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<!DOCTYPE html>
<html lang='en-US' xml:lang='en-US'>
<head> <title>Speed: The GCS ENCS Cluster</title>
<meta charset='utf-8' />
<meta content='TeX4ht (https://tug.org/tex4ht/)' name='generator' />
<meta content='width=device-width,initial-scale=1' name='viewport' />
<link href='speed-manual.css' rel='stylesheet' type='text/css' />
<meta content='speed-manual.tex' name='src' />
<script>window.MathJax = { tex: { tags: "ams", }, }; </script>
<script async='async' id='MathJax-script' src='https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml-full.js' type='text/javascript'></script>
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</head><body>
<div class='maketitle'>
<h2 class='titleHead'>Speed: The GCS ENCS Cluster</h2>
<div class='author'> Serguei A. Mokhov <br class='and' />Gillian A. Roper <br class='and' />Carlos Alarcón Meza <br class='and' />Farah Salhany <br class='and' />Network, Security and HPC Group<span class='thank-mark'><a href='#tk-1'><span class='tcrm-1000'>∗</span></a></span>
<br /> <span class='cmr-9'>Gina Cody School of Engineering and Computer Science</span>
<br /> <span class='cmr-9'>Concordia University</span>
<br /> <span class='cmr-9'>Montreal, Quebec, Canada</span>
<br /> <a class='url' href='rt-ex-hpc~AT~encs.concordia.ca'><span class='cmtt-9'>rt-ex-hpc~AT~encs.concordia.ca</span></a><br /></div>
<br />
<div class='date'><span class='cmbx-10'>Version 7.3</span></div>
<div class='thanks'><br /><a id='tk-1'></a><span class='thank-mark'><span class='tcrm-1000'>∗</span></span>The group acknowledges the initial manual version VI produced by Dr. Scott Bunnell while with us
as well as Dr. Tariq Daradkeh for his instructional support of the users and contribution of
examples.</div></div><section class='abstract' role='doc-abstract'>
<h3 class='abstracttitle'>
<span class='cmbx-9'>Abstract</span>
</h3>
<!-- l. 91 --><p class='noindent'><span class='cmr-9'>This document serves as a quick start guide to using the Gina Cody School of Engineering
and Computer Science (GCS ENCS) compute server farm, known as “Speed.” Managed by
the HPC/NAG group of the Academic Information Technology Services (AITS) at GCS,
Concordia University, Montreal, Canada.</span>
</p>
</section>
<h3 class='likesectionHead' id='contents'><a id='x1-1000'></a>Contents</h3>
<div class='tableofcontents'>
<span class='sectionToc'>1 <a href='#introduction' id='QQ2-1-2'>Introduction</a></span>
<br /> <span class='subsectionToc'>1.1 <a href='#citing-us' id='QQ2-1-3'>Citing Us</a></span>
<br /> <span class='subsectionToc'>1.2 <a href='#resources' id='QQ2-1-4'>Resources</a></span>
<br /> <span class='subsectionToc'>1.3 <a href='#team' id='QQ2-1-5'>Team</a></span>
<br /> <span class='subsectionToc'>1.4 <a href='#what-speed-consists-of' id='QQ2-1-6'>What Speed Consists of</a></span>
<br /> <span class='subsectionToc'>1.5 <a href='#what-speed-is-ideal-for' id='QQ2-1-10'>What Speed Is Ideal For</a></span>
<br /> <span class='subsectionToc'>1.6 <a href='#what-speed-is-not' id='QQ2-1-11'>What Speed Is Not</a></span>
<br /> <span class='subsectionToc'>1.7 <a href='#available-software' id='QQ2-1-12'>Available Software</a></span>
<br /> <span class='subsectionToc'>1.8 <a href='#requesting-access' id='QQ2-1-13'>Requesting Access</a></span>
<br /><span class='sectionToc'>2 <a href='#job-management' id='QQ2-1-14'>Job Management</a></span>
<br /> <span class='subsectionToc'>2.1 <a href='#getting-started' id='QQ2-1-15'>Getting Started</a></span>
<br /> <span class='subsubsectionToc'>2.1.1 <a href='#ssh-connections' id='QQ2-1-16'>SSH Connections</a></span>
<br /> <span class='subsubsectionToc'>2.1.2 <a href='#environment-set-up' id='QQ2-1-17'>Environment Set Up</a></span>
<br /> <span class='subsectionToc'>2.2 <a href='#job-submission-basics' id='QQ2-1-18'>Job Submission Basics</a></span>
<br /> <span class='subsubsectionToc'>2.2.1 <a href='#directives' id='QQ2-1-19'>Directives</a></span>
<br /> <span class='subsubsectionToc'>2.2.2 <a href='#working-with-modules' id='QQ2-1-20'>Working with Modules</a></span>
<br /> <span class='subsubsectionToc'>2.2.3 <a href='#user-scripting' id='QQ2-1-21'>User Scripting</a></span>
<br /> <span class='subsectionToc'>2.3 <a href='#sample-job-script' id='QQ2-1-22'>Sample Job Script</a></span>
<br /> <span class='subsectionToc'>2.4 <a href='#common-job-management-commands' id='QQ2-1-25'>Common Job Management Commands</a></span>
<br /> <span class='subsectionToc'>2.5 <a href='#advanced-sbatch-options' id='QQ2-1-26'>Advanced <span class='cmtt-10'>sbatch </span>Options</a></span>
<br /> <span class='subsectionToc'>2.6 <a href='#array-jobs' id='QQ2-1-27'>Array Jobs</a></span>
<br /> <span class='subsectionToc'>2.7 <a href='#requesting-multiple-cores-ie-multithreading-jobs' id='QQ2-1-28'>Requesting Multiple Cores (i.e., Multithreading Jobs)</a></span>
<br /> <span class='subsectionToc'>2.8 <a href='#interactive-jobs' id='QQ2-1-29'>Interactive Jobs</a></span>
<br /> <span class='subsubsectionToc'>2.8.1 <a href='#command-line' id='QQ2-1-30'>Command Line</a></span>
<br /> <span class='subsubsectionToc'>2.8.2 <a href='#graphical-applications' id='QQ2-1-31'>Graphical Applications</a></span>
<br /> <span class='subsubsectionToc'>2.8.3 <a href='#jupyter-notebooks' id='QQ2-1-33'>Jupyter Notebooks</a></span>
<br /> <span class='paragraphToc'>2.8.3.1 <a href='#jupyter-notebook-in-singularity' id='QQ2-1-34'>Jupyter Notebook in Singularity</a></span>
<br /> <span class='paragraphToc'>2.8.3.2 <a href='#jupyter-notebook-in-conda' id='QQ2-1-38'>Jupyter Notebook in Conda</a></span>
<br /> <span class='paragraphToc'>2.8.3.3 <a href='#jupyter-notebook-in-python-venv' id='QQ2-1-41'>Jupyter Notebook in Python venv</a></span>
<br /> <span class='subsubsectionToc'>2.8.4 <a href='#visual-studio-code' id='QQ2-1-42'>Visual Studio Code</a></span>
<br /> <span class='subsectionToc'>2.9 <a href='#scheduler-environment-variables' id='QQ2-1-44'>Scheduler Environment Variables</a></span>
<br /> <span class='subsectionToc'>2.10 <a href='#ssh-keys-for-mpi' id='QQ2-1-47'>SSH Keys for MPI</a></span>
<br /> <span class='subsectionToc'>2.11 <a href='#creating-virtual-environments' id='QQ2-1-48'>Creating Virtual Environments</a></span>
<br /> <span class='subsubsectionToc'>2.11.1 <a href='#anaconda' id='QQ2-1-49'>Anaconda</a></span>
<br /> <span class='paragraphToc'>2.11.1.1 <a href='#conda-env-without-prefix' id='QQ2-1-50'>Conda Env without <span class='cmtt-10'>--prefix</span></a></span>
<br /> <span class='subsubsectionToc'>2.11.2 <a href='#python' id='QQ2-1-51'>Python</a></span>
<br /> <span class='subsectionToc'>2.12 <a href='#example-job-script-fluent' id='QQ2-1-52'>Example Job Script: Fluent</a></span>
<br /> <span class='subsectionToc'>2.13 <a href='#example-job-efficientdet' id='QQ2-1-55'>Example Job: EfficientDet</a></span>
<br /> <span class='subsectionToc'>2.14 <a href='#java-jobs' id='QQ2-1-56'>Java Jobs</a></span>
<br /> <span class='subsectionToc'>2.15 <a href='#scheduling-on-the-gpu-nodes' id='QQ2-1-57'>Scheduling on the GPU Nodes</a></span>
