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[BUG] cudf.to_csv fails when dataframe has a timedelta dtypes #6225

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galipremsagar opened this issue Sep 14, 2020 · 4 comments · Fixed by #6076
Closed

[BUG] cudf.to_csv fails when dataframe has a timedelta dtypes #6225

galipremsagar opened this issue Sep 14, 2020 · 4 comments · Fixed by #6076
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@karthikeyann
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bug Something isn't working cuIO cuIO issue libcudf Affects libcudf (C++/CUDA) code.

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@galipremsagar
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galipremsagar commented Sep 14, 2020 •
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Describe the bug
Looks like we don't have the support for timedelta types in csv writer. and reader.

Steps/Code to reproduce bug

In[21]: df = cudf.DataFrame({'a':cudf.Series([1, 2, 3], dtype='timedelta64[ns]')})
In[22]: df.to_csv('temp')
Traceback (most recent call last):
  File "/home/pgali/anaconda3/envs/cudf_dev/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3417, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-22-d7bef929cdc2>", line 1, in <module>
    df.to_csv('temp')
  File "/home/pgali/anaconda3/envs/cudf_dev/lib/python3.7/site-packages/cudf/core/dataframe.py", line 6515, in to_csv
    chunksize,
  File "/home/pgali/anaconda3/envs/cudf_dev/lib/python3.7/contextlib.py", line 74, in inner
    return func(*args, **kwds)
  File "/home/pgali/anaconda3/envs/cudf_dev/lib/python3.7/site-packages/cudf/io/csv.py", line 154, in to_csv
    rows_per_chunk=rows_per_chunk,
  File "cudf/_lib/csv.pyx", line 375, in cudf._lib.csv.write_csv
  File "cudf/_lib/csv.pyx", line 420, in cudf._lib.csv.write_csv
RuntimeError: cuDF failure at: /home/pgali/Desktop/cudf/cpp/src/io/csv/writer_impl.cu:336: Unsupported column type.
/snap/pycharm-community/209/plugins/python-ce/helpers/pydev/_pydev_bundle/_pydev_imports_tipper.py:213: FutureWarning: _AXIS_NAMES has been deprecated.
  obj = getattr(obj_to_complete, d)
/snap/pycharm-community/209/plugins/python-ce/helpers/pydev/_pydev_bundle/_pydev_imports_tipper.py:213: FutureWarning: _AXIS_NUMBERS has been deprecated.
  obj = getattr(obj_to_complete, d)
In[23]: df.to_pandas().to_csv('temp')
In[24]: pd.read_csv('temp')
Out[24]: 
   Unnamed: 0                          a
0           0  0 days 00:00:00.000000001
1           1  0 days 00:00:00.000000002
2           2  0 days 00:00:00.000000003
In[25]: cudf.read_csv('temp')
Out[25]: 
   Unnamed: 0                          a
0           0  0 days 00:00:00.000000001
1           1  0 days 00:00:00.000000002
2           2  0 days 00:00:00.000000003
In[26]: cudf.read_csv('temp')['a']
Out[26]: 
0    0 days 00:00:00.000000001
1    0 days 00:00:00.000000002
2    0 days 00:00:00.000000003
Name: a, dtype: object

Expected behavior
to_csv should be able to write to the file.
from_csv should be able to correctly infer the dtype.

Environment overview (please complete the following information)

  • Environment location: Bare-metal
  • Method of cuDF install: from source

Environment details
Please run and paste the output of the cudf/print_env.sh script here, to gather any other relevant environment details

Click here to see environment details
 **git***
 commit 49558bdfa8f493ffc26d435a2f644bc2c092cc21 (HEAD -> 6001, origin/6001)
 Author: galipremsagar <[email protected]>
 Date:   Mon Sep 14 09:18:36 2020 -0500
 
 replace prints with logging
 **git submodules***
 
 ***OS Information***
 DISTRIB_ID=Ubuntu
 DISTRIB_RELEASE=20.04
 DISTRIB_CODENAME=focal
 DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
 NAME="Ubuntu"
 VERSION="20.04.1 LTS (Focal Fossa)"
 ID=ubuntu
 ID_LIKE=debian
 PRETTY_NAME="Ubuntu 20.04.1 LTS"
 VERSION_ID="20.04"
 HOME_URL="https://www.ubuntu.com/"
 SUPPORT_URL="https://help.ubuntu.com/"
 BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
 PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
 VERSION_CODENAME=focal
 UBUNTU_CODENAME=focal
 Linux pgali-HP-Z8-G4-Workstation 5.4.0-47-generic #51-Ubuntu SMP Fri Sep 4 19:50:52 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
 
