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High-performance Spiking Neural Networks Library Written From Scratch with C++ and Python Interfaces.

License: Other

C++ 72.92% CMake 1.87% Python 6.24% Cuda 13.04% C 0.56% Jupyter Notebook 5.38%

cxx python snn stdp cuda high-performance r-stdp computational-neuroscience cudnn neuroscience

spyker's People

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kdr121 rachmadvwp stephentaylor1998

spyker's Issues

Request for files

Hello.

Is it possible to include the Spyker implementation of the model of Mozafari et al. you mentioned in your paper ?

Thank you.

Preprocessing padding

Parameter to choose the padding method in preprocessing methods (e.g. DoG, LoG, ..).

For real images, it creates high activation on the edges.

Compile error with CUDA

Hi.

I am trying to build the Python interface using CUDA.

Unfortunately, I obtain this error message :

  -- Looking for a CUDA compiler
  -- Looking for a CUDA compiler - /home/ggoupy/anaconda3/bin/nvcc
  -- The CUDA compiler identification is NVIDIA 12.0.140
  -- Check for working CUDA compiler: /home/ggoupy/anaconda3/bin/nvcc
  -- Check for working CUDA compiler: /home/ggoupy/anaconda3/bin/nvcc -- works
  -- Detecting CUDA compiler ABI info
  -- Detecting CUDA compiler ABI info - done
  CMake Error at CMakeLists.txt:103 (find_package):
    By not providing "FindCUDAToolkit.cmake" in CMAKE_MODULE_PATH this project
    has asked CMake to find a package configuration file provided by
    "CUDAToolkit", but CMake did not find one.

    Could not find a package configuration file provided by "CUDAToolkit" with
    any of the following names:

      CUDAToolkitConfig.cmake
      cudatoolkit-config.cmake

    Add the installation prefix of "CUDAToolkit" to CMAKE_PREFIX_PATH or set
    "CUDAToolkit_DIR" to a directory containing one of the above files.  If
    "CUDAToolkit" provides a separate development package or SDK, be sure it
    has been installed.

I tried to install CUDA from the ubuntu package manager, but also from runfile and with conda. Always the same error.

I am not used to C++ compilation and this is the first time I install CUDA so I may have done something wrong (even if I followed the Nvidia instructions).

Unable to compile

Hello.

I am trying to build the Python interface but I run across a compilation error :

  Scanning dependencies of target spyker
  [ 92%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/backprop.cpp.o
  [ 92%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/canny.cpp.o
  [ 93%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/fire.cpp.o
  [ 93%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/code.cpp.o
  [ 93%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/conv.cpp.o
  [ 93%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/dog.cpp.o
  [ 93%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/fc.cpp.o
  [ 93%] Building CXX object CMakeFiles/spyker.dir/src/spyker/cpu/inhibit.cpp.o
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/fc.cpp: In constructor ‘Spyker::Core::CPU::FC::FC(Spyker::Len3, Spyker::Len2, Spyker::Len3, Spyker::Type)’:
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/fc.cpp:36:23: error: ‘desc’ is not a member of ‘dnnl::matmul’
     36 |         dnnl::matmul::desc desc(input, kernel, output);
        |                       ^~~~
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/fc.cpp:37:43: error: ‘desc’ was not declared in this scope
     37 |         dnnl::matmul::primitive_desc prim(desc, onednn_static->engine);
        |                                           ^~~~
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp: In constructor ‘Spyker::Core::CPU::Conv::Conv(Spyker::Len4, Spyker::Len4, Spyker::Len4, Spyker::Len2, Spyker::Len4, Spyker::Type)’:
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:38:36: error: ‘desc’ is not a member of ‘dnnl::convolution_forward’
     38 |         dnnl::convolution_forward::desc desc(dnnl::prop_kind::forward_inference,                 //
        |                                    ^~~~
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:40:63: error: expected primary-expression before ‘,’ token
     40 |                                              input, kernel, {}, output, {_stride.y, _stride.x},  //
        |                                                               ^
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:40:73: error: expected primary-expression before ‘{’ token
     40 |                                              input, kernel, {}, output, {_stride.y, _stride.x},  //
        |                                                                         ^
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:40:95: error: expected primary-expression before ‘,’ token
     40 |                                              input, kernel, {}, output, {_stride.y, _stride.x},  //
        |                                                                                               ^
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:41:46: error: expected primary-expression before ‘{’ token
     41 |                                              {_pad.t, _pad.z}, {_pad.y, _pad.x});
        |                                              ^
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:41:62: error: expected primary-expression before ‘,’ token
     41 |                                              {_pad.t, _pad.z}, {_pad.y, _pad.x});
        |                                                              ^
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:41:64: error: expected primary-expression before ‘{’ token
     41 |                                              {_pad.t, _pad.z}, {_pad.y, _pad.x});
        |                                                                ^
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:41:80: error: expected primary-expression before ‘)’ token
     41 |                                              {_pad.t, _pad.z}, {_pad.y, _pad.x});
        |                                                                                ^
  /tmp/pip-req-build-lhj6rq17/src/spyker/cpu/conv.cpp:42:56: error: ‘desc’ was not declared in this scope
     42 |         dnnl::convolution_forward::primitive_desc prim(desc, onednn_static->engine);
        |                                                        ^~~~
  make[2]: *** [CMakeFiles/spyker.dir/build.make:128: CMakeFiles/spyker.dir/src/spyker/cpu/fc.cpp.o] Error 1
  make[2]: *** Waiting for unfinished jobs....
  make[2]: *** [CMakeFiles/spyker.dir/build.make:102: CMakeFiles/spyker.dir/src/spyker/cpu/conv.cpp.o] Error 1
  make[1]: *** [CMakeFiles/Makefile2:289: CMakeFiles/spyker.dir/all] Error 2
  make: *** [Makefile:130: all] Error 2
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-req-build-lhj6rq17/setup.py", line 99, in <module>
      setup(
    File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 144, in setup
      return distutils.core.setup(**attrs)
    File "/usr/lib/python3.8/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/usr/lib/python3.8/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 223, in run
      self.run_command('build')
    File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/usr/lib/python3.8/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/tmp/pip-req-build-lhj6rq17/setup.py", line 39, in run
      self.build_extension(ext)
    File "/tmp/pip-req-build-lhj6rq17/setup.py", line 96, in build_extension
      subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)
    File "/usr/lib/python3.8/subprocess.py", line 364, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--', '-j8']' returned non-zero exit status 2.
error
  ERROR: Failed building wheel for spyker
  Running setup.py clean for spyker
  Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-lhj6rq17/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-lhj6rq17/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
  running clean
  removing 'build/temp.linux-x86_64-3.8' (and everything under it)
  removing 'build/lib.linux-x86_64-3.8' (and everything under it)
  'build/bdist.linux-x86_64' does not exist -- can't clean it
  'build/scripts-3.8' does not exist -- can't clean it
  removing 'build'
Failed to build spyker
Cleaning up...
  Removing source in /tmp/pip-req-build-lhj6rq17
Removed build tracker: '/tmp/pip-req-tracker-5vwbnst5'
ERROR: Failed to build one or more wheels
Exception information:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 186, in _main
    status = self.run(options, args)
  File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 188, in run
    raise CommandError(
pip._internal.exceptions.CommandError: Failed to build one or more wheels

