148 lines
4.3 KiB
Markdown
148 lines
4.3 KiB
Markdown
(flux-page)=
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# Using Nextflow with Flux
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:::{versionadded} 22.11.0-edge
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:::
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## Overview
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The [Flux Framework](https://flux-framework.org/) is a modern resource manager that can span the space between cloud and HPC. If your center does not provide Flux, you can [build Flux yourself](https://flux-framework.readthedocs.io/en/latest/quickstart.html#building-the-code) and launch it as a job using your resource manager of choice (e.g. SLURM or a cloud provider).
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In the [`docker/flux`](https://github.com/nextflow-io/nextflow/tree/master/docker/flux) directory we provide a [Dockerfile for interacting with Flux](https://github.com/nextflow-io/nextflow/tree/master/docker/flux/.devcontainer/Dockerfile) along with a [VSCode Developer Container](https://code.visualstudio.com/docs/devcontainers/containers) environment that you can put at the root of the project to be provided with a Flux agent and the dependencies needed to build Nextflow. There are two ways to use this:
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- Build a container from scratch and bind your code to it (e.g. for development or testing)
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- Use VSCode and DevContainers to create a more seamless environment
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Both strategies are described below. For this tutorial, you will generally want to prepare a pipeline to use the `flux` executor, create an environment with Flux, start a Flux instance, and interact with it.
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## Prepare your pipeline
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To run your pipeline with Flux, you'll want to specify it in your config. Here is an example `nextflow.config`:
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```groovy
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manifest {
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mainScript = 'demo.nf'
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homePage = 'https://github.com/nextflow-io/nextflow/tree/master/docker/flux'
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description = 'Demo using Nextflow with Flux'
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}
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process {
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executor = 'flux'
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}
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```
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For additional Flux settings, see the {ref}`flux-executor` section.
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Here is an example pipeline that we will use:
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```nextflow
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workflow {
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breakfast = channel.of '🥞️', '🥑️', '🥧️', '🍵️', '🍞️'
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haveMeal(breakfast)
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}
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process haveMeal {
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debug true
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input:
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val food
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script:
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"""
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printf '$food for breakfast!'
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"""
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}
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```
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## Prepare your environment
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You can either build the Docker image from the root of the Nextflow repository:
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```console
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$ docker build -f docker/flux/.devcontainer/Dockerfile --platform linux/amd64 -o type=docker -t nextflow-flux .
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```
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And then shell into the container for a development environment. You'll need to bind the present working directory to `/code` to see your local changes in the container:
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```console
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$ docker run -it -v $PWD:/code nextflow-flux
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```
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You can also move the `.devcontainer` directory to the root of your repository, and open it in VSCode:
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```console
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$ cp -R docker/flux/.devcontainer .devcontainer
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```
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Then open in VSCode, and select **Re-open in container**:
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```console
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$ code .
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```
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Then you should be able to open a terminal (**Terminal** -> **New Terminal**) to interact with the command line. Try running `make` again! Whichever of these two approaches you take, you should be in a container environment with the `flux` command available.
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## Start a Flux instance
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Once in your container, you can start an interactive Flux instance (from which you can submit jobs on the command line to test with Nextflow) as follows:
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```console
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$ flux start --test-size=4
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```
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### Getting familiar with Flux
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Here is an example of submitting a job and getting the log for it.
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First submit the job:
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```console
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$ flux submit echo "HELLO MOTO"
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ƒEzWqspb
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```
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Then get the log for it:
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```console
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$ flux job attach ƒEzWqspb
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HELLO MOTO
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```
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Try submitting a longer job:
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```console
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$ flux submit sleep 60
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```
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And then seeing it in the jobs listing.
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```console
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$ flux jobs
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JOBID USER NAME ST NTASKS NNODES TIME INFO
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ƒ4tkMUAAT root sleep R 1 1 2.546s ab6634a491bb
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```
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## Submitting with Nextflow
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Prepare your `nextflow.config` and `demo.nf` in the same directory.
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```console
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$ ls .
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demo.nf nextflow.config
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```
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Finally, run the pipeline with Flux:
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```console
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$ nextflow -c nextflow.config run demo.nf
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N E X T F L O W ~ version 22.10.0
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Launching `demo.nf` [clever_blackwell] DSL2 - revision: f8cda838cb
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executor > flux (5)
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[4c/f162db] process > haveMeal (3) [100%] 5 of 5 ✔
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🥞️ for breakfast!
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🍞️ for breakfast!
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🍵️ for breakfast!
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🥑️ for breakfast!
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🥧️ for breakfast!
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```
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