Cudf: [BUG] Column selection fails in read_parquet for df with nulls
Describe the bug
I am getting a Invalid null mask for non-zero null count. error when trying to round trip a simple DataFrame to/from parquet. The problem occurs when both of the following are true:
- The DataFrame has an "object" column with 1+ null values.
- The
read_parquetcall is specifying a specific set ofcolumns
Steps/Code to reproduce bug
import cudf
path = "test.parquet"
df = cudf.datasets.timeseries()
df["name"] = df["name"].astype("object")
df["name"].iloc[1] = None
df.to_parquet(path, index=False)
cudf.read_parquet(path) # Works fine
cudf.read_parquet(path, columns=["id", "name"]) # Works fine
cudf.read_parquet(path, columns=["name", "id"])
Trace
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-31-6f0182eeef31> in <module>
----> 1 cudf.read_parquet(path, columns=["name", "id"])
~/workspace/rapids_dev/cudf/python/cudf/cudf/io/parquet.py in read_parquet(filepath_or_buffer, engine, columns, row_groups, skip_rows, num_rows, strings_to_categorical, use_pandas_metadata, *args, **kwargs)
212 num_rows=num_rows,
213 strings_to_categorical=strings_to_categorical,
--> 214 use_pandas_metadata=use_pandas_metadata,
215 )
216 else:
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/parquet.pyx in cudf._lib.parquet.read_parquet()
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/parquet.pyx in cudf._lib.parquet.read_parquet()
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/table.pyx in cudf._lib.table.Table.from_unique_ptr()
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/column.pyx in cudf._lib.column.Column.from_unique_ptr()
RuntimeError: cuDF failure at: /home/nfs/rzamora/workspace/rapids_dev/cudf/cpp/src/column/column_view.cpp:56: Invalid null mask for non-zero null count.
Note that I get the same error for cudf.read_parquet(path, columns=["x", "y"]) (so the object column doesn't need to be in the columns selection)
Expected behavior
There should be no RuntimeError error.
Environment overview (please complete the following information)
- Environment location: Bare-metal
- Method of cuDF install: conda
Environment details
Click here to see environment details
**git***
commit e51115fba4ffef293467ccb7acc94395e808ac62 (HEAD, upstream/branch-0.15)
Merge: 7e73aa467 b8d78a8bf
Author: Keith Kraus <[email protected]>
Date: Wed Aug 19 04:22:07 2020 -0400
Merge pull request #5735 from sriramch/add_months
[REVIEW] allow timestamps to be constructed only from duration
**git submodules***
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Wed Aug 19 17:04:45 2020
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| 4 Tesla V100-SXM2... On | 00000000:85:00.0 Off | 0 |
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| 5 Tesla V100-SXM2... On | 00000000:86:00.0 Off | 0 |
| N/A 30C P0 41W / 300W | 12MiB / 32510MiB | 0% Default |
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| 6 Tesla V100-SXM2... On | 00000000:89:00.0 Off | 0 |
| N/A 32C P0 43W / 300W | 12MiB / 32510MiB | 0% Default |
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| 7 Tesla V100-SXM2... On | 00000000:8A:00.0 Off | 0 |
| N/A 28C P0 42W / 300W | 12MiB / 32510MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 79453 C ...mora/miniconda3/envs/nvt_dev/bin/python 1439MiB |
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***CMake***
/datasets/rzamora/miniconda3/envs/nvt_dev/bin/cmake
cmake version 3.18.0
CMake suite maintained and supported by Kitware (kitware.com/cmake).