<br /> <span class='subsubsectionToc'>2.15.1 <a href='#p-on-multigpu-multinode' id='QQ2-1-58'>P6 on Multi-GPU, Multi-Node</a></span>
<br /> <span class='subsubsectionToc'>2.15.2 <a href='#cuda' id='QQ2-1-59'>CUDA</a></span>
<br /> <span class='subsubsectionToc'>2.15.3 <a href='#special-notes-for-sending-cuda-jobs-to-the-gpu-queues' id='QQ2-1-60'>Special Notes for Sending CUDA Jobs to the GPU Queues</a></span>
<br /> <span class='subsubsectionToc'>2.15.4 <a href='#openiss-examples' id='QQ2-1-61'>OpenISS Examples</a></span>
<br /> <span class='paragraphToc'>2.15.4.1 <a href='#openiss-and-reid' id='QQ2-1-62'>OpenISS and REID</a></span>
<br /> <span class='paragraphToc'>2.15.4.2 <a href='#openiss-and-yolov' id='QQ2-1-63'>OpenISS and YOLOv3</a></span>
<br /> <span class='subsectionToc'>2.16 <a href='#singularity-containers' id='QQ2-1-64'>Singularity Containers</a></span>
<br /><span class='sectionToc'>3 <a href='#conclusion' id='QQ2-1-65'>Conclusion</a></span>
<br /> <span class='subsectionToc'>3.1 <a href='#important-limitations' id='QQ2-1-66'>Important Limitations</a></span>
<br /> <span class='subsectionToc'>3.2 <a href='#tipstricks' id='QQ2-1-67'>Tips/Tricks</a></span>
<br /> <span class='subsectionToc'>3.3 <a href='#use-cases' id='QQ2-1-68'>Use Cases</a></span>
<br /><span class='sectionToc'>A <a href='#history' id='QQ2-1-69'>History</a></span>
<br /> <span class='subsectionToc'>A.1 <a href='#acknowledgments' id='QQ2-1-70'>Acknowledgments</a></span>
<br /> <span class='subsectionToc'>A.2 <a href='#migration-from-uge-to-slurm' id='QQ2-1-71'>Migration from UGE to SLURM</a></span>
<br /> <span class='subsectionToc'>A.3 <a href='#phases' id='QQ2-1-73'>Phases</a></span>
<br /> <span class='subsubsectionToc'>A.3.1 <a href='#phase-' id='QQ2-1-74'>Phase 5</a></span>
<br /> <span class='subsubsectionToc'>A.3.2 <a href='#phase-1' id='QQ2-1-75'>Phase 4</a></span>
<br /> <span class='subsubsectionToc'>A.3.3 <a href='#phase-2' id='QQ2-1-76'>Phase 3</a></span>
<br /> <span class='subsubsectionToc'>A.3.4 <a href='#phase-3' id='QQ2-1-77'>Phase 2</a></span>
<br /> <span class='subsubsectionToc'>A.3.5 <a href='#phase-4' id='QQ2-1-78'>Phase 1</a></span>
<br /><span class='sectionToc'>B <a href='#frequently-asked-questions' id='QQ2-1-79'>Frequently Asked Questions</a></span>
<br /> <span class='subsectionToc'>B.1 <a href='#where-do-i-learn-about-linux' id='QQ2-1-80'>Where do I learn about Linux?</a></span>
<br /> <span class='subsectionToc'>B.2 <a href='#how-to-use-bash-shell-on-speed' id='QQ2-1-83'>How to use bash shell on Speed?</a></span>
<br /> <span class='subsubsectionToc'>B.2.1 <a href='#how-do-i-set-bash-as-my-login-shell' id='QQ2-1-84'>How do I set bash as my login shell?</a></span>
<br /> <span class='subsubsectionToc'>B.2.2 <a href='#how-do-i-move-into-a-bash-shell-on-speed' id='QQ2-1-85'>How do I move into a bash shell on Speed?</a></span>
<br /> <span class='subsubsectionToc'>B.2.3 <a href='#how-do-i-use-the-bash-shell-in-an-interactive-session-on-speed' id='QQ2-1-86'>How do I use the bash shell in an interactive session on Speed?</a></span>
<br /> <span class='subsubsectionToc'>B.2.4 <a href='#how-do-i-run-scripts-written-in-bash-on-speed' id='QQ2-1-87'>How do I run scripts written in bash on <span class='cmtt-10'>Speed</span>?</a></span>
<br /> <span class='subsectionToc'>B.3 <a href='#how-to-resolve-disk-quota-exceeded-errors' id='QQ2-1-88'>How to resolve “Disk quota exceeded” errors?</a></span>
<br /> <span class='subsubsectionToc'>B.3.1 <a href='#probable-cause' id='QQ2-1-89'>Probable Cause</a></span>
<br /> <span class='subsubsectionToc'>B.3.2 <a href='#possible-solutions' id='QQ2-1-90'>Possible Solutions</a></span>
<br /> <span class='subsubsectionToc'>B.3.3 <a href='#example-of-setting-working-directories-for-comsol' id='QQ2-1-91'>Example of setting working directories for <span class='cmtt-10'>COMSOL</span></a></span>
<br /> <span class='subsubsectionToc'>B.3.4 <a href='#example-of-setting-working-directories-for-python-modules' id='QQ2-1-92'>Example of setting working directories for <span class='cmtt-10'>Python Modules</span></a></span>
<br /> <span class='subsectionToc'>B.4 <a href='#how-do-i-check-my-jobs-status' id='QQ2-1-93'>How do I check my job’s status?</a></span>
<br /> <span class='subsectionToc'>B.5 <a href='#why-is-my-job-pending-when-nodes-are-empty' id='QQ2-1-94'>Why is my job pending when nodes are empty?</a></span>
<br /> <span class='subsubsectionToc'>B.5.1 <a href='#disabled-nodes' id='QQ2-1-95'>Disabled nodes</a></span>
<br /> <span class='subsubsectionToc'>B.5.2 <a href='#error-in-job-submit-request' id='QQ2-1-96'>Error in job submit request.</a></span>
<br /> <span class='subsectionToc'>B.6 <a href='#how-to-handle-tmp-overflow-on-speed-nodes' id='QQ2-1-97'>How to Handle <span class='cmtt-10'>/tmp </span>Overflow on Speed Nodes?</a></span>
<br /> <span class='subsubsectionToc'>B.6.1 <a href='#cause' id='QQ2-1-98'>Cause</a></span>
<br /> <span class='subsubsectionToc'>B.6.2 <a href='#solution' id='QQ2-1-99'>Solution</a></span>
<br /><span class='sectionToc'>C <a href='#sister-facilities' id='QQ2-1-100'>Sister Facilities</a></span>
<br /><span class='sectionToc'>D <a href='#software-installed-on-speed' id='QQ2-1-101'>Software Installed On Speed</a></span>
<br /> <span class='subsectionToc'>D.1 <a href='#el' id='QQ2-1-102'>EL7</a></span>
<br /> <span class='subsectionToc'>D.2 <a href='#el1' id='QQ2-1-103'>EL9</a></span>
<br /><span class='sectionToc'><a href='#annotated-bibliography'>Annotated Bibliography</a></span>
</div>
<h3 class='sectionHead' id='introduction'><span class='titlemark'>1 </span> <a id='x1-20001'></a>Introduction</h3>
<!-- l. 7 --><p class='noindent'>This document contains basic information required to use “Speed”, along with tips, tricks, examples,
and references to projects and papers that have used Speed. User contributions of sample jobs and/or
references are welcome.
</p><!-- l. 11 --><p class='noindent'><span class='cmbx-10'>Note: </span>On October 20, 2023, we completed the migration to SLURM from Grid Engine (UGE/AGE)
as our job scheduler. This manual has been updated to use SLURM’s syntax and commands. If you
are a long-time GE user, refer to Appendix <a href='#migration-from-uge-to-slurm'>A.2<!-- tex4ht:ref: appdx:uge-to-slurm --></a> for key highlights needed to translate your GE jobs to
SLURM as well as environment changes. These changes are also elaborated throughout this document
and our examples.
</p><!-- l. 20 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='citing-us'><span class='titlemark'>1.1 </span> <a id='x1-30001.1'></a>Citing Us</h4>
<!-- l. 23 --><p class='noindent'>If you wish to cite this work in your acknowledgements, you can use our general DOI found on our
GitHub page <a class='url' href='https://dx.doi.org/10.5281/zenodo.5683642'><span class='cmtt-10'>https://dx.doi.org/10.5281/zenodo.5683642</span></a> or a specific version of the manual and
scripts from that link individually. You can also use the “cite this repository” feature of
GitHub.
