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  1. Spark
  2. SPARK-28547

Make it work for wide (> 10K columns data)

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    Details

    • Type: Improvement
    • Status: Resolved
    • Priority: Critical
    • Resolution: Incomplete
    • Affects Version/s: 3.0.0
    • Fix Version/s: None
    • Component/s: Spark Core
    • Labels:
      None
    • Environment:

      Ubuntu server, Spark 2.4.3 Scala with >64GB RAM per node, 32 cores (tried different configurations of executors)

      Description

      Spark is super-slow for all wide data (when there are >15kb columns and >15kb rows). Most of the genomics/transcriptomic data is wide because number of genes is usually >20kb and number of samples ass well. Very popular GTEX dataset is a good example ( see for instance RNA-Seq data at https://storage.googleapis.com/gtex_analysis_v7/rna_seq_data where gct is just a .tsv file with two comments in the beginning). Everything done in wide tables (even simple "describe" functions applied to all the genes-columns) either takes hours or gets frozen (because of lost executors) irrespective of memory and numbers of cores. While the same operations work fast (minutes) and well with pure pandas (without any spark involved).
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            • Assignee:
              Unassigned
              Reporter:
              antonkulaga antonkulaga
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              • Created:
                Updated:
                Resolved: