[jira] [Updated] (ARROW-3933) [Python] Segfault reading Parquet files from GNOMAD

["Wes McKinney (JIRA)" <ji...@apache.org>]

     [ https://issues.apache.org/jira/browse/ARROW-3933?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Wes McKinney updated ARROW-3933:
--------------------------------
    Component/s: Python

> [Python] Segfault reading Parquet files from GNOMAD
> ---------------------------------------------------
>
>                 Key: ARROW-3933
>                 URL: https://issues.apache.org/jira/browse/ARROW-3933
>             Project: Apache Arrow
>          Issue Type: Bug
>          Components: C++, Python
>         Environment: Ubuntu 18.04 or Mac OS X
>            Reporter: David Konerding
>            Priority: Minor
>              Labels: parquet
>             Fix For: 0.12.0
>
>
> I am getting segfault trying to run a basic program Ubuntu 18.04 VM (AWS). Error also occurs out of box on Mac OS X.
> $ sudo snap install --classic google-cloud-sdk
> $ gsutil cp gs://gnomad-public/release/2.0.2/vds/exomes/gnomad.exomes.r2.0.2.sites.vds/rdd.parquet/part-r-00000-31fcf9bd-682f-4c20-bbe5-b0bd08699104.snappy.parquet .
> $ conda install pyarrow
> $ python test.py
> Segmentation fault (core dumped)
> test.py:
> import pyarrow.parquet as pq
> path = "part-r-00000-31fcf9bd-682f-4c20-bbe5-b0bd08699104.snappy.parquet"
> pq.read_table(path)
> gdb output:
> Thread 3 "python" received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 0x7fffdf199700 (LWP 13703)]
> 0x00007fffdfc2a470 in parquet::arrow::StructImpl::GetDefLevels(short const**, unsigned long*) () from /home/ubuntu/miniconda2/lib/python2.7/site-packages/pyarrow/../../../libparquet.so.11
> I tested fastparquet, it reads the file just fine.



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