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https://github.com/jdblischak/smk-simple-slurm

A simple Snakemake profile for Slurm without --cluster-config
https://github.com/jdblischak/smk-simple-slurm

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A simple Snakemake profile for Slurm without --cluster-config

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# Simple Slurm



> A simple Snakemake profile for Slurm without `--cluster-generic-*-cmd`



- [Simple Slurm](#simple-slurm)

  - [Features](#features)

  - [Limitations](#limitations)

  - [Quick start](#quick-start)

  - [Customizations](#customizations)

    - [A fixed argument to `sbatch`, e.g. `--account`](#a-fixed-argument-to-sbatch-eg---account)

    - [A variable argument to `sbatch`, e.g. `--time`](#a-variable-argument-to-sbatch-eg---time)

    - [Using a cluster status script](#using-a-cluster-status-script)

    - [Multiple clusters](#multiple-clusters)

  - [Use speed with caution](#use-speed-with-caution)

  - [License](#license)



The option [`--cluster-config`][cluster-config] is removed in `snakemake>8.0.0`, but it's still

possible to set default and rule-specific resources for [submitting jobs to a

remote scheduler][cluster-execution] using a combination of

`--default-resources` and the `resources` field in individual rules. This

profile is a simplified alternative to the more comprehensive [official Slurm

profile for Snakemake][slurm-official]. For more background, this [blog

post][sichong-post] by Sichong Peng nicely explains this strategy for replacing

`--cluster-config`.



> [!WARNING]

> The Slurm profile and documentation in this repository have been updated to only support

> Snakemake versions >= 8.0.0. This is because Snakemake 8

> completely overhauled how it submits jobs to external clusters, which broke

> this and all the other existing profiles.

> If you plan to continue to use Snakemake 7, you can find the Snakemake 7

> version of the docs in the [v7 branch of this repository][v7].



## Features



* Only requires a single configuration file to get started submitting jobs to

  Slurm



* Easily add or remove options to pass to `sbatch`



* Automatically saves the log files as `logs/{rule}/{rule}-{wildcards}-%j.out`,

  where `{rule}` is the name of the rule, `{wildcards}` is any wildcards passed

  to the rule, and `%j` is the job number



* Automatically names jobs using the pattern `smk-{rule}-{wildcards}`



* Fast! It can quickly submit jobs and check their status because it doesn't

  invoke a Python script for these steps, which adds up when you have thousands

  of jobs (however, please see the section [Use speed with

  caution](#use-speed-with-caution))



* No reliance on the now-removed option `--cluster-config` or hard-to-read command-line flags (`--cluster-generic-*-cmd`)

  to customize job resources



* By default it relies on Snakemake's built-in ability to understand the job

  statuses PENDING, RUNNING, COMPLETING, and OUT_OF_MEMORY



* (Optional, but recommended) You can pass a simple script (see

  [`extras/`](extras/)) to [`--cluster-generic-status-cmd`][cluster-status] to additionally

  handle the job statuses TIMEOUT and CANCELED



* **New** Support for [cluster-cancel][] feature introduced in Snakemake 7.0.0

  (see [`examples/cluster-cancel/`](examples/cluster-cancel/))



* **New** Full support for [multi-cluster setups][multi_cluster] (using a custom

  status script requires Snakemake 7.1.1+). See the section [Multiple

  clusters](#multiple-clusters) below



* **New** Adaptable for use with [AWS ParallelCluster][aws-parallelcluster]. See

  [Christian Brueffer's][cbrueffer] profile

  [snakemake-aws-parallelcluster-slurm][]



