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[BUG] cuml PCA transform() requires n_rows > 1 #2804

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ngs2410 opened this issue Sep 9, 2020 · 2 comments · Fixed by #2829
Closed

[BUG] cuml PCA transform() requires n_rows > 1 #2804

ngs2410 opened this issue Sep 9, 2020 · 2 comments · Fixed by #2829
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@cjnolet
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bug Something isn't working

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@ngs2410
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ngs2410 commented Sep 9, 2020

Describe the bug
cuml PCA .transform() requires n_rows > 1 which is surprising as sklearn PCA doesn't have the same requirement.

I caught this trying to make predictions using a previously saved model that included a pipeline with a cuml PCA model. In my case, predictions are over a single example. My workaround will be to tile the example but it feels like this should not be necessary.

Traceback (most recent call last):
  File "test3.py", line 9, in <module>
    y = model.transform(predict)
  File "/home/ngs/miniconda3/envs/cuml14/lib/python3.7/site-packages/cuml/common/memory_utils.py", line 56, in cupy_rmm_wrapper
    return func(*args, **kwargs)
  File "cuml/decomposition/pca.pyx", line 716, in cuml.decomposition.pca.PCA.transform
RuntimeError: Exception occured! file=/opt/conda/envs/rapids/conda-bld/libcuml_1598033241212/work/cpp/src/pca/pca.cuh line=230: Parameter n_rows: number of rows cannot be less than two

Steps/Code to reproduce bug

This code throws the exception using cuml PCA but works fine using sklearn PCA:

import numpy as np
# from sklearn.decomposition import PCA
from cuml.decomposition import PCA

train = np.asfortranarray(np.random.randn(10,10))
predict = np.asfortranarray(np.random.randn(1,10))
model = PCA(n_components=4)
model.fit(train)
y = model.transform(predict)

Expected behavior
I expected cuml PCA transform() to be able to transform a single example.

Environment details:

Click here to see environment details
 **git***
 Not inside a git repository
 
 ***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 boots 5.4.0-42-generic #46-Ubuntu SMP Fri Jul 10 00:24:02 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
 
 ***GPU Information***
 Tue Sep  8 17:42:25 2020
 +-----------------------------------------------------------------------------+
 | NVIDIA-SMI 440.100      Driver Version: 440.100      CUDA Version: 10.2     |
 |-------------------------------+----------------------+----------------------+
 | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
 | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
 |===============================+======================+======================|
 |   0  GeForce GTX 166...  Off  | 00000000:01:00.0  On |                  N/A |
 |  0%   49C    P8    15W / 120W |   1275MiB /  5936MiB |      6%      Default |
 +-------------------------------+----------------------+----------------------+
 |   1  GeForce GTX 108...  Off  | 00000000:21:00.0 Off |                  N/A |
 |  0%   42C    P8    10W / 250W |     12MiB / 11178MiB |      0%      Default |
 +-------------------------------+----------------------+----------------------+
 
 +-----------------------------------------------------------------------------+
 | Processes:                                                       GPU Memory |
 |  GPU       PID   Type   Process name                             Usage      |
 |=============================================================================|
 |    0      2065      G   /usr/lib/xorg/Xorg                           198MiB |
 |    0      3002      G   /usr/lib/xorg/Xorg                           538MiB |
 |    0      3205      G   /usr/bin/gnome-shell                         296MiB |
 |    0      5636      G   ...quest-channel-token=7969671501842603176   228MiB |
 +-----------------------------------------------------------------------------+
 
