From 353e55608a2e4f7123987a05cee998800804e0e3 Mon Sep 17 00:00:00 2001 From: Cannon Lock Date: Tue, 17 Dec 2024 12:28:19 -0600 Subject: [PATCH 1/7] Update HTC Guide Page --- _data/guide-menu.yaml | 10 - _data/guide-menu.yml | 108 ----------- _data/htc-guide-menu.yml | 176 ++++++++++++++++++ _includes/components/guide-button-link.liquid | 21 +++ _includes/components/guide-section.liquid | 14 ++ _uw-research-computing/htc/guides.html | 93 +++------ 6 files changed, 236 insertions(+), 186 deletions(-) delete mode 100644 _data/guide-menu.yaml delete mode 100644 _data/guide-menu.yml create mode 100644 _data/htc-guide-menu.yml create mode 100644 _includes/components/guide-button-link.liquid create mode 100644 _includes/components/guide-section.liquid diff --git a/_data/guide-menu.yaml b/_data/guide-menu.yaml deleted file mode 100644 index 175ca67e..00000000 --- a/_data/guide-menu.yaml +++ /dev/null @@ -1,10 +0,0 @@ -- name: External Resources - children: - - name: Software Carpentry ( Online courses and videos; readings ) - href: "http://software-carpentry.org/lessons/" - - name: HTCondor Manual - href: "https://htcondor.org/manual/" - - name: Slurm Manual - href: "http://slurm.schedmd.com/" - - name: DoIT Software Training for Students ( free on-campus courses ) - href: "http://www.doit.wisc.edu/training/student/" \ No newline at end of file diff --git a/_data/guide-menu.yml b/_data/guide-menu.yml deleted file mode 100644 index 9ce25606..00000000 --- a/_data/guide-menu.yml +++ /dev/null @@ -1,108 +0,0 @@ -- name: Basics and Policies - children: - - name: HTC System Transitioning to a New Linux Version (CentOS Stream 8) - href: /uw-research-computing/os-transition-htc.html - - name: Using CHTC's HTC Submit Nodes - href: /uw-research-computing/use-submit-node.html - - name: Connecting to CHTC - href: /uw-research-computing/connecting.html - - name: Automating CHTC Log In - href: /uw-research-computing/configure-ssh.html - - name: Transferring Files Between CHTC and Research Drive - href: /uw-research-computing/transfer-data-researchdrive.html - - name: Using Globus to Transfer Files to and from CHTC - href: /uw-research-computing/globus.html - - name: Remotely Access a Pricate Github Repository - href: /uw-research-computing/github-remote-access.html - - name: Checking Disk Quota Usage - href: /uw-research-computing/check-quota.html - - name: Get Help - href: /uw-research-computing/get-help.html -- name: Job Submission - children: - - name: Running Your First HTC Jobs - href: /uw-research-computing/helloworld.html - - name: Learning About Your Jobs Using condor_q - href: /uw-research-computing/condor_q.html - - name: Submitting Multiple Jobs - href: /uw-research-computing/multiple-jobs.html - - name: Workflows with HTCondor's DAGMan - href: /uw-research-computing/dagman-workflows.html - - name: Submitting Multiple Jobs in Different Directories - href: /uw-research-computing/multiple-job-dirs.html -- name: Handling Data in Jobs - children: - - name: Transfer Small Input and Output - href: /uw-research-computing/file-availability.html - - name: Transfer Large Input Files Via Squid - href: /uw-research-computing/file-avail-squid.html - - name: Use Large Input and Output Files Via Staging - href: /uw-research-computing/file-avail-largedata.html -- name: Software Solutions - children: - - name: Compiling Software in an Interactive Job - href: /uw-research-computing/inter-submit.html - - name: Running Matlab Jobs - href: /uw-research-computing/matlab-jobs.html - - name: Running Python Jobs - href: /uw-research-computing/python-jobs.html - - name: Using Conda Environments to Run Python Jobs - href: /uw-research-computing/conda-installation.html - - name: Running R Jobs - href: /uw-research-computing/r-jobs.html - - name: Running Julia Jobs - href: /uw-research-computing/julia-jobs.html - - name: Running Java Jobs - href: /uw-research-computing/java-jobs.html - - name: Using Software Installed in a Docker Container - href: /uw-research-computing/docker-jobs.html - - name: Create a Docker Container - href: /uw-research-computing/docker-build.html - - name: Licensed Software on the HTC System - href: /uw-research-computing/licensed-software.html - - name: Submitting Jobs that use MPI - href: /uw-research-computing/mpi-jobs.html -- name: Special Use Case - children: - - name: Submitting Jobs that use GPUs - href: /uw-research-computing/gpu-jobs.html - - name: Run Machine Learning Jobs - href: /uw-research-computing/machine-learning-htc.html - - name: Scaling Beyond Local HTC Capacity - href: /uw-research-computing/scaling-htc.html - - name: Restart Jobs with Checkpointing - href: /uw-research-computing/checkpointing.html - - name: Submitting Jobs with Checkpointing - href: /uw-research-computing/checkpointing.html - - name: Submitting High Memory Jobs - href: /uw-research-computing/high-memory-jobs.html - - name: Submitting Jobs that use MPI - href: /uw-research-computing/mpi-jobs.html -- name: Troubleshooting - children: - - name: Windows/Linux Incompatibility - href: /uw-research-computing/dos-unix.html - - name: Explore and Test Docker Containers - href: /uw-research-computing/docker-test.html -- name: HPC Cluster Guides - children: - - name: Connecting to CHTC - href: /uw-research-computing/connecting.html - - name: HPC Cluster Overview Guide - href: /uw-research-computing/hpc-overview.html - - name: HPC Software - href: /uw-research-computing/hpc-software.html - - name: HPC Job Submission - href: /uw-research-computing/hpc-job-submission.html - - name: Transitioning to a New HPC Cluster - href: /uw-research-computing/hpc-transition-2023.html -- name: External Resources - children: - - name: Software Carpentry ( Online courses and videos; readings ) - href: "http://software-carpentry.org/lessons/" - - name: HTCondor Manual - href: "https://htcondor.org/manual/" - - name: Slurm Manual - href: "http://slurm.schedmd.com/" - - name: DoIT Software Training for Students ( free on-campus courses ) - href: "http://www.doit.wisc.edu/training/student/" \ No newline at end of file diff --git a/_data/htc-guide-menu.yml b/_data/htc-guide-menu.yml new file mode 100644 index 00000000..a801b34c --- /dev/null +++ b/_data/htc-guide-menu.yml @@ -0,0 +1,176 @@ +- text: "Get started" + icon: "bi bi-rocket-takeoff" + links: + - text: "System overview" + url: "/uw-research-computing/htc-overview" + icon: "" + - text: "Roadmap to getting started" + url: "/uw-research-computing/htc-roadmap" + icon: "" + - text: "Log into CHTC" + url: "/uw-research-computing/connecting" + icon: "" + +- text: "Submit jobs" + icon: "bi bi-send" + links: + - text: "Submit jobs using HTCondor " + icon: "" + links: + - text: "Job submission basics" + url: "/uw-research-computing/htcondor-job-submission" + icon: "" + - text: "Submit multiple jobs" + url: "/uw-research-computing/multiple-jobs" + icon: "" + - text: "Submit multiple jobs in different directories" + url: "/uw-research-computing/multiple-job-dirs" + icon: "" + - text: "Submit an interactive job" + url: "/uw-research-computing/inter-submit" + icon: "" + - text: "Monitor your job" + url: "/uw-research-computing/condor_q" + icon: "" + - text: "Recipes for HTC Workflows" + url: "https://github.com/CHTC/recipes/tree/main/workflows-htc" + icon: "" + - text: "Arguments and shell scripting " + icon: "" + links: + - text: "Basic scripting and job submission with arguments" + url: "/uw-research-computing/htc-basic-scripting" + icon: "" + - text: "Practice: Pass arguments from the submit file to the executable script" + url: "/uw-research-computing/htc-passing-arguments" + icon: "bi bi-clipboard-check" + - text: "Practice: Pass multiple arguments to multiple jobs with one submit file" + url: "/uw-research-computing/htc-passing-arguments-multiple" + icon: "bi bi-clipboard-check" + +- text: "Manage data" + icon: "bi bi-file-earmark-text" + links: + - text: "Data storage locations" + url: "/uw-research-computing/file-availability" + icon: "" + - text: "Check disk quota and usage" + url: "/uw-research-computing/check-quota" + icon: "" + - text: "Transfer data in jobs" + url: "/uw-research-computing/file-availability#handling-data-in-jobs" + icon: "" + - text: "Transfer files to/from CHTC " + icon: "" + links: + - text: "Local computer" + url: "/uw-research-computing/transfer-files-computer" + icon: "" + - text: "ResearchDrive" + url: "/uw-research-computing/transfer-data-researchdrive" + icon: "" + - text: "Globus" + url: "/uw-research-computing/globus" + icon: "" + - text: "Private GitHub repo" + url: "/uw-research-computing/github-remote-access" + icon: "" + +- text: "Software" + icon: "bi bi-pc-display" + links: + - text: "Overview and policies" + url: "/uw-research-computing/software-overview-htc" + icon: "" + - text: "Containers " + icon: "" + links: + - text: "Build a software environment with containers " + icon: "" + links: + - text: "What even are containers?" + url: "/uw-research-computing/software-overview-htc#containers" + icon: "" + links: + - text: "Apptainer/Singularity" + url: "/uw-research-computing/apptainer-build" + icon: "" + - text: "Practice: Build a container" + url: "/uw-research-computing/apptainer-htc-advanced-example" + icon: "bi bi-clipboard-check" + - text: "Docker" + url: "/uw-research-computing/docker-build" + icon: "" + - text: "Recipes repository" + url: "https://github.com/CHTC/recipes/tree/main/software" + icon: "" + - text: "Convert Docker images to Apptainer/Singularity images" + url: "/uw-research-computing/htc-docker-to-apptainer" + icon: "" + - text: "Licensed software and modules" + url: "/uw-research-computing/licensed-software" + icon: "" + +- text: "Workflows" + icon: "bi bi-diagram-2" + links: + - text: "Checkpoint jobs" + url: "/uw-research-computing/checkpointing" + icon: "" + - text: "DAGMan workflow manager " + icon: "" + links: + - text: "Submit workflows with DAGman" + url: "/uw-research-computing/htc/dagman-workflows" + icon: "" + - text: "Practice: Run a simple DAGMan workflow" + url: "/uw-research-computing/htc/dagman-simple-example" + icon: "bi bi-clipboard-check" + - text: "Practice: Run an diamond DAGMan workflow" + url: "/uw-research-computing/htc/tutorial-dagman-intermediate" + icon: "bi bi-clipboard-check" + +- text: "Special use cases" + icon: "bi bi-cpu" + links: + - text: "Use GPUs" + url: "/uw-research-computing/gpu-jobs" + icon: "" + - text: "Machine learning jobs" + url: "/uw-research-computing/machine-learning-htc" + icon: "" + - text: "Scale beyond local HTC capacity" + url: "/uw-research-computing/scaling-htc" + icon: "" + - text: "Custom Linux versions" + url: "/uw-research-computing/os-request-htc" + icon: "" + +- text: "Troubleshooting" + icon: "bi bi-question-circle" + links: + - text: "Status page" + url: "http://status.chtc.wisc.edu" + icon: "" + - text: "Known issues" + url: "/uw-research-computing/htc-known-issues" + icon: "" + - text: "Windows/Linux incompatibility" + url: "/uw-research-computing/dos-unix" + icon: "" + - text: "Get help" + url: "/uw-research-computing/get-help.html" + icon: "" + +- text: "External Resources" + icon: "bi bi-box-arrow-up-right" + links: + - text: "HTCondor manual" + url: "https://htcondor.org/manual/" + icon: "" + - text: "Software Carpentry" + url: "https://software-carpentry.org/lessons/" + icon: "" + - text: "UW-Madison software training for students" + url: "https://sts.doit.wisc.edu/workshops/" + icon: "" \ No newline at end of file diff --git a/_includes/components/guide-button-link.liquid b/_includes/components/guide-button-link.liquid new file mode 100644 index 00000000..0e598239 --- /dev/null +++ b/_includes/components/guide-button-link.liquid @@ -0,0 +1,21 @@ +{% if link.url %} + + + {% if link.icon and link.icon != "" %} + + {% endif %} + {{ link.text }} + +{% else %} + + + {{ link.text }} + +{% endif %} +{% if link.links %} +
+ {% for link in link.links %} + {% include components/guide-button-link.liquid %} + {% endfor %} +
+{% endif %} diff --git a/_includes/components/guide-section.liquid b/_includes/components/guide-section.liquid new file mode 100644 index 00000000..a51b44e5 --- /dev/null +++ b/_includes/components/guide-section.liquid @@ -0,0 +1,14 @@ +
+
+