</p><!-- l. 29 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='resources'><span class='titlemark'>1.2 </span> <a id='x1-40001.2'></a>Resources</h4>
<ul class='itemize1'>
<li class='itemize'>
<!-- l. 34 --><p class='noindent'>Public GitHub page where the manual and sample job scripts are maintained at<br class='newline' /><a class='url' href='https://github.com/NAG-DevOps/speed-hpc'><span class='cmtt-10'>https://github.com/NAG-DevOps/speed-hpc</span></a> </p>
<ul class='itemize2'>
<li class='itemize'>Pull requests (PRs) are subject to review and are welcome:<br class='newline' /><a class='url' href='https://github.com/NAG-DevOps/speed-hpc/pulls'><span class='cmtt-10'>https://github.com/NAG-DevOps/speed-hpc/pulls</span></a></li></ul>
</li>
<li class='itemize'>
<!-- l. 42 --><p class='noindent'>Speed Manual: </p>
<ul class='itemize2'>
<li class='itemize'>PDF version of the manual: <a class='url' href='https://github.com/NAG-DevOps/speed-hpc/blob/master/doc/speed-manual.pdf'><span class='cmtt-10'>https://github.com/NAG-DevOps/speed-hpc/blob/master/doc/speed-manual.pdf</span></a>
</li>
<li class='itemize'>HTML version of the manual: <a class='url' href='https://nag-devops.github.io/speed-hpc/'><span class='cmtt-10'>https://nag-devops.github.io/speed-hpc/</span></a></li></ul>
</li>
<li class='itemize'>Concordia official page for “Speed” cluster, which includes access request instructions.
<a class='url' href='https://www.concordia.ca/ginacody/aits/speed.html'><span class='cmtt-10'>https://www.concordia.ca/ginacody/aits/speed.html</span></a>
</li>
<li class='itemize'>All Speed users are subscribed to the <span class='cmtt-10'>hpc-ml </span>mailing list.</li></ul>
<!-- l. 60 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='team'><span class='titlemark'>1.3 </span> <a id='x1-50001.3'></a>Team</h4>
<!-- l. 63 --><p class='noindent'>Speed is supported by: </p>
<ul class='itemize1'>
<li class='itemize'>Serguei Mokhov, PhD, Manager, Networks, Security and HPC, AITS
</li>
<li class='itemize'>Gillian Roper, Senior Systems Administrator, HPC, AITS
</li>
<li class='itemize'>Carlos Alarcón Meza, Systems Administrator, HPC and Networking, AITS
</li>
<li class='itemize'>Farah Salhany, IT Instructional Specialist, AITS</li></ul>
<!-- l. 75 --><p class='noindent'>We receive support from the rest of AITS teams, such as NAG, SAG, FIS, and DOG.
</p><!-- l. 77 --><p class='noindent'><a class='url' href='https://www.concordia.ca/ginacody/aits.html'><span class='cmtt-10'>https://www.concordia.ca/ginacody/aits.html</span></a>
</p><!-- l. 81 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='what-speed-consists-of'><span class='titlemark'>1.4 </span> <a id='x1-60001.4'></a>What Speed Consists of</h4>
<ul class='itemize1'>
<li class='itemize'>Twenty four (24) 32-core compute nodes, each with 512 GB of memory and approximately
1 TB of local volatile-scratch disk space (pictured in Figure <a href='#-speed'>1<!-- tex4ht:ref: fig:speed-pics --></a>).
</li>
<li class='itemize'>Twelve (12) NVIDIA Tesla P6 GPUs, with 16 GB of GPU memory (compatible with the
CUDA, OpenGL, OpenCL, and Vulkan APIs).
</li>
<li class='itemize'>4 VIDPRO nodes (ECE. Dr. Amer), with 6 P6 cards, and 6 V100 cards (32GB), and
256GB of RAM.
</li>
<li class='itemize'>7 new SPEED2 servers with 256 CPU cores each 4x A100 80 GB GPUs, partitioned into
4x 20GB MIGs each; larger local storage for TMPDIR (see Figure <a href='#-speed-cluster-hardware-architecture'>2<!-- tex4ht:ref: fig:speed-architecture-full --></a>).
</li>
<li class='itemize'>One AMD FirePro S7150 GPU, with 8 GB of memory (compatible with the Direct X,
OpenGL, OpenCL, and Vulkan APIs).
</li>
<li class='itemize'>Salus compute node (CSSE CLAC, Drs. Bergler and Kosseim), 56 cores and 728GB of
RAM, see Figure <a href='#-speed-cluster-hardware-architecture'>2<!-- tex4ht:ref: fig:speed-architecture-full --></a>.
</li>
<li class='itemize'>Magic subcluster partition (ECE, Dr. Khendek, 11 nodes, see Figure <a href='#-speed-cluster-hardware-architecture'>2<!-- tex4ht:ref: fig:speed-architecture-full --></a>).
</li>
<li class='itemize'>Nebular subcluster partition (CIISE, Drs. Yan, Assi, Ghafouri, et al., Nebulae GPU
node with 2x RTX 6000 Ada 48GB cards, Stellar compute node, and Matrix 177TB
storage/compute node, see Figure <a href='#-speed-cluster-hardware-architecture'>2<!-- tex4ht:ref: fig:speed-architecture-full --></a>).</li></ul>
<figure class='figure' id='-speed'>
<a id='x1-60011'></a>
<!-- l. 111 --><p class='noindent'><img alt='PIC' height='412' src='images/speed-pics.png' width='412' />
</p>
<figcaption class='caption'><span class='id'>Figure 1: </span><span class='content'>Speed</span></figcaption><!-- tex4ht:label?: x1-60011 -->
</figure>
<figure class='figure' id='-speed-cluster-hardware-architecture'>
<a id='x1-60022'></a>
<!-- l. 118 --><p class='noindent'><img alt='PIC' height='412' src='images/speed-architecture-full.png' width='412' />
</p>
<figcaption class='caption'><span class='id'>Figure 2: </span><span class='content'>Speed Cluster Hardware Architecture</span></figcaption><!-- tex4ht:label?: x1-60022 -->
</figure>
<figure class='figure' id='-speed-slurm-architecture'>
<a id='x1-60033'></a>
<!-- l. 125 --><p class='noindent'><img alt='PIC' height='412' src='images/slurm-arch.png' width='412' />
</p>
<figcaption class='caption'><span class='id'>Figure 3: </span><span class='content'>Speed SLURM Architecture</span></figcaption><!-- tex4ht:label?: x1-60033 -->
</figure>
<h4 class='subsectionHead' id='what-speed-is-ideal-for'><span class='titlemark'>1.5 </span> <a id='x1-70001.5'></a>What Speed Is Ideal For</h4>
<ul class='itemize1'>
<li class='itemize'>Design, develop, test, and run parallel, batch, and other algorithms and scripts with
partial data sets. “Speed” has been optimized for compute jobs that are multi-core aware,
require a large memory space, or are iteration intensive.
</li>
<li class='itemize'>
<!-- l. 142 --><p class='noindent'>Prepare jobs for large clusters such as: </p>
<ul class='itemize2'>
<li class='itemize'>Digital Research Alliance of Canada (Calcul Quebec and Compute Canada)
</li>
<li class='itemize'>Cloud platforms</li></ul>
</li>
<li class='itemize'>Jobs that are too demanding for a desktop.
</li>
<li class='itemize'>Single-core batch jobs; multithreaded jobs typically up to 32 cores (i.e., a single
machine).
</li>
<li class='itemize'>Multi-node multi-core jobs (MPI).
</li>
<li class='itemize'>Anything that can fit into a 500-GB memory space and a <span class='cmbx-10'>speed scratch </span>space of
approximately 10 TB.
</li>
<li class='itemize'>CPU-based jobs.
</li>
<li class='itemize'>CUDA GPU jobs.
</li>
<li class='itemize'>Non-CUDA GPU jobs using OpenCL.</li></ul>
<!-- l. 165 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='what-speed-is-not'><span class='titlemark'>1.6 </span> <a id='x1-80001.6'></a>What Speed Is Not</h4>
<ul class='itemize1'>
<li class='itemize'>Speed is not a web host and does not host websites.
</li>
<li class='itemize'>Speed is not meant for Continuous Integration (CI) automation deployments for Ansible
or similar tools.