 ***CPU***
 Architecture:                    x86_64
 CPU op-mode(s):                  32-bit, 64-bit
 Byte Order:                      Little Endian
 Address sizes:                   43 bits physical, 48 bits virtual
 CPU(s):                          128
 On-line CPU(s) list:             0-127
 Thread(s) per core:              2
 Core(s) per socket:              64
 Socket(s):                       1
 NUMA node(s):                    1
 Vendor ID:                       AuthenticAMD
 CPU family:                      23
 Model:                           49
 Model name:                      AMD Ryzen Threadripper 3990X 64-Core Processor
 Stepping:                        0
 Frequency boost:                 enabled
 CPU MHz:                         2208.591
 CPU max MHz:                     2900.0000
 CPU min MHz:                     2200.0000
 BogoMIPS:                        5800.23
 Virtualization:                  AMD-V
 L1d cache:                       2 MiB
 L1i cache:                       2 MiB
 L2 cache:                        32 MiB
 L3 cache:                        256 MiB
 NUMA node0 CPU(s):               0-127
 Vulnerability Itlb multihit:     Not affected
 Vulnerability L1tf:              Not affected
 Vulnerability Mds:               Not affected
 Vulnerability Meltdown:          Not affected
 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 AMD retpoline, IBPB conditional, STIBP conditional, RSB filling
 Vulnerability Srbds:             Not affected
 Vulnerability Tsx async abort:   Not affected
 Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 hw_pstate sme ssbd mba sev ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr wbnoinvd arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif umip rdpid overflow_recov succor smca
 
 ***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/bin/nvcc
 nvcc: NVIDIA (R) Cuda compiler driver
 Copyright (c) 2005-2019 NVIDIA Corporation
 Built on Sun_Jul_28_19:07:16_PDT_2019
 Cuda compilation tools, release 10.1, V10.1.243
 
 ***Python***
 /home/ngs/miniconda3/envs/cuml14/bin/python
 Python 3.7.7
 
 ***Environment Variables***
 PATH                            : /home/ngs/miniconda3/envs/cuml14/bin:/home/ngs/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
 LD_LIBRARY_PATH                 :
 NUMBAPRO_NVVM                   :
 NUMBAPRO_LIBDEVICE              :
 CONDA_PREFIX                    : /home/ngs/miniconda3/envs/cuml14
 PYTHON_PATH                     :
 
