a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-advanced\/dependent-jobs\/\">dependency<\/a> option allows you to be sure that one job runs before another.<\/li>\n<li>Don\u2019t request specific nodes.<\/li>\n<li>Don\u2019t request more memory than you need.<\/li>\n<li>Don\u2019t request more cpus than you are launching tasks, or threads for.<\/li>\n<li>Avoid using the \u201c\u2013\u2013contiguous\u201d or \u201c\u2013\u2013exclusive\u201d options, as these will limit which nodes your job can run on.<\/li>\n<\/ul>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"req-mem\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Requesting more memory_0\" id=\"shortcode-accordion-10-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-10-panel\">\n            Requesting more memory\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-10-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-10-trigger\" inert>\n        <html><body>\n<p>Requesting a specific amount of memory in your script can be done using the \u201c\u2013\u2013mem\u201d option. This amount is in megabytes (1000 MB is 1 GB). If you wanted 150 GB of memory, just multiply that number by 1000 to get the amount in MB. The example below shows the line on your script that you would add if you wanted to allocate 150 gigabytes of memory:<\/p>\n<p style=\"padding-left: 30px;\">#SBATCH \u2013\u2013mem=150000<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"req-cpu\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Requesting more CPUs_0\" id=\"shortcode-accordion-11-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-11-panel\">\n            Requesting more CPUs\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-11-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-11-trigger\" inert>\n        <html><body>\n<p>If you would like your job to use a certain number of cpus, you may request this using the \u201c\u2013\u2013cpus-per-task\u201d option. For example, if you would like each task in your script (each instance of srun you have) to use 3 cpus, you would add the following line to the script:<\/p>\n<p style=\"padding-left: 30px;\">#SBATCH \u2013\u2013cpus-per-task=3<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"req-gpu\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Requesting the GPU_0\" id=\"shortcode-accordion-12-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-12-panel\">\n            Requesting the GPU\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-12-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-12-trigger\" inert>\n        <html><body>\n<p>Please refer to our documentation page <a href=\"https:\/\/in.nau.edu\/arc\/gpus\/#submitting-a-gpu-job\">GPUs on Monsoon<\/a> to learn how to request GPUs.<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"gpu-avail\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"GPU availability_0\" id=\"shortcode-accordion-13-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-13-panel\">\n            GPU availability\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-13-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-13-trigger\" inert>\n        <html><body>\n<p>Please refer to our documentation page <a href=\"https:\/\/in.nau.edu\/arc\/gpus\/#checking-available-gpus\">GPUs on Monsoon<\/a> to learn how to view GPU availability.<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"job-resources\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Job resources_0\" id=\"shortcode-accordion-14-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-14-panel\">\n            Job resources\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-14-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-14-trigger\" inert>\n        <html><body>\n<p>You can determine the efficiency of your jobs with the\u00a0jobstats utility.\u00a0 Running \u201cjobstats\u201d without any flags will return all your jobs of the previous 24 hours. To see older jobs, add the -S flag followed by a date in the format YYYY-MM-DD. Example: \u201cjobstats -S 2019-01-01\u201d.<br>\nHere is some sample output of running jobstats:<br>\n\ufffc<br>\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-tall-banner-image wp-image-1093\" src=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/Screen-Shot-2019-05-02-at-1.01.38-PM-960x62.png\" alt=\"\" width=\"960\" height=\"62\" srcset=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/Screen-Shot-2019-05-02-at-1.01.38-PM-960x62.png 960w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/Screen-Shot-2019-05-02-at-1.01.38-PM-300x18.png 300w\" sizes=\"auto, (max-width: 960px) 100vw, 960px\" \/><\/p>\n<p>Your efficiency is calculated with a variety of factors, including the number of CPUs you use, how long your job runs, and your memory usage.<\/p>\n<p>Additional options are available. Use \u201cjobstats -h\u201d to see all available options.