To go through this tutorial, you need the following software installed:
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. You can use the Dockerfile in examples/flux 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 -t flux-snake .
And then you can run the container with or without any such bind:
$ docker run -it --rm flux-snake
Once you shelled into the container, you can view and start a Flux instance:
$ flux getattr size $ flux start --test-size=4 $ flux getattr size
And see resources available:
$ flux resource status STATUS NNODES NODELIST avail 4 5a74dc238d[98,98,98,98]
Flux currently has support for
runtime, which should be set to a number
(seconds) and defaults to 0, meaning unlimited runtime. Flux currently does not
Now let’s run Snakemake with the Flux executor. There is an example
in the flux examples folder that will show running a “Hello World!” example,
and this file should be in your fluxuser home:
$ ls Snakefile snakemake
Here is how to run the workflow:
$ snakemake --flux --jobs=1
The flags above refer to:
--flux: tell Snakemake to use the flux executor
Once you submit the job, you’ll immediately see the familiar Snakemake console output. The jobs happen very quickly, but the default wait time between checks is 10 seconds so it will take a bit longer.
Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. 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 Aug 12 21:09:32 2022] rule multilingual_hello_world: output: hello/world.txt jobid: 1 reason: Missing output files: hello/world.txt wildcards: greeting=hello resources: tmpdir=/tmp Checking status for job ƒ3sWJLhD [Fri Aug 12 21:09:42 2022] Finished job 1. 1 of 3 steps (33%) done Select jobs to execute... [Fri Aug 12 21:09:42 2022] rule multilingual_hello_world: output: hola/world.txt jobid: 2 reason: Missing output files: hola/world.txt wildcards: greeting=hola resources: tmpdir=/tmp Checking status for job ƒ8JAY1Kd [Fri Aug 12 21:09:52 2022] Finished job 2. 2 of 3 steps (67%) done Select jobs to execute... [Fri Aug 12 21:09:52 2022] localrule all: input: hello/world.txt, hola/world.txt jobid: 0 reason: Input files updated by another job: hola/world.txt, hello/world.txt resources: tmpdir=/tmp [Fri Aug 12 21:09:52 2022] Finished job 0. 3 of 3 steps (100%) done Complete log: .snakemake/log/2022-08-12T210932.564786.snakemake.log
At this point you can inspect the local directory to see your job output!
$ ls Snakefile hello hola $ cat hello/world.txt hello, World!