 ***GPU Information***
 Mon Sep 14 10:00:17 2020
 +-----------------------------------------------------------------------------+
 | NVIDIA-SMI 450.66       Driver Version: 450.66       CUDA Version: 11.0     |
 |-------------------------------+----------------------+----------------------+
 | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
 | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
 |                               |                      |               MIG M. |
 |===============================+======================+======================|
 |   0  Quadro RTX 8000     Off  | 00000000:22:00.0 Off |                  Off |
 | 33%   32C    P8     5W / 260W |    589MiB / 48601MiB |      0%      Default |
 |                               |                      |                  N/A |
 +-------------------------------+----------------------+----------------------+
 |   1  Quadro RTX 8000     Off  | 00000000:2D:00.0  On |                  Off |
 | 33%   35C    P8    19W / 260W |    340MiB / 48592MiB |      6%      Default |
 |                               |                      |                  N/A |
 +-------------------------------+----------------------+----------------------+
 
 +-----------------------------------------------------------------------------+
 | Processes:                                                                  |
 |  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
 |        ID   ID                                                   Usage      |
 |=============================================================================|
 |    0   N/A  N/A       966      G   /usr/lib/xorg/Xorg                  4MiB |
 |    0   N/A  N/A      1831      G   /usr/lib/xorg/Xorg                  4MiB |
 |    0   N/A  N/A     22570      C   .../envs/cudf_dev/bin/python      575MiB |
 |    1   N/A  N/A       966      G   /usr/lib/xorg/Xorg                 39MiB |
 |    1   N/A  N/A      1831      G   /usr/lib/xorg/Xorg                133MiB |
 |    1   N/A  N/A      2034      G   /usr/bin/gnome-shell              148MiB |
 |    1   N/A  N/A     12967      G   /usr/lib/firefox/firefox            3MiB |
 |    1   N/A  N/A     16497      G   /usr/lib/firefox/firefox            3MiB |
 +-----------------------------------------------------------------------------+
 
 ***CPU***
 Architecture:                    x86_64
 CPU op-mode(s):                  32-bit, 64-bit
 Byte Order:                      Little Endian
 Address sizes:                   46 bits physical, 48 bits virtual
 CPU(s):                          12
 On-line CPU(s) list:             0-11
 Thread(s) per core:              2
 Core(s) per socket:              6
 Socket(s):                       1
 NUMA node(s):                    1
 Vendor ID:                       GenuineIntel
 CPU family:                      6
 Model:                           85
 Model name:                      Intel(R) Xeon(R) Gold 6128 CPU @ 3.40GHz
 Stepping:                        4
 CPU MHz:                         1200.529
 CPU max MHz:                     3700.0000
 CPU min MHz:                     1200.0000
 BogoMIPS:                        6800.00
 Virtualization:                  VT-x
 L1d cache:                       192 KiB
 L1i cache:                       192 KiB
 L2 cache:                        6 MiB
 L3 cache:                        19.3 MiB
 NUMA node0 CPU(s):               0-11
 Vulnerability Itlb multihit:     KVM: Vulnerable
 Vulnerability L1tf:              Mitigation; PTE Inversion
 Vulnerability Mds:               Mitigation; Clear CPU buffers; SMT vulnerable
 Vulnerability Meltdown:          Mitigation; PTI
 Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
 Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization
 Vulnerability Spectre v2:        Mitigation; Full generic retpoline, IBPB conditional, IBRS_FW, STIBP conditional, RSB filling
 Vulnerability Srbds:             Not affected
 Vulnerability Tsx async abort:   Mitigation; Clear CPU buffers; SMT vulnerable
 Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d
 
 ***CMake***
 /home/pgali/anaconda3/envs/cudf_dev/bin/cmake
 cmake version 3.18.2
 
 CMake suite maintained and supported by Kitware (kitware.com/cmake).
 