## Limitations



* If you use [job grouping][grouping], then you can't dynamically name the jobs

  and log files based on the name of the rules. This doesn't prevent you from

  using this profile and benefiting from its other features, but it is less

  convenient. Also note that [job grouping isn't easy to use in the first

  place][grouping-issue], since it sums resources like `mem_mb` and `threads`,

  but that is a limitation of Snakemake itself, and not anything in particular

  with this profile **UPDATE:** As of Snakemake 7.11, there is improved support

  for [managing the maximum resources requested when submitting a grouped

  job][resources-and-group-jobs] that executes multiple rules. It's still

  non-trivial, but now at least possible. See the example in

  [`examples/job-grouping/`](examples/job-grouping/) for a demonstration of how

  to use the new features



* Wildcards can't contain `/` if you want to use them in the name of the Slurm

  log file. This is a Slurm requirement (which makes sense, since it has to

  create a file on the filesystem). You'll either have to change how you manage

  the wildcards or remove the `{wildcards}` from the pattern passed to `--output`,

  e.g. `--output=logs/{rule}/{rule}-%j.out`.

  Note that you can still submit wildcards containing `/` to `--job-name`



* Requires Snakemake version 8.0.0 or later (released 2023-12-20, see

  [changelog](https://github.com/snakemake/snakemake/blob/main/CHANGELOG.md#800-2023-12-20)). You can test this directly in your `Snakefile` with

  [`min_version()`][min_version]. If you require an older version of Snakemake, please see the [`v7` branch](https://github.com/jdblischak/smk-simple-slurm/tree/v7)



## Quick start



1. Download the configuration file [`config.v8+.yaml`](simple/config.v8+.yaml) to your

   Snakemake project. It has to be in a subdirectory, e.g. `simple/`



1. Open it in your favorite text editor and replace all the placeholders

   surrounded in angle brackets (`<>`) with the options you use to submit jobs

   on your cluster



1. You can override any of the defaults by adding a `resources` field to a rule,

   e.g.



    ```python

    rule much_memory:

        resources:

            mem_mb=64000

    ```



1. Invoke snakemake with the profile:



    ```sh

    snakemake --profile simple/

    ```



## Customizations



See the directory [`examples/`](examples/) for examples you can experiment with

on your cluster.



### A fixed argument to `sbatch`, e.g. `--account`



To pass an additional argument to `sbatch` that will be fixed across all job

submissions, add it directly to the arguments passed to `sbatch` in the field

`cluster-generic-submit-cmd`. For example, to specify an account to use for all job submissions, you can add the `--account` argument as shown below:



```yaml

executor: cluster-generic

cluster-generic-submit-cmd:

  mkdir -p logs/{rule} &&

  sbatch

    --partition={resources.partition}

    --qos={resources.qos}

    --cpus-per-task={threads}

    --mem={resources.mem_mb}

    --job-name=smk-{rule}-{wildcards}

    --output=logs/{rule}/{rule}-{wildcards}-%j.out

    --account=myaccount

```



### A variable argument to `sbatch`, e.g. `--time`



To pass an additional argument to `sbatch` that can vary across job submissions,

add it to the arguments passed to `sbatch` in the field `cluster`, list a

default value in the field `default-resources`, and update any rules that

require a value different from the default.



For example, the `config.v8+.yaml` below sets a default time of 1 hour, and the

example rule overrides this default for a total of 3 hours. Note that the quotes

around the default time specification are required, even though you don't need

quotes when specifying the default for either `partition` or `qos`.



```yaml

executor: cluster-generic

cluster-generic-submit-cmd:

  mkdir -p logs/{rule} &&

  sbatch

    --partition={resources.partition}

    --qos={resources.qos}

    --cpus-per-task={threads}

    --mem={resources.mem_mb}

    --job-name=smk-{rule}-{wildcards}

    --output=logs/{rule}/{rule}-{wildcards}-%j.out

    --time={resources.time}

default-resources:

  - partition=

  - qos=

  - mem_mb=1000

  - time="01:00:00"

```



```python

# A rule in Snakefile

rule more_time:

    resources:

        time = "03:00:00"

```



Note that `sbatch` accepts time defined using various formats. Above I used

`hours:minutes:seconds`, but the simple slurm profile is agnostic to how you

choose to configure this. It's a good idea to be consistent across rules, but

it's not required. From Slurm 19.05.7:



> A time limit of zero requests that no time limit be imposed. Acceptable time

> formats include "minutes", "minutes:seconds", "hours:minutes:seconds",

> "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds".



