From 5ae2180fb96429d6b6e8ad5db1adaf52b0382115 Mon Sep 17 00:00:00 2001 From: mohalkh5 Date: Mon, 8 Jun 2026 19:50:33 -0600 Subject: [PATCH 1/4] adding persistence1 docs --- docs/index.md | 1 + docs/running-jobs/persistence1.md | 42 +++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 docs/running-jobs/persistence1.md diff --git a/docs/index.md b/docs/index.md index 77a996d3..921c1e71 100644 --- a/docs/index.md +++ b/docs/index.md @@ -74,6 +74,7 @@ running-jobs/roce-enabled running-jobs/job-resources running-jobs/slurm-commands running-jobs/squeue-status-codes +running-jobs/persistence1 ``` diff --git a/docs/running-jobs/persistence1.md b/docs/running-jobs/persistence1.md new file mode 100644 index 00000000..8ce2851a --- /dev/null +++ b/docs/running-jobs/persistence1.md @@ -0,0 +1,42 @@ +# Persistence1 + +Persistence1 is a dedicated service for running long-lived workflow managers that coordinate jobs on Alpine. + +Many workflow management tools, including Nextflow, Snakemake, and KinBot, require a process that remains active for days or weeks while monitoring workflow progress and submitting jobs to the cluster. Because these applications must remain running for extended periods, they are not suitable for execution as standard Slurm jobs and should not be run on login nodes. + +Persistence1 provides a dedicated environment where users can run workflow managers and other workflow orchestration tools that require continuous execution while maintaining access to Alpine resources. It is not intended for running computational intensive workloads directly, interactive analysis, high-memory applications or replacing Slurm job submissions. + + +## Getting Started + +Access to `persistence1` is managed through a dedicated user group and must be requested before use. + +* To request access, submit a request through the [support request form](https://colorado.service-now.com/req_portal?id=ucb_sc_rc_form). +* In the form, select Other as the Nature of Request. +* Include the following information in your request: + - your CU Boulder IdentiKey + - a brief description of the workflow manager or application you intend to run + + +## Connecting to Persistence1 + +After access has been granted, you can connect to `persistence1` from a CURC login node: + +``` +[rcops@login-ci3 ~]$ ssh persistence1 +``` + +## Working on Persistence1 + +Persistence1 provides access to the same filesystems and software environment available on Alpine. + +Users can: + +* access their `/home`, `/projects` and `/scratch/alpine` directory +* run container-based workflows through Apptainer +* create and manage conda environments using Miniforge +* run workflow managers such as Nextflow + +## Getting Help + +If you have questions about access, software availability, or workflow configuration on Persistence1, submit a request through [support request form](https://colorado.service-now.com/req_portal?id=ucb_sc_rc_form). \ No newline at end of file From 467700e14dc603d45b7d865c88127661c064b9ed Mon Sep 17 00:00:00 2001 From: mohalkh5 Date: Thu, 11 Jun 2026 13:16:29 -0600 Subject: [PATCH 2/4] Apply suggestions from code review Co-authored-by: monaghaa <33913248+monaghaa@users.noreply.github.com> --- docs/running-jobs/persistence1.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/running-jobs/persistence1.md b/docs/running-jobs/persistence1.md index 8ce2851a..ee9bd53c 100644 --- a/docs/running-jobs/persistence1.md +++ b/docs/running-jobs/persistence1.md @@ -1,6 +1,6 @@ -# Persistence1 +# Running workflow managers on Persistence1 -Persistence1 is a dedicated service for running long-lived workflow managers that coordinate jobs on Alpine. +`Persistence1` is a dedicated service for running long-lived workflow managers that coordinate jobs on Alpine. Many workflow management tools, including Nextflow, Snakemake, and KinBot, require a process that remains active for days or weeks while monitoring workflow progress and submitting jobs to the cluster. Because these applications must remain running for extended periods, they are not suitable for execution as standard Slurm jobs and should not be run on login nodes. @@ -12,9 +12,9 @@ Persistence1 provides a dedicated environment where users can run workflow manag Access to `persistence1` is managed through a dedicated user group and must be requested before use. * To request access, submit a request through the [support request form](https://colorado.service-now.com/req_portal?id=ucb_sc_rc_form). -* In the form, select Other as the Nature of Request. +* In the form, select "Other" as the "Nature of Request". * Include the following information in your request: - - your CU Boulder IdentiKey + - your CURC username - a brief description of the workflow manager or application you