Oregon State University Research HPC portal and documentation web site.https://docs.hpc.oregonstate.edu/Edward Davisen Fri, 30 Jan 2026 20:05:58 -0000 Fri, 30 Jan 2026 20:05:58 -0000 1440 MkDocs RSS plugin - v1.15.0 <h1>renv 1.1.4</h1><ul><li>Fixed an issue where <code>renv</code> could erroneously record packages installed from Posit Package Manager snapshots as being installed from CRAN. ...</li></ul>https://docs.hpc.oregonstate.edu/cqls/presentations/2025-11-12-supercomputing/renv/library/macos/R-4.4/aarch64-apple-darwin20/renv/NEWS/ Fri, 30 Jan 2026 20:06:00 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/presentations/2025-11-12-supercomputing/renv/library/macos/R-4.4/aarch64-apple-darwin20/renv/NEWS/ <h1>CEOAS Research Computing</h1><p><a href="./jupyterhub.md">JupyterHub</a><a href="./partitions.md">Partitions</a><a href="./software.md">Software</a></p>https://docs.hpc.oregonstate.edu/ceoas/ Sun, 25 Jan 2026 04:42:26 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/ceoas/ <h1>CEOAS JupyterHub</h1><p>For CEOAS users running Jupyter notebooks and other interactive software on the cluster, CEOAS has a JupyterHub server available to on-cam...</p>https://docs.hpc.oregonstate.edu/ceoas/jupyterhub/ Sun, 25 Jan 2026 04:42:26 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/ceoas/jupyterhub/ <h1>Partitions</h1><p>The CEOAS partitions are summarized as follows:</p><p>| partition | description || --------- | ----------- || ceoas | General-use partition for CE...</p>https://docs.hpc.oregonstate.edu/ceoas/partitions/ Sun, 25 Jan 2026 04:42:26 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/ceoas/partitions/ <h1>CEOAS Software</h1><p>Under construction. Please watch warmly until it is ready.</p>https://docs.hpc.oregonstate.edu/ceoas/software/ Sun, 25 Jan 2026 04:42:26 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/ceoas/software/ <h1>Oregon State University Research HPC Documentation</h1><div class="grid cards" markdown>- :material-clock-fast:{ .lg .middle } **Quick Links** --- ...https://docs.hpc.oregonstate.edu/ Mon, 22 Dec 2025 22:38:50 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/ <h1>General Use Policies</h1><p>All individuals using the CQLS infrastructure are required to adhere toappropriate data management, software licensing and the[Oreg...</p>https://docs.hpc.oregonstate.edu/cqls/about/policies/ Mon, 22 Dec 2025 22:38:50 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/about/policies/ <h1>Generating RSA SSH Key Using ssh-keygen</h1><p>In order to facilitate logging in without having to type your ONID password every time, you can generate a ssh key...</p>https://docs.hpc.oregonstate.edu/cqls/connecting/sshkey/ Mon, 22 Dec 2025 22:38:50 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/connecting/sshkey/ <h1>New User 'onboarding' / FAQs</h1><h2>Assumptions</h2><p>You have experience using the command-line; if not, see Training below</p><h2>Accounts</h2><h3>How do I login? (SSH...</h3>https://docs.hpc.oregonstate.edu/cqls/faq/ Mon, 22 Dec 2025 22:38:50 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/faq/ davised <h1>Submitting data to the NCBI Sequence Read Archive (SRA)</h1><h2>Pre-processing steps</h2><ul><li>[ ] Collect fastq.gz files for each sample</li><li>[ ] Rename fastq.gz files from long name to short name per sample</li><li>[ ] Get biosample data early (especially if it's from collaborators)</li></ul>https://docs.hpc.oregonstate.edu/cqls/tips/submitting-sra-data/ Mon, 22 Dec 2025 22:38:50 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/tips/submitting-sra-data/ <h1>Connecting to the Wildwood HPC cluster</h1><p>Connecting to the Wildwood HPC cluster may take a slightly different form foreach user, depending on how they were...