Thus to instead use `minutes`, you could achieve the same effect as above with:



```yaml

executor: cluster-generic

cluster-generic-submit-cmd:

  mkdir -p logs/{rule} &&

  sbatch

    --partition={resources.partition}

    --qos={resources.qos}

    --cpus-per-task={threads}

    --mem={resources.mem_mb}

    --job-name=smk-{rule}-{wildcards}

    --output=logs/{rule}/{rule}-{wildcards}-%j.out

    --time={resources.time}

default-resources:

  - partition=

  - qos=

  - mem_mb=1000

  - time=60

```



```python

# A rule in Snakefile

rule more_time:

    resources:

        time = 180

```



See [`examples/time-integer/`](examples/time-integer/) and

[`examples/time-string/`](examples/time-string/) for examples you can play with.

Note that specifying the time as a string requires a minimum Snakemake version

of 5.15.0.



### Using a cluster status script



By default, snakemake can monitor jobs submitted to slurm. I realized this when

reading this detailed [blog post][no-cluster-status], in which the author

decided not to use the `cluster-status.py` script provided by the [official

Slurm profile][slurm-official]. Thus if you don't find that your jobs are

silently failing often, then there's no need to worry about this extra

configuration step.



However, if you start to have jobs silently fail often, e.g. with status

`TIMEOUT` for exceeding their time limit, then you can add a custom script to

monitor the job status with the option [`--cluster-generic-status-cmd`][cluster-status].



The directory [`extras/`](extras/) contains multiple options for checking the

status of the jobs. You can choose which one you'd like to use:



* `status-sacct.py` - This is the example from the [Snakemake

  documentation][cluster-status]. It uses `sacct` to query the status of each

  job by its ID



* `status-sacct.sh` - (**recommended**) This is a Bash translation of the example

  from the [Snakemake documentation][cluster-status]. The Python script is

  simply shell-ing out to `sacct`, so running Bash directly removes the overhead

  of repeatedly starting Python each time you check a job



* `status-scontrol.sh` - This is a Bash script that uses `scontrol` to query the

  status of each job by its ID. The `scontrol` command is from

  [`slurm-status.py`](https://github.com/Snakemake-Profiles/slurm/blob/master/%7B%7Bcookiecutter.profile_name%7D%7D/slurm-status.py#L35)

  in the [official profile][slurm-official]. If your HPC cluster doesn't have

  `sacct` configured, you can use this option



* `status-sacct-multi.sh` - Support for multi-cluster setup (see section

  [Multiple clusters](#multiple-clusters))



To use one of these status scripts:



1. Download the script to your profile directory where `config.yaml` is located



1. Make the script executable, e.g. `chmod +x status-sacct.sh`



1. Add the field `cluster-generic-status-cmd` to your `config.yaml`, e.g. `cluster-generic-status-cmd: status-sacct.sh`



1. Add the flag `--parsable` to your `sbatch` command (requires Slurm version

   14.03.0rc1 or later)



### Multiple clusters



It's possible for Slurm to submit jobs to [multiple different

clusters][multi_cluster]. Below is my advice on how to configure this. However,

I've worked with multiple HPC clusters running Slurm, and have never encountered

this situation. Thus I'd appreciate any contributions to improve the

documentation below.



1. If you have access to multiple clusters, but only need to submit jobs to the

   default cluster, then you shouldn't have to modify anything in this profile



1. If you want to always submit your jobs to a cluster other than the default,

   or use multiple clusters, then pass the option `--clusters` to `sbatch`, e.g.

   to submit your jobs to either cluster "c1" or "c2"



    ```yaml

    # config.v8+.yaml

    executor: cluster-generic

    cluster-generic-submit-cmd:

      mkdir -p logs/{rule} &&

      sbatch

        --clusters=c1,c2

    ```



1. To set a default cluster and override it for specific rules, use

   `--default-resources`. For example, to run on "c1" by default but "c2" for a

   specific rule:



    ```yaml

    # config.v8+.yaml

    executor: cluster-generic

    cluster-generic-submit-cmd:

      mkdir -p logs/{rule} &&

      sbatch

        --clusters={resources.clusters}

    default-resources:

      - clusters=c1

    ```



    ```python

    # Snakefile

    rule different_cluster:

        resources:

            clusters="c2"

    ```



1. Using a custom cluster status script in a multi-cluster setup requires

   Snakemake 7.1.1+ (or Snakemake 8.0.0+ if you are using the new `--cluster-generic-*-cmd` flags). After you add the flag `--parsable` to `sbatch`, it will return `jobid;cluster_name`. I adapted `status-sacct.sh` to handle this

   situation. Please see [`examples/multi-cluster/`](examples/multi-cluster) to

   try out `status-sacct-multi.sh`



## Use speed with caution



A big benefit of the simplicity of this profile is the speed in which jobs can

be submitted and their statuses checked. The [official Slurm profile for

Snakemake][slurm-official] provides a lot of extra fine-grained control, but

this is all defined in Python scripts, which then have to be invoked for each

job submission and status check. I needed this speed for a pipeline that had an

aggregation rule that needed to be run tens of thousands of times, and the run

time for each job was under 10 seconds. In this situation, the job submission

rate and status check rate were huge bottlenecks.



However, you should use this speed with caution! On a shared HPC cluster, many

users are making requests to the Slurm scheduler. If too many requests are made

at once, the performance will suffer for all users. If the rules in your

Snakemake pipeline take at least more than a few minutes to complete, then it's

overkill to constantly check the status of multiple jobs in a single second. In

other words, only increase `max-jobs-per-second` and/or

`max-status-checks-per-second` if either the submission rate or status checks to

confirm job completion are clear bottlenecks.



## License



This is all boiler plate code. Please feel free to use it for whatever purpose

you like. No need to attribute or cite this repo, but of course it comes with no

warranties. To make it official, it's released under the [CC0][] license. See

[`LICENSE`](LICENSE) for details.



[aws-parallelcluster]: https://aws.amazon.com/hpc/parallelcluster/

[cbrueffer]: https://github.com/cbrueffer

[CC0]: https://creativecommons.org/publicdomain/zero/1.0/

[changelog]: https://snakemake.readthedocs.io/en/stable/project_info/history.html

[cluster-cancel]: https://snakemake.readthedocs.io/en/stable/tutorial/additional_features.html#using-cluster-cancel

[cluster-config]: https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#cluster-configuration-deprecated

[cluster-execution]: https://snakemake.readthedocs.io/en/stable/executing/cluster.html

[cluster-status]: https://snakemake.readthedocs.io/en/stable/tutorial/additional_features.html#using-cluster-status

[grouping]: https://snakemake.readthedocs.io/en/stable/executing/grouping.html

[grouping-issue]: https://github.com/snakemake/snakemake/issues/872

[min_version]: https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#depend-on-a-minimum-snakemake-version

[multi_cluster]: https://slurm.schedmd.com/multi_cluster.html

[no-cluster-status]: http://bluegenes.github.io/Using-Snakemake_Profiles/

[resources-and-group-jobs]: https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#resources-and-group-jobs

[sichong-post]: https://www.sichong.site/workflow/2021/11/08/how-to-manage-workflow-with-resource-constraint.html

[slurm-official]: https://github.com/Snakemake-Profiles/slurm

[snakemake-aws-parallelcluster-slurm]: https://github.com/cbrueffer/snakemake-aws-parallelcluster-slurm

[v7]: https://github.com/jdblischak/smk-simple-slurm/tree/v7