+ + {{ section.text }} +

+
+
+ {% assign links = section.links %} + {% for link in links %} + {% include components/guide-button-link.liquid %} + {% endfor %} +
+
\ No newline at end of file diff --git a/_uw-research-computing/htc/guides.html b/_uw-research-computing/htc/guides.html index 8cf3745b..3d61c69a 100644 --- a/_uw-research-computing/htc/guides.html +++ b/_uw-research-computing/htc/guides.html @@ -1,74 +1,31 @@ --- highlighter: none -layout: markdown-page +layout: default title: HTC Computing Guides --- -

-Below is a list of guides for some of the most common tasks our users need to -carry out as they begin and continue to use the HTC resources at the CHTC. -

- -

User Expectations

- -Read through these user expectations and policies before using CHTC services. - - - - -{% assign category_order = "Basics and Policies,Job Submission,Handling Data in Jobs,Software Solutions,Special Use Cases,Troubleshooting" | split: "," %} - -

HTC Documentation

-{% assign documentation = site.uw-research-computing | where_exp: "x", "x.guide.tag contains 'htc'" %} -
-{% for category in category_order %} - {% assign category_documents = documentation | where_exp: "x", "x.guide.category == category" | sort: "guide.order" %} - {% if category_documents.size != 0 %} -
-
-
- {% if category == "Basics and Policies" %} - {% assign img_src = "/uw-research-computing/guide-icons/checkmark.png" %} - {% endif %} - {% if category == "Job Submission" %} - {% assign img_src = "/uw-research-computing/guide-icons/laptop_arrow.png" %} - {% endif %} - {% if category == "Handling Data in Jobs" %} - {% assign img_src = "/uw-research-computing/guide-icons/data.png" %} - {% endif %} - {% if category == "Software Solutions" %} - {% assign img_src = "/uw-research-computing/guide-icons/gear.png" %} - {% endif %} - {% if category == "Special Use Cases" %} - {% assign img_src = "/uw-research-computing/guide-icons/processor.png" %} - {% endif %} - {% if category == "Troubleshooting" %} - {% assign img_src = "/uw-research-computing/guide-icons/trouble.png" %} - {% endif %} - -

{{ category }}

-
- {% for document in category_documents %} - {%if document.guide.tag contains 'bold' %} - {{ document.alt_title | default: document.title }} - {% else %} - {{ document.alt_title | default: document.title }} - {% endif %} - {% endfor %} -
-
- {% endif %} -{% endfor %} -
- -Icon Credits +
+

HTC Computing Guides

+
+
+ {% for section in site.data.htc-guide-menu %} +
+ {% include components/guide-section.liquid %} +
+ {% endfor %} +
+
+
+