</li>
<li class='itemize'>Does not run Kubernetes or other container orchestration software.
</li>
<li class='itemize'>Does not run Docker. (<span class='cmbx-10'>Note: </span>Speed does run Singularity and many Docker containers
can be converted to Singularity containers with a single command. See Section <a href='#singularity-containers'>2.16<!-- tex4ht:ref: sect:singularity-containers --></a>.)
</li>
<li class='itemize'>Speed is not for jobs executed outside of the scheduler. (Jobs running outside of the
scheduler will be killed and all data lost.)</li></ul>
<!-- l. 179 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='available-software'><span class='titlemark'>1.7 </span> <a id='x1-90001.7'></a>Available Software</h4>
<!-- l. 182 --><p class='noindent'>There are a wide range of open-source and commercial software available and installed on “Speed.”
This includes Abaqus <span class='cite'>[<a href='#Xabaqus'>1</a>]</span>, AllenNLP, Anaconda, ANSYS, Bazel, COMSOL, CPLEX, CUDA, Eclipse,
Fluent <span class='cite'>[<a href='#Xfluent'>2</a>]</span>, Gurobi, MATLAB <span class='cite'>[<a href='#Xmatlab'>15</a>, <a href='#Xscholarpedia-matlab'>29</a>]</span>, OMNeT++, OpenCV, OpenFOAM, OpenMPI, OpenPMIx,
ParaView, PyTorch, QEMU, R, Rust, and Singularity among others. Programming environments
include various versions of Python, C++/Java compilers, TensorFlow, OpenGL, OpenISS, and
MARF <span class='cite'>[<a href='#Xmarf'>30</a>]</span>.
</p><!-- l. 188 --><p class='noindent'>In particular, there are over 2200 programs available in <span class='cmtt-10'>/encs/bin </span>and <span class='cmtt-10'>/encs/pkg </span>under Scientific
Linux 7 (EL7). We are building an equivalent array of programs for the EL9 SPEED2 nodes. To see
the packages available, run <span class='cmtt-10'>ls -al /encs/pkg/ </span>on <span class='cmtt-10'>speed.encs</span>. See a complete list in
Appendix <a href='#software-installed-on-speed'>D<!-- tex4ht:ref: sect:software-list --></a>.
</p><!-- l. 192 --><p class='noindent'><span class='cmbx-10'>Note: </span>We do our best to accommodate custom software requests. Python environments can use
user-custom installs from within scratch directory.
</p><!-- l. 197 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='requesting-access'><span class='titlemark'>1.8 </span> <a id='x1-100001.8'></a>Requesting Access</h4>
<!-- l. 200 --><p class='noindent'>After reviewing the “What Speed is” (Section <a href='#what-speed-is-ideal-for'>1.5<!-- tex4ht:ref: sect:speed-is-for --></a>) and “What Speed is Not” (Section <a href='#what-speed-is-not'>1.6<!-- tex4ht:ref: sect:speed-is-not --></a>), request
access to the “Speed” cluster by emailing: <span class='cmtt-10'>rt-ex-hpc AT encs.concordia.ca</span>.
</p>
<ul class='itemize1'>
<li class='itemize'>GCS ENCS faculty and staff may request access directly.
</li>
<li class='itemize'>
<!-- l. 206 --><p class='noindent'>GCS students must include the following in their request message: </p>
<ul class='itemize2'>
<li class='itemize'>GCS ENCS username
</li>
<li class='itemize'>Name and email (CC) of the approver – either a supervisor, course instructor, or a
department representative (e.g., in the case of undergraduate or M.Eng. students it
can be the Chair, associate chair, a technical officer, or a department administrator)
for approval.
</li>
<li class='itemize'>Written request from the approver for the GCS ENCS username to be granted access
to “Speed.”</li></ul>
</li>
<li class='itemize'>Non-GCS students taking a GCS course will have their GCS ENCS account created
automatically, but still need the course instructor’s approval to use the service.
</li>
<li class='itemize'>Non-GCS faculty and students need to get a “sponsor” within GCS, so that a guest GCS ENCS
account is created first. A sponsor can be any GCS Faculty member you collaborate with.
Failing that, request the approval from our Dean’s Office; via our Associate Deans Drs. Eddie
Hoi Ng or Emad Shihab.
</li>
<li class='itemize'>External entities collaborating with GCS Concordia researchers should also go through the
Dean’s Office for approvals.</li></ul>
<!-- l. 221 --><p class='noindent'>For detailed instructions, refer to the Concordia <a href='https://www.concordia.ca/ginacody/aits/speed.html'>Computing (HPC) Facility: Speed</a> webpage.
</p><!-- l. 4 --><p class='noindent'>
</p>
<h3 class='sectionHead' id='job-management'><span class='titlemark'>2 </span> <a id='x1-110002'></a>Job Management</h3>
<!-- l. 7 --><p class='noindent'>We use SLURM as the workload manager. It supports primarily two types of jobs: batch and
interactive. Batch jobs are used to run unattended tasks, whereas, interactive jobs are are ideal for
setting up virtual environments, compilation, and debugging.
</p><!-- l. 11 --><p class='noindent'><span class='cmbx-10'>Note: </span>In the following instructions, anything bracketed like, <span class='obeylines-h'><span class='verb'><span class='cmtt-10'><></span></span></span>, indicates a label/value to be replaced
(the entire bracketed term needs replacement).
</p><!-- l. 14 --><p class='noindent'>Job instructions in a script start with <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>#SBATCH</span></span></span> prefix, for example:
</p>
<pre class='verbatim' id='verbatim-1'>
#SBATCH --mem=100M -t 600 -J <job-name> -A <slurm account>
#SBATCH -p pg --gpus=1 --mail-type=ALL</pre>
<!-- l. 18 --><p class='nopar'>
</p><!-- l. 20 --><p class='noindent'>For complex compute steps within a script, use <span class='cmtt-10'>srun</span>. We recommend using <span class='cmtt-10'>salloc </span>for interactive
jobs as it supports multiple steps. However, <span class='cmtt-10'>srun </span>can also be used to start interactive jobs (see
Section <a href='#interactive-jobs'>2.8<!-- tex4ht:ref: sect:interactive-jobs --></a>). Common and required job parameters include:
</p><!-- l. 25 --><p class='noindent'>Common and required job parameters include: </p>
<ul class='itemize1'>
<li class='itemize'>Memory (<span class='cmtt-10'>--mem=<mem>[M|G|T]</span>),
</li>
<li class='itemize'>Partition/Queue (<span class='cmtt-10'>-p <partition></span>),
</li>
<li class='itemize'>Job name (<span class='cmtt-10'>--job-name=<name> </span>or <span class='cmtt-10'>-J <name></span>),
</li>
<li class='itemize'>Wall Clock Limit (<span class='cmtt-10'>-t <min> or -t <days-hh:mm:ss></span>),
</li>
<li class='itemize'>Event Notification (<span class='cmtt-10'>--mail-type=<events></span>),
</li>
<li class='itemize'>Email Address (<span class='cmtt-10'>--mail-user=<address></span>),
</li>
<li class='itemize'>Slurm Account (<span class='cmtt-10'>--account=<account> or -A <account></span>),
</li>
<li class='itemize'>Tasks Per Node (<span class='cmtt-10'>--tasks-per-node=<count></span>),
</li>
<li class='itemize'>CPUs Per Task (<span class='cmtt-10'>--cpus-per-task=<count></span>),
</li>
<li class='itemize'>CPU Count ntasks (<span class='cmtt-10'>-n <count></span>).</li></ul>
<!-- l. 3 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='getting-started'><span class='titlemark'>2.1 </span> <a id='x1-120002.1'></a>Getting Started</h4>
<!-- l. 6 --><p class='noindent'>Before getting started, please review the “What Speed is” (Section <a href='#what-speed-is-ideal-for'>1.5<!-- tex4ht:ref: sect:speed-is-for --></a>) and “What Speed is Not”
(Section <a href='#what-speed-is-not'>1.6<!-- tex4ht:ref: sect:speed-is-not --></a>). Once your GCS ENCS account has been granted access to “Speed”, use
your GCS ENCS account credentials to create an SSH connection to <span class='cmtt-10'>speed </span>(an alias for
<span class='cmtt-10'>speed-submit.encs.concordia.ca</span>).
</p><!-- l. 12 --><p class='noindent'>All users are expected to have a basic understanding of Linux and its commonly used commands (see
Appendix <a href='#frequently-asked-questions'>B<!-- tex4ht:ref: sect:faqs --></a> for resources).
