From a3be834d19770d61f85c9a8de6b1c6ef18fbc6c0 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 20 Feb 2026 14:05:11 -0600 Subject: [PATCH 1/2] add coldfront doc links --- .github/workflows/a11y-scan.yml | 13 +++++ docs/_config.yml | 24 -------- docs/_toc.yml | 79 -------------------------- docs/tutorials/globus_box_transfers.md | 6 +- docs/tutorials/slurm/best_practices.md | 4 +- 5 files changed, 18 insertions(+), 108 deletions(-) delete mode 100644 docs/_config.yml delete mode 100644 docs/_toc.yml diff --git a/.github/workflows/a11y-scan.yml b/.github/workflows/a11y-scan.yml index ec26e4bc..1db76dbf 100644 --- a/.github/workflows/a11y-scan.yml +++ b/.github/workflows/a11y-scan.yml @@ -9,6 +9,19 @@ jobs: with: urls: | # Provide a newline-delimited list of URLs to scan; more information below. https://southernmethodistuniversity.github.io/hpc_docs/ + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/qs_instructor.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/qs_student.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/add_change_project.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/add_class.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/add_remove_users.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/request_change_allocation.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/add_metadata.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/usage_stats.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/archive_project.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/renewals.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/running_jobs.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/faq.html + https://southernmethodistuniversity.github.io/hpc_docs/coldfront/optout.html repository: "SouthernMethodistUniversity/hpc_docs" token: ${{ secrets.A11Y_SCAN_ACCESS_TOKEN }} cache_key: "hpc_docs_a11y_scan" # Provide a filename that will be used when caching results. We recommend including the name or domain of the site being scanned. diff --git a/docs/_config.yml b/docs/_config.yml deleted file mode 100644 index 189db228..00000000 --- a/docs/_config.yml +++ /dev/null @@ -1,24 +0,0 @@ -title: "SMU HPC Documentation" -author: "Southern Methodist University" -logo: "./images/smu_logo.jpg" -copyright: "2023-2025" -execute: - execute_notebooks: "off" -html: - favicon: "./images/favicon.ico" - extra-css: - - no_code_block_number.css -parse: - myst_enable_extensions: - - colon_fence - - dollarmath - - linkify - - substitution - - tasklist - - html_image -sphinx: - config: - numfig: True - numfig_secnum_depth: 0 - numfig_format: - code-block: "%s" diff --git a/docs/_toc.yml b/docs/_toc.yml deleted file mode 100644 index e5dd09b5..00000000 --- a/docs/_toc.yml +++ /dev/null @@ -1,79 +0,0 @@ -root: index.md -format: jb-book -defaults: - numbered: false -parts: -- caption: Announcements - chapters: - - file: work_deprecation.md -- caption: Getting Started - chapters: - - file: about.md - sections: - - file: about/systems.md - - file: about/queues.md - - file: about/faculty_partner.md - - url: https://www.smu.edu/oit/ai - title: SMU AI Guidance - - url: https://www.smu.edu/provost/research/sponsoredprojects/proposal_development/datamanagementplans - title: Data Management Plans - - file: policies/policies.md - - file: accounts.md - - file: coldfront/quick_start.md - title: ColdFront - sections: - - file: coldfront/qs_instructor.md - - file: coldfront/qs_student.md - - file: coldfront/add_change_project.md - - file: coldfront/add_class.md - - file: coldfront/add_remove_users.md - - file: coldfront/request_change_allocation.md - - file: coldfront/add_metadata.md - - file: coldfront/usage_stats.md - - file: coldfront/archive_project.md - - file: coldfront/renewals.md - - file: coldfront/running_jobs.md - - file: coldfront/faq.md - - file: coldfront/optout.md - - file: access.md -- caption: How to Use - chapters: - - file: portal.md - - file: quickstart.md - - file: tutorials/slurm/slurm.md - sections: - - file: tutorials/slurm/best_practices.md - - file: tutorials/unix/unix.md - title: Basic Linux - - file: tutorials/containers/containers.md -- caption: Storage and File Management - chapters: - - file: tutorials/globus_box_transfers.md - title: Globus and Box -- caption: Applications - chapters: - - file: tutorials/modules/modules.md - - file: examples/conda/README.md - sections: - - file: examples/conda/migration.md - - file: tutorials/r/overview.md - sections: - - file: tutorials/r/environments.md - - file: tutorials/r/slurm.md - - file: applications/vscode.md - - file: tutorials/navigating_jupyterlab.md - title: JupyterLab - - file: applications/other_applications.md - sections: - - file: examples/amber/index.md - - file: examples/gaussian/index.md - - file: examples/openfoam/index.md - - file: examples/stata/index.md -- caption: Workshops and Trainings - chapters: - - url: https://southernmethodistuniversity.github.io/SMU_SuperPOD_101/ - title: SuperPOD 101 - - file: tutorials/clone_constellate.md -- caption: Getting Help / Troubleshooting - chapters: - - file: about/contact.md diff --git a/docs/tutorials/globus_box_transfers.md b/docs/tutorials/globus_box_transfers.md index d85fd660..6f59f09b 100644 --- a/docs/tutorials/globus_box_transfers.md +++ b/docs/tutorials/globus_box_transfers.md @@ -66,15 +66,15 @@ Click the start button above the side the data is coming from to start the trans You may want to adjust the transfer settings (for example, to only update new or changed files) -:::{Note} +:::{note} You do not have to stay on the Globus site while the transfer is happening. It will send an email when completed. ::: -:::{Note} +:::{note} The transfers can be slow. We typically see between 1-5 MBPS between Box and M3 (connection speeds to other services may vary). ::: -:::{Note} +:::{note} Box has a file size limit of 50GB ::: diff --git a/docs/tutorials/slurm/best_practices.md b/docs/tutorials/slurm/best_practices.md index cbf7e1d6..3d6e1765 100644 --- a/docs/tutorials/slurm/best_practices.md +++ b/docs/tutorials/slurm/best_practices.md @@ -80,7 +80,7 @@ $ reportseff -u $USER --since d=1 3575979 CANCELLED 00:00:43 1.2% 14.0% 12.6% ``` -:::{Note} +:::{note} If you command outputs a large number of jobs, the formatting is sometimes not clean. ::: @@ -100,7 +100,7 @@ If your program is behaving as expected, consider reducing the number of cores y The memory efficiency represents the percentage of the requested memory that was used by your job. Realistically, anything about `50%` memory efficiency is good. Due to how memory is measured, programs that dynamically allocate and deallocate memory may fail as a result of running out of memory even if the reported usage is "low." If you know your program allocates most of the memory it uses at the beginning, aiming for `80-90%` efficiency is a good target. -:::{Note} +:::{note} Memory efficiency is hard to measure. SLURM periodically samples memory usage, so it often misses large spikes of increased memory usage that occurs between samples. It is not unsual for jobs to temporarily use 2x or more memory than reported. ::: From 9c919f8f5c81a4487ff8f3701bc651d6f736177f Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Fri, 20 Feb 2026 14:15:28 -0600 Subject: [PATCH 2/2] add back accidentally deleted files --- docs/_config.yml | 24 +++++++++++++++ docs/_toc.yml | 79 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 docs/_config.yml create mode 100644 docs/_toc.yml diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 00000000..bdb787fb --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,24 @@ +title: "SMU HPC Documentation" +author: "Southern Methodist University" +logo: "./images/smu_logo.jpg" +copyright: "2023-2025" +execute: + execute_notebooks: "off" +html: + favicon: "./images/favicon.ico" + extra-css: + - no_code_block_number.css +parse: + myst_enable_extensions: + - colon_fence + - dollarmath + - linkify + - substitution + - tasklist + - html_image +sphinx: + config: + numfig: True + numfig_secnum_depth: 0 + numfig_format: + code-block: "%s" \ No newline at end of file diff --git a/docs/_toc.yml b/docs/_toc.yml new file mode 100644 index 00000000..e5dd09b5 --- /dev/null +++ b/docs/_toc.yml @@ -0,0 +1,79 @@ +root: index.md +format: jb-book +defaults: + numbered: false +parts: +- caption: Announcements + chapters: + - file: work_deprecation.md +- caption: Getting Started + chapters: + - file: about.md + sections: + - file: about/systems.md + - file: about/queues.md + - file: about/faculty_partner.md + - url: https://www.smu.edu/oit/ai + title: SMU AI Guidance + - url: https://www.smu.edu/provost/research/sponsoredprojects/proposal_development/datamanagementplans + title: Data Management Plans + - file: policies/policies.md + - file: accounts.md + - file: coldfront/quick_start.md + title: ColdFront + sections: + - file: coldfront/qs_instructor.md + - file: coldfront/qs_student.md + - file: coldfront/add_change_project.md + - file: coldfront/add_class.md + - file: coldfront/add_remove_users.md + - file: coldfront/request_change_allocation.md + - file: coldfront/add_metadata.md + - file: coldfront/usage_stats.md + - file: coldfront/archive_project.md + - file: coldfront/renewals.md + - file: coldfront/running_jobs.md + - file: coldfront/faq.md + - file: coldfront/optout.md + - file: access.md +- caption: How to Use + chapters: + - file: portal.md + - file: quickstart.md + - file: tutorials/slurm/slurm.md + sections: + - file: tutorials/slurm/best_practices.md + - file: tutorials/unix/unix.md + title: Basic Linux + - file: tutorials/containers/containers.md +- caption: Storage and File Management + chapters: + - file: tutorials/globus_box_transfers.md + title: Globus and Box +- caption: Applications + chapters: + - file: tutorials/modules/modules.md + - file: examples/conda/README.md + sections: + - file: examples/conda/migration.md + - file: tutorials/r/overview.md + sections: + - file: tutorials/r/environments.md + - file: tutorials/r/slurm.md + - file: applications/vscode.md + - file: tutorials/navigating_jupyterlab.md + title: JupyterLab + - file: applications/other_applications.md + sections: + - file: examples/amber/index.md + - file: examples/gaussian/index.md + - file: examples/openfoam/index.md + - file: examples/stata/index.md +- caption: Workshops and Trainings + chapters: + - url: https://southernmethodistuniversity.github.io/SMU_SuperPOD_101/ + title: SuperPOD 101 + - file: tutorials/clone_constellate.md +- caption: Getting Help / Troubleshooting + chapters: + - file: about/contact.md