Guide Sections

+
+ {% for section in site.data.htc-guide-menu %} + + {{ section.text }} + + {% endfor %} +
+
+
+
+
\ No newline at end of file From b9a7aac4c1eaeef08f79e0749fe3ac2febb35d91 Mon Sep 17 00:00:00 2001 From: Cannon Lock Date: Fri, 10 Jan 2025 13:29:51 -0600 Subject: [PATCH 2/7] Update HTC and HPC guide pages --- .github/workflows/test-links.yml | 2 +- _data/hpc-guide-menu.yml | 99 +++++++++++++++++ _data/htc-guide-menu.yml | 66 ++++++++--- _includes/components/guide-button-link.liquid | 4 +- _includes/get/flat_guide.liquid | 1 + _includes/guide-sidebar.liquid | 34 +++--- _uw-research-computing/account-details.md | 2 - _uw-research-computing/apptainer-build.md | 3 +- _uw-research-computing/apptainer-hpc.md | 3 +- .../apptainer-htc-advanced-example.md | 3 +- _uw-research-computing/apptainer-htc.md | 3 +- .../basic-shell-commands.md | 3 +- _uw-research-computing/check-quota.md | 3 +- _uw-research-computing/checkpointing.md | 3 +- _uw-research-computing/condor_q.md | 3 +- _uw-research-computing/configure-ssh.md | 3 +- _uw-research-computing/connecting.md | 3 +- .../data-recovery-fall2024.md | 5 +- _uw-research-computing/docker-build.md | 3 +- _uw-research-computing/docker-jobs.md | 3 +- _uw-research-computing/docker-test.md | 3 +- _uw-research-computing/dos-unix.md | 1 - .../file-avail-largedata.md | 3 +- _uw-research-computing/file-avail-squid.md | 3 +- _uw-research-computing/file-availability.md | 3 +- .../github-remote-access.md | 3 +- _uw-research-computing/globus.md | 3 +- _uw-research-computing/gpu-jobs.md | 3 +- _uw-research-computing/high-memory-jobs.md | 3 +- _uw-research-computing/hpc-el9-spack.md | 5 +- _uw-research-computing/hpc-job-monitoring.md | 5 +- _uw-research-computing/hpc-job-submission.md | 5 +- _uw-research-computing/hpc-known-issues.md | 3 +- _uw-research-computing/hpc-overview.md | 7 +- _uw-research-computing/hpc-spack-install.md | 3 +- _uw-research-computing/hpc-spack-modules.md | 3 +- _uw-research-computing/hpc-spack-setup.md | 3 +- _uw-research-computing/hpc/guides.html | 103 +++++------------- _uw-research-computing/htc-basic-scripting.md | 3 +- .../htc-docker-to-apptainer.md | 3 +- _uw-research-computing/htc-known-issues.md | 1 - .../htc-modules-transition-to-el9.md | 3 +- _uw-research-computing/htc-modules.md | 3 +- _uw-research-computing/htc-overview.md | 5 +- .../htc-passing-arguments-multiple.md | 3 +- .../htc-passing-arguments.md | 3 +- _uw-research-computing/htc-roadmap.md | 6 +- .../htc/dagman-simple-example.md | 3 +- .../htc/dagman-workflows.md | 3 +- .../htc/tutorial-dagman-intermediate.md | 3 +- .../htcondor-job-submission.md | 3 +- _uw-research-computing/htcondor-quick-ref.md | 3 +- _uw-research-computing/inter-submit.md | 3 +- _uw-research-computing/licensed-software.md | 3 +- .../machine-learning-htc.md | 3 +- _uw-research-computing/multiple-job-dirs.md | 3 +- _uw-research-computing/multiple-jobs.md | 3 +- _uw-research-computing/os-request-htc.md | 5 +- _uw-research-computing/scaling-htc.md | 3 +- .../software-overview-htc.md | 3 +- .../transfer-data-researchdrive.md | 3 +- .../transfer-files-computer.md | 3 +- 62 files changed, 258 insertions(+), 230 deletions(-) create mode 100644 _data/hpc-guide-menu.yml create mode 100644 _includes/get/flat_guide.liquid diff --git a/.github/workflows/test-links.yml b/.github/workflows/test-links.yml index 06f818fb..280b9d38 100644 --- a/.github/workflows/test-links.yml +++ b/.github/workflows/test-links.yml @@ -6,6 +6,6 @@ jobs: runs-on: ubuntu-latest steps: - - uses: CannonLock/test_links@master + - uses: CHTC/test_links@master with: file_ignore: "/./staff/.*/,/./includes/.*/,/./doc/.*/" \ No newline at end of file diff --git a/_data/hpc-guide-menu.yml b/_data/hpc-guide-menu.yml new file mode 100644 index 00000000..953c9831 --- /dev/null +++ b/_data/hpc-guide-menu.yml @@ -0,0 +1,99 @@ +- text: "Get started" + icon: "bi bi-rocket-takeoff" + links: + - text: "HPC system transition to a new Linux Version (CentOS Stream 9)" + url: "/uw-research-computing/archived/hpc-el8-to-el9" + icon: "" + - text: "CHTC /staging and /projects next steps" + url: "/uw-research-computing/data-recovery-fall2024" + icon: "" + highlight: true + - text: "System overview" + url: "/uw-research-computing/hpc-overview" + icon: "" + - text: "Log in to CHTC" + url: "/uw-research-computing/connecting" + icon: "" + - text: "Automate CHTC login" + url: "/uw-research-computing/configure-ssh" + icon: "" + - text: "Basic shell commands" + url: "/uw-research-computing/basic-shell-commands" + icon: "" + +- text: "Submit jobs" + icon: "bi bi-send" + links: + - text: "Submitting and managing jobs using SLURM" + url: "/uw-research-computing/hpc-job-submission" + icon: "" + - text: "Reviewing job information using SLURM" + url: "/uw-research-computing/hpc-job-monitoring" + icon: "" + +- text: "Manage data" + icon: "bi bi-file-earmark-text" + links: + - text: "Transfer files to/from CHTC" + icon: "" + links: + - text: "Local computer" + url: "/uw-research-computing/transfer-files-computer" + icon: "" + - text: "ResearchDrive" + url: "/uw-research-computing/transfer-data-researchdrive" + icon: "" + - text: "Private GitHub repo" + url: "/uw-research-computing/github-remote-access" + icon: "" + +- text: "Software" + icon: "bi bi-pc-display" + links: + - text: "Overview and Policies" + url: "/uw-research-computing/hpc-software" + icon: "" + - text: "Spack" + icon: "" + links: + - text: "Set up" + url: "/uw-research-computing/hpc-spack-setup" + icon: "" + - text: "Install software" + url: "/uw-research-computing/hpc-spack-install" + icon: "" + - text: "Create custom modules" + url: "/uw-research-computing/hpc-spack-modules" + icon: "" + - text: "Recreate Spack installs on a new operating system" + url: "/uw-research-computing/hpc-el9-spack" + icon: "" + - text: "Containers" + icon: "" + links: + - text: "Use Apptainer containers" + url: "/uw-research-computing/apptainer-hpc" + icon: "" + - text: "Build an Apptainer container" + url: "/uw-research-computing/apptainer-build" + icon: "" + +- text: "Troubleshooting" + icon: "bi bi-question-circle" + links: + - text: "Known issues on the HPC" + url: "/uw-research-computing/hpc-known-issues" + icon: "" + +- text: "External resources" + icon: "bi bi-box-arrow-up-right" + links: + - text: "Slurm manual" + url: "http://slurm.schedmd.com/" + icon: "" + - text: "Software Carpentry" + url: "http://software-carpentry.org/lessons/" + icon: "" + - text: "UW-Madison software training for students" + url: "http://www.doit.wisc.edu/training/student/" + icon: "" \ No newline at end of file diff --git a/_data/htc-guide-menu.yml b/_data/htc-guide-menu.yml index a801b34c..2f7863ad 100644 --- a/_data/htc-guide-menu.yml +++ b/_data/htc-guide-menu.yml @@ -1,6 +1,10 @@ - text: "Get started" icon: "bi bi-rocket-takeoff" links: + - text: "CHTC /staging and /projects next steps" + url: "/uw-research-computing/data-recovery-fall2024" + icon: "" + highlight: true - text: "System overview" url: "/uw-research-computing/htc-overview" icon: "" @@ -10,6 +14,12 @@ - text: "Log into CHTC" url: "/uw-research-computing/connecting" icon: "" + - text: "Quick reference: Basic shell commands" + url: "/uw-research-computing/basic-shell-commands" + icon: "bi bi-book" + - text: "Quick reference: HTCondor commands" + url: "/uw-research-computing/htcondor-quick-ref" + icon: "bi bi-book" - text: "Submit jobs" icon: "bi bi-send" @@ -32,9 +42,6 @@ - text: "Monitor your job" url: "/uw-research-computing/condor_q" icon: "" - - text: "Recipes for HTC Workflows" - url: "https://github.com/CHTC/recipes/tree/main/workflows-htc" - icon: "" - text: "Arguments and shell scripting " icon: "" links: @@ -51,15 +58,18 @@ - text: "Manage data" icon: "bi bi-file-earmark-text" links: - - text: "Data storage locations" + - text: "Transfer small input and output" url: "/uw-research-computing/file-availability" icon: "" + - text: "Transfer large input files via Squid" + url: "/uw-research-computing/file-avail-squid" + icon: "" + - text: "Transfer large input and output files via /staging" + url: "/uw-research-computing/file-avail-largedata" + icon: "" - text: "Check disk quota and usage" url: "/uw-research-computing/check-quota" icon: "" - - text: "Transfer data in jobs" - url: "/uw-research-computing/file-availability#handling-data-in-jobs" - icon: "" - text: "Transfer files to/from CHTC " icon: "" links: @@ -88,28 +98,47 @@ - text: "Build a software environment with containers " icon: "" links: - - text: "What even are containers?" + - text: "What are containers?" url: "/uw-research-computing/software-overview-htc#containers" icon: "" + - text: "Apptainer/Singularity" + url: "/uw-research-computing/apptainer-build" + icon: "" links: - - text: "Apptainer/Singularity" - url: "/uw-research-computing/apptainer-build" - icon: "" - - text: "Practice: Build a container" - url: "/uw-research-computing/apptainer-htc-advanced-example" - icon: "bi bi-clipboard-check" + - text: "Practice: Build a container" + url: "/uw-research-computing/apptainer-htc-advanced-example" + icon: "bi bi-clipboard-check" - text: "Docker" url: "/uw-research-computing/docker-build" icon: "" + links: + - text: "Explore and test Docker containers" + url: "/uw-research-computing/docker-test" + icon: "" - text: "Recipes repository" url: "https://github.com/CHTC/recipes/tree/main/software" icon: "" - text: "Convert Docker images to Apptainer/Singularity images" url: "/uw-research-computing/htc-docker-to-apptainer" icon: "" + - text: "Use Apptainer containers" + url: "/uw-research-computing/apptainer-htc" + icon: "" + - text: "Use Docker containers" + url: "/uw-research-computing/docker-jobs" + icon: "" + - text: "Compile software in an interactive job" + url: "/uw-research-computing/inter-submit" + icon: "" - text: "Licensed software and modules" url: "/uw-research-computing/licensed-software" icon: "" + - text: "Use software available in modules" + url: "/uw-research-computing/htc-modules" + icon: "" + - text: "HTC modules transition to EL9" + url: "/uw-research-computing/htc-modules-transition-to-el9" + icon: "" - text: "Workflows" icon: "bi bi-diagram-2" @@ -136,12 +165,15 @@ - text: "Use GPUs" url: "/uw-research-computing/gpu-jobs" icon: "" - - text: "Machine learning jobs" - url: "/uw-research-computing/machine-learning-htc" - icon: "" - text: "Scale beyond local HTC capacity" url: "/uw-research-computing/scaling-htc" icon: "" + - text: "Submit high memory jobs" + url: "/uw-research-computing/high-memory-jobs" + icon: "" + - text: "Machine learning jobs" + url: "/uw-research-computing/machine-learning-htc" + icon: "" - text: "Custom Linux versions" url: "/uw-research-computing/os-request-htc" icon: "" diff --git a/_includes/components/guide-button-link.liquid b/_includes/components/guide-button-link.liquid index 0e598239..ea89c16d 100644 --- a/_includes/components/guide-button-link.liquid +++ b/_includes/components/guide-button-link.liquid @@ -1,5 +1,5 @@ {% if link.url %} - + {% if link.icon and link.icon != "" %} @@ -8,7 +8,7 @@ {% else %} - + {{ link.text }} {% endif %} diff --git a/_includes/get/flat_guide.liquid b/_includes/get/flat_guide.liquid new file mode 100644 index 00000000..28cc77ef --- /dev/null +++ b/_includes/get/flat_guide.liquid @@ -0,0 +1 @@ +{% assign %} \ No newline at end of file diff --git a/_includes/guide-sidebar.liquid b/_includes/guide-sidebar.liquid index 5e15bae3..87eab154 100644 --- a/_includes/guide-sidebar.liquid +++ b/_includes/guide-sidebar.liquid @@ -1,6 +1,6 @@ {% assign page_tag = page.tag[0] %} {% assign data = site.uw-research-computing | where_exp: "x", "x.tag contains page.tag" | sort: "category" %} -{% assign category_order = "Basics and Policies,Job Submission,Handling Data in Jobs,Software Solutions,Special Use Cases,Troubleshooting" | split: "," %} +{% assign category_order = "Get started,Submit jobs,Manage data,Software,Troubleshooting,External Resources" | split: "," %}
{% if page.guide.tag contains 'htc' and page.guide.tag contains 'hpc' %} @@ -22,11 +22,11 @@ {% assign active = pages_in_category | where_exp: "x", "x.url == page.url" %}
-