</p><!-- l. 17 --><p class='noindent'>
</p>
<h5 class='subsubsectionHead' id='ssh-connections'><span class='titlemark'>2.1.1 </span> <a id='x1-130002.1.1'></a>SSH Connections</h5>
<!-- l. 20 --><p class='noindent'>Requirements to create SSH connection to “Speed”:
</p><ol class='enumerate1'>
<li class='enumerate' id='x1-13002x1'><span class='cmbx-10'>Active GCS ENCS user account: </span>Ensure you have an active GCS ENCS user account
with permission to connect to Speed (see Section <a href='#requesting-access'>1.8<!-- tex4ht:ref: sect:access-requests --></a>).
</li>
<li class='enumerate' id='x1-13004x2'><span class='cmbx-10'>VPN Connection </span>(for off-campus access): If you are off-campus, you wil need to
establish an active connection to Concordia’s VPN, which requires a Concordia netname.
</li>
<li class='enumerate' id='x1-13006x3'><span class='cmbx-10'>Terminal Emulator for Windows: </span>Windows systems use a terminal emulator such as
PuTTY, Cygwin, or MobaXterm.
</li>
<li class='enumerate' id='x1-13008x4'><span class='cmbx-10'>Terminal for macOS: </span>macOS systems have a built-in Terminal app or <span class='cmtt-10'>xterm </span>that comes
with XQuartz.</li></ol>
<!-- l. 30 --><p class='noindent'>To create an SSH connection to Speed, open a terminal window and type the following command,
replacing <span class='obeylines-h'><span class='verb'><span class='cmtt-10'><ENCSusername></span></span></span> with your ENCS account’s username:
</p>
<pre class='verbatim' id='verbatim-2'>
ssh <ENCSusername>@speed.encs.concordia.ca</pre>
<!-- l. 33 --><p class='nopar'>
</p><!-- l. 35 --><p class='noindent'>For detailed instructions on securely connecting to a GCS server, refer to the AITS FAQ: <a href='https://www.concordia.ca/ginacody/aits/support/faq/ssh-to-gcs.html'>How do I
securely connect to a GCS server?</a>
</p><!-- l. 40 --><p class='noindent'>
</p>
<h5 class='subsubsectionHead' id='environment-set-up'><span class='titlemark'>2.1.2 </span> <a id='x1-140002.1.2'></a>Environment Set Up</h5>
<!-- l. 46 --><p class='noindent'>After creating an SSH connection to Speed, you will need to make sure the <span class='cmtt-10'>srun</span>, <span class='cmtt-10'>sbatch</span>, and <span class='cmtt-10'>salloc</span>
commands are available to you. To check this, type each command at the prompt and press Enter. If
“command not found” is returned, you need to make sure your <span class='tctt-1000'>$</span><span class='cmtt-10'>PATH </span>includes <span class='cmtt-10'>/local/bin</span>. You can
check your path by typing:
</p>
<pre class='verbatim' id='verbatim-3'>
echo $PATH</pre>
<!-- l. 52 --><p class='nopar'>
</p><!-- l. 54 --><p class='noindent'>The next step is to set up your cluster-specific storage “speed-scratch”, to do so, execute the following
command from within your home directory.
</p>
<pre class='verbatim' id='verbatim-4'>
mkdir -p /speed-scratch/$USER && cd /speed-scratch/$USER</pre>
<!-- l. 58 --><p class='nopar'>
</p><!-- l. 60 --><p class='noindent'>Next, copy a job template to your cluster-specific storage </p>
<ul class='itemize1'>
<li class='itemize'>From Windows drive G: to Speed:<br class='newline' /><span class='obeylines-h'><span class='verb'><span class='cmtt-10'>cp /winhome/<1st letter of $USER>/$USER/<script>.sh /speed-scratch/$USER/</span></span></span>
</li>
<li class='itemize'>From Linux drive U: to Speed:<br class='newline' /><span class='obeylines-h'><span class='verb'><span class='cmtt-10'>cp ~/<script>.sh /speed-scratch/$USER/</span></span></span></li></ul>
<!-- l. 68 --><p class='noindent'><span class='cmbx-10'>Tip: </span>the default shell for GCS ENCS users is <span class='cmtt-10'>tcsh</span>. If you would like to use <span class='cmtt-10'>bash</span>, please contact
<span class='cmtt-10'>rt-ex-hpc AT encs.concordia.ca</span>.
</p><!-- l. 71 --><p class='noindent'><span class='cmbx-10'>Note: </span>If you encounter a “command not found” error after logging in to Speed, your user account
may have defunct Grid Engine environment commands. See Appendix <a href='#migration-from-uge-to-slurm'>A.2<!-- tex4ht:ref: appdx:uge-to-slurm --></a> for instructions on how to
resolve this issue.
</p><!-- l. 3 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='job-submission-basics'><span class='titlemark'>2.2 </span> <a id='x1-150002.2'></a>Job Submission Basics</h4>
<!-- l. 6 --><p class='noindent'>Preparing your job for submission is fairly straightforward. Start by basing your job script on one of
the examples available in the <span class='cmtt-10'>src/ </span>directory of our <a href='https://github.com/NAG-DevOps/speed-hpc'>GitHub repository</a>. You can clone the repository to
get the examples to start with via the command line:
</p>
<pre class='verbatim' id='verbatim-5'>
git clone --depth=1 https://github.com/NAG-DevOps/speed-hpc.git
cd speed-hpc/src</pre>
<!-- l. 14 --><p class='nopar'>
</p><!-- l. 16 --><p class='noindent'>The job script is a shell script that contains directives, module loads, and user scripting. To quickly
run some sample jobs, use the following commands:
</p>
<pre class='verbatim' id='verbatim-6'>
sbatch -p ps -t 10 env.sh
sbatch -p ps -t 10 bash.sh
sbatch -p ps -t 10 manual.sh
sbatch -p pg -t 10 lambdal-singularity.sh</pre>
<!-- l. 23 --><p class='nopar'>
</p><!-- l. 27 --><p class='noindent'>
</p>
<h5 class='subsubsectionHead' id='directives'><span class='titlemark'>2.2.1 </span> <a id='x1-160002.2.1'></a>Directives</h5>
<!-- l. 5 --><p class='noindent'>Directives are comments included at the beginning of a job script that set the shell and the options for
the job scheduler. The shebang directive is always the first line of a script. In your job script, this
directive sets which shell your script’s commands will run in. On “Speed”, we recommend that your
script use a shell from the <span class='cmtt-10'>/encs/bin </span>directory.<br class='newline' />
</p><!-- l. 12 --><p class='noindent'>To use the <span class='cmtt-10'>tcsh </span>shell, start your script with <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>#!/encs/bin/tcsh</span></span></span>. For <span class='cmtt-10'>bash</span>, start with
<span class='obeylines-h'><span class='verb'><span class='cmtt-10'>#!/encs/bin/bash</span></span></span>.<br class='newline' />
</p><!-- l. 15 --><p class='noindent'>Directives that start with <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>#SBATCH</span></span></span> set the options for the cluster’s SLURM job scheduler. The
following provides an example of some essential directives:
</p>
<pre class='verbatim' id='verbatim-7'>
#SBATCH --job-name=<jobname> ## or -J. Give the job a name
#SBATCH --mail-type=<type> ## set type of email notifications
#SBATCH --chdir=<directory> ## or -D, set working directory for the job
#SBATCH --nodes=1 ## or -N, node count required for the job
#SBATCH --ntasks=1 ## or -n, number of tasks to be launched
#SBATCH --cpus-per-task=<corecount> ## or -c, core count requested, e.g. 8 cores
#SBATCH --mem=<memory> ## assign memory for this job,
## e.g., 32G memory per node</pre>
<!-- l. 28 --><p class='nopar'>
</p><!-- l. 31 --><p class='noindent'>Replace the following to adjust the job script for your project(s) </p>
<ul class='itemize1'>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><jobname></span></span></span> with a job name for the job. This name will be displayed in the job queue.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><directory></span></span></span> with the fullpath to your job’s working directory, e.g., where your code,
source files and where the standard output files will be written to. By default, <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>--chdir</span></span></span>
sets the current directory as the job’s working directory.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><type></span></span></span> with the type of e-mail notifications you wish to receive. Valid options are: NONE,
BEGIN, END, FAIL, REQUEUE, ALL.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><corecount></span></span></span> with the degree of multithreaded parallelism (i.e., cores) allocated to your
job. Up to 32 by default.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><memory></span></span></span> with the amount of memory, in GB, that you want to be allocated per node.