<br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"create-ent-group\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Creating and Managing an Enterprise Group_0\" id=\"shortcode-accordion-15-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-15-panel\">\n            Creating and Managing an Enterprise Group\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-15-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-15-trigger\" inert>\n        <html><body>\n<p>ARC\u2019s Monsoon cluster uses NAU\u2019s \u201cEnterprise Groups\u201d to define what researchers may access a given project-directory in the\u00a0<span style=\"font-size: 16px; font-family: monospace; border: 1px solid; border-radius: 4px; padding: 0px 4px 0px; border-color: #BBBBBB;\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\" data-darkreader-inline-bgcolor=\"\">\/projects<\/span>\u00a0area.<\/p>\n<p><strong>Note<\/strong>: Monsoon staff are unable to modify membership of anyone\u2019s Enterprise Group.<\/p>\n<h2>Monsoon and Enterprise Groups<\/h2>\n<p>On Monsoon, Enterprise Groups govern who can access a given project.<\/p>\n<p>A PI can add\/remove members to\/from their Enterprise Group to control who can access their project. (Monsoon staff are unable to modify membership or ownership of Enterprise Groups.)<\/p>\n<h3>Creating and Managing an Enterprise Group<\/h3>\n<p>Enterprise Groups are managed by Monsoon\u2019s PI\u2019s themselves through the Directory Services tab at\u00a0<a href=\"https:\/\/my-old.nau.edu\/\">https:\/\/my-old.nau.edu\/<\/a>.<\/p>\n<p>To learn how to create and manage Enterprise Groups, please read the\u00a0official NAU documentation on Enterprise Groups:\u00a0<a href=\"https:\/\/nau.service-now.com\/sp?id=kb_article&amp;article=KB0014689\">LDAP and Enterprise Group Maintenance [KB0014689]<\/a>.<\/p>\n<p><strong>Note<\/strong>: although it is possible to add\u00a0<strong>non-<\/strong>Monsoon users to an Enterprise Group, those users will not have access to files (anywhere) on Monsoon.<\/p>\n<h3>Reviewing a Project\u2019s Membership Via Command-Line on Monsoon<\/h3>\n<p>Researchers with existing projects can view the name of their project\u2019s Enterprise Group, and review its membership, like this:<\/p>\n<p><code>$ ls -ld\u00a0\/projects\/hpcpub<br>\ndrwxrws---+ 2 abc123\u00a0ITS-HPC-staf\u00a04096 Sep 24 11:26 \/projects\/hpcpub<br>\n$ getent group\u00a0ITS-HPC-staff<br>\nITS-HPC-staff:*:11055:abc123,def456,ghi789<\/code><\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"licensing\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Licensing_0\" id=\"shortcode-accordion-16-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-16-panel\">\n            Licensing\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-16-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-16-trigger\" inert>\n        <html><body>\n<p>Licenses can be requested like any other resource in your SLURM scripts using #SBATCH \u2013\u2013licenses:&lt;program&gt;:&lt;# of licenses&gt;. Read the documentation on <a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-advanced\/\">licensing<\/a> for more information.<br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"using-screen\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Keep commands running after disconnecting SSH_0\" id=\"shortcode-accordion-17-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-17-panel\">\n            Keep commands running after disconnecting SSH\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-17-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-17-trigger\" inert>\n        <html><body>\n<p>Monsoon users can use the \u2018screen\u2019 command to keep commands running even after closing their terminal session\/SSH client, as long as they run \u2018screen\u2019 first.<\/p>\n<ol>\n<li>Start a command-line shell on one of Monsoon\u2019s login nodes<\/li>\n<li>Start a \u2018screen\u2019 session by running the \u2018<strong>screen<\/strong>\u2018 command<\/li>\n<li>Initiate the desired programs\/processes<\/li>\n<li>Optionally close the window\/exit the SSH client<\/li>\n<\/ol>\n<p><em>(\u2018screen\u2019 is also used as a safeguard against unstable network communications)<\/em><\/p>\n<p>To re-connect to a closed\/lost \u2018screen\u2019 session:<\/p>\n<ol>\n<li>Ensure you are logged in to the same system<br>\n(e.g.:wind, rain, dtn1, ondemand)<\/li>\n<li>Run \u2018<strong>screen -r<\/strong>\u2018<\/li>\n<\/ol>\n<p>For more in-depth information on using \u2018screen\u2019, please see our <a href=\"https:\/\/in.nau.edu\/hpc\/using-the-screen-command\/\">Using the \u2018screen\u2019 command<\/a> page.