{"version": "https://jsonfeed.org/version/1", "title": "Oregon State University Research HPC Documentation", "home_page_url": "https://docs.hpc.oregonstate.edu/", "feed_url": "https://docs.hpc.oregonstate.edu/feed_json_updated.json", "description": "Oregon State University Research HPC portal and documentation web site.\n", "icon": null, "authors": [{"name": "Edward Davis"}], "language": "en", "items": [{"id": "https://docs.hpc.oregonstate.edu/cqls/presentations/2025-11-12-supercomputing/renv/library/macos/R-4.4/aarch64-apple-darwin20/renv/NEWS/", "url": "https://docs.hpc.oregonstate.edu/cqls/presentations/2025-11-12-supercomputing/renv/library/macos/R-4.4/aarch64-apple-darwin20/renv/NEWS/", "title": "renv 1.1.4", "content_html": "<h1>renv 1.1.4</h1>\n<ul>\n<li>Fixed an issue where <code>renv</code> could erroneously record packages installed\n  from Posit Package Manager snapshots as being installed from CRAN. ...</li>\n</ul>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/presentations/2025-11-12-supercomputing/renv/library/macos/R-4.4/aarch64-apple-darwin20/renv/NEWS.png", "date_modified": "2026-01-30T20:06:00.024565+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/ceoas/", "url": "https://docs.hpc.oregonstate.edu/ceoas/", "title": "CEOAS Research Computing", "content_html": "<h1>CEOAS Research Computing</h1>\n<p><a href=\"./jupyterhub.md\">JupyterHub</a>\n<a href=\"./partitions.md\">Partitions</a>\n<a href=\"./software.md\">Software</a></p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/ceoas/index.png", "date_modified": "2026-01-25T04:42:26+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/ceoas/jupyterhub/", "url": "https://docs.hpc.oregonstate.edu/ceoas/jupyterhub/", "title": "JupyterHub", "content_html": "<h1>CEOAS JupyterHub</h1>\n<p>For CEOAS users running Jupyter notebooks and other interactive software on the cluster, CEOAS has a JupyterHub server available to on-cam...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/ceoas/jupyterhub.png", "date_modified": "2026-01-25T04:42:26+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/ceoas/partitions/", "url": "https://docs.hpc.oregonstate.edu/ceoas/partitions/", "title": "Partitions", "content_html": "<h1>Partitions</h1>\n<p>The CEOAS partitions are summarized as follows:</p>\n<p>| partition | description |\n| --------- | ----------- |\n| ceoas | General-use partition for CE...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/ceoas/partitions.png", "date_modified": "2026-01-25T04:42:26+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/ceoas/software/", "url": "https://docs.hpc.oregonstate.edu/ceoas/software/", "title": "Software", "content_html": "<h1>CEOAS Software</h1>\n<p>Under construction. Please watch warmly until it is ready.</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/ceoas/software.png", "date_modified": "2026-01-25T04:42:26+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/", "url": "https://docs.hpc.oregonstate.edu/", "title": "Home", "content_html": "<h1>Oregon State University Research HPC Documentation</h1>\n<div class=\"grid cards\" markdown>\n\n-   :material-clock-fast:{ .lg .middle } **Quick Links**\n\n    ---\n\n ...", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/index.png", "date_modified": "2025-12-22T22:38:50+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/about/policies/", "url": "https://docs.hpc.oregonstate.edu/cqls/about/policies/", "title": "Policies", "content_html": "<h1>General Use Policies</h1>\n<p>All individuals using the CQLS infrastructure are required to adhere to\nappropriate data management, software licensing and the\n[Oreg...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/about/policies.png", "date_modified": "2025-12-22T22:38:50+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/connecting/sshkey/", "url": "https://docs.hpc.oregonstate.edu/cqls/connecting/sshkey/", "title": "SSH Key Generation", "content_html": "<h1>Generating RSA SSH Key Using ssh-keygen</h1>\n<p>In order to facilitate logging in without having to type your ONID password every time, you can generate a ssh key...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/connecting/sshkey.png", "date_modified": "2025-12-22T22:38:50+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/faq/", "url": "https://docs.hpc.oregonstate.edu/cqls/faq/", "title": "New User 'onboarding' / FAQs", "content_html": "<h1>New User 'onboarding' / FAQs</h1>\n<h2>Assumptions</h2>\n<p>You have experience using the command-line; if not, see Training below</p>\n<h2>Accounts</h2>\n<h3>How do I login? (SSH...</h3>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/faq/index.png", "date_modified": "2025-12-22T22:38:50+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/tips/submitting-sra-data/", "url": "https://docs.hpc.oregonstate.edu/cqls/tips/submitting-sra-data/", "title": "Submitting data to the NCBI Sequence Read Archive (SRA)", "content_html": "<h1>Submitting data to the NCBI Sequence Read Archive (SRA)</h1>\n<h2>Pre-processing steps</h2>\n<ul>\n<li>[ ] Collect fastq.gz files for each sample</li>\n<li>[ ] Rename fastq.gz files from long name to short name per sample</li>\n<li>[ ] Get biosample data early (especially if it's from collaborators)</li>\n</ul>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/tips/posts/2023-06-09-submitting-sra-data/index.en.png", "date_modified": "2025-12-22T22:38:50+00:00", "authors": [{"name": "davised"}], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/connecting/", "url": "https://docs.hpc.oregonstate.edu/cqls/connecting/", "title": "Connecting to the Wildwood HPC cluster", "content_html": "<h1>Connecting to the Wildwood HPC cluster</h1>\n<p>Connecting to the Wildwood HPC cluster may take a slightly different form for\neach user, depending on how they were...