Up to 500 depending on the node.<br class='newline' /><span class='cmbx-10'>Note</span>: All jobs MUST set a value for the <span class='cmtt-10'>--mem </span>option.</li></ul>
<!-- l. 44 --><p class='noindent'>Example with short option equivalents:
</p>
<pre class='verbatim' id='verbatim-8'>
#SBATCH -J myjob ## Job’s name set to ’myjob’
#SBATCH --mail-type=ALL ## Receive all email type notifications
#SBATCH -D ./ ## Use current directory as working directory
#SBATCH -N 1 ## Node count required for the job
#SBATCH -n 1 ## Number of tasks to be launched
#SBATCH -c 8 ## Request 8 cores
#SBATCH --mem=32G ## Allocate 32G memory per node</pre>
<!-- l. 54 --><p class='nopar'>
</p><!-- l. 57 --><p class='noindent'><span class='cmbx-10'>Tip: </span>If you are unsure about memory footprints, err on assigning a generous memory space to
your job, so that it does not get prematurely terminated. You can refine <span class='cmtt-10'>--mem </span>values
for future jobs by monitoring the size of a job’s active memory space on <span class='cmtt-10'>speed-submit</span>
with:
</p>
<pre class='verbatim' id='verbatim-9'>
sacct -j <jobID>
sstat -j <jobID></pre>
<!-- l. 65 --><p class='nopar'>
</p><!-- l. 67 --><p class='noindent'>This can be customized to show specific columns:
</p>
<pre class='verbatim' id='verbatim-10'>
sacct -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID>
sstat -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID></pre>
<!-- l. 72 --><p class='nopar'>
</p><!-- l. 74 --><p class='noindent'>Memory-footprint efficiency values (<span class='cmtt-10'>seff</span>) are also provided for completed jobs in the final email
notification as “maxvmsize”. <span class='cmti-10'>Jobs that request a low-memory footprint are more likely to load on a
busy cluster.</span><br class='newline' />
</p><!-- l. 79 --><p class='noindent'>Other essential options are <span class='cmtt-10'>--time</span>, or <span class='cmtt-10'>-t</span>, and <span class='cmtt-10'>--account</span>, or <span class='cmtt-10'>-A</span>. </p>
<ul class='itemize1'>
<li class='itemize'><span class='cmtt-10'>--time=<time> </span>– is the estimate of wall clock time required for your job to run. As
previously mentioned, the maximum is 7 days for batch and 24 hours for interactive jobs.
Jobs with a smaller <span class='cmtt-10'>time </span>value will have a higher priority and may result in your job
being scheduled sooner.
</li>
<li class='itemize'><span class='cmtt-10'>--account=<name> </span>– specifies which Account, aka project or association, that the Speed
resources your job uses should be attributed to. When moving from GE to SLURM users
most users were assigned to Speed’s two default accounts <span class='cmtt-10'>speed1 </span>and <span class='cmtt-10'>speed2</span>. However,
users that belong to a particular research group or project are will have a default Account
like the following <span class='cmtt-10'>aits</span>, <span class='cmtt-10'>vidpro</span>, <span class='cmtt-10'>gipsy</span>, <span class='cmtt-10'>ai2</span>, <span class='cmtt-10'>mpackir</span>, <span class='cmtt-10'>cmos</span>, among others.</li></ul>
<!-- l. 34 --><p class='noindent'>Directives are comments included at the beginning of a job script that set the shell and the options for
the job scheduler.
</p><!-- l. 37 --><p class='noindent'>The shebang directive is always the first line of a script. In your job script, this directive sets which
shell your script’s commands will run in. On “Speed”, we recommend that your script use a shell from
the <span class='cmtt-10'>/encs/bin </span>directory.
</p><!-- l. 41 --><p class='noindent'>To use <span class='cmtt-10'>tcsh </span>shell, start your script with <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>#!/encs/bin/tcsh</span></span></span>, for <span class='cmtt-10'>bash</span>, start with <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>#!/encs/bin/bash</span></span></span>
</p><!-- l. 44 --><p class='noindent'>Directives that start with <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>#SBATCH</span></span></span> set the options for the cluster’s SLURM job scheduler. The
following provides an example of some essential directives:
</p>
<pre class='verbatim' id='verbatim-11'>
#SBATCH --job-name=<jobname> ## or -J. Give the job a name
#SBATCH --mail-type=<type> ## set type of email notifications
#SBATCH --chdir=<directory> ## or -D, set working directory for the job
#SBATCH --nodes=1 ## or -N, node count required for the job
#SBATCH --ntasks=1 ## or -n, number of tasks to be launched
#SBATCH --cpus-per-task=<corecount> ## or -c, core count requested, e.g. 8 cores
#SBATCH --mem=<memory> ## assign memory for this job,
## e.g., 32G memory per node</pre>
<!-- l. 57 --><p class='nopar'>
</p><!-- l. 60 --><p class='noindent'>Replace the following to adjust the job script for your project(s) </p>
<ul class='itemize1'>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><jobname></span></span></span> with a job name for the job. This name will be displayed in the job queue.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><directory></span></span></span> with the fullpath to your job’s working directory, e.g., where your code,
source files and where the standard output files will be written to. By default, <span class='obeylines-h'><span class='verb'><span class='cmtt-10'>--chdir</span></span></span>
sets the current directory as the job’s working directory.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><type></span></span></span> with the type of e-mail notifications you wish to receive. Valid options are: NONE,
BEGIN, END, FAIL, REQUEUE, ALL.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><corecount></span></span></span> with the degree of multithreaded parallelism (i.e., cores) allocated to your
job. Up to 32 by default.
</li>
<li class='itemize'><span class='obeylines-h'><span class='verb'><span class='cmtt-10'><memory></span></span></span> with the amount of memory, in GB, that you want to be allocated per node.
Up to 500 depending on the node.<br class='newline' /><span class='cmbx-10'>Note</span>: All jobs MUST set a value for the <span class='cmtt-10'>--mem </span>option.</li></ul>
<!-- l. 73 --><p class='noindent'>Example with short option equivalents:
</p>
<pre class='verbatim' id='verbatim-12'>
#SBATCH -J myjob ## Job’s name set to ’myjob’
#SBATCH --mail-type=ALL ## Receive all email type notifications
#SBATCH -D ./ ## Use current directory as working directory
#SBATCH -N 1 ## Node count required for the job
#SBATCH -n 1 ## Number of tasks to be launched
#SBATCH -c 8 ## Request 8 cores
#SBATCH --mem=32G ## Allocate 32G memory per node</pre>
<!-- l. 83 --><p class='nopar'>
</p><!-- l. 86 --><p class='noindent'><span class='cmbx-10'>Tip: </span>If you are unsure about memory footprints, err on assigning a generous memory space to
your job, so that it does not get prematurely terminated. You can refine <span class='cmtt-10'>--mem </span>values
for future jobs by monitoring the size of a job’s active memory space on <span class='cmtt-10'>speed-submit</span>
with:
</p>
<pre class='verbatim' id='verbatim-13'>
sacct -j <jobID>
sstat -j <jobID></pre>
<!-- l. 94 --><p class='nopar'>
</p><!-- l. 96 --><p class='noindent'>This can be customized to show specific columns:
</p>
<pre class='verbatim' id='verbatim-14'>
sacct -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID>
sstat -o jobid,maxvmsize,ntasks%7,tresusageouttot%25 -j <jobID></pre>
<!-- l. 101 --><p class='nopar'>
</p><!-- l. 103 --><p class='noindent'>Memory-footprint efficiency values <span class='cmtt-10'>seff </span>are also provided for completed jobs in the final email
notification as “maxvmsize”.
</p><!-- l. 106 --><p class='noindent'><span class='cmti-10'>Jobs that request a low-memory footprint are more likely to load on a busy cluster.</span>
</p><!-- l. 108 --><p class='noindent'>Other essential options are <span class='cmtt-10'>--time</span>, or <span class='cmtt-10'>-t</span>, and <span class='cmtt-10'>--account</span>, or <span class='cmtt-10'>-A</span>. </p>
<ul class='itemize1'>
<li class='itemize'><span class='cmtt-10'>--time=<time> </span>– is the estimate of wall clock time required for your job to run. As
previously mentioned, the maximum is 7 days for batch and 24 hours for interactive jobs.
Jobs with a smaller <span class='cmtt-10'>time </span>value will have a higher priority and may result in your job
being scheduled sooner.