 ***g++***
 /usr/bin/g++
 g++ (Ubuntu 9.3.0-10ubuntu2) 9.3.0
 Copyright (C) 2019 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) 2005-2020 NVIDIA Corporation
 Built on Wed_Jul_22_19:09:09_PDT_2020
 Cuda compilation tools, release 11.0, V11.0.221
 Build cuda_11.0_bu.TC445_37.28845127_0
 
 ***Python***
 /home/pgali/anaconda3/envs/cudf_dev/bin/python
 Python 3.7.8
 
 ***Environment Variables***
 PATH                            : /home/pgali/anaconda3/envs/cudf_dev/bin:/home/pgali/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/cuda/bin
 LD_LIBRARY_PATH                 : :/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64
 NUMBAPRO_NVVM                   :
 NUMBAPRO_LIBDEVICE              :
 CONDA_PREFIX                    : /home/pgali/anaconda3/envs/cudf_dev
 PYTHON_PATH                     :
 
 ***conda packages***
 /home/pgali/anaconda3/condabin/conda
 # packages in environment at /home/pgali/anaconda3/envs/cudf_dev:
 #
 # Name                    Version                   Build  Channel
 _libgcc_mutex             0.1                 conda_forge    conda-forge
 _openmp_mutex             4.5                       1_gnu    conda-forge
 abseil-cpp                20200225.2           he1b5a44_2    conda-forge
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 argon2-cffi               20.1.0           py37h8f50634_1    conda-forge
 arrow-cpp                 1.0.1           py37h1234567_1_cuda    conda-forge
 arrow-cpp-proc            1.0.1                      cuda    conda-forge
 async_generator           1.10                       py_0    conda-forge
 attrs                     20.2.0             pyh9f0ad1d_0    conda-forge
 aws-sdk-cpp               1.7.164              hba45d7a_2    conda-forge
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 backports                 1.0                        py_2    conda-forge
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 black                     19.10b0                    py_4    conda-forge
 bleach                    3.1.5              pyh9f0ad1d_0    conda-forge
 bokeh                     2.2.1            py37hc8dfbb8_0    conda-forge
 boost-cpp                 1.72.0               h7b93d67_2    conda-forge
 brotli                    1.0.9                he1b5a44_0    conda-forge
 brotlipy                  0.7.0           py37h8f50634_1000    conda-forge
 bzip2                     1.0.8                h516909a_3    conda-forge
 c-ares                    1.16.1               h516909a_3    conda-forge
 ca-certificates           2020.6.20            hecda079_0    conda-forge
 certifi                   2020.6.20        py37hc8dfbb8_0    conda-forge
 cffi                      1.14.1           py37h2b28604_0    conda-forge
 cfgv                      3.2.0                      py_0    conda-forge
 chardet                   3.0.4           py37hc8dfbb8_1006    conda-forge
 clang                     8.0.1                hc9558a2_2    conda-forge
 clang-tools               8.0.1                hc9558a2_2    conda-forge
 clangxx                   8.0.1                         2    conda-forge
 click                     7.1.2              pyh9f0ad1d_0    conda-forge
 cloudpickle               1.6.0                      py_0    conda-forge
 cmake                     3.18.2               h5c55442_0    conda-forge
 cmake_setuptools          0.1.3                      py_0    rapidsai
 commonmark                0.9.1                      py_0    conda-forge
 cryptography              3.1              py37hb09aad4_0    conda-forge
 cudatoolkit               11.0.221             h6bb024c_0    nvidia
 cudf                      0.16.0a0+1709.g95229579dc.dirty          pypi_0    pypi
 cudnn                     8.0.0                cuda11.0_0    nvidia
 cupy                      7.8.0            py37h0ce7dbb_0    rapidsai
 curl                      7.71.1               he644dc0_5    conda-forge
 cython                    0.29.21          py37h3340039_0    conda-forge
 cytoolz                   0.10.1           py37h516909a_0    conda-forge
 dask                      2.25.0+15.g3327b2e1          pypi_0    pypi
 dask-cudf                 0.16.0a0+1717.g6188ce518c          pypi_0    pypi
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 distlib                   0.3.1              pyh9f0ad1d_0    conda-forge
 distributed               2.25.0+9.g4115f55c          pypi_0    pypi
 dlpack                    0.3                  he1b5a44_1    conda-forge
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 editdistance              0.5.3            py37h3340039_1    conda-forge
 entrypoints               0.3             py37hc8dfbb8_1001    conda-forge
 expat                     2.2.9                he1b5a44_2    conda-forge
 fastavro                  1.0.0.post1      py37h8f50634_0    conda-forge
 fastrlock                 0.5              py37h3340039_0    conda-forge
 filelock                  3.0.12             pyh9f0ad1d_0    conda-forge
 flake8                    3.8.3                      py_1    conda-forge
 flatbuffers               1.12.0               he1b5a44_0    conda-forge
 freetype                  2.10.2               he06d7ca_0    conda-forge
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 future                    0.18.2           py37hc8dfbb8_1    conda-forge
 gflags                    2.2.2             he1b5a44_1004    conda-forge
 glog                      0.4.0                h49b9bf7_3    conda-forge
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 grpc-cpp                  1.30.2               heedbac9_0    conda-forge
 heapdict                  1.0.1                      py_0    conda-forge
 hypothesis                5.28.0                     py_0    conda-forge
 icu                       67.1                 he1b5a44_0    conda-forge
 identify                  1.5.0              pyh9f0ad1d_0    conda-forge
 idna                      2.10               pyh9f0ad1d_0    conda-forge
 imagesize                 1.2.0                      py_0    conda-forge
 importlib-metadata        1.7.0            py37hc8dfbb8_0    conda-forge
 importlib_metadata        1.7.0                         0    conda-forge
 iniconfig                 1.0.1              pyh9f0ad1d_0    conda-forge