+ -

+
{% for page in pages_in_category %} @@ -39,7 +39,8 @@ {% endif %} {% endfor %}
- {% elsif page.guide.tag contains 'htc' %} + {% endif %} + {% if page.guide.tag contains 'htc' %} {% assign htc_pages = site.uw-research-computing | where_exp: "x", "x.guide.tag contains 'htc'" | sort: "category" %} {% assign categories = "" | split: "" %} @@ -57,14 +58,17 @@ {% assign pages_in_category = htc_pages | where_exp: "x", "x.guide.category == category" | sort: "guide.order" %} {% assign active = pages_in_category | where_exp: "x", "x.url == page.url" %} + {% if page.guide.tag contains 'htc' and page.guide.tag contains 'hpc' %} + {% assign active = "" | split: "" %} + {% endif %}
-

- -

-
+ +
{% for page in pages_in_category %}
@@ -76,7 +80,8 @@ {% endif %} {% endfor %}
- {% elsif page.guide.tag contains 'hpc' %} + {% endif %} + {% if page.guide.tag contains 'hpc' %} {% assign hpc_pages = site.uw-research-computing | where_exp: "x", "x.guide.tag contains 'hpc'" | sort: "category" %} {% assign categories = "" | split: "" %} @@ -94,14 +99,17 @@ {% assign pages_in_category = hpc_pages | where_exp: "x", "x.guide.category == category" | sort: "guide.order" %} {% assign active = pages_in_category | where_exp: "x", "x.url == page.url" %} + {% if page.guide.tag contains 'htc' and page.guide.tag contains 'hpc' %} + {% assign active = "" | split: "" %} + {% endif %}
-

