nextflow
node_crunch
nextflow | node_crunch | |
---|---|---|
9 | 15 | |
2,557 | 78 | |
1.4% | - | |
9.7 | 0.0 | |
about 4 hours ago | 6 months ago | |
Groovy | Rust | |
Apache License 2.0 | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
nextflow
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Nextflow: Data-Driven Computational Pipelines
> It's been a while since you can rerun/resume Nextflow pipelines
Yes, you can resume, but you need your whole upstream DAG to be present. Snakemake can rerun a job when only the dependencies of that job are present, which allows to neatly manage the disk usage, or archive an intermediate state of a project and rerun things from there.
> and yes, you can have dry runs in Nextflow
You have stubs, which really isn't the same thing.
> I have no idea what you're referring to with the 'arbitrary limit of 1000 parallel jobs' though
I was referring to this issue: https://github.com/nextflow-io/nextflow/issues/1871. Except, the discussion doesn't give the issue a full justice. Nextflow spans each job in a separate thread, and when it tries to span 1000+ condor jobs it die with a cryptic error message. The option of -Dnxf.pool.type=sync and -Dnxf.pool.maxThreads=N prevents the ability to resume and attempts to rerun the pipeline.
> As for deleting temporary files, there are features that allow you to do a few things related to that, and other features being implemented.
There are some hacks for this - but nothing I would feel safe to integrate into a production tool. They are implementing something - you're right - and it's been the case for several years now, so we'll see.
Snakemake has all that out of the box.
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Alternatives to nextflow?
For now, I think that the best place to track this / get your voice heard is this GitHub Discussions post (which covers many things - error reporting is one of them). https://github.com/nextflow-io/nextflow/discussions/3107
- HyperQueue: ergonomic HPC task executor written in Rust
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Nextflow vs Snakemake
We could spend the day pointing to things we wish were different, but that doesn't change the fact that Nextflow is the leader when it comes to workflow orchestration. And feel free to create a new issue in the GitHub repository if you wish to request a feature :)
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Feel very hard writing nextflow pipeline.
The nextflow devs have been talking about this for a while on GitHub. Looks like they're implementing something along these lines using schema like they do for nf-core. GitHub discussion.
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Need a statically typed Python replacement
Groovy definitely scales up just fine I think but I never used it myself outside of little snippets embedded in my DSL, I know its considered by some to be "dead" so its interesting to see what other JVM-ecosystem users think of it.
node_crunch
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Rust MPI -- Will there ever be a fully oxidized implementation?
I've written my own crate called node-crunch for distributed computing.
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Eclipse Zenoh: 0.7.0 release
This looks really nice! It has encryption and compression is planned for the next release. I've developed node_crunch, a crate for distributed computing and designed the protocols myself. I think that Zenoh could make my life a lot easier ;-) I'll definitely try it out!
- HyperQueue: ergonomic HPC task executor written in Rust
- Mandelbrot rendering with Rust
- possibility of blas natively in Rust
- An optimization story
- Rust and Scientific/High-Performance Computing
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[Feedback] Genetic Algorithm to Solve Sudoku Puzzles
You may be interested in darwin-rs, a crate for evolutionary algorithm that I'm working on. It uses multiple threads to speed things up, but I'm currently implementing node-crunch support, so that it can run on a cluster.
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Added Glasses and Soft Shadows to my Ray Tracer
Nice! I'm currently working on node_crunch a crate for distributed computing. I've modified an existing ray tracer to run on a cluster. If you're interested you can have a look at the code.
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What sort of mature, open-source libraries do you feel Rust should have but currently lacks?
I'm currently working on node_crunch.
What are some alternatives?
galaxy - Data intensive science for everyone.
darwin-rs - darwin-rs, evolutionary algorithms with rust
argo - Workflow Engine for Kubernetes
libint - Libint: high-performance library for computing Gaussian integrals in quantum mechanics
ploomber - The fastest ⚡️ way to build data pipelines. Develop iteratively, deploy anywhere. ☁️
rsmpi - MPI bindings for Rust
singularity - Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
constellation - Constellation is the first Confidential Kubernetes. Constellation shields entire Kubernetes clusters from the (cloud) infrastructure using confidential computing.
Airflow - Apache Airflow - A platform to programmatically author, schedule, and monitor workflows
StaticArrays.jl - Statically sized arrays for Julia
devops-resources - DevOps resources - Linux, Jenkins, AWS, SRE, Prometheus, Docker, Python, Ansible, Git, Kubernetes, Terraform, OpenStack, SQL, NoSQL, Azure, GCP
libcint - general GTO integrals for quantum chemistry