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Merged
MSiggel merged 1 commit into from
Apr 10, 2026
Merged

docs: add HPC customization notice where simulate.config is referenced #5

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4 changes: 4 additions & 0 deletions docs/content/docs/quick-start.mdx
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Expand Up @@ -99,6 +99,10 @@ nextflow run workflows/simulate.nf \
--config_yaml output_systems/sample_input.yaml
```

<Callout type="warn" title="Cluster-specific configuration">
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.
</Callout>

</Step>
</Steps>

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4 changes: 4 additions & 0 deletions docs/content/docs/user-guide/tutorial-mixedbox-campaign.mdx
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Expand Up @@ -146,6 +146,10 @@ nextflow run workflows/simulate.nf \
--config_yaml tutorial_campaign/mixedbox_chain_length_series_20.yaml
```

<Callout type="warn" title="Cluster-specific configuration">
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.
</Callout>

This executes the fixed sequence implemented in `workflows/simulate.nf`:

1. minimization
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4 changes: 4 additions & 0 deletions docs/content/docs/user-guide/workflows.mdx
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Expand Up @@ -50,6 +50,10 @@ nextflow run workflows/simulate.nf \
--config_yaml results/systems.yaml
```

<Callout type="warn" title="Cluster-specific configuration">
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.
</Callout>

`simulate.nf` executes this fixed sequence for each hash listed in the summary YAML:

1. Minimization using `em.mdp`
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