 ipykernel                 5.3.4            py37h43977f1_0    conda-forge
 ipython                   7.18.1           py37hc6149b9_0    conda-forge
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 isort                     5.0.7            py37hc8dfbb8_0    conda-forge
 jedi                      0.17.2           py37hc8dfbb8_0    conda-forge
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 krb5                      1.17.1               hfafb76e_3    conda-forge
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 ld_impl_linux-64          2.34                 hc38a660_9    conda-forge
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 libcblas                  3.8.0               17_openblas    conda-forge
 libcurl                   7.71.1               hcdd3856_5    conda-forge
 libedit                   3.1.20191231         he28a2e2_2    conda-forge
 libev                     4.33                 h516909a_1    conda-forge
 libevent                  2.1.10               hcdb4288_2    conda-forge
 libffi                    3.2.1             he1b5a44_1007    conda-forge
 libgcc-ng                 9.3.0               h24d8f2e_16    conda-forge
 libgfortran-ng            7.5.0               hdf63c60_16    conda-forge
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 libllvm10                 10.0.1               he513fc3_3    conda-forge
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 libopenblas               0.3.10          pthreads_hb3c22a3_4    conda-forge
 libpng                    1.6.37               hed695b0_2    conda-forge
 libprotobuf               3.12.4               h8b12597_0    conda-forge
 librmm                    0.16.0a200910   cuda11.0_g9d02c5b_365    rapidsai-nightly
 libsodium                 1.0.18               h516909a_0    conda-forge
 libssh2                   1.9.0                hab1572f_5    conda-forge
 libstdcxx-ng              9.3.0               hdf63c60_16    conda-forge
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 libutf8proc               2.5.0                h516909a_2    conda-forge
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 more-itertools            8.5.0                      py_0    conda-forge
 msgpack-python            1.0.0            py37h99015e2_1    conda-forge
 nbclient                  0.5.0                      py_0    conda-forge
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 pillow                    7.2.0            py37h718be6c_1    conda-forge
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 ptyprocess                0.6.0                   py_1001    conda-forge
 py                        1.9.0              pyh9f0ad1d_0    conda-forge
 pyarrow                   1.0.1           py37h1234567_1_cuda    conda-forge
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 python                    3.7.8           h6f2ec95_1_cpython    conda-forge
 python-dateutil           2.8.1                      py_0    conda-forge
 python_abi                3.7                     1_cp37m    conda-forge
 pytz                      2020.1             pyh9f0ad1d_0    conda-forge
 pyyaml                    5.3.1            py37h8f50634_0    conda-forge
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 rapidjson                 1.1.0             he1b5a44_1002    conda-forge
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 rmm                       0.16.0a200910   cuda_11.0_py37_g9d02c5b_365    rapidsai-nightly
 send2trash                1.5.0                      py_0    conda-forge
 setuptools                49.6.0           py37hc8dfbb8_0    conda-forge
 six                       1.15.0             pyh9f0ad1d_0    conda-forge
 snappy                    1.1.8                he1b5a44_3    conda-forge
 snowballstemmer           2.0.0                      py_0    conda-forge
 sortedcontainers          2.2.2              pyh9f0ad1d_0    conda-forge
 spdlog                    1.7.0                hc9558a2_2    conda-forge
 sphinx                    3.2.1                      py_0    conda-forge
 sphinx-copybutton         0.3.0              pyh9f0ad1d_0    conda-forge
 sphinx-markdown-tables    0.0.14             pyh9f0ad1d_1    conda-forge
 sphinx_rtd_theme          0.5.0              pyh9f0ad1d_0    conda-forge
 sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
 sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
 sphinxcontrib-htmlhelp    1.0.3                      py_0    conda-forge
 sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
 sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
 sphinxcontrib-serializinghtml 1.1.4                      py_0    conda-forge
 sphinxcontrib-websupport  1.2.4              pyh9f0ad1d_0    conda-forge
 sqlite                    3.33.0               h4cf870e_0    conda-forge
 streamz                   0.5.6                    pypi_0    pypi
 tblib                     1.6.0                      py_0    conda-forge
 terminado                 0.8.3            py37hc8dfbb8_1    conda-forge
 testpath                  0.4.4                      py_0    conda-forge
 thrift-cpp                0.13.0               h62aa4f2_3    conda-forge
 tk                        8.6.10               hed695b0_0    conda-forge
 toml                      0.10.1             pyh9f0ad1d_0    conda-forge
 toolz                     0.10.0                     py_0    conda-forge
 tornado                   6.0.4            py37h8f50634_1    conda-forge
 traitlets                 5.0.4                      py_0    conda-forge
 typed-ast                 1.4.1            py37h516909a_0    conda-forge
 typing_extensions         3.7.4.2                    py_0    conda-forge
 urllib3                   1.25.10                    py_0    conda-forge
 virtualenv                20.0.20          py37hc8dfbb8_1    conda-forge
 wcwidth                   0.2.5              pyh9f0ad1d_1    conda-forge
 webencodings              0.5.1                      py_1    conda-forge
 wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
 xz                        5.2.5                h516909a_1    conda-forge
 yaml                      0.2.5                h516909a_0    conda-forge
 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_1009    conda-forge
 zstd                      1.4.5                h6597ccf_2    conda-forge