- -

-
+ +
{% for page in pages_in_category %}
diff --git a/_uw-research-computing/account-details.md b/_uw-research-computing/account-details.md index 0c259ffe..9410fec4 100644 --- a/_uw-research-computing/account-details.md +++ b/_uw-research-computing/account-details.md @@ -1,9 +1,7 @@ --- layout: guide title: How to Request a CHTC Account -alt_title: How to Request a CHTC Account guide: - order: 2 category: Basics and Policies --- diff --git a/_uw-research-computing/apptainer-build.md b/_uw-research-computing/apptainer-build.md index abe76752..bd41b78d 100644 --- a/_uw-research-computing/apptainer-build.md +++ b/_uw-research-computing/apptainer-build.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Building an Apptainer Container guide: - order: 12 - category: Software Solutions + category: Software tag: - htc - hpc diff --git a/_uw-research-computing/apptainer-hpc.md b/_uw-research-computing/apptainer-hpc.md index 9143d29f..ed7f6a64 100644 --- a/_uw-research-computing/apptainer-hpc.md +++ b/_uw-research-computing/apptainer-hpc.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Using Apptainer Containers on HPC guide: - order: 5 - category: Software Solutions + category: Software tag: - hpc --- diff --git a/_uw-research-computing/apptainer-htc-advanced-example.md b/_uw-research-computing/apptainer-htc-advanced-example.md index 5d692afc..1dabd342 100644 --- a/_uw-research-computing/apptainer-htc-advanced-example.md +++ b/_uw-research-computing/apptainer-htc-advanced-example.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Advanced Apptainer Example - SUMO guide: - order: 13 - category: Software Solutions + category: Software tag: - htc --- diff --git a/_uw-research-computing/apptainer-htc.md b/_uw-research-computing/apptainer-htc.md index 5da5b23b..08f8a254 100644 --- a/_uw-research-computing/apptainer-htc.md +++ b/_uw-research-computing/apptainer-htc.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Use Apptainer Containers guide: - order: 11 - category: Software Solutions + category: Software tag: - htc --- diff --git a/_uw-research-computing/basic-shell-commands.md b/_uw-research-computing/basic-shell-commands.md index 4849762b..6d878b68 100644 --- a/_uw-research-computing/basic-shell-commands.md +++ b/_uw-research-computing/basic-shell-commands.md @@ -4,8 +4,7 @@ layout: guide title: Basic shell commands alt_title: Basic shell commands guide: - order: 4 - category: Basics and Policies + category: Get started tag: - htc - hpc diff --git a/_uw-research-computing/check-quota.md b/_uw-research-computing/check-quota.md index cfc83a59..db627df7 100644 --- a/_uw-research-computing/check-quota.md +++ b/_uw-research-computing/check-quota.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Check Disk Quota and Usage guide: - order: 7 - category: Basics and Policies + category: Manage data tag: - htc --- diff --git a/_uw-research-computing/checkpointing.md b/_uw-research-computing/checkpointing.md index a34411c1..10f62ece 100644 --- a/_uw-research-computing/checkpointing.md +++ b/_uw-research-computing/checkpointing.md @@ -4,8 +4,7 @@ layout: guide title: Checkpointing Jobs category: Special Use Cases guide: - order: 3 - category: Special Use Cases + category: Workflows tag: - htc --- diff --git a/_uw-research-computing/condor_q.md b/_uw-research-computing/condor_q.md index 92e879c3..4e945bca 100644 --- a/_uw-research-computing/condor_q.md +++ b/_uw-research-computing/condor_q.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Learn About Your Jobs Using condor_q guide: - order: 2 - category: Job Submission + category: Submit jobs tag: - htc --- diff --git a/_uw-research-computing/configure-ssh.md b/_uw-research-computing/configure-ssh.md index f1a9a270..f098102d 100644 --- a/_uw-research-computing/configure-ssh.md +++ b/_uw-research-computing/configure-ssh.md @@ -2,8 +2,7 @@ layout: guide title: Automate CHTC login guide: - order: 4 - category: Basics and Policies + category: Get started tag: - htc - hpc diff --git a/_uw-research-computing/connecting.md b/_uw-research-computing/connecting.md index 6959e114..2a349fb3 100644 --- a/_uw-research-computing/connecting.md +++ b/_uw-research-computing/connecting.md @@ -4,8 +4,7 @@ layout: guide title: Log in to CHTC alt_title: Log in to CHTC guide: - order: 2 - category: Basics and Policies + category: Get started tag: - htc - hpc diff --git a/_uw-research-computing/data-recovery-fall2024.md b/_uw-research-computing/data-recovery-fall2024.md index 0b209307..8b255157 100644 --- a/_uw-research-computing/data-recovery-fall2024.md +++ b/_uw-research-computing/data-recovery-fall2024.md @@ -2,11 +2,8 @@ highlighter: none layout: guide title: "CHTC /staging and /projects Next Steps" -published: true guide: - button_class: bg-warning - order: 0 - category: Basics and Policies + category: Get started tag: - hpc - htc diff --git a/_uw-research-computing/docker-build.md b/_uw-research-computing/docker-build.md index 8b6586f4..ce8bb049 100644 --- a/_uw-research-computing/docker-build.md +++ b/_uw-research-computing/docker-build.md @@ -2,8 +2,7 @@ layout: guide title: Build a Docker Container Image guide: - order: 9 - category: Software Solutions + category: Software tag: - htc --- diff --git a/_uw-research-computing/docker-jobs.md b/_uw-research-computing/docker-jobs.md index a0f6343e..da0ac45f 100644 --- a/_uw-research-computing/docker-jobs.md +++ b/_uw-research-computing/docker-jobs.md @@ -4,8 +4,7 @@ layout: guide title: Running HTC Jobs Using Docker Containers alt_title: Use Software Installed in a Docker Container guide: - order: 8 - category: Software Solutions + category: Software tag: - htc --- diff --git a/_uw-research-computing/docker-test.md b/_uw-research-computing/docker-test.md index 7577979a..b60629fe 100644 --- a/_uw-research-computing/docker-test.md +++ b/_uw-research-computing/docker-test.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Explore and Test Docker Containers guide: - order: 1 - category: Troubleshooting + category: Software tag: - htc --- diff --git a/_uw-research-computing/dos-unix.md b/_uw-research-computing/dos-unix.md index c32231b0..f5e6c490 100644 --- a/_uw-research-computing/dos-unix.md +++ b/_uw-research-computing/dos-unix.md @@ -3,7 +3,6 @@ highlighter: none layout: guide title: Windows / Linux Incompatibility guide: - order: 0 category: Troubleshooting tag: - htc diff --git a/_uw-research-computing/file-avail-largedata.md b/_uw-research-computing/file-avail-largedata.md index 6f9036f6..3faa1cf9 100644 --- a/_uw-research-computing/file-avail-largedata.md +++ b/_uw-research-computing/file-avail-largedata.md @@ -4,8 +4,7 @@ layout: file_avail title: Managing Large Data in HTC Jobs alt_title: Use Large Input and Output Files Via Staging guide: - order: 2 - category: Handling Data in Jobs + category: Manage data tag: - htc --- diff --git a/_uw-research-computing/file-avail-squid.md b/_uw-research-computing/file-avail-squid.md index 4a99c994..f43bbb97 100644 --- a/_uw-research-computing/file-avail-squid.md +++ b/_uw-research-computing/file-avail-squid.md @@ -3,8 +3,7 @@ highlighter: none layout: file_avail title: Transfer Large Input Files Via Squid guide: - order: 1 - category: Handling Data in Jobs + category: Manage data tag: - htc --- diff --git a/_uw-research-computing/file-availability.md b/_uw-research-computing/file-availability.md index 1cf8d3ea..7244e4eb 100644 --- a/_uw-research-computing/file-availability.md +++ b/_uw-research-computing/file-availability.md @@ -4,8 +4,7 @@ layout: file_avail title: Small Input and Output File Availability Via HTCondor alt_title: Transfer Small Input and Output guide: - order: 0 - category: Handling Data in Jobs + category: Manage data tag: - htc --- diff --git a/_uw-research-computing/github-remote-access.md b/_uw-research-computing/github-remote-access.md index cd0b03a6..e8fa6e6b 100644 --- a/_uw-research-computing/github-remote-access.md +++ b/_uw-research-computing/github-remote-access.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Access a Private GitHub Repository Remotely guide: - order: 6 - category: Basics and Policies + category: Manage data tag: - htc - hpc diff --git a/_uw-research-computing/globus.md b/_uw-research-computing/globus.md index 1f498d94..676960a5 100644 --- a/_uw-research-computing/globus.md +++ b/_uw-research-computing/globus.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Use Globus to Transfer Files to and from CHTC guide: - order: 5 - category: Basics and Policies + category: Manage data tag: - htc --- diff --git a/_uw-research-computing/gpu-jobs.md b/_uw-research-computing/gpu-jobs.md index 4b68aef0..80986184 100644 --- a/_uw-research-computing/gpu-jobs.md +++ b/_uw-research-computing/gpu-jobs.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Use GPUs guide: - order: 0 - category: Special Use Cases + category: Special use cases tag: - htc --- diff --git a/_uw-research-computing/high-memory-jobs.md b/_uw-research-computing/high-memory-jobs.md index d73d4812..0242a2dc 100644 --- a/_uw-research-computing/high-memory-jobs.md +++ b/_uw-research-computing/high-memory-jobs.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Submit High Memory Jobs guide: - order: 4 - category: Special Use Cases + category: Special use cases tag: - htc --- diff --git a/_uw-research-computing/hpc-el9-spack.md b/_uw-research-computing/hpc-el9-spack.md index 98a880d9..60a26e92 100644 --- a/_uw-research-computing/hpc-el9-spack.md +++ b/_uw-research-computing/hpc-el9-spack.md @@ -3,9 +3,8 @@ highlighter: none layout: hpc_layout title: Recreating Spack Installs on a New Operating System published: true -guide: - order: 4 - category: Software Solutions +guide: + category: Software tag: - hpc --- diff --git a/_uw-research-computing/hpc-job-monitoring.md b/_uw-research-computing/hpc-job-monitoring.md index 31a4b22b..52bed8bf 100644 --- a/_uw-research-computing/hpc-job-monitoring.md +++ b/_uw-research-computing/hpc-job-monitoring.md @@ -2,9 +2,8 @@ highlighter: none layout: hpc_layout title: Reviewing Job Information Using SLURM -guide: - order: 1 - category: Job Submission +guide: + category: Submit jobs tag: - hpc --- diff --git a/_uw-research-computing/hpc-job-submission.md b/_uw-research-computing/hpc-job-submission.md index fc3ba62e..4e71b4be 100644 --- a/_uw-research-computing/hpc-job-submission.md +++ b/_uw-research-computing/hpc-job-submission.md @@ -2,9 +2,8 @@ highlighter: none layout: hpc_layout title: Submitting and Managing Jobs Using SLURM -guide: - order: 0 - category: Job Submission +guide: + category: Submit jobs tag: - hpc --- diff --git a/_uw-research-computing/hpc-known-issues.md b/_uw-research-computing/hpc-known-issues.md index 2b5ebbf1..fe5c1286 100644 --- a/_uw-research-computing/hpc-known-issues.md +++ b/_uw-research-computing/hpc-known-issues.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Known Issues on the HPC guide: - order: 8 - category: Basics and Policies + category: Troubleshooting tag: - hpc --- diff --git a/_uw-research-computing/hpc-overview.md b/_uw-research-computing/hpc-overview.md index 06228e6f..8a4c544e 100644 --- a/_uw-research-computing/hpc-overview.md +++ b/_uw-research-computing/hpc-overview.md @@ -1,10 +1,9 @@ --- highlighter: none layout: hpc_layout -title: HPC Cluster Overview -guide: - order: 1 - category: Basics and Policies +title: HPC System Overview +guide: + category: Get started tag: - hpc --- diff --git a/_uw-research-computing/hpc-spack-install.md b/_uw-research-computing/hpc-spack-install.md index 6623891c..e91b341c 100644 --- a/_uw-research-computing/hpc-spack-install.md +++ b/_uw-research-computing/hpc-spack-install.md @@ -3,8 +3,7 @@ highlighter: none layout: hpc_layout title: Install Software Using Spack guide: - order: 2 - category: Software Solutions + category: Software tag: -hpc --- diff --git a/_uw-research-computing/hpc-spack-modules.md b/_uw-research-computing/hpc-spack-modules.md index 743ac571..3f234673 100644 --- a/_uw-research-computing/hpc-spack-modules.md +++ b/_uw-research-computing/hpc-spack-modules.md @@ -3,8 +3,7 @@ highlighter: none layout: hpc_layout title: Create Custom Modules Using Spack guide: - order: 3 - category: Software Solutions + category: Software tag: -hpc --- diff --git a/_uw-research-computing/hpc-spack-setup.md b/_uw-research-computing/hpc-spack-setup.md index b8a95512..3afdbd28 100644 --- a/_uw-research-computing/hpc-spack-setup.md +++ b/_uw-research-computing/hpc-spack-setup.md @@ -3,8 +3,7 @@ highlighter: none layout: hpc_layout title: Set Up Spack on HPC guide: - order: 1 - category: Software Solutions + category: Software tag: -hpc --- diff --git a/_uw-research-computing/hpc/guides.html b/_uw-research-computing/hpc/guides.html index 9b53196e..cfc70453 100644 --- a/_uw-research-computing/hpc/guides.html +++ b/_uw-research-computing/hpc/guides.html @@ -1,84 +1,31 @@ --- highlighter: none -layout: markdown-page +layout: default title: HPC Computing Guides --- -