 ***conda packages***
 /home/ngs/miniconda3/condabin/conda
 # packages in environment at /home/ngs/miniconda3/envs/cuml14:
 #
 # 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
 absl-py                   0.10.0                   pypi_0    pypi
 arrow-cpp                 0.17.1          py37h1234567_11_cuda    conda-forge
 arrow-cpp-proc            1.0.0                      cuda    conda-forge
 astroid                   2.4.2            py37hc8dfbb8_0    conda-forge
 astunparse                1.6.3                    pypi_0    pypi
 aws-sdk-cpp               1.7.164              hba45d7a_2    conda-forge
 bokeh                     2.1.1            py37hc8dfbb8_0    conda-forge
 boost-cpp                 1.72.0               h7b93d67_2    conda-forge
 boto3                     1.14.47            pyh9f0ad1d_0    conda-forge
 botocore                  1.17.47            pyh9f0ad1d_0    conda-forge
 brotli                    1.0.7             he1b5a44_1004    conda-forge
 brotlipy                  0.7.0           py37h8f50634_1000    conda-forge
 bzip2                     1.0.8                h516909a_3    conda-forge
 c-ares                    1.16.1               h516909a_1    conda-forge
 ca-certificates           2020.6.20            hecda079_0    conda-forge
 cachetools                4.1.1                    pypi_0    pypi
 certifi                   2020.6.20        py37hc8dfbb8_0    conda-forge
 cffi                      1.14.1           py37he30daa8_0
 chardet                   3.0.4                    pypi_0    pypi
 click                     7.1.2              pyh9f0ad1d_0    conda-forge
 cloudpickle               1.5.0                      py_0    conda-forge
 cryptography              3.0              py37hb09aad4_0    conda-forge
 cudatoolkit               10.1.243             h6bb024c_0    nvidia
 cudf                      0.15.0a200821   cuda_10.1_py37_g1a3b3f217_4960    rapidsai-nightly
 cudnn                     7.6.0                cuda10.1_0    nvidia
 cuml                      0.15.0a200821   cuda10.1_py37_g5b13b4a61_2142    rapidsai-nightly
 cupy                      7.8.0            py37h0632833_0    conda-forge
 curl                      7.71.1               he644dc0_5    conda-forge
 cycler                    0.10.0                     py_2    conda-forge
 cytoolz                   0.10.1           py37h516909a_0    conda-forge
 dask                      2.23.0                     py_0    conda-forge
 dask-core                 2.23.0                     py_0    conda-forge
 dask-cudf                 0.15.0a200821   py37_g1a3b3f217_4960    rapidsai-nightly
 distributed               2.23.0           py37hc8dfbb8_0    conda-forge
 dlpack                    0.3                  he1b5a44_1    conda-forge
 dnspython                 1.16.0                     py_1    conda-forge
 docutils                  0.15.2                   py37_0    conda-forge
 double-conversion         3.1.5                he1b5a44_2    conda-forge
 ecdsa                     0.13                       py_0    conda-forge
 faiss-proc                1.0.0                      cuda    rapidsai-nightly
 fastavro                  0.24.2           py37h8f50634_0    conda-forge
 fastrlock                 0.5              py37h3340039_0    conda-forge
 filelock                  3.0.12                   pypi_0    pypi
 flock                     0.1                      pypi_0    pypi
 freetype                  2.10.2               he06d7ca_0    conda-forge
 fsspec                    0.8.0                      py_0    conda-forge
 gast                      0.3.3                    pypi_0    pypi
 gflags                    2.2.2             he1b5a44_1004    conda-forge
 glog                      0.4.0                h49b9bf7_3    conda-forge
 gmp                       6.2.0                he1b5a44_2    conda-forge
 google-auth               1.20.1                   pypi_0    pypi
 google-auth-oauthlib      0.4.1                    pypi_0    pypi
 google-pasta              0.2.0                    pypi_0    pypi
 grpc-cpp                  1.30.2               heedbac9_0    conda-forge
 grpcio                    1.31.0                   pypi_0    pypi
 h5py                      2.10.0                   pypi_0    pypi
 heapdict                  1.0.1                      py_0    conda-forge
 icu                       67.1                 he1b5a44_0    conda-forge
 idna                      2.10               pyh9f0ad1d_0    conda-forge
 iexfinance                0.4.3                    pypi_0    pypi
 importlib-metadata        1.7.0                    pypi_0    pypi
 isort                     4.3.21           py37hc8dfbb8_1    conda-forge
 jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
 jmespath                  0.10.0             pyh9f0ad1d_0    conda-forge
 joblib                    0.16.0                     py_0    conda-forge
 jpeg                      9d                   h516909a_0    conda-forge
 keras-preprocessing       1.1.2                    pypi_0    pypi