Additional context
Surfaced while running fuzz tests #6001
@galipremsagar galipremsagar added bug Something isn't working Needs Triage Need team to review and classify cuIO cuIO issue labels Sep 14, 2020
@karthikeyann
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This PR #6076 adds this feature.

@galipremsagar galipremsagar linked a pull request Sep 14, 2020 that will close this issue
[REVIEW] duration csv writer, reader support #6076
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@galipremsagar
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Thanks @karthikeyann 👍

@galipremsagar galipremsagar added libcudf Affects libcudf (C++/CUDA) code. and removed Needs Triage Need team to review and classify labels Sep 14, 2020
@karthikeyann
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@galipremsagar pd.read_csv doesn't infer the timedelta type. It is read as string.

@galipremsagar galipremsagar changed the title [BUG] cudf.to_csv/cudf.from_csv fails when dataframe has a timedelta dtypes [BUG] cudf.to_csv fails when dataframe has a timedelta dtypes Sep 14, 2020
@galipremsagar
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I see, updated the description accordingly @karthikeyann

@karthikeyann karthikeyann mentioned this issue Sep 16, 2020
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@galipremsagar galipremsagar mentioned this issue Sep 18, 2020
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[REVIEW] duration csv writer, reader support karthikeyann/cudf
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@karthikeyann @galipremsagar