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rseng-big-data-processinglisted

Covers processing research data that outgrows one machine's memory: out-of-core and chunked computation, Dask for scaling the scientific Python stack, Spark for distributed tabular pipelines, lazy evaluation, partitioning strategies, idempotent and restartable batch jobs, and knowing when NOT to distribute. Use when datasets no longer fit in memory, when the user mentions Dask, Spark, out-of-core or larger-than-memory data, when a pandas/NumPy workflow hits memory limits, or when designing batch pipelines over many files. (Cluster job submission and job arrays are rseng-hpc-computing; pipeline orchestration engines are rseng-workflows; profile first with rseng-performance-profiling.)
fdiblen/rseng-agent-skills · ★ 20 · Data & Documents · score 81
Install: claude install-skill fdiblen/rseng-agent-skills
# Big data processing for research "Big" starts where the current tool breaks: the dataset that no longer fits in RAM, the loop over files that no longer finishes overnight. The escalation path matters more than any framework - each step up costs complexity, debuggability and reproducibility, so take the smallest step that works. ## The escalation ladder 1. Optimize in place first: columnar formats with predicate pushdown (Parquet - rseng-scientific-file-formats), dtype downcasting, reading only needed columns; profile before scaling (rseng-performance-profiling) - many "big data" problems are memory-layout problems. 2. Out-of-core on one machine: chunked iteration (read-process- write per chunk), memory-mapped arrays, or Dask's lazy collections on a single node. One machine with streaming processing handles far more than intuition suggests, with none of the distributed complexity. 3. Embarrassingly parallel batch: independent per-file/per-chunk jobs as cluster job arrays (rseng-hpc-computing) or a workflow engine (rseng-workflows) - the RIGHT answer for most research sweeps, and simpler than any framework. 4. Distributed frameworks: Dask (scales NumPy/pandas/xarray idioms; native in the Pangeo geoscience stack) or Spark (SQL-flavored tabular pipelines, industry-standard cluster tooling) when computation genuinely needs cross-partition coordination: shuffles, joins, global aggregations over larger-than-node data. Skipping strai