-Below is a list of guides for some of the most common tasks our users need to -carry out as they begin and continue to use the HPC resources at the CHTC. -

- -

User Expectations

- -Read through these user expectations and policies before using CHTC services. - - - - -{% assign category_order = "Basics and Policies,Job Submission,Handling Data in Jobs,Software Solutions,Special Use Cases,Troubleshooting" | split: "," %} - -

HPC Documentation

-{% assign documentation = site.uw-research-computing | where_exp: "x", "x.guide.tag contains 'hpc'" %} -
- {% for category in category_order %} - {% assign category_documents = documentation | where_exp: "x", "x.guide.category == category" | sort: "guide.order" %} - {% if category_documents.size != 0 %} -
-
-
- {% if category == "Basics and Policies" %} - {% assign img_src = "/uw-research-computing/guide-icons/checkmark.png" %} - {% endif %} - {% if category == "Job Submission" %} - {% assign img_src = "/uw-research-computing/guide-icons/laptop_arrow.png" %} - {% endif %} - {% if category == "Handling Data in Jobs" %} - {% assign img_src = "/uw-research-computing/guide-icons/data.png" %} - {% endif %} - {% if category == "Software Solutions" %} - {% assign img_src = "/uw-research-computing/guide-icons/gear.png" %} - {% endif %} - {% if category == "Special Use Cases" %} - {% assign img_src = "/uw-research-computing/guide-icons/processor.png" %} - {% endif %} - {% if category == "Troubleshooting" %} - {% assign img_src = "/uw-research-computing/guide-icons/trouble.png" %} - {% endif %} - -

{{ category }}

-
- {% for document in category_documents %} - {%if document.guide.tag contains 'bold' %} - {{ document.alt_title | default: document.title }} - {% else %} - {{ document.alt_title | default: document.title }} - {% endif %} - {% endfor %} -
-
- {% endif %} - {% endfor %} -
- -

External Documentation

-
- Software Carpentry ( Online courses and videos; readings ) - HTCondor Manual - Slurm Manual - DoIT Software Training for Students ( free on-campus courses ) -
- - - -Icon Credits +
+

HPC Computing Guides

+
+
+ {% for section in site.data.hpc-guide-menu %} +
+ {% include components/guide-section.liquid %} +
+ {% endfor %} +
+
+
+