<br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n        <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Parallelism_0\" id=\"shortcode-accordion-18-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-18-panel\">\n            Parallelism\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-18-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-18-trigger\" inert>\n        <html><body>\n<p>Many programs on Monsoon are written to make use of parallelization, either in the form of threading, MPI, or both. To check what type of parallelization an application supports, you can look at the libraries it was compiled with. First, find where you app is located using the \u201cwhich\u201d command. Then run \u201cldd \/path\/to\/my\/app.\u201d A list of libraries will be printed out. If you see \u201clibpthread\u201d or \u201clibgomp\u201d, then it is likely that your software is capable of multi-threading (shared memory). Please read our segment on <a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-advanced\/parallelism\/\">shared-memory parallelism<\/a> for more info on setting up your Slurm script.<\/p>\n<p>If you see libmpi* listed, then it is likely that your software is capable of MPI (distributed memory). Please read our segment on <a href=\"https:\/\/in.nau.edu\/hpc\/overview\/using-the-cluster-advanced\/parallelism\/\">distributed-memory parallelism<\/a> for more info on setting up your Slurm job script.<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"x11\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Running X11 Jobs on Monsoon_0\" id=\"shortcode-accordion-19-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-19-panel\">\n            Running X11 Jobs on Monsoon\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-19-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-19-trigger\" inert>\n        <html><body>\n<p>Some programs run on the cluster will be more convenient to run and debug with a GUI. Due to this, the Monsoon cluster supports forwarding X11 windows over your ssh session.<\/p>\n<h2 id=\"running-x-forwarding\">Running X-Forwarding<\/h2>\n<p>Enable X-forwarding to your local machine is fairly straightforward.<\/p>\n<h3 id=\"maclinux\">Mac\/Linux<\/h3>\n<p>When connecting to monsoon using SSH, add the <code>-Y<\/code> flag<\/p>\n<pre><code>ssh abc123@monsoon.hpc.nau.edu -Y<\/code><\/pre>\n<h3 id=\"windows\">Windows<\/h3>\n<p>On PuTTY, in the left menu navigate to <code>SSH-&gt;X11<\/code> and check <code>Enable X11 forwarding<\/code><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-landscape-image wp-image-1065\" src=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/x_forwarding_putty-454x348.png\" alt=\"\" width=\"454\" height=\"348\"><\/p>\n<p>After connecting to Monsoon, running the GUI program with <code>srun<\/code> will create your window.<\/p>\n<pre><code>srun xeyes<\/code><\/pre>\n<p>For some programs, such as matlab, in order to ensure the window appears, add the <code>\u2013\u2013pty<\/code> flag to <code>srun<\/code>.<\/p>\n<pre><code>module load matlab\r\nsrun \u2013\u2013pty -t 5:00 \u2013\u2013mem=2000 matlab  # Start an interactive matlab session<\/code><\/pre>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"restoring-files\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Restoring Deleted Files_0\" id=\"shortcode-accordion-20-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-20-panel\">\n            Restoring Deleted Files\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-20-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-20-trigger\" inert>\n        <html><body>\n<h5>What if I delete a file that I need?<\/h5>\n<p>Snapshot of all home user directories are taken twice a day. What this means is if you accidentally delete a file from your home directory that you need back, if it was created before a snapshot window, you will be able to restore that file. If you do an ls of the snapshot directory (ls \/home\/.snapshot), you may see something like the following:<\/p>\n<pre><code>\r\n@GMT-2019.02.09-05.00.01 @GMT-2019.02.10-18.00.01 @GMT-2019.02.12-05.00.01 latest\r\n@GMT-2019.02.09-18.00.02 @GMT-2019.02.11-05.00.01 @GMT-2019.02.12-18.00.01\r\n@GMT-2019.02.10-05.00.01 @GMT-2019.02.11-18.00.01 @GMT-2019.02.13-05.00.01\r\n<\/code><\/pre>\n<p>Each of the directories starting with @GMT are a backup. if my userid is ricky I can check my files like the following:<\/p>\n<pre><code>\r\nls -la \/home\/.snapshot\/@GMT-2019.02.12-18.00.01\/ricky\r\n<\/code><\/pre>\n<p>if I know I had my file before 6pm on the 12th. I would see all of the files that I had at the time of the snapshot. If there were a file called dask_test.py that I needed to restore from that snapshot, I could type in the following:<\/p>\n<pre><code>\r\ncp \/home\/.snapshot\/@GMT-2019.02.12-18.00.01\/ricky\/dask_test.py \/home\/ricky\r\n<\/code><\/pre>\n<p>Your file would then be restored.