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  1. Apache Arrow
  2. ARROW-3792

[Python] Segmentation fault when writing empty RecordBatches to Parquet

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Details

    • Bug
    • Status: Resolved
    • Major
    • Resolution: Fixed
    • 0.11.1
    • 0.12.0
    • C++, Python
    • Fedora 28, pyarrow installed with pip
      Fedora 29, pyarrow installed from conda-forge

    Description

      Background

      I am trying to convert a very sparse dataset to parquet (~3% rows in a range are populated). The file I am working with spans upto ~63M rows. I decided to iterate in batches of 500k rows, 127 batches in total. Each row batch is a RecordBatch. I create 4 batches at a time, and write to a parquet file incrementally. Something like this:

      batches = [..]  # 4 batches
      tbl = pa.Table.from_batches(batches)
      pqwriter.write_table(tbl, row_group_size=15000)
      # same issue with pq.write_table(..)
      

      I was getting a segmentation fault at the final step, I narrowed it down to a specific iteration. I noticed that iteration had empty batches; specifically, [0, 0, 2876, 14423]. The number of rows for each RecordBatch for the whole dataset is below:

      [14050, 16398, 14080, 14920, 15527, 14288, 15040, 14733, 15345, 15799,
      15728, 15942, 14734, 15241, 15721, 15255, 14167, 14009, 13753, 14800,
      14554, 14287, 15393, 14766, 16600, 15675, 14072, 13263, 12906, 14167,
      14455, 15428, 15129, 16141, 15478, 16257, 14639, 14887, 14919, 15535,
      13973, 14334, 13286, 15038, 15951, 17252, 15883, 19903, 16967, 16878,
      15845, 12205, 8761, 0, 0, 0, 0, 0, 2876, 14423, 13557, 12723, 14330,
      15452, 13551, 12723, 12396, 13531, 13539, 11512, 13175, 13941, 14634,
      15515, 14239, 13856, 13873, 14154, 14822, 13543, 14653, 15328, 16171,
      15101, 150 55, 15194, 14058, 13706, 14747, 14650, 14694, 15397, 15122,
      16055, 16635, 14153, 14665, 14781, 15462, 15426, 16150, 14632, 14532,
      15139, 15324, 15279, 16075, 16394, 16834, 15391, 16320, 1650 4, 17248,
      15913, 15341, 14754, 16637, 15695, 16642, 18143, 19481, 19072, 15742,
      18807, 18789, 14258, 0, 0]
      

      On excluding the empty RecordBatch-es, the segfault goes away, but unfortunately I couldn't create a proper minimal example with synthetic data.

      Not quite minimal example

      The data I am using is from the 1000 Genome project, which has been public for many years, so we can be reasonably sure the data is good. The following steps should help you replicate the issue.

      1. Download the data file (and index), about 330MB:
        $ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz{,.tbi}
        
      2. Install the Cython library pysam, a thin wrapper around the reference implementation of the VCF file spec. You will need zlib headers, but that's probably not a problem
        $ pip3 install --user pysam
        
      3. Now you can use the attached script to replicate the crash.

      Extra information

      I have tried attaching gdb, the backtrace when the segfault occurs is shown below (maybe it helps, this is how I realised empty batches could be the reason).

      (gdb) bt
      #0  0x00007f3e7676d670 in parquet::TypedColumnWriter<parquet::DataType<(parquet::Type::type)6> >::WriteMiniBatch(long, short const*, short const*, parquet::ByteArray const*) ()
         from /home/user/miniconda3/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.11
      #1  0x00007f3e76733d1e in arrow::Status parquet::arrow::(anonymous namespace)::ArrowColumnWriter::TypedWriteBatch<parquet::DataType<(parquet::Type::type)6>, arrow::BinaryType>(arrow::Array const&, long, short const*, short const*) ()
         from /home/user/miniconda3/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.11
      #2  0x00007f3e7673a3d4 in parquet::arrow::(anonymous namespace)::ArrowColumnWriter::Write(arrow::Array const&) ()
         from /home/user/miniconda3/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.11
      #3  0x00007f3e7673df09 in parquet::arrow::FileWriter::Impl::WriteColumnChunk(std::shared_ptr<arrow::ChunkedArray> const&, long, long) ()
         from /home/user/miniconda3/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.11
      #4  0x00007f3e7673c74d in parquet::arrow::FileWriter::WriteColumnChunk(std::shared_ptr<arrow::ChunkedArray> const&, long, long) ()
         from /home/user/miniconda3/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.11
      #5  0x00007f3e7673c8d2 in parquet::arrow::FileWriter::WriteTable(arrow::Table const&, long) ()
         from /home/user/miniconda3/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.11
      #6  0x00007f3e731e3a51 in __pyx_pw_7pyarrow_8_parquet_13ParquetWriter_5write_table(_object*, _object*, _object*) ()
         from /home/user/miniconda3/lib/python3.6/site-packages/pyarrow/_parquet.cpython-36m-x86_64-linux-gnu.so
      

      Attachments

        1. minimal_bug_arrow3792.py
          1 kB
          Tanya Schlusser
        2. pq-bug.py
          1 kB
          Suvayu Ali

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              wesm Wes McKinney
              suvayu Suvayu Ali
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