37건 · 관련도순
Diagnose and remediate cluster-wide HyperPod (EKS or Slurm) problems — creation / deployment failures (CloudFormation, EFA health check, lifecycle scripts, capacity), EKS access, node replacement, CloudFormation nested-stack errors, post-maintenance rollback state, dangling nodes, autoscaler conflicts. Includes `--validate` pre-flight. Read-only.
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Diagnose NCCL failures and adjacent training-pod failures on HyperPod GPU clusters (EKS or Slurm) — training hangs, AllReduce / collective-op timeouts, EFA or libfabric errors, rendezvous failures, EFA TCP fallback, /dev/shm or memlock issues, NCCL version mismatch across pods, container OOM / exit-137 / OOMKilled, GPU OOM (CUDA out of memory), CrashLoopBackOff / Pending pods, MASTER_ADDR DNS, NetworkPolicy blocking. Not for single-node hardware faults (→ hyperpod-node-debugger § G) or cluster-creation EFA / SSM failures (→ hyperpod-cluster-debugger § A / § F).
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Expert knowledge for Azure CycleCloud development including troubleshooting, best practices, decision making, architecture & design patterns, security, configuration, integrations & coding patterns, and deployment. Use when automating CycleCloud via API/CLI/SDK, configuring Slurm clusters, tuning HB/HC VMs, or securing access, and other Azure CycleCloud related development tasks. Not for Azure Batch (use azure-batch), Azure HDInsight (use azure-hdinsight), Azure Databricks (use azure-databricks), Azure Kubernetes Service (AKS) (use azure-kubernetes-service).
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Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized, cloud-native, and nf-core pipelines.
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Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow for Groovy dataflow or nf-core integration.
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Think and work like an expert High-Performance Computing Specialist. Use when a task calls for High-Performance Computing Specialist judgment. Reasons from NUMA topology and hybrid MPI+OpenMP+CUDA decomposition through Slurm fairshare/backfill job design, strong/weak scaling (Amdahl/Gustafson), Darshan/mpiP/Nsight profiling, and parallel HDF5/MPI-IO on Lustre while treating I/O storms, collectives bottlenecks, and rank-binding mistakes as first-class failure modes.
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Runs the GPU part of a vlm-ocr pipeline on Leiden University's ALICE cluster. Decides whether a corpus needs ALICE, picks a GPU partition for the model, sets up storage, a pinned vLLM environment and offline weights, ships code and scans, runs a gate job and chained bulk jobs with the bundled SLURM template, and brings the page records home for post-processing. Use with vlm-ocr when OCRing scans on ALICE or deciding whether to.
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Run the GPU part of a $vlm-ocr pipeline on Leiden University's ALICE cluster: decide whether a corpus needs ALICE, pick a GPU partition for the model, set up storage, a pinned vLLM environment and offline weights, ship code and scans, run a gate job and chained bulk jobs with the bundled SLURM template, and bring the page records home for post-processing. Use with $vlm-ocr when OCRing scans on ALICE or deciding whether to.
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Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed. Use when deciding channel/dataflow (Nextflow) vs rule-based (Snakemake) authoring; wiring queue vs value channels and fixing shared-reference exhaustion with .first(); composing DSL2 modules and subworkflows with take/main/emit; selecting container/conda profiles and pinning images by digest for portability across local/SLURM/LSF/AWS Batch/Google Batch/Kubernetes executors; diagnosing why -resume misses the cache (nondeterministic input order, mtime on network filesystems, mutable :latest tags) with cache 'lenient' and -dump-hashes; managing work/ vs publishDir and dynamic retry escalation; and choosing whether to adopt an nf-core community pipeline or author from scratch.
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Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and selecting a container engine and institutional config via -profile. Use when deciding to adopt a community pipeline versus author one from scratch; picking a pipeline and pinning its -r revision; selecting -profile test/docker/singularity/conda plus an institutional config from nf-core/configs; building and validating a samplesheet CSV against the pipeline schema (nf-schema); choosing --genome/iGenomes versus custom references; configuring resources and max_memory for SLURM/AWS Batch; using -resume and -stub; and reading MultiQC outputs.
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Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.
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Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.
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Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.
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