Snakemake executor plugin: flux

This is the Flux Framework external executor plugin for snakemake.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-executor-plugin-flux

Usage

In order to use the plugin, run Snakemake (>=8.0) in the folder where your workflow code and config resides (containing either workflow/Snakefile or Snakefile) with the corresponding value for the executor flag:

snakemake --executor flux --default-resources --jobs N ...

with N being the number of jobs you want to run in parallel and ... being any additional arguments you want to use (see below). The machine on which you run Snakemake must have the executor plugin installed, and, depending on the type of the executor plugin, have access to the target service of the executor plugin (e.g. an HPC middleware like slurm with the sbatch command, or internet access to submit jobs to some cloud provider, e.g. azure).

The flag --default-resources ensures that Snakemake auto-calculates the mem and disk resources for each job, based on the input file size. The values assumed there are conservative and should usually suffice. However, you can always override those defaults by specifying the resources in your Snakemake rules or via the --set-resources flag.

Depending on the executor plugin, you might either rely on a shared local filesystem or use a remote filesystem or storage. For the latter, you have to additionally use a suitable storage plugin (see section storage plugins in the sidebar of this catalog) and eventually check for further recommendations in the sections below.

All arguments can also be persisted via a profile, such that they don’t have to be specified on each invocation. Here, this would mean the following entries inside of the profile

executor: flux
default_resources: []

For specifying other default resources than the built-in ones, see the docs.

Further details

Snakemake Executor Flux

This is an example implementation for an external snakemake plugin. Since we already have one for Flux (and it can run in a container) the example is for Flux. You can use this repository as a basis to design your own executor to work with snakemake!

Usage

Tutorial

For this tutorial you will need Docker installer.

Flux-framework is a flexible resource scheduler that can work on both high performance computing systems and cloud (e.g., Kubernetes). Since it is more modern (e.g., has an official Python API) we define it under a cloud resource. For this example, we will show you how to set up a “single node” local Flux container to interact with snakemake using the plugin here. You can use the Dockerfile that will provide a container with Flux and snakemake Note that we install from source and bind to /home/fluxuser/snakemake with the intention of being able to develop (if desired).

First, build the container:

$ docker build -f example/Dockerfile -t flux-snake .

We will add the plugin here to /home/fluxuser/plugin, install it, and shell in as the fluxuser to optimally interact with flux. After the container builds, shell in:

$ docker run -it flux-snake bash

And start a flux instance:

$ flux start --test-size=4

Go into the examples directory (where the Snakefile is) and run snakemake, targeting your executor plugin.

$ cd ./example

# This says "use the custom executor module named snakemake_executor_plugin_flux"
$ snakemake --jobs 1 --executor flux

Building DAG of jobs...
Using shell: /bin/bash
Job stats:
job                         count    min threads    max threads
------------------------  -------  -------------  -------------
all                             1              1              1
multilingual_hello_world        2              1              1
total                           3              1              1

Select jobs to execute...

[Fri Jun 16 19:24:22 2023]
rule multilingual_hello_world:
    output: hola/world.txt
    jobid: 2
    reason: Missing output files: hola/world.txt
    wildcards: greeting=hola
    resources: tmpdir=/tmp

Job 2 has been submitted with flux jobid ƒcjn4t3R (log: .snakemake/flux_logs/multilingual_hello_world/greeting_hola.log).
[Fri Jun 16 19:24:32 2023]
Finished job 2.
1 of 3 steps (33%) done
Select jobs to execute...

[Fri Jun 16 19:24:32 2023]
rule multilingual_hello_world:
    output: hello/world.txt
    jobid: 1
    reason: Missing output files: hello/world.txt
    wildcards: greeting=hello
    resources: tmpdir=/tmp

Job 1 has been submitted with flux jobid ƒhAPLa79 (log: .snakemake/flux_logs/multilingual_hello_world/greeting_hello.log).
[Fri Jun 16 19:24:42 2023]
Finished job 1.
2 of 3 steps (67%) done
Select jobs to execute...

[Fri Jun 16 19:24:42 2023]
localrule all:
    input: hello/world.txt, hola/world.txt
    jobid: 0
    reason: Input files updated by another job: hello/world.txt, hola/world.txt
    resources: tmpdir=/tmp

[Fri Jun 16 19:24:42 2023]
Finished job 0.
3 of 3 steps (100%) done
Complete log: .snakemake/log/2023-06-16T192422.186675.snakemake.log

And that’s it! Continue reading to learn more about plugin design, and how you can also design your own executor plugin for use or development (that doesn’t need to be added to upstream snakemake).

Developer

To do the same run but bind the local plugin directory:

docker run -it -v $PWD/:/home/fluxuser/plugin flux-snake bash

The instructions for creating and scaffolding this plugin are here. Instructions for writing your plugin with examples are provided via the snakemake-executor-plugin-interface.