 kiwisolver                1.2.0            py37h99015e2_0    conda-forge
 krb5                      1.17.1               hfafb76e_2    conda-forge
 langdetect                1.0.7                      py_0    conda-forge
 lazy-object-proxy         1.4.3            py37h8f50634_2    conda-forge
 lcms2                     2.11                 hbd6801e_0    conda-forge
 ld_impl_linux-64          2.33.1               h53a641e_7
 libblas                   3.8.0               17_openblas    conda-forge
 libcblas                  3.8.0               17_openblas    conda-forge
 libcudf                   0.15.0a200821   cuda10.1_g1a3b3f217_4960    rapidsai-nightly
 libcuml                   0.15.0a200821   cuda10.1_g5b13b4a61_2142    rapidsai-nightly
 libcumlprims              0.15.0a200820       cuda10.1_61    rapidsai-nightly
 libcurl                   7.71.1               hcdd3856_5    conda-forge
 libedit                   3.1.20191231         h14c3975_1
 libev                     4.33                 h516909a_0    conda-forge
 libevent                  2.1.10               hcdb4288_2    conda-forge
 libfaiss                  1.6.3           he68dc02_1_cuda    conda-forge
 libffi                    3.3                  he6710b0_2
 libgcc-ng                 9.3.0               h24d8f2e_15    conda-forge
 libgfortran-ng            7.5.0               hdf63c60_15    conda-forge
 libgomp                   9.3.0               h24d8f2e_15    conda-forge
 libhwloc                  2.1.0                h3c4fd83_0    conda-forge
 libiconv                  1.16                 h516909a_0    conda-forge
 liblapack                 3.8.0               17_openblas    conda-forge
 libllvm10                 10.0.1               he513fc3_1    conda-forge
 libnghttp2                1.41.0               hab1572f_1    conda-forge
 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                    0.15.0a200821   cuda10.1_g178c2cd_723    rapidsai-nightly
 libssh2                   1.9.0                hab1572f_5    conda-forge
 libstdcxx-ng              9.1.0                hdf63c60_0
 libtiff                   4.1.0                hc7e4089_6    conda-forge
 libwebp-base              1.1.0                h516909a_3    conda-forge
 libxml2                   2.9.10               h68273f3_2    conda-forge
 llvmlite                  0.34.0           py37h5202443_0    conda-forge
 locket                    0.2.0                      py_2    conda-forge
 lz4-c                     1.9.2                he1b5a44_3    conda-forge
 markdown                  3.2.2                    pypi_0    pypi
 markupsafe                1.1.1            py37h8f50634_1    conda-forge
 matplotlib                3.3.1                         1    conda-forge
 matplotlib-base           3.3.1            py37hd478181_1    conda-forge
 mccabe                    0.6.1                      py_1    conda-forge
 msgpack-python            1.0.0            py37h99015e2_1    conda-forge
 mysql-common              8.0.21                        0    conda-forge
 mysql-connector-c         6.1.11            h876a3cc_1006    conda-forge
 mysql-connector-python    8.0.21           py37h023e13c_0    conda-forge
 mysql-libs                8.0.21               hf3661c5_0    conda-forge
 nccl                      2.7.8.1              h51cf6c1_0    conda-forge
 ncurses                   6.2                  he6710b0_1
 numba                     0.51.0           py37h9fdb41a_0    conda-forge
 numpy                     1.19.1           py37h7ea13bd_2    conda-forge
 oauthlib                  3.1.0                    pypi_0    pypi
 olefile                   0.46                       py_0    conda-forge
 openssl                   1.1.1g               h516909a_1    conda-forge
 opt-einsum                3.3.0                    pypi_0    pypi
 packaging                 20.4               pyh9f0ad1d_0    conda-forge
 pandas                    1.1.0            py37h3340039_0    conda-forge
 parquet-cpp               1.5.1                         2    conda-forge
 partd                     1.1.0                      py_0    conda-forge
 pillow                    7.2.0            py37h718be6c_1    conda-forge
 pip                       20.2.2                   py37_0
 protobuf                  3.12.4           py37h3340039_0    conda-forge
 psutil                    5.7.2            py37h8f50634_0    conda-forge
 pyaml                     20.4.0             pyh9f0ad1d_0    conda-forge
 pyarrow                   0.17.1          py37h1234567_11_cuda    conda-forge
 pyasn1                    0.4.8                    pypi_0    pypi
 pyasn1-modules            0.2.8                    pypi_0    pypi
 pycparser                 2.20               pyh9f0ad1d_2    conda-forge
 pycryptodome              3.9.7            py37hb05bdb2_1    conda-forge
 pylint                    2.5.3            py37hc8dfbb8_0    conda-forge
 pyopenssl                 19.1.0                     py_1    conda-forge
 pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
 pysocks                   1.7.1            py37hc8dfbb8_1    conda-forge