intend to run @@ -28,15 +28,15 @@ After access has been granted, you can connect to `persistence1` from a CURC log ## Working on Persistence1 -Persistence1 provides access to the same filesystems and software environment available on Alpine. +`Persistence1` provides access to the same filesystems on CURC compute nodes, as well as a subset of relevant software. Users can: -* access their `/home`, `/projects` and `/scratch/alpine` directory -* run container-based workflows through Apptainer -* create and manage conda environments using Miniforge -* run workflow managers such as Nextflow +* access their `/home`, `/projects` `/scratch/alpine`, and (if available) PetaLibrary directories. +* run container-based workflow managers through Apptainer +* use the Miniforge module to create and manage conda environments that contain workflow managers +* directly load and use modules for popular workflow managers such as Nextflow ## Getting Help -If you have questions about access, software availability, or workflow configuration on Persistence1, submit a request through [support request form](https://colorado.service-now.com/req_portal?id=ucb_sc_rc_form). \ No newline at end of file +If you have questions about access, software availability, or workflow configuration on `Persistence1`, submit a request through [support request form](https://colorado.service-now.com/req_portal?id=ucb_sc_rc_form). \ No newline at end of file From 406af41c079443d8edb75b04e7fa1e9866b0d27d Mon Sep 17 00:00:00 2001 From: mohalkh5 Date: Thu, 11 Jun 2026 13:18:08 -0600 Subject: [PATCH 3/4] Apply suggestion from code review Co-authored-by: monaghaa <33913248+monaghaa@users.noreply.github.com> --- docs/running-jobs/persistence1.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/running-jobs/persistence1.md b/docs/running-jobs/persistence1.md index ee9bd53c..7968daef 100644 --- a/docs/running-jobs/persistence1.md +++ b/docs/running-jobs/persistence1.md @@ -4,7 +4,10 @@ Many workflow management tools, including Nextflow, Snakemake, and KinBot, require a process that remains active for days or weeks while monitoring workflow progress and submitting jobs to the cluster. Because these applications must remain running for extended periods, they are not suitable for execution as standard Slurm jobs and should not be run on login nodes. -Persistence1 provides a dedicated environment where users can run workflow managers and other workflow orchestration tools that require continuous execution while maintaining access to Alpine resources. It is not intended for running computational intensive workloads directly, interactive analysis, high-memory applications or replacing Slurm job submissions. +`Persistence1` provides a dedicated environment where users can run workflow managers and other workflow orchestration tools that require continuous execution while maintaining access to Alpine resources. + +````{important} +`Persistence1` is not intended for running computationally intensive workloads directly, interactive analysis, high-memory applications or replacing Slurm job submissions. ## Getting Started From 180682c880d740f311a848f609a8ea4828339dc6 Mon Sep 17 00:00:00 2001 From: mohalkh5 Date: Fri, 12 Jun 2026 08:11:08 -0600 Subject: [PATCH 4/4] Fix formatting for usage note --- docs/running-jobs/persistence1.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/running-jobs/persistence1.md b/docs/running-jobs/persistence1.md index 7968daef..61212914 100644 --- a/docs/running-jobs/persistence1.md +++ b/docs/running-jobs/persistence1.md @@ -6,8 +6,9 @@ Many workflow management tools, including Nextflow, Snakemake, and KinBot, requi `Persistence1` provides a dedicated environment where users can run workflow managers and other workflow orchestration tools that require continuous execution while maintaining access to Alpine resources. -````{important} -`Persistence1` is not intended for running computationally intensive workloads directly, interactive analysis, high-memory applications or replacing Slurm job submissions. +```{important} +`Persistence1` is not intended for running computationally intensive workloads directly, interactive analysis, high-memory applications or replacing Slurm job submissions. +``` ## Getting Started @@ -42,4 +43,4 @@ Users can: ## Getting Help -If you have questions about access, software availability, or workflow configuration on `Persistence1`, submit a request through [support request form](https://colorado.service-now.com/req_portal?id=ucb_sc_rc_form). \ No newline at end of file +If you have questions about access, software availability, or workflow configuration on `Persistence1`, submit a request through [support request form](https://colorado.service-now.com/req_portal?id=ucb_sc_rc_form).