Guide Sections

+
+ {% for section in site.data.hpc-guide-menu %} + + {{ section.text }} + + {% endfor %} +
+
+
+
+
\ No newline at end of file diff --git a/_uw-research-computing/htc-basic-scripting.md b/_uw-research-computing/htc-basic-scripting.md index 16d5f643..10c3248d 100644 --- a/_uw-research-computing/htc-basic-scripting.md +++ b/_uw-research-computing/htc-basic-scripting.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Basic Scripting and Job Submission with Arguments" guide: - order: 5 - category: Job Submission + category: Submit jobs tag: - htc --- diff --git a/_uw-research-computing/htc-docker-to-apptainer.md b/_uw-research-computing/htc-docker-to-apptainer.md index 0e8b7083..a8847f26 100644 --- a/_uw-research-computing/htc-docker-to-apptainer.md +++ b/_uw-research-computing/htc-docker-to-apptainer.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Convert Docker images to Apptainer images" guide: - order: 8 - category: Software Solutions + category: Software tag: - htc --- diff --git a/_uw-research-computing/htc-known-issues.md b/_uw-research-computing/htc-known-issues.md index 70e2df43..54ff6bb6 100644 --- a/_uw-research-computing/htc-known-issues.md +++ b/_uw-research-computing/htc-known-issues.md @@ -3,7 +3,6 @@ highlighter: none layout: guide title: Known Issues on the HTC guide: - order: 3 category: Troubleshooting tag: - htc diff --git a/_uw-research-computing/htc-modules-transition-to-el9.md b/_uw-research-computing/htc-modules-transition-to-el9.md index e23ce7fb..6aa93a66 100644 --- a/_uw-research-computing/htc-modules-transition-to-el9.md +++ b/_uw-research-computing/htc-modules-transition-to-el9.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: HTC Modules Transition to EL9 guide: - order: 5 - category: Special Use Cases + category: Software tag: - htc --- diff --git a/_uw-research-computing/htc-modules.md b/_uw-research-computing/htc-modules.md index 8e79ee25..72718f18 100644 --- a/_uw-research-computing/htc-modules.md +++ b/_uw-research-computing/htc-modules.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Use Software Available in Modules guide: - order: 5 - category: Special Use Cases + category: Software tag: - htc --- diff --git a/_uw-research-computing/htc-overview.md b/_uw-research-computing/htc-overview.md index d29ec23a..c92dc353 100644 --- a/_uw-research-computing/htc-overview.md +++ b/_uw-research-computing/htc-overview.md @@ -1,10 +1,9 @@ --- highlighter: none layout: guide -title: HTC System Overview +title: System Overview guide: - order: 0 - category: Basics and Policies + category: Get started tag: - htc --- diff --git a/_uw-research-computing/htc-passing-arguments-multiple.md b/_uw-research-computing/htc-passing-arguments-multiple.md index 1ca089b5..ec84ca18 100644 --- a/_uw-research-computing/htc-passing-arguments-multiple.md +++ b/_uw-research-computing/htc-passing-arguments-multiple.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Practice: Passing Multiple Arguments to Multiple Jobs with One Submit File" guide: - order: 7 - category: Job Submission + category: Submit jobs tag: - htc --- diff --git a/_uw-research-computing/htc-passing-arguments.md b/_uw-research-computing/htc-passing-arguments.md index 05e80c7a..5cdf7022 100644 --- a/_uw-research-computing/htc-passing-arguments.md +++ b/_uw-research-computing/htc-passing-arguments.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Practice: Passing Arguments from the Submit File to the Executable Script" guide: - order: 6 - category: Job Submission + category: Submit jobs tag: - htc --- diff --git a/_uw-research-computing/htc-roadmap.md b/_uw-research-computing/htc-roadmap.md index e8e464cd..e08a0466 100644 --- a/_uw-research-computing/htc-roadmap.md +++ b/_uw-research-computing/htc-roadmap.md @@ -1,11 +1,9 @@ --- highlighter: none layout: guide -title: HTC Getting Started Roadmap -alt_title: HTC Getting Started Roadmap +title: Roadmap to getting started guide: - order: 3 - category: Basics and Policies + category: Get started tag: - htc --- diff --git a/_uw-research-computing/htc/dagman-simple-example.md b/_uw-research-computing/htc/dagman-simple-example.md index 934e43f7..df6d13ab 100644 --- a/_uw-research-computing/htc/dagman-simple-example.md +++ b/_uw-research-computing/htc/dagman-simple-example.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Simple Example of a DAGMan workflow" guide: - order: 10 - category: Job Submission + category: Workflows tag: - htc --- diff --git a/_uw-research-computing/htc/dagman-workflows.md b/_uw-research-computing/htc/dagman-workflows.md index fd4a5c18..def9b73d 100644 --- a/_uw-research-computing/htc/dagman-workflows.md +++ b/_uw-research-computing/htc/dagman-workflows.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Overview: Submit Workflows with HTCondor's DAGMan" guide: - order: 9 - category: Job Submission + category: Workflows tag: - htc --- diff --git a/_uw-research-computing/htc/tutorial-dagman-intermediate.md b/_uw-research-computing/htc/tutorial-dagman-intermediate.md index cf1739f6..74a3ee1f 100644 --- a/_uw-research-computing/htc/tutorial-dagman-intermediate.md +++ b/_uw-research-computing/htc/tutorial-dagman-intermediate.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Intermediate DAGMan: Uses and Features" guide: - order: 11 - category: Job Submission + category: Workflows tag: - htc --- diff --git a/_uw-research-computing/htcondor-job-submission.md b/_uw-research-computing/htcondor-job-submission.md index c1df41a3..24a1b4d9 100644 --- a/_uw-research-computing/htcondor-job-submission.md +++ b/_uw-research-computing/htcondor-job-submission.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Practice: Submit HTC Jobs using HTCondor" guide: - order: 1 - category: Job Submission + category: Submit jobs tag: - htc --- diff --git a/_uw-research-computing/htcondor-quick-ref.md b/_uw-research-computing/htcondor-quick-ref.md index 50153aee..b8273cab 100644 --- a/_uw-research-computing/htcondor-quick-ref.md +++ b/_uw-research-computing/htcondor-quick-ref.md @@ -3,8 +3,7 @@ layout: guide title: "Quick reference: HTCondor commands" alt_title: "Quick reference: HTCondor commands" guide: - order: 5 - category: Basics and Policies + category: Get started tag: htc --- diff --git a/_uw-research-computing/inter-submit.md b/_uw-research-computing/inter-submit.md index 55e68133..0e1882f0 100644 --- a/_uw-research-computing/inter-submit.md +++ b/_uw-research-computing/inter-submit.md @@ -4,8 +4,7 @@ layout: guide title: Compiling or Testing Code with an Interactive Job alt_title: Compile Software in an Interactive Job guide: - order: 1 - category: Software Solutions + category: Software tag: - htc --- diff --git a/_uw-research-computing/licensed-software.md b/_uw-research-computing/licensed-software.md index 85172309..7e0cb769 100644 --- a/_uw-research-computing/licensed-software.md +++ b/_uw-research-computing/licensed-software.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Use Licensed Software guide: - order: 10 - category: Software Solutions + category: Software tag: - htc --- diff --git a/_uw-research-computing/machine-learning-htc.md b/_uw-research-computing/machine-learning-htc.md index 1ec7afb8..77e83653 100644 --- a/_uw-research-computing/machine-learning-htc.md +++ b/_uw-research-computing/machine-learning-htc.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Run Machine Learning Jobs guide: - order: 1 - category: Special Use Cases + category: Special use cases tag: - htc --- diff --git a/_uw-research-computing/multiple-job-dirs.md b/_uw-research-computing/multiple-job-dirs.md index 01470a5e..e3f0c121 100644 --- a/_uw-research-computing/multiple-job-dirs.md +++ b/_uw-research-computing/multiple-job-dirs.md @@ -4,8 +4,7 @@ layout: guide title: Submitting Multiple Jobs in Individual Directories alt_title: Submitting Multiple Jobs in Different Directories guide: - order: 4 - category: Job Submission + category: Submit jobs tag: - htc --- diff --git a/_uw-research-computing/multiple-jobs.md b/_uw-research-computing/multiple-jobs.md index 330af5a2..7f6bf215 100644 --- a/_uw-research-computing/multiple-jobs.md +++ b/_uw-research-computing/multiple-jobs.md @@ -4,8 +4,7 @@ layout: guide title: Submitting Multiple Jobs Using HTCondor alt_title: Submitting Multiple Jobs Using HTCondor guide: - order: 2 - category: Job Submission + category: Submit jobs tag: - htc --- diff --git a/_uw-research-computing/os-request-htc.md b/_uw-research-computing/os-request-htc.md index 88ea30c5..0999382d 100644 --- a/_uw-research-computing/os-request-htc.md +++ b/_uw-research-computing/os-request-htc.md @@ -2,9 +2,8 @@ highlighter: none layout: guide title: Use Custom Linux Versions in CHTC -guide: - order: 7 - category: Special Use Cases +guide: + category: Special use cases tag: - htc --- diff --git a/_uw-research-computing/scaling-htc.md b/_uw-research-computing/scaling-htc.md index 12c36304..8efd32ef 100644 --- a/_uw-research-computing/scaling-htc.md +++ b/_uw-research-computing/scaling-htc.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Scale Beyond Local HTC Capacity guide: - order: 2 - category: Special Use Cases + category: Special use cases tag: - htc --- diff --git a/_uw-research-computing/software-overview-htc.md b/_uw-research-computing/software-overview-htc.md index fc706666..1b86b2dc 100644 --- a/_uw-research-computing/software-overview-htc.md +++ b/_uw-research-computing/software-overview-htc.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: "Overview: How to Use Software" guide: - order: 0 - category: Software Solutions + category: Software tag: - htc - bold diff --git a/_uw-research-computing/transfer-data-researchdrive.md b/_uw-research-computing/transfer-data-researchdrive.md index 201c3794..2a4548e3 100644 --- a/_uw-research-computing/transfer-data-researchdrive.md +++ b/_uw-research-computing/transfer-data-researchdrive.md @@ -2,8 +2,7 @@ layout: guide title: Transfer Files Between CHTC and ResearchDrive guide: - order: 4 - category: Basics and Policies + category: Manage data tag: - htc - hpc diff --git a/_uw-research-computing/transfer-files-computer.md b/_uw-research-computing/transfer-files-computer.md index d4e94d9f..87364404 100644 --- a/_uw-research-computing/transfer-files-computer.md +++ b/_uw-research-computing/transfer-files-computer.md @@ -3,8 +3,7 @@ highlighter: none layout: guide title: Transfer Files between CHTC and your Computer guide: - order: 2 - category: Basics and Policies + category: Manage data tag: - htc - hpc From 4dc96d05b63655c9190ef96cfe114bcedfe574f5 Mon Sep 17 00:00:00 2001 From: Cannon Lock Date: Fri, 10 Jan 2025 14:03:56 -0600 Subject: [PATCH 3/7] Requested Updates --- _data/hpc-guide-menu.yml | 1 + _data/main-menu.yml | 16 ++++++---------- _includes/components/guide-button-link.liquid | 2 +- 3 files changed, 8 insertions(+), 11 deletions(-) diff --git a/_data/hpc-guide-menu.yml b/_data/hpc-guide-menu.yml index 953c9831..8deb5954 100644 --- a/_data/hpc-guide-menu.yml +++ b/_data/hpc-guide-menu.yml @@ -4,6 +4,7 @@ - text: "HPC system transition to a new Linux Version (CentOS Stream 9)" url: "/uw-research-computing/archived/hpc-el8-to-el9" icon: "" + highlight: true - text: "CHTC /staging and /projects next steps" url: "/uw-research-computing/data-recovery-fall2024" icon: "" diff --git a/_data/main-menu.yml b/_data/main-menu.yml index 7cfd0ab7..bf36ab58 100644 --- a/_data/main-menu.yml +++ b/_data/main-menu.yml @@ -18,11 +18,8 @@ nav_items: - url: /fellowships/index.html name: Fellowships - id: uw-research-computing - name: UW Research Computing + name: Research Computing url: /uw-research-computing/index.html - - id: guides - name: Guides - url: /uw-research-computing/guides.html - id: technologies name: Technologies url: /technologies.html @@ -31,9 +28,8 @@ nav_items: url: /research.html - id: news name: News - url: /news-navigation.html - sub_menu: - - url: /news.html - name: CHTC News - - url: /events.html - name: Events + url: /news.html + - url: /events.html + name: Events + id: events + diff --git a/_includes/components/guide-button-link.liquid b/_includes/components/guide-button-link.liquid index ea89c16d..727c2ab3 100644 --- a/_includes/components/guide-button-link.liquid +++ b/_includes/components/guide-button-link.liquid @@ -7,7 +7,7 @@ {{ link.text }} {% else %} - + {{ link.text }} From ae31cff1beadc2d9d662cb0821efe3b7bdf451c7 Mon Sep 17 00:00:00 2001 From: Cannon Lock Date: Fri, 17 Jan 2025 13:01:15 -0600 Subject: [PATCH 4/7] #d5d5d5 Folder backgrounds --- _includes/components/guide-button-link.liquid | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/components/guide-button-link.liquid b/_includes/components/guide-button-link.liquid index 727c2ab3..08c356f7 100644 --- a/_includes/components/guide-button-link.liquid +++ b/_includes/components/guide-button-link.liquid @@ -7,7 +7,7 @@ {{ link.text }} {% else %} - + {{ link.text }} From c4da763161b988cada5f407c79e33a6128b32efb Mon Sep 17 00:00:00 2001 From: Cannon Lock Date: Fri, 17 Jan 2025 13:17:42 -0600 Subject: [PATCH 5/7] Make headers bigger and correct d5d5d5 debacle --- _includes/components/guide-button-link.liquid | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/components/guide-button-link.liquid b/_includes/components/guide-button-link.liquid index 08c356f7..fde8c70e 100644 --- a/_includes/components/guide-button-link.liquid +++ b/_includes/components/guide-button-link.liquid @@ -7,7 +7,7 @@ {{ link.text }} {% else %} - + {{ link.text }} From 458b6dd6c7bc50a5eb296b91833d74d71a5bdb6f Mon Sep 17 00:00:00 2001 From: Cannon Lock Date: Fri, 17 Jan 2025 13:53:05 -0600 Subject: [PATCH 6/7] Redirect guide page to research computing page --- _redirects/guides.md | 5 + _uw-research-computing/guides.html | 143 ----------------------------- 2 files changed, 5 insertions(+), 143 deletions(-) create mode 100644 _redirects/guides.md delete mode 100644 _uw-research-computing/guides.html diff --git a/_redirects/guides.md b/_redirects/guides.md new file mode 100644 index 00000000..8cc3f99b --- /dev/null +++ b/_redirects/guides.md @@ -0,0 +1,5 @@ +--- +layout: redirect +redirect_url: https://chtc.cs.wisc.edu/uw-research-computing/index.html +permalink: /uw-research-computing/guides.html +--- \ No newline at end of file diff --git a/_uw-research-computing/guides.html b/_uw-research-computing/guides.html deleted file mode 100644 index eef05da6..00000000 --- a/_uw-research-computing/guides.html +++ /dev/null @@ -1,143 +0,0 @@ ---- -highlighter: none -layout: markdown-page -title: Computing Guides ---- - - -

