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minor fixes adapting to behavior observed with snakemake 6.0.5 #37

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Mar 23, 2021
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minor fixes adapting to behavior observed with snakemake 6.0.5 #37

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10 changes: 7 additions & 3 deletions _episodes/13-cluster.md
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ cluster: "sbatch --time={resources.time_min} --mem={resources.mem_mb}
-e slurm/logs/{rule}_{wildcards}"
jobs: 25
default-resources: [cpus=1, mem_mb=1000, time_min=5]
resources: [cpus=100, mem_mb=1000000]
resources: [cpus=100, mem_mb=100000]
```
{: .source}

Expand All @@ -206,14 +206,18 @@ This file has several components.
the cluster.
Here we've used SLURM's `sbatch` command and arguments for setting time limits
and resources with snakemake wildcards defining the requested values.
We've also specified where to save SLURM logs and what to call them; note that
this folder must already exist.

We've also specified where to save SLURM logs and what to call them. **Note** that
this folder must already exist. If the folders don't exist, snakemake will hang.

Values for any command line argument to snakemake can be defined in our
profile, although a value is required (e.g. the `--use-conda` argument could be
included in our profile with `use-conda: true`).

`jobs` specifies the maximum number of jobs that will be submitted at one time.
We also specified the `default-resources` that will be requested for each job,
while `resources` defines the resource limits.

With these parameters, snakemake will use no more than 100 cpus and 100000 MB
(100 GB) at a time between all currently submitted jobs.
While it does not come into play here, a generally sensible default is slightly
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