<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"requesting-node-gen\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Requesting Certain Node Generations_0\" id=\"shortcode-accordion-21-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-21-panel\">\n            Requesting Certain Node Generations\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-21-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-21-trigger\" inert>\n        <html><body>\n<p>Monsoon has four generations of nodes ordered by age (oldest first):<\/p>\n<ul>\n<li>Sandy Bridge Xeon, 4 socket, 8 core per socket, 2.20GHz, 384GB mem\u00a0 \u00a0 \u00a0 # request with #SBATCH -C sb<\/li>\n<li>Haswell Xeon, 2 socket, 12 core per socket, 2.50GHz, 128GB mem\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 # request with #SBATCH -C hw<\/li>\n<li>Broadwell Xeon, 2 socket, 14 core per\u00a0socket, 2.40GHz, 128GB mem\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 # request with #SBATCH -C bw<\/li>\n<li>Skylake Xeon, 2 socket, 14\u00a0core per socket, 2.60GHz, 196GB mem\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 # request with #SBATCH -C sl<\/li>\n<\/ul>\n<p>To select a certain generation, just put #SBATCH -C &lt;generation&gt; in the job. For instance to have a job run on Broadwell nodes only:<\/p>\n<pre>#!\/bin\/bash\r\n#SBATCH \u2013\u2013job-name=myjob\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 # job name\r\n#SBATCH \u2013\u2013output=\/scratch\/abc123\/output.txt\u00a0# job output\r\n#SBATCH \u2013\u2013time=6:00\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\r\n#SBATCH \u2013\u2013workdir=\/scratch\/abc123\u00a0 \u00a0 \u00a0 \u00a0 \u00a0  # work directory\r\n#SBATCH \u2013\u2013mem=1000\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 # 2GB of memory\r\n#SBATCH -C bw\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 # select the Broadwell generation\r\n\r\n# load a module, for example\r\nmodule load python\/2.7.5\r\n\r\n# run your application, precede the application command with srun\r\n# a couple example applications ...\r\nsrun date\r\nsrun sleep 30\r\nsrun date\r\n<\/pre>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"request-gpu-model\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"How to request specific model of GPU_0\" id=\"shortcode-accordion-22-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-22-panel\">\n            How to request specific model of GPU\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-22-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-22-trigger\" inert>\n        <html><body>\n<p>Please refer to our documentation page <a href=\"https:\/\/in.nau.edu\/arc\/gpus\/\">GPUs on Monsoon<\/a> to learn how to request specific GPU models.<\/p>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"missing-folder\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"RStudio Missing Project Folder_0\" id=\"shortcode-accordion-23-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-23-panel\">\n            RStudio Missing Project Folder\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-23-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-23-trigger\" inert>\n        <html><body>\n<div>\n<div>\/project areas are not available when running through RStudio due to our automounting of projects. To resolve this, please create a ~\/.Rprofile file, if not already created, and append the following to it:<\/div>\n<div><\/div>\n<div>system(\u201cecho \u2018Ensuring my project directory is mounted \u2026'\u201d)<\/div>\n<div class=\"copy-paste-block\">\n<div>\n<p>system(\u201cls \/projects\/&lt;insert proj name&gt;\/PROJ_DETAILS\u201d)<\/p>\n<div><\/div>\n<div>The echo is optional.<\/div>\n<div><\/div>\n<div>Now when R or RStudio starts, the project folder will be mounted, and available.<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"rgdal\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Support for rgdal_0\" id=\"shortcode-accordion-24-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-24-panel\">\n            Support for rgdal\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-24-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-24-trigger\" inert>\n        <html><body>\n<p>Often researchers utilizing R, and geospatial tools will lean on a package called \u201crgdal\u201d. In order to utilize rgdal on monsoon, a number of external software packages must first be made available to R both for the initial \u201crgdal\u201d installation, as well as for subsequent usage.<\/p>\n<p>We have prepared a full explanation of the process on our HPC forum, here: <a href=\"https:\/\/ask.cyberinfrastructure.org\/t\/how-do-i-install-use-the-rgdal-package-for-r-on-monsoon\/1695\">How do I install\/use the \u2018rgdal\u2019 package for R on Monsoon?<\/a><\/p>\n<p>Similarly, a more generalized explanation of how to use R modules with Monsoon is here: <a href=\"https:\/\/ask.cyberinfrastructure.org\/t\/what-is-the-preferred-way-to-install-r-packages-libraries-on-monsoon\/1694\">What is the preferred way to install R packages\/libraries on Monsoon?<\/a><br>\n<\/p><\/body><\/html>\n    <\/div>\n<\/div>\n\n<!