How to implement a GPU neighbor sampling kernel properly in pyg-lib #298

Gibyeng · 2024-02-07T03:28:29Z

Gibyeng
Feb 7, 2024

I am writing a GPU-based neighbor sampling kernel, but I got a problem.
This is what I have done.

Create file "neighbor_kenel.cu" in "csrc/sampler/cuda"
In the "neighbor_kernel.cu", I defined namespace "pyg" and "sampler" and "neighbor_sample_kernel" function, just like the one in "random_walk_kernel.cu".
Register the kernel as follows

TORCH_LIBRARY_IMPL(pyg, CUDA, m) {
  m.impl(TORCH_SELECTIVE_NAME("pyg::neighbor_sample"),
         TORCH_FN(neighbor_sample_kernel));
}

In the python side, I am trying to call the "neighbor_sample_kernel" in this way.

device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
d_rowptr = rowptr.to(device)
d_col = col.to(device)
d_seed = seed.to(device)
for seed in tqdm(node_perm.split(batch_size)):
    pyg_lib.sampler.neighbor_sample(
        d_rowptr,
        d_col,
        d_seed,
        num_neighbors,
        node_time=node_time,
        edge_time=None,
        seed_time=None,
        edge_weight=edge_weight,
        replace=args.replace,
        directed=args.directed,
        disjoint=args.disjoint,
        temporal_strategy=args.temporal_strategy,
        return_edge_id=True,
    )

Then I got this error

NotImplementedError: Could not run 'pyg::neighbor_sample' with arguments from the 'CUDA' backend. This could be because the operator doesn't exist for this backend, or was omitted during the selective/custom build process (if using custom build).

Thank you in advance.

rusty1s · 2024-02-07T12:49:59Z

rusty1s
Feb 7, 2024
Maintainer

This looks correct. Can you confirm that your kernel gets actually compiled during building?

6 replies

rusty1s Feb 8, 2024
Maintainer

Can you show me the installation log of it? I also think you need to run via python setup.py install.

Gibyeng Feb 8, 2024
Author

this is the log after I run python ./setup.py build

running build
running build_py
running build_ext
-- Caffe2: CUDA detected: 11.8
-- Caffe2: CUDA nvcc is: /usr/local/cuda/bin/nvcc
-- Caffe2: CUDA toolkit directory: /usr/local/cuda
-- Caffe2: Header version is: 11.8
-- /usr/local/cuda/lib64/libnvrtc.so shorthash is 672ee683
-- USE_CUDNN is set to 0. Compiling without cuDNN support
-- USE_CUSPARSELT is set to 0. Compiling without cuSPARSELt support
-- Autodetected CUDA architecture(s):  7.5 7.5
-- Added CUDA NVCC flags for: -gencode;arch=compute_75,code=sm_75
CMake Warning at /home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:22 (message):
  static library kineto_LIBRARY-NOTFOUND not found.
Call Stack (most recent call first):
  /home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:127 (append_torchlib_if_found)
  CMakeLists.txt:79 (find_package)


-- CMAKE_BUILD_TYPE: RELEASE
-- CMAKE_CXX_FLAGS_DEBUG: -g -O0
-- CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG
-- Configuring done (5.5s)
CMake Warning (dev) in CMakeLists.txt:
  Policy CMP0104 is not set: CMAKE_CUDA_ARCHITECTURES now detected for NVCC,
  empty CUDA_ARCHITECTURES not allowed.  Run "cmake --help-policy CMP0104"
  for policy details.  Use the cmake_policy command to set the policy and
  suppress this warning.

  CUDA_ARCHITECTURES is empty for target "pyg".
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning at CMakeLists.txt:55 (add_library):
  Cannot generate a safe runtime search path for target pyg because files in
  some directories may conflict with libraries in implicit directories:

    runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/7 may be hidden by files in:
      /home/xxx/anaconda3/envs/pyG-env/lib

  Some of these libraries may not be found correctly.


-- Generating done (0.2s)
-- Build files have been written to: /home/xxx/Documents/pyg-lib/build/temp.linux-x86_64-cpython-311
[1/2] Building CUDA object CMakeFiles/...csrc/sampler/cuda/neighbor_kernel.cu.o
/home/xxx/Documents/pyg-lib/pyg_lib/csrc/sampler/cuda/neighbor_kernel.cu(16): warning #177-D: function "pyg::sampler::<unnamed>::blocks" was declared but never referenced

[2/2] Linking CXX shared library /home...lib.linux-x86_64-cpython-311/libpyg.so

Gibyeng Feb 8, 2024
Author

And this is the log, after I run python setup.py install.

running install
/home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
/home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  self.initialize_options()
running bdist_egg
running egg_info
writing pyg_lib.egg-info/PKG-INFO
writing dependency_links to pyg_lib.egg-info/dependency_links.txt
writing requirements to pyg_lib.egg-info/requires.txt
writing top-level names to pyg_lib.egg-info/top_level.txt
reading manifest file 'pyg_lib.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*' found under directory 'docs'
warning: no previously-included files matching '*' found under directory 'benchmark'
adding license file 'LICENSE'
adding license file 'LICENSE_radix_sort'
writing manifest file 'pyg_lib.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
-- Caffe2: CUDA detected: 11.8
-- Caffe2: CUDA nvcc is: /usr/local/cuda/bin/nvcc
-- Caffe2: CUDA toolkit directory: /usr/local/cuda
-- Caffe2: Header version is: 11.8
-- /usr/local/cuda/lib64/libnvrtc.so shorthash is 672ee683
-- USE_CUDNN is set to 0. Compiling without cuDNN support
-- USE_CUSPARSELT is set to 0. Compiling without cuSPARSELt support
-- Autodetected CUDA architecture(s):  7.5 7.5
-- Added CUDA NVCC flags for: -gencode;arch=compute_75,code=sm_75
CMake Warning at /home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:22 (message):
  static library kineto_LIBRARY-NOTFOUND not found.
Call Stack (most recent call first):
  /home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:127 (append_torchlib_if_found)
  CMakeLists.txt:79 (find_package)