</li>
<li class='itemize'><span class='cmtt-10'>--account=<name> </span>– specifies which Account, aka project or association, that the Speed
resources your job uses should be attributed to. When moving from GE to SLURM users
most users were assigned to Speed’s two default accounts <span class='cmtt-10'>speed1 </span>and <span class='cmtt-10'>speed2</span>. However,
users that belong to a particular research group or project are will have a default Account
like the following <span class='cmtt-10'>aits</span>, <span class='cmtt-10'>vidpro</span>, <span class='cmtt-10'>gipsy</span>, <span class='cmtt-10'>ai2</span>, <span class='cmtt-10'>mpackir</span>, <span class='cmtt-10'>cmos</span>, among others.</li></ul>
<!-- l. 128 --><p class='noindent'>
</p>
<h5 class='subsubsectionHead' id='working-with-modules'><span class='titlemark'>2.2.2 </span> <a id='x1-170002.2.2'></a>Working with Modules</h5>
<!-- l. 131 --><p class='noindent'>After setting the directives in your job script, the next section typically involves loading the necessary
software modules. The <span class='cmtt-10'>module </span>command is used to manage the user environment, make sure to load
all the modules your job depends on. You can check available modules with the module avail
command. Loading the correct modules ensures that your environment is properly set up for
execution.
</p><!-- l. 137 --><p class='noindent'>To list for a particular program (<span class='cmtt-10'>matlab</span>, for example):
</p>
<pre class='verbatim' id='verbatim-15'>
module avail
module -t avail matlab ## show the list for a particular program (e.g., matlab)
module -t avail m ## show the list for all programs starting with ‘m’</pre>
<!-- l. 143 --><p class='nopar'>
</p><!-- l. 146 --><p class='noindent'>For example, insert the following in your script to load the <span class='cmtt-10'>matlab/R2023a </span>module:
</p>
<pre class='verbatim' id='verbatim-16'>
module load matlab/R2023a/default</pre>
<!-- l. 149 --><p class='nopar'>
</p><!-- l. 151 --><p class='noindent'><span class='cmbx-10'>Note: </span>you can remove a module from active use by replacing <span class='cmtt-10'>load </span>by <span class='cmtt-10'>unload</span>.
</p><!-- l. 153 --><p class='noindent'>To list loaded modules:
</p>
<pre class='verbatim' id='verbatim-17'>
module list</pre>
<!-- l. 156 --><p class='nopar'>
</p><!-- l. 158 --><p class='noindent'>To purge all software in your working environment:
</p>
<pre class='verbatim' id='verbatim-18'>
module purge</pre>
<!-- l. 161 --><p class='nopar'>
</p><!-- l. 165 --><p class='noindent'>
</p>
<h5 class='subsubsectionHead' id='user-scripting'><span class='titlemark'>2.2.3 </span> <a id='x1-180002.2.3'></a>User Scripting</h5>
<!-- l. 171 --><p class='noindent'>The final part of the job script involves the commands that will be executed by the job. This section
should include all necessary commands to set up and run the tasks your script is designed to perform.
You can use any Linux command in this section, ranging from a simple executable call to a complex
loop iterating through multiple commands.
</p><!-- l. 176 --><p class='noindent'><span class='cmbx-10'>Best Practice</span>: prefix any compute-heavy step with <span class='cmtt-10'>srun</span>. This ensures you gain proper insights on
the execution of your job.
</p><!-- l. 179 --><p class='noindent'>Each software program may have its own execution framework, as it’s the script’s author (e.g., you)
responsibility to review the software’s documentation to understand its requirements. Your script
should be written to clearly specify the location of input and output files and the degree of parallelism
needed.
</p><!-- l. 183 --><p class='noindent'>Jobs that involve multiple interactions with data input and output files, should make use of <span class='cmtt-10'>TMPDIR</span>, a
scheduler-provided workspace nearly 1 TB in size. <span class='cmtt-10'>TMPDIR </span>is created on the local disk of the compute
node at the start of a job, offering faster I/O operations compared to shared storage (provided over
NFS).
</p><!-- l. 3 --><p class='noindent'>
</p>
<h4 class='subsectionHead' id='sample-job-script'><span class='titlemark'>2.3 </span> <a id='x1-190002.3'></a>Sample Job Script</h4>
<!-- l. 6 --><p class='noindent'>Here’s a basic job script, <a class='url' href='env.sh'><span class='cmtt-10'>env.sh</span></a> shown in Figure <a href='#-source-code-for-envsh'>4<!-- tex4ht:ref: fig:env.sh --></a>. You can copy it from our <a href='https://github.com/NAG-DevOps/speed-hpc'>GitHub
repository</a>.
</p>
<figure class='figure' id='-source-code-for-envsh'>
<a id='x1-190214'></a>
<!-- l. 11 --><pre class='lstinputlisting' id='listing-1'><span class='label'><a id='x1-19002r1'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>!/</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>encs</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>/</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>bin</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>/</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>tcsh</span></span>
<span class='label'><a id='x1-19003r2'></a></span>
<span class='label'><a id='x1-19004r3'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>SBATCH</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>--job-name=envs</span> </span><span class='cmitt-10x-x-70'> </span><span style='color:#000000'><span class='cmitt-10x-x-70'>##</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>Give the job a name</span>
</span><span class='label'><a id='x1-19005r4'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>SBATCH</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>--mail-type=ALL</span> </span><span class='cmitt-10x-x-70'> </span><span style='color:#000000'><span class='cmitt-10x-x-70'>##</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>Receive all email type notifications</span>
</span><span class='label'><a id='x1-19006r5'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>SBATCH</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>--chdir=./</span> </span><span class='cmitt-10x-x-70'> </span><span style='color:#000000'><span class='cmitt-10x-x-70'>##</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>Use currect directory as working directory</span>
</span><span class='label'><a id='x1-19007r6'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>SBATCH</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>--nodes=1</span>
</span><span class='label'><a id='x1-19008r7'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>SBATCH</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>--ntasks=1</span>
</span><span class='label'><a id='x1-19009r8'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>SBATCH</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>--cpus-per-task=1</span> </span><span class='cmitt-10x-x-70'> </span><span style='color:#000000'><span class='cmitt-10x-x-70'>##</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>Request 1 cpus</span>
</span><span class='label'><a id='x1-19010r9'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'><span class='cmitt-10x-x-70'>SBATCH</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>--mem=1G</span> </span><span class='cmitt-10x-x-70'> </span><span style='color:#000000'><span class='cmitt-10x-x-70'>##</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>Assign 1G memory per node</span>
</span><span class='label'><a id='x1-19011r10'></a></span>
<span class='label'><a id='x1-19012r11'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>Reset TMPDIR to a larger storage</span>
</span><span class='label'><a id='x1-19013r12'></a></span><span style='color:#000000'><span class='cmtt-8x-x-87'>mkdir</span></span><span style='color:#000000'> <span class='cmtt-8x-x-87'>-p /speed-scratch/</span><span class='tctt-0800x-x-87'>$</span><span class='cmtt-8x-x-87'>USER/tmp</span>
</span><span class='label'><a id='x1-19014r13'></a></span><span style='color:#000000'><span class='cmtt-8x-x-87'>setenv</span></span><span style='color:#000000'> <span class='cmtt-8x-x-87'>TMPDIR /speed-scratch/</span><span class='tctt-0800x-x-87'>$</span><span class='cmtt-8x-x-87'>USER/tmp</span>
</span><span class='label'><a id='x1-19015r14'></a></span>
<span class='label'><a id='x1-19016r15'></a></span><span style='color:#000000'><span class='cmtt-8x-x-87'>date</span></span>
<span class='label'><a id='x1-19017r16'></a></span><span style='color:#000000'><span class='cmtt-8x-x-87'>srun</span></span><span style='color:#000000'> <span class='cmtt-8x-x-87'>env</span>
</span><span class='label'><a id='x1-19018r17'></a></span><span style='color:#000000'><span class='cmtt-8x-x-87'>date</span></span>
<span class='label'><a id='x1-19019r18'></a></span>
<span class='label'><a id='x1-19020r19'></a></span><span style='color:#000000'><span class='cmitt-10x-x-70'>#</span></span><span style='color:#000000'> <span class='cmitt-10x-x-70'>EOF</span></span>
</pre>
<figcaption class='caption'><span class='id'>Figure 4: </span><span class='content'>Source code for <a class='url' href='env.sh'><span class='cmtt-10'>env.sh</span></a></span></figcaption><!-- tex4ht:label?: x1-190214 -->
</figure>
<!-- l. 17 --><p class='noindent'>The first line is the shell declaration (also know as a shebang) and sets the shell to <span class='cmti-10'>tcsh</span>. The lines that
begin with <span class='cmtt-10'>#SBATCH </span>are directives for the scheduler.
