Decision: Parallel backend and pipeline tool

[seabbs]

We need to decide which pipelining tool and computational backends we are going to use.

At the moment we have a partial Dagger.jl implementation but its unclear how we can scale this across different types of compute (i.e local, connections via ssh, slurm and Azure batch). It is also unclear what kind of pipeline tools that Dagger.jl offers (like the task graph, progress monitoring etc). See here for issue looking into some of this: JuliaParallel/Dagger.jl#512

Another option is the JobSchedulers.jl and Pipelines.jl ecosystem which would be closer to a traditional command line based workflow. However it is currently unclear if these packages support non-local compute. See here for an issue on this: cihga39871/JobSchedulers.jl#15

A final alternative is to take a mixed approach of the two or to take a simpler approach that uses more of the standard base Julia tooling.

Making any decision is not time critical as we can use local compute for our current pipeline but as an example of Julia best practices we want to have a clear steer on scalable approaches for the future.

[SamuelBrand1]

After some time looking at this and f2f discussion, I now favour using either nextflow or airflow as the eventually/scalable backend.

Upsides

• Well documented.
• Example usages are easily available and seem numerous.
• Connection to Azure Batch resources seem maintained.

Downsides

• Lose the feature of self-constructing computational DAG by moving away from Dagger.jl (I think, open to push back or ideas on how to combine).

Thoughts @zsusswein ?

[seabbs]

Yeah I can see the arguments for this.

I would note though that one of the main issues is not lack of cloud support in Dagger.jl (via Distributed.j) as it actually has quite a lot. The problem is that Azure cloud support in Julia is poorly integrated/implemented and so doesn't work with the rest of the ecosystem.

In terms of the DAG I see the manual DAG construction you do in airflow etc as very similar. I think the real hit we take is we move from an all Julia workflow to one with a glue language and Julia which seems like shame (but for the points you raise seems like it makes sense).

I think for now we should press on but plan to refactor as a demonstration project that we can pitch if/when there is interest or if there is interest from others (i.e @zsusswein)

[zsusswein]

A few quick thoughts:

• Pipeline tooling is usually opinionated -- I think that's both a pro and a con. I'd try to (a) avoid choosing a tool that doesn't match your opinions and (b) figure out how it plays with both cloud and local runs before you go with it. I'm not super clear on when/where this becomes a cloud problem, so not sure how big a deal that is.
• Moving from all-Julia to multi-language is a real hit. I buy the argument that it's worth it. But also, I'd push for moving to containerization earlier as result.
• What's the right level of abstraction for parallelization? Are you running the whole pipeline in one container? Or are you spawning a container from a shared base image per-task in your DAG? (I vote for the latter). This is moot pre-container, but the kind of thing I'd design for early on.

[seabbs]

Moving from all-Julia to multi-language is a real hit.

I strongly agree and if we could anything other than azure batch we would be able to continue all in Julia but alas. That being said I can see an argument for a standard approach to pipelining and that might as well be very fully featured (i.e some of the above options).

containerization earlier as result

Noting that containers in julia look quite trivial: https://discourse.julialang.org/t/recommended-recipe-for-deploying-a-julia-app-in-docker-with-efficient-precompilation/95591/2. I would also say that in most good pipeline tools exactly where a specific task is actually being run is abstracted and so I would lightly pushback against this or perhaps rephrase to its key to think about how the tools you are using would require you to do this

Or are you spawning a container from a shared base image per-task in your DAG? (I vote for the latter).

Currently the latter. The nice thing about Distributed.jl is this is all abstracted so we don't need to make an internal choice about where it rruns and on what (like in the future ecosystem)

[SamuelBrand1]

Shall we move this to discussion?

[seabbs]

yes

[SamuelBrand1]

Here is a nice example of nextflow being used to organise an analysis pipeline with a mix of julia and stan code:

https://github.com/Julia-Tempering/autoMALA-mev

[SamuelBrand1]

Given the nice nextflow example linked above, these docs look useful https://www.nextflow.io/docs/latest/azure.html