-- CMAKE_BUILD_TYPE: RELEASE
-- CMAKE_CXX_FLAGS_DEBUG: -g -O0
-- CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG
-- Configuring done (1.6s)
CMake Warning (dev) in CMakeLists.txt:
  Policy CMP0104 is not set: CMAKE_CUDA_ARCHITECTURES now detected for NVCC,
  empty CUDA_ARCHITECTURES not allowed.  Run "cmake --help-policy CMP0104"
  for policy details.  Use the cmake_policy command to set the policy and
  suppress this warning.

  CUDA_ARCHITECTURES is empty for target "pyg".
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning at CMakeLists.txt:55 (add_library):
  Cannot generate a safe runtime search path for target pyg because files in
  some directories may conflict with libraries in implicit directories:

    runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/7 may be hidden by files in:
      /home/xxx/anaconda3/envs/pyG-env/lib

  Some of these libraries may not be found correctly.


-- Generating done (0.0s)
-- Build files have been written to: /home/xxx/Documents/pyg-lib/build/temp.linux-x86_64-cpython-311
ninja: no work to do.
creating build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-cpython-311/libpyg.so -> build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/pyg_lib
copying build/lib.linux-x86_64-cpython-311/pyg_lib/_triton.py -> build/bdist.linux-x86_64/egg/pyg_lib
creating build/bdist.linux-x86_64/egg/pyg_lib/partition
copying build/lib.linux-x86_64-cpython-311/pyg_lib/partition/__init__.py -> build/bdist.linux-x86_64/egg/pyg_lib/partition
creating build/bdist.linux-x86_64/egg/pyg_lib/ops
copying build/lib.linux-x86_64-cpython-311/pyg_lib/ops/__init__.py -> build/bdist.linux-x86_64/egg/pyg_lib/ops
copying build/lib.linux-x86_64-cpython-311/pyg_lib/ops/scatter_reduce.py -> build/bdist.linux-x86_64/egg/pyg_lib/ops
copying build/lib.linux-x86_64-cpython-311/pyg_lib/__init__.py -> build/bdist.linux-x86_64/egg/pyg_lib
copying build/lib.linux-x86_64-cpython-311/pyg_lib/home.py -> build/bdist.linux-x86_64/egg/pyg_lib
creating build/bdist.linux-x86_64/egg/pyg_lib/sampler
copying build/lib.linux-x86_64-cpython-311/pyg_lib/sampler/__init__.py -> build/bdist.linux-x86_64/egg/pyg_lib/sampler
copying build/lib.linux-x86_64-cpython-311/pyg_lib/testing.py -> build/bdist.linux-x86_64/egg/pyg_lib
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/_triton.py to _triton.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/partition/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/ops/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/ops/scatter_reduce.py to scatter_reduce.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/home.py to home.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/sampler/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyg_lib/testing.py to testing.cpython-311.pyc
creating stub loader for libpyg.so
byte-compiling build/bdist.linux-x86_64/egg/libpyg.py to libpyg.cpython-311.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying pyg_lib.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyg_lib.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyg_lib.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyg_lib.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyg_lib.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
__pycache__.libpyg.cpython-311: module references __file__
pyg_lib.__pycache__.__init__.cpython-311: module references __file__
creating 'dist/pyg_lib-0.3.1-py3.11-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing pyg_lib-0.3.1-py3.11-linux-x86_64.egg
removing '/home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/pyg_lib-0.3.1-py3.11-linux-x86_64.egg' (and everything under it)
creating /home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/pyg_lib-0.3.1-py3.11-linux-x86_64.egg
Extracting pyg_lib-0.3.1-py3.11-linux-x86_64.egg to /home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages
Adding pyg-lib 0.3.1 to easy-install.pth file

Installed /home/xxx/anaconda3/envs/pyG-env/lib/python3.11/site-packages/pyg_lib-0.3.1-py3.11-linux-x86_64.egg
Processing dependencies for pyg-lib==0.3.1
Finished processing dependencies for pyg-lib==0.3.1

Gibyeng Feb 8, 2024
Author

It seems the kernel is called as expected after I run python setup.py install. I think the problem has been solved. thank you for your help.

rusty1s Feb 8, 2024
Maintainer

Super :)

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How to implement a GPU neighbor sampling kernel properly in pyg-lib #298

Gibyeng Feb 7, 2024

Replies: 1 comment · 6 replies

rusty1s Feb 7, 2024 Maintainer

rusty1s Feb 8, 2024 Maintainer

Gibyeng Feb 8, 2024 Author

Gibyeng Feb 8, 2024 Author

Gibyeng Feb 8, 2024 Author

rusty1s Feb 8, 2024 Maintainer

Gibyeng
Feb 7, 2024

Replies: 1 comment 6 replies

rusty1s
Feb 7, 2024
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rusty1s Feb 8, 2024
Maintainer

Gibyeng Feb 8, 2024
Author

Gibyeng Feb 8, 2024
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Gibyeng Feb 8, 2024
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rusty1s Feb 8, 2024
Maintainer