From ff39e4b2401b7a1ae42a76c7d941a5fa488b623c Mon Sep 17 00:00:00 2001 From: MSiggel <11818778+MSiggel@users.noreply.github.com> Date: Fri, 10 Apr 2026 09:27:30 +0200 Subject: [PATCH] Add HPC customization warnings where simulate.config is referenced The shipped simulate.config contains SLURM settings specific to one cluster. Pages that show the simulate command now warn users to adapt the config and link to the Running on HPC Clusters guide. Closes #4 Co-Authored-By: Claude Opus 4.6 (1M context) --- docs/content/docs/quick-start.mdx | 4 ++++ docs/content/docs/user-guide/tutorial-mixedbox-campaign.mdx | 4 ++++ docs/content/docs/user-guide/workflows.mdx | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/docs/content/docs/quick-start.mdx b/docs/content/docs/quick-start.mdx index 7f38376..b8422cf 100644 --- a/docs/content/docs/quick-start.mdx +++ b/docs/content/docs/quick-start.mdx @@ -99,6 +99,10 @@ nextflow run workflows/simulate.nf \ --config_yaml output_systems/sample_input.yaml ``` + +The shipped `simulate.config` contains SLURM settings tuned for a specific cluster. Edit this file to match your HPC environment before running. See [Running on HPC Clusters](/docs/user-guide/running-on-hpc) for details. + + diff --git a/docs/content/docs/user-guide/tutorial-mixedbox-campaign.mdx b/docs/content/docs/user-guide/tutorial-mixedbox-campaign.mdx index d5683a9..4f77c09 100644 --- a/docs/content/docs/user-guide/tutorial-mixedbox-campaign.mdx +++ b/docs/content/docs/user-guide/tutorial-mixedbox-campaign.mdx @@ -146,6 +146,10 @@ nextflow run workflows/simulate.nf \ --config_yaml tutorial_campaign/mixedbox_chain_length_series_20.yaml ``` + +The shipped `simulate.config` contains SLURM settings tuned for a specific cluster. Edit this file to match your HPC environment before running. See [Running on HPC Clusters](/docs/user-guide/running-on-hpc) for details. + + This executes the fixed sequence implemented in `workflows/simulate.nf`: 1. minimization diff --git a/docs/content/docs/user-guide/workflows.mdx b/docs/content/docs/user-guide/workflows.mdx index bb3e656..4be6dce 100644 --- a/docs/content/docs/user-guide/workflows.mdx +++ b/docs/content/docs/user-guide/workflows.mdx @@ -50,6 +50,10 @@ nextflow run workflows/simulate.nf \ --config_yaml results/systems.yaml ``` + +The shipped `simulate.config` contains SLURM settings (queue name, module loads, GPU/CPU/memory requests) tuned for a specific cluster. Edit this file to match your HPC environment before running. See [Running on HPC Clusters](/docs/user-guide/running-on-hpc) for guidance. + + `simulate.nf` executes this fixed sequence for each hash listed in the summary YAML: 1. Minimization using `em.mdp`