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/connecting/index.png", "date_modified": "2025-12-22T21:53:27+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/quick-start/local-drives/", "url": "https://docs.hpc.oregonstate.edu/cqls/quick-start/local-drives/", "title": "Using Local Drives", "content_html": "<h1>Using local drives on the compute nodes</h1>\n<p>The Wildwood HPC cluster has local drives mapped to the <code>/scratch</code> volume. This is a change from the old infrastru...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/quick-start/local-drives.png", "date_modified": "2025-12-22T21:53:27+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/tips/using-matlab-on-cqls-hpc/", "url": "https://docs.hpc.oregonstate.edu/cqls/tips/using-matlab-on-cqls-hpc/", "title": "Using MATLAB on CQLS HPC", "content_html": "<h1>Using MATLAB on CQLS HPC</h1>\n<h2>Introduction to MATLAB on the CQLS infrastructure</h2>\n<p>Users that are looking to work with MathWorks MATLAB software are able to access\nit at the command line. First off, MATLAB will not run on the front end machines\n<code>shell.hpc.oregonstate.edu</code> and <code>files.hpc.oregonstate.edu</code>. Users are able to\nrun the software stack on the processing machines using the <code>-nodisplay</code> option\nwhen accessing MATLAB via the command line.  </p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/tips/posts/2023-02-15-using-matlab-on-cqls-hpc/index.en.png", "date_modified": "2025-12-22T21:53:27+00:00", "authors": [{"name": "davised"}, {"name": "sullichr"}], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/software/nextflow/", "url": "https://docs.hpc.oregonstate.edu/cqls/software/nextflow/", "title": "Using Nextflow for scientific computing", "content_html": "<h1>Using Nextflow for scientific computing</h1>\n<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>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/software/nextflow/index.png", "date_modified": "2025-11-10T22:47:16+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/presentations/2025-10-31-HPC/index_files/libs/revealjs/plugin/reveal-chalkboard/", "url": "https://docs.hpc.oregonstate.edu/cqls/presentations/2025-10-31-HPC/index_files/libs/revealjs/plugin/reveal-chalkboard/", "title": "Chalkboard", "content_html": "<h1>Chalkboard</h1>\n<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>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/presentations/2025-10-31-HPC/index_files/libs/revealjs/plugin/reveal-chalkboard/README.png", "date_modified": "2025-11-06T00:10:10+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/software/list/", "url": "https://docs.hpc.oregonstate.edu/cqls/software/list/", "title": "Software List", "content_html": "<h1>Software List (Updated October 14, 2025)</h1>\n<p>|        name        | arch  |  latest   | updated  |             versions              |            provides     ...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/software/list.png", "date_modified": "2025-10-14T17:52:35+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/connecting/vscode/", "url": "https://docs.hpc.oregonstate.edu/cqls/connecting/vscode/", "title": "VS Code", "content_html": "<h1>Using VS Code remote ssh settings</h1>\n<h2>Using the Remote - Tunnel extension</h2>\n<p>The <a href=\"https://code.visualstudio.com/docs/remote/tunnels\">Remote - Tunnels</a> extens...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/connecting/vscode.png", "date_modified": "2025-10-01T20:05:34+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/quick-start/queuing/", "url": "https://docs.hpc.oregonstate.edu/cqls/quick-start/queuing/", "title": "Queuing System Info", "content_html": "<h1>Using the HPC queuing systems</h1>\n<p><a href=\"https://slurm.schedmd.com\">Slurm</a> is the primary queuing system available on the Wildwood HPC infrastructure. If you\nhave u...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/quick-start/queuing.png", "date_modified": "2025-09-23T20:36:19+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/software/request/", "url": "https://docs.hpc.oregonstate.edu/cqls/software/request/", "title": "Software Request", "content_html": "<h1>Requesting new software</h1>\n<p>Please continue requesting software installs using the new software request\nform:</p>\n<p><a href=\"//support.cqls.oregonstate.edu/\">Request form</a>...</p>", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/software/request.png", "date_modified": "2025-09-16T18:41:38+00:00", "authors": [], "tags": null}, {"id": "https://docs.hpc.oregonstate.edu/cqls/", "url": "https://docs.hpc.oregonstate.edu/cqls/", "title": "CQLS Research Computing", "content_html": "<h1>CQLS Research Computing</h1>\n<div class=\"grid cards\" markdown>\n\n-   :material-clock-fast:{ .lg .middle } **Quick Links**\n\n    ---\n\n    * [:material-connection:...", "image": "https://docs.hpc.oregonstate.edu/assets/images/social/cqls/index.png", "date_modified": "2025-09-02T22:03:55+00:00", "authors": [], "tags": null}]}