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docs: fix headings in further.md
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johanneskoester authored Nov 7, 2024
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# The Executor Plugin for HPC Clusters using the SLURM Batch System

## The general Idea
### The general Idea

To use this plugin, log in to your cluster's head node (sometimes called the "login" node), activate your environment as usual, and start Snakemake. Snakemake will then submit your jobs as cluster jobs.

## Specifying Account and Partition
### Specifying Account and Partition

Most SLURM clusters have two mandatory resource indicators for
accounting and scheduling, the account and a
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```
instead of the `threads` parameter. Parameters in the `resources` section will take precedence.

## MPI jobs
### MPI jobs

Snakemake\'s SLURM backend also supports MPI jobs, see
`snakefiles-mpi`{.interpreted-text role="ref"} for details. When using
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localrules: <rule_a>, <rule_b>
```

## Advanced Resource Specifications
### Advanced Resource Specifications

A workflow rule may support several
[resource specifications](https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources).
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cpus_per_task: 40
```
### Additional Command Line Flags
#### Additional Command Line Flags
This plugin defines additional command line flags.
As always, these can be set on the command line or in a profile.
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Be sure to use sensible settings for your cluster and make use of parallel execution (e.g. threads) and [global profiles](#using-profiles) to avoid I/O contention.


## Summary:
### Summary:

When put together, a frequent command line looks like:

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