-- shortcode-accordion -->\n<div class=\"shortcode-accordion shortcode-accordion--closed\" style=\"position: relative;\" >\n    <span class=\"anchor\" id=\"using-conda-env-in-jupyter\" style=\"visibility: hidden; position: absolute;\" aria-hidden=\"true\"><\/span>    <h4 class=\"shortcode-accordion__header\">\n        <button type=\"button\" class=\"shortcode-accordion__trigger\" data-header=\"Using conda environments in the ondemand jupyter app_0\" id=\"shortcode-accordion-25-trigger\" aria-expanded=\"false\" aria-controls=\"shortcode-accordion-25-panel\">\n            Using conda environments in the ondemand jupyter app\n            <span class=\"shortcode-accordion__header__arrow\" aria-hidden=\"true\"><\/span>\n        <\/button>\n    <\/h4>\n    <div class=\"shortcode-accordion__body\" id=\"shortcode-accordion-25-panel\" role=\"region\" aria-labelledby=\"shortcode-accordion-25-trigger\" inert>\n        <html><body>\n<p>The jupyter app for ondemand (located <a href=\"https:\/\/ondemand.hpc.nau.edu\/pun\/sys\/dashboard\/batch_connect\/sys\/jupyter\/session_contexts\/new\">here<\/a>) automatically looks for any conda environments you may have installed on monsoon. If any of these environments has python and ipykernel, then the app loads them up and you can select them as a kernel named *-conda-env. This gives you access to specialized python modules that are not in the base environment, like <a href=\"https:\/\/www.crummy.com\/software\/BeautifulSoup\/bs4\/doc\/\">BeautifulSoup<\/a> for example.<\/p>\n<p>Here\u2019s how you can select a kernel on the home screen on juptyer:<br>\n<a href=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-home-cropped-1.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-2365\" src=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-home-cropped-1.png\" alt=\"demo of how to select jupyter kernel from within home page\" width=\"1158\" height=\"300\" srcset=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-home-cropped-1.png 1158w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-home-cropped-1-300x78.png 300w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-home-cropped-1-1024x265.png 1024w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-home-cropped-1-768x199.png 768w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-home-cropped-1-600x155.png 600w\" sizes=\"auto, (max-width: 1158px) 100vw, 1158px\" \/><\/a><br>\nOr from within a notebook:<\/p>\n<p><a href=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-notebook-cropped.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-2363\" src=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-notebook-cropped.png\" alt=\"demo of how to select jupyter kernel from within notebook\" width=\"1167\" height=\"369\" srcset=\"https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-notebook-cropped.png 1167w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-notebook-cropped-300x95.png 300w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-notebook-cropped-1024x324.png 1024w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-notebook-cropped-768x243.png 768w, https:\/\/in.nau.edu\/wp-content\/uploads\/sites\/208\/select-jupyter-kernel-notebook-cropped-600x190.png 600w\" sizes=\"auto, (max-width: 1167px) 100vw, 1167px\" \/><\/a><\/p>\n<p>Here\u2019s how you can install the ipykernel package in your conda env (replace \u201cmyenv\u201d with your conda environment name):<\/p>\n<pre><code>module load anaconda3\r\nconda activate myenv\r\nconda install ipykernel\r\n<\/code><\/pre>\n<p>If the conda install is successful you should be able to load ipykernel without error like this:<\/p>\n<pre><code>python3 -c 'import ipykernel'\r\n<\/code><\/pre>\n<p>And there will be a jupyter-kernelspec executable in the environment:<\/p>\n<pre><code># if this command prints out a path different from your environment's \/bin\r\n# then jupyter won't see it\r\n# this would be from an error with the ipykernel install for your conda env\r\nwhich jupyter-kernelspec\r\n<\/code><\/pre>\n<p>If you are still using python2 then you may have to install backports like this:<\/p>\n<pre><code>conda install backports.functools_lru_cache\r\n<\/code><\/pre>\n<\/body><\/html>\n    <\/div>\n<\/div>\n\n","protected":false},"excerpt":{"rendered":"<p>FAQs<\/p>\n","protected":false},"author":469,"featured_media":454,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ring_central_script_selection":"","footnotes":""},"class_list":["post-39","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/pages\/39","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/users\/469"}],"replies":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/comments?post=39"}],"version-history":[{"count":77,"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/pages\/39\/revisions"}],"predecessor-version":[{"id":4208,"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/pages\/39\/revisions\/4208"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/media\/454"}],"wp:attachment":[{"href":"https:\/\/in.nau.edu\/arc\/wp-json\/wp\/v2\/media?parent=39"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}