 python                    3.7.7                hcff3b4d_5
 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
 re2                       2020.07.06           he1b5a44_1    conda-forge
 readline                  8.0                  h7b6447c_0
 regex                     2020.7.14                pypi_0    pypi
 requests                  2.24.0                   pypi_0    pypi
 requests-oauthlib         1.3.0                    pypi_0    pypi
 rmm                       0.15.0a200821   cuda_10.1_py37_g178c2cd_723    rapidsai-nightly
 rsa                       4.6                      pypi_0    pypi
 s3transfer                0.3.3            py37hc8dfbb8_1    conda-forge
 sacremoses                0.0.43                   pypi_0    pypi
 scikit-learn              0.23.2           py37h6785257_0    conda-forge
 scikit-optimize           0.7.4                      py_0    conda-forge
 scipy                     1.4.1                    pypi_0    pypi
 sentencepiece             0.1.91                   pypi_0    pypi
 setuptools                49.6.0                   py37_0
 six                       1.15.0             pyh9f0ad1d_0    conda-forge
 snakeviz                  2.1.0              pyh9f0ad1d_0    conda-forge
 snappy                    1.1.8                he1b5a44_3    conda-forge
 sortedcontainers          2.2.2              pyh9f0ad1d_0    conda-forge
 spdlog                    1.7.0                hc9558a2_2    conda-forge
 sqlite                    3.33.0               h62c20be_0
 ta                        0.5.25                   pypi_0    pypi
 tblib                     1.6.0                      py_0    conda-forge
 tensorboard               2.3.0                    pypi_0    pypi
 tensorboard-plugin-wit    1.7.0                    pypi_0    pypi
 tensorflow                2.3.0                    pypi_0    pypi
 tensorflow-estimator      2.3.0                    pypi_0    pypi
 tensorflow-hub            0.9.0                    pypi_0    pypi
 tensorflow-text           2.3.0                    pypi_0    pypi
 termcolor                 1.1.0                    pypi_0    pypi
 threadpoolctl             2.1.0              pyh5ca1d4c_0    conda-forge
 thrift-cpp                0.13.0               h62aa4f2_3    conda-forge
 tk                        8.6.10               hbc83047_0
 tokenizers                0.8.1rc1                 pypi_0    pypi
 toml                      0.10.1             pyh9f0ad1d_0    conda-forge
 toolz                     0.10.0                     py_0    conda-forge
 tornado                   6.0.4            py37h8f50634_1    conda-forge
 tqdm                      4.48.2                   pypi_0    pypi
 transformers              3.0.2                    pypi_0    pypi
 treelite                  0.92             py37h023e13c_2    conda-forge
 treelite-runtime          0.92                     pypi_0    pypi
 typed-ast                 1.4.1            py37h516909a_0    conda-forge
 typing_extensions         3.7.4.2                    py_0    conda-forge
 ucx                       1.8.1+g6b29558       ha5db111_0    rapidsai-nightly
 ucx-py                    0.15.0a200820+g6b29558        py37_212    rapidsai-nightly
 uriparser                 0.9.3                he1b5a44_1    conda-forge
 urllib3                   1.25.10                    py_0    conda-forge
 werkzeug                  1.0.1                    pypi_0    pypi
 wheel                     0.34.2                   py37_0
 wrapt                     1.11.2           py37h8f50634_0    conda-forge
 xgboost                   1.1.1                    pypi_0    pypi
 xz                        5.2.5                h7b6447c_0
 yaml                      0.2.5                h516909a_0    conda-forge
 zict                      2.0.0                      py_0    conda-forge
 zipp                      3.1.0                    pypi_0    pypi
 zlib                      1.2.11               h7b6447c_3
 zstd                      1.4.5                h6597ccf_2    conda-forge

@ngs2410 ngs2410 added ? - Needs Triage Need team to review and classify bug Something isn't working labels Sep 9, 2020
@cjnolet cjnolet self-assigned this Sep 10, 2020
@wphicks
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wphicks commented Sep 15, 2020

Failing assertion that leads to the exception is here.

@wphicks wphicks removed the ? - Needs Triage Need team to review and classify label Sep 15, 2020
@wphicks
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wphicks commented Sep 15, 2020

Whoops, submitted that comment before I was done. Adding on... I don't immediately see why this assertion would be necessary except if the whiten option is true. In the case of n_rows == 1, whitening obviously does not make sense, so we can probably add some special handling there.

This was referenced Sep 16, 2020
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[REVIEW] Small fixes for mid-release bug squash cjnolet/cuml
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@cjnolet @ngs2410 @wphicks