</p>https://docs.hpc.oregonstate.edu/cqls/connecting/ Mon, 22 Dec 2025 21:53:27 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/connecting/ <h1>Using local drives on the compute nodes</h1><p>The Wildwood HPC cluster has local drives mapped to the <code>/scratch</code> volume. This is a change from the old infrastru...</p>https://docs.hpc.oregonstate.edu/cqls/quick-start/local-drives/ Mon, 22 Dec 2025 21:53:27 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/quick-start/local-drives/ davised sullichr <h1>Using MATLAB on CQLS HPC</h1><h2>Introduction to MATLAB on the CQLS infrastructure</h2><p>Users that are looking to work with MathWorks MATLAB software are able to accessit at the command line. First off, MATLAB will not run on the front end machines<code>shell.hpc.oregonstate.edu</code> and <code>files.hpc.oregonstate.edu</code>. Users are able torun the software stack on the processing machines using the <code>-nodisplay</code> optionwhen accessing MATLAB via the command line. </p>https://docs.hpc.oregonstate.edu/cqls/tips/using-matlab-on-cqls-hpc/ Mon, 22 Dec 2025 21:53:27 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/tips/using-matlab-on-cqls-hpc/ <h1>Using Nextflow for scientific computing</h1><p>The CQLS recommends using <a href="https://www.nextflow.io">Nextflow</a> especially the <a href="https://nf-co.re">nf-core pipelines</a>...</p>https://docs.hpc.oregonstate.edu/cqls/software/nextflow/ Mon, 10 Nov 2025 22:47:16 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/software/nextflow/ <h1>Chalkboard</h1><p>With this plugin you can add a chalkboard to reveal.js. The plugin provides two possibilities to include handwritten notes to your presentation...</p>https://docs.hpc.oregonstate.edu/cqls/presentations/2025-10-31-HPC/index_files/libs/revealjs/plugin/reveal-chalkboard/ Thu, 06 Nov 2025 00:10:10 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/presentations/2025-10-31-HPC/index_files/libs/revealjs/plugin/reveal-chalkboard/ <h1>Software List (Updated October 14, 2025)</h1><p>| name | arch | latest | updated | versions | provides ...</p>https://docs.hpc.oregonstate.edu/cqls/software/list/ Tue, 14 Oct 2025 17:52:35 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/software/list/ <h1>Using VS Code remote ssh settings</h1><h2>Using the Remote - Tunnel extension</h2><p>The <a href="https://code.visualstudio.com/docs/remote/tunnels">Remote - Tunnels</a> extens...</p>https://docs.hpc.oregonstate.edu/cqls/connecting/vscode/ Wed, 01 Oct 2025 20:05:34 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/connecting/vscode/ <h1>Using the HPC queuing systems</h1><p><a href="https://slurm.schedmd.com">Slurm</a> is the primary queuing system available on the Wildwood HPC infrastructure. If youhave u...</p>https://docs.hpc.oregonstate.edu/cqls/quick-start/queuing/ Tue, 23 Sep 2025 20:36:19 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/quick-start/queuing/ <h1>Requesting new software</h1><p>Please continue requesting software installs using the new software requestform:</p><p><a href="//support.cqls.oregonstate.edu/">Request form</a>...</p>https://docs.hpc.oregonstate.edu/cqls/software/request/ Tue, 16 Sep 2025 18:41:38 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/software/request/ <h1>CQLS Research Computing</h1><div class="grid cards" markdown>- :material-clock-fast:{ .lg .middle } **Quick Links** --- * [:material-connection:...https://docs.hpc.oregonstate.edu/cqls/ Tue, 02 Sep 2025 22:03:55 +0000Oregon State University Research HPC Documentationhttps://docs.hpc.oregonstate.edu/cqls/