***g++***
/usr/bin/g++
g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
***nvcc***
/usr/local/cuda/bin/nvcc
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Wed_Oct_23_19:24:38_PDT_2019
Cuda compilation tools, release 10.2, V10.2.89
***Python***
/datasets/rzamora/miniconda3/envs/nvt_dev/bin/python
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yarl 1.4.2 py37h7b6447c_0
zeromq 4.3.2 he1b5a44_3 conda-forge
zict 2.0.0 py_0 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h516909a_1007 conda-forge
zstd 1.4.5 h6597ccf_2 conda-forge
Additional context
Causing NVTabular tests to fail with latest cudf
rjzamora
All 12 comments
Somewhere a column_view is being constructed with a non-zero null_count but a nullptr null_mask.
harrism
on 20 Aug 2020
Updated (simpler) Repro:
import cudf
path = "test.parquet"
df = cudf.DataFrame({"a": ["a", None, "c"], "b": [1, 2, 3]})
df.to_parquet(path, index=False)
cudf.read_parquet(path, columns=["a", "b"]) # GOOD
cudf.read_parquet(path, columns=["b", "a"])
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-38-96c014a638fa> in <module>
----> 1 cudf.read_parquet(path, columns=["b", "a"])
~/workspace/rapids_dev/cudf/python/cudf/cudf/io/parquet.py in read_parquet(filepath_or_buffer, engine, columns, row_groups, skip_rows, num_rows, strings_to_categorical, use_pandas_metadata, *args, **kwargs)
212 num_rows=num_rows,
213 strings_to_categorical=strings_to_categorical,
--> 214 use_pandas_metadata=use_pandas_metadata,
215 )
216 else:
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/parquet.pyx in cudf._lib.parquet.read_parquet()
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/parquet.pyx in cudf._lib.parquet.read_parquet()
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/table.pyx in cudf._lib.table.Table.from_unique_ptr()
~/workspace/rapids_dev/cudf/python/cudf/cudf/_lib/column.pyx in cudf._lib.column.Column.from_unique_ptr()
RuntimeError: cuDF failure at: /home/nfs/rzamora/workspace/rapids_dev/cudf/cpp/src/column/column_view.cpp:56: Invalid null mask for non-zero null count.
DataFrame (for clarity):
a b
0 a 1
1 <NA> 2
2 c 3
Got local repro with the updated code. Looking for root cause.
vuule
on 20 Aug 2020
@nvdbaranec in case this looks related to his recent PR.
vuule
on 20 Aug 2020
Progress so far:
It looks like the error actually comes from the integer column. After page data decode, null count for col "b" is three (should be zero), while it's zero for col "a" (should be one).
The integer col "b" is created as not nullable (correctly), so this aligns with the error message.
I still haven't found how this is caused by column selection. Current assumption is that there is a mix-up between selected column index and output column index at some point, in code related to data validity.
vuule
on 20 Aug 2020
Just saw this. Taking a look.
nvdbaranec
on 20 Aug 2020
Some more isolation info:
issue also reproes with
df = cudf.DataFrame({"a": [1, None, 3], "b": [1, 2, 3]}) or
df = cudf.DataFrame({"a": [1, 2, 3], "b": [1, None, 3]})
but not with
df = cudf.DataFrame({"a": [1, None, 3], "b": [1, None, 3]})
In the repro case the valid count is still incorrect in both columns.
vuule
on 20 Aug 2020
Confirmed I can repro this purely on the cpp side as well. Definitely related to reading the columns out of order. Probably an easy fix.
nvdbaranec
on 20 Aug 2020
@nvdbaranec and I found the root cause and have a tentative fix.
Dave will take over and open a PR once the fix is thoroughly tested.
vuule
on 20 Aug 2020
🚀4
Vukasin gets the credit here - he zenned the issue.
nvdbaranec
on 20 Aug 2020
👎1
👍1
Thanks for digging in here @vuule !
rjzamora
on 20 Aug 2020
Vukasin gets the credit here - he zenned the issue.
It was a clear team effort. I insist on a 50/50 split :)
vuule
on 20 Aug 2020
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Most helpful comment
@nvdbaranec and I found the root cause and have a tentative fix.
Dave will take over and open a PR once the fix is thoroughly tested.