Here is the config :

['cmake', '/tmp/pip-req-build-lhj6rq17', '-DENABLE_PYTHON=ON', '-DENABLE_TESTS=OFF', '-DENABLE_EXAMPLES=OFF', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-req-build-lhj6rq17/build/lib.linux-x86_64-3.8/spyker/', '-DPYTHON_EXECUTABLE=/usr/bin/python3', '-DCMAKE_BUILD_TYPE=Release']
  -- The CXX compiler identification is GNU 9.4.0
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Looking for sgemm_
  -- Looking for sgemm_ - not found
  -- Looking for C++ include pthread.h
  -- Looking for C++ include pthread.h - found
  -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
  -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
  -- Looking for pthread_create in pthreads
  -- Looking for pthread_create in pthreads - not found
  -- Looking for pthread_create in pthread
  -- Looking for pthread_create in pthread - found
  -- Found Threads: TRUE
  -- Looking for sgemm_
  -- Looking for sgemm_ - found
  -- Found BLAS: /usr/lib/x86_64-linux-gnu/libopenblas.so
  -- Looking for cblas_saxpy
  -- Looking for cblas_saxpy - found
  -- Found CBLAS: /usr/lib/x86_64-linux-gnu/libopenblas.so
  -- Looking for cheev_
  -- Looking for cheev_ - found
  -- A library with LAPACK API found.
  -- Looking for LAPACKE_dgels
  -- Looking for LAPACKE_dgels - not found
  -- Found LAPACKE: /usr/lib/x86_64-linux-gnu/liblapacke.so
  CMake Warning (dev) at CMakeLists.txt:83 (set):
    implicitly converting 'LIST' to 'STRING' type.
  This warning is for project developers.  Use -Wno-dev to suppress it.

  -- The C compiler identification is GNU 9.4.0
  -- Check for working C compiler: /usr/bin/cc
  -- Check for working C compiler: /usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- DNNL_TARGET_ARCH: X64
  -- DNNL_LIBRARY_NAME: dnnl
  -- Found OpenMP_C: -fopenmp (found version "4.5")
  -- Found OpenMP_CXX: -fopenmp (found version "4.5")
  -- Found OpenMP: TRUE (found version "4.5")
  -- Could NOT find Doxyrest (missing: DOXYREST_EXECUTABLE)
  -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.8.10", minimum required is "2.7")
  -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE)
  -- Found Git: /usr/bin/git (found version "2.25.1")
  -- Enabled workload: INFERENCE
  -- Enabled primitives: CONVOLUTION;MATMUL
  -- Enabled primitive CPU ISA: ALL
  -- Enabled primitive GPU ISA: ALL
  -- Primitive cache is enabled
  -- The ASM compiler identification is GNU
  -- Found assembler: /usr/bin/cc
  -- Looking for a CUDA compiler
  -- Looking for a CUDA compiler - NOTFOUND
  -- Found OpenMP_CXX: -fopenmp
  -- Found OpenMP: TRUE
  -- pybind11 v2.11.0 dev1
  -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.8.10", minimum required is "3.6")
  -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  --
  -- Summary:
  -- Optimization Flags: ------------ -march=native
  -- CUDA Archutecutre List: --------
  -- Python Interface: -------------- ON
  -- CUDA: -------------------------- OFF
  -- CUDNN: ------------------------- OFF
  -- DNNL: -------------------------- ON
  -- BLAS: -------------------------- ON
  --
  -- Configuring done

Do you know what the cause of the issue could be ?

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