</p>
<ul class='itemize1'>
<li class='itemize'><span class='cmtt-10'>-J </span>(or <span class='cmtt-10'>--job-name</span>) sets <span class='cmti-10'>envs </span>as the job name.
</li>
<li class='itemize'><span class='cmtt-10'>--mail-type </span>sets the type of notifications.
</li>
<li class='itemize'><span class='cmtt-10'>--chdir </span>sets the working directory.
</li>
<li class='itemize'><span class='cmtt-10'>--nodes </span>specifies the number of required nodes.
</li>
<li class='itemize'><span class='cmtt-10'>--ntasks </span>specifies the number of tasks.
</li>
<li class='itemize'><span class='cmtt-10'>--cpus-per-task </span>requests 1 cpus.
</li>
<li class='itemize'>
<!-- l. 27 --><p class='noindent'><span class='cmtt-10'>--mem= </span>requests memory.
</p><!-- l. 29 --><p class='noindent'><span class='cmbx-10'>Note: </span>Jobs require the <span class='cmtt-10'>--mem </span>option to be set either in the script or on the command
line; <span class='cmbx-10'>job submission will be rejected if it’s missing.</span></p></li></ul>
<!-- l. 33 --><p class='noindent'>The script then:
</p><ol class='enumerate1'>
<li class='enumerate' id='x1-19023x1'>Creates a directory.
</li>
<li class='enumerate' id='x1-19025x2'>Sets TMPDIR to a larger storage.
</li>
<li class='enumerate' id='x1-19027x3'>Prints current date.
</li>
<li class='enumerate' id='x1-19029x4'>Prints env variables.
</li>
<li class='enumerate' id='x1-19031x5'>Prints current date again.</li></ol>
<!-- l. 42 --><p class='noindent'>The scheduler command, <span class='cmtt-10'>sbatch</span>, is used to submit (non-interactive) jobs. From an ssh session on
“speed-submit”, submit this job with
</p>
<pre class='verbatim' id='verbatim-19'>
sbatch ./env.sh</pre>
<!-- l. 46 --><p class='nopar'>
</p><!-- l. 48 --><p class='noindent'>You will see, <span class='cmtt-10'>Submitted batch job <JOB ID></span>. The commands <span class='cmtt-10'>squeue </span>and <span class='cmtt-10'>sinfo </span>can be used to
look at the queue and the status of the cluster
</p>
<pre class='verbatim' id='verbatim-20'>
[serguei@speed-submit src] % squeue -l
Thu Oct 19 11:38:54 2023
JOBID PARTITION NAME USER STATE TIME TIME_LIMI NODES NODELIST(REASON)
2641 ps interact b_user RUNNING 19:16:09 1-00:00:00 1 speed-07
2652 ps interact a_user RUNNING 41:40 1-00:00:00 1 speed-07
2654 ps envs serguei RUNNING 0:01 7-00:00:00 1 speed-07
[serguei@speed-submit src] % sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
ps* up 7-00:00:00 8 drng@ speed-[09-11,15-16,20-21,36]
ps* up 7-00:00:00 3 drng speed-[38,42-43]
ps* up 7-00:00:00 2 drain magic-node-[04,08]
ps* up 7-00:00:00 4 mix magic-node-07,salus,speed-[07,37]
ps* up 7-00:00:00 7 alloc magic-node-06,speed-[08,12,22-24,29]
ps* up 7-00:00:00 13 idle magic-node-[05,09-10],speed-[19,30-35,39-41]
pg up 7-00:00:00 1 drain* speed-05
pg up 7-00:00:00 2 mix speed-[01,17]
pt up 7-00:00:00 4 drng speed-[27,38,42-43]
pt up 7-00:00:00 2 mix speed-[17,37]
pt up 7-00:00:00 3 idle speed-[39-41]
pa up 7-00:00:00 1 drng speed-27
pa up 7-00:00:00 1 mix speed-01
pa up 7-00:00:00 2 idle speed-[03,25]
cl up 7-00:00:00 1 drain* speed-05
cl up 7-00:00:00 4 drng speed-[27,38,42-43]
cl up 7-00:00:00 3 mix speed-[01,17,37]
cl up 7-00:00:00 6 idle speed-[03,19,25,39-41]
pc up 7-00:00:00 1 mix salus
pm up 7-00:00:00 2 drain magic-node-[04,08]
pm up 7-00:00:00 1 mix magic-node-07
pm up 7-00:00:00 1 alloc magic-node-06
pm up 7-00:00:00 3 idle magic-node-[05,09-10]
pn up 7-00:00:00 1 down* stellar
pn up 7-00:00:00 2 idle matrix,nebulae</pre>
<!-- l. 88 --><p class='nopar'>
</p><!-- l. 91 --><p class='noindent'>Once the job finishes, there will be a new file in the directory that the job was started from,
with the syntax of, <span class='cmtt-10'>slurm-<job id>.out</span>. This file represents the standard output (and
error, if there is any) of the job in question. Important information is often written to this
file.
</p>
<h4 class='subsectionHead' id='common-job-management-commands'><span class='titlemark'>2.4 </span> <a id='x1-200002.4'></a>Common Job Management Commands</h4>
<!-- l. 6 --><p class='noindent'>Here is a summary of useful job management commands for handling various aspects of job
submission and monitoring on the Speed cluster:
</p>
<ul class='itemize1'>
<li class='itemize'>
<!-- l. 10 --><p class='noindent'>Submitting a job:
</p>
<pre class='verbatim' id='verbatim-21'>
sbatch -A <ACCOUNT> --mem=<MEMORY> -p <PARTITION> ./<myscript>.sh</pre>
<!-- l. 13 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 15 --><p class='noindent'>Checking your job(s) status:
</p>
<pre class='verbatim' id='verbatim-22'>
squeue -u <ENCSusername></pre>
<!-- l. 18 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 20 --><p class='noindent'>Displaying cluster status:
</p>
<pre class='verbatim' id='verbatim-23'>
squeue</pre>
<!-- l. 23 --><p class='nopar'> </p>
<ul class='itemize2'>
<li class='itemize'>Use <span class='cmtt-10'>-A </span>for per account (e.g., <span class='cmtt-10'>-A vidpro</span>, <span class='cmtt-10'>-A aits</span>)
</li>
<li class='itemize'>Use <span class='cmtt-10'>-p </span>for per partition (e.g., <span class='cmtt-10'>-p ps</span>, <span class='cmtt-10'>-p pg</span>, <span class='cmtt-10'>-p pt</span>), etc.</li></ul>
</li>
<li class='itemize'>
<!-- l. 29 --><p class='noindent'>Displaying job information:
</p>
<pre class='verbatim' id='verbatim-24'>
squeue --job <job-ID></pre>
<!-- l. 32 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 34 --><p class='noindent'>Displaying individual job steps: (to see which step failed if you used <span class='cmtt-10'>srun</span>)
</p>
<pre class='verbatim' id='verbatim-25'>
squeue -las</pre>
<!-- l. 37 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 39 --><p class='noindent'>Monitoring job and cluster status: (view <span class='cmtt-10'>sinfo </span>and watch the queue for your job(s))
</p>
<pre class='verbatim' id='verbatim-26'>
watch -n 1 "sinfo -Nel -pps,pt,pg,pa && squeue -la"</pre>
<!-- l. 42 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 44 --><p class='noindent'>Canceling a job:
</p>
<pre class='verbatim' id='verbatim-27'>
scancel <job-ID></pre>
<!-- l. 47 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 49 --><p class='noindent'>Holding a job:
</p>
<pre class='verbatim' id='verbatim-28'>
scontrol hold <job-ID></pre>
<!-- l. 52 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 54 --><p class='noindent'>Releasing a job:
</p>
<pre class='verbatim' id='verbatim-29'>
scontrol release <job-ID></pre>
<!-- l. 57 --><p class='nopar'>
</p></li>
<li class='itemize'>
<!-- l. 59 --><p class='noindent'>Getting job statistics: (including useful metrics like “maxvmem”)
</p>
<pre class='verbatim' id='verbatim-30'>
sacct -j <job-ID></pre>
<!-- l. 62 --><p class='nopar'> <span class='cmtt-10'>maxvmem </span>is one of the more useful stats that you can elect to display as a format
option.
</p>
<pre class='verbatim' id='verbatim-31'>
% sacct -j 2654
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
2654 envs ps speed1 1 COMPLETED 0:0