-Below is a list of guides for some of the most common tasks our users need to -carry out as they begin and continue to use the resources at the CHTC. -Some of these are general computing solutions; others are specific to HTCondor -or to the configuration of CHTC computing resources. -

-

-Guides will be added to the list as we can provide them. Please contact us -(email at bottom of page) if you find any of the information to be incorrect. -

- - - -

User Expectations

- -Read through these user expectations and policies before using CHTC services. - - - - -{% assign category_order = "Basics and Policies,Job Submission,Handling Data in Jobs,Software Solutions,Special Use Cases,Troubleshooting" | split: "," %} - -

HTC Documentation

-{% assign documentation = site.uw-research-computing | where_exp: "x", "x.guide.tag contains 'htc'" %} -
-{% for category in category_order %} - {% assign category_documents = documentation | where_exp: "x", "x.guide.category == category" | sort: "guide.order" %} - {% if category_documents.size != 0 %} -
-
-
- {% if category == "Basics and Policies" %} - {% assign img_src = "/uw-research-computing/guide-icons/checkmark.png" %} - {% endif %} - {% if category == "Job Submission" %} - {% assign img_src = "/uw-research-computing/guide-icons/laptop_arrow.png" %} - {% endif %} - {% if category == "Handling Data in Jobs" %} - {% assign img_src = "/uw-research-computing/guide-icons/data.png" %} - {% endif %} - {% if category == "Software Solutions" %} - {% assign img_src = "/uw-research-computing/guide-icons/gear.png" %} - {% endif %} - {% if category == "Special Use Cases" %} - {% assign img_src = "/uw-research-computing/guide-icons/processor.png" %} - {% endif %} - {% if category == "Troubleshooting" %} - {% assign img_src = "/uw-research-computing/guide-icons/trouble.png" %} - {% endif %} - -

{{ category }}

-
- {% for document in category_documents %} - {%if document.guide.tag contains 'bold' %} - {{ document.alt_title | default: document.title }} - {% else %} - {{ document.alt_title | default: document.title }} - {% endif %} - {% endfor %} -
-
- {% endif %} -{% endfor %} -
- -

HPC Documentation

-{% assign documentation = site.uw-research-computing | where_exp: "x", "x.guide.tag contains 'hpc'" %} -
- {% for category in category_order %} - {% assign category_documents = documentation | where_exp: "x", "x.guide.category == category" | sort: "guide.order" %} - {% if category_documents.size != 0 %} -
-
-
- {% if category == "Basics and Policies" %} - {% assign img_src = "/uw-research-computing/guide-icons/checkmark.png" %} - {% endif %} - {% if category == "Job Submission" %} - {% assign img_src = "/uw-research-computing/guide-icons/laptop_arrow.png" %} - {% endif %} - {% if category == "Handling Data in Jobs" %} - {% assign img_src = "/uw-research-computing/guide-icons/data.png" %} - {% endif %} - {% if category == "Software Solutions" %} - {% assign img_src = "/uw-research-computing/guide-icons/gear.png" %} - {% endif %} - {% if category == "Special Use Cases" %} - {% assign img_src = "/uw-research-computing/guide-icons/processor.png" %} - {% endif %} - {% if category == "Troubleshooting" %} - {% assign img_src = "/uw-research-computing/guide-icons/trouble.png" %} - {% endif %} - -

{{ category }}

-
- {% for document in category_documents %} - {{ document.alt_title | default: document.title }} - {% endfor %} -
-
- {% endif %} - {% endfor %} -
- -

External Documentation

-
- Software Carpentry ( Online courses and videos; readings ) - HTCondor Manual - Slurm Manual - DoIT Software Training for Students ( free on-campus courses ) -
- - - -Icon Credits From 78823e61ee7f8c862990c5ea29ee8bb8e8878c3a Mon Sep 17 00:00:00 2001 From: Amber Lim <59936462+xamberl@users.noreply.github.com> Date: Fri, 17 Jan 2025 14:01:59 -0600 Subject: [PATCH 7/7] Update guides.md Per Christina's suggestion, change redirect to how-tos --- _redirects/guides.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_redirects/guides.md b/_redirects/guides.md index 8cc3f99b..01cf2299 100644 --- a/_redirects/guides.md +++ b/_redirects/guides.md @@ -1,5 +1,5 @@ --- layout: redirect -redirect_url: https://chtc.cs.wisc.edu/uw-research-computing/index.html +redirect_url: https://chtc.cs.wisc.edu/uw-research-computing/how-tos.html permalink: /uw-research-computing/guides.html ---- \ No newline at end of file +---