The generalised_shapelets from patrick-kidger

generalised_shapelets's Introduction

JAX scientific ML ecosystem:

Probably the reason you're here. I would highlight:

Equinox: elegant neural networks.
Diffrax: numerical ODE/SDE solvers.
jaxtyping: shape/dtype annotations for arrays.
Lineax: linear/least-squares solvers. (new!)
Optimistix: root finding, least squares, etc. (new!)

Other links:

Twitter:
Google scholar: here
Personal website: kidger.site
Neural ODE/SDE textbook: arXiv/2202.02435

Me:

I currently wear multiple hats across bio/ML/CS at Cradle.bio. These days I am generally interested in scientific ML, and specifically the application of ML to unsolved problems in biology!

I also hold an honorary lectureship at Imperial College London. In past lives I previously wore the same multitude of hats at Google X, and did my PhD at the University of Oxford.

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generalised_shapelets's Issues

Compilation Problem with Pip Install

I am unable to correctly install the package using the provided command because the build is failing:

pip install "git+https://github.com/patrick-kidger/generalised_shapelets/#egg=torchshapelets&subdirectory=torchshapelets"

The problem seems to be with OpenMp

I am using

Ubuntu 20.04
Python 3.8.10
Pytorch 1.10
x86_64-linux-gnu-gcc as my compiler

The error log is :

ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_1t8npic/torchshapelets/torchshapelets/setup.py'"'"'; __file__='"'"'/tmp/pip-install-_1t8npic/torchshapelets/torchshapelets/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-68btjbfr
       cwd: /tmp/pip-install-_1t8npic/torchshapelets/torchshapelets
  Complete output (39 lines):
  running bdist_wheel
  /home/etienne/.local/lib/python3.8/site-packages/torch/utils/cpp_extension.py:381: UserWarning: Attempted to use ninja as the BuildExtension backend but we could not find ninja.. Falling back to using the slow distutils backend.
    warnings.warn(msg.format('we could not find ninja.'))
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/torchshapelets
  copying src/torchshapelets/regularisation.py -> build/lib.linux-x86_64-3.8/torchshapelets
  copying src/torchshapelets/discrepancies.py -> build/lib.linux-x86_64-3.8/torchshapelets
  copying src/torchshapelets/__init__.py -> build/lib.linux-x86_64-3.8/torchshapelets
  copying src/torchshapelets/shapelet_transform.py -> build/lib.linux-x86_64-3.8/torchshapelets
  running build_ext
  building '_impl' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/src
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/etienne/.local/lib/python3.8/site-packages/torch/include -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/TH -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/THC -I/usr/include/python3.8 -c src/discrepancies.cpp -o build/temp.linux-x86_64-3.8/src/discrepancies.o -fvisibility=hidden -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=_impl -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/etienne/.local/lib/python3.8/site-packages/torch/include -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/TH -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/THC -I/usr/include/python3.8 -c src/pytorchbind.cpp -o build/temp.linux-x86_64-3.8/src/pytorchbind.o -fvisibility=hidden -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=_impl -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/etienne/.local/lib/python3.8/site-packages/torch/include -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/TH -I/home/etienne/.local/lib/python3.8/site-packages/torch/include/THC -I/usr/include/python3.8 -c src/shapelet_transform.cpp -o build/temp.linux-x86_64-3.8/src/shapelet_transform.o -fvisibility=hidden -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=_impl -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  src/shapelet_transform.cpp: In function ‘std::tuple<at::Tensor, at::Tensor> torchshapelets::shapelet_transform(at::Tensor, at::Tensor, at::Tensor, at::Tensor, at::Tensor, int64_t, const std::function<at::Tensor(at::Tensor, at::Tensor, at::Tensor, at::Tensor)>&, at::Tensor)’:
  src/shapelet_transform.cpp:313:9: error: ‘num_shapelets’ not specified in enclosing ‘parallel’
    313 |         for (int64_t shapelet_index = 0; shapelet_index < num_shapelets; ++shapelet_index) {
        |         ^~~
  src/shapelet_transform.cpp:310:17: error: enclosing ‘parallel’
    310 |         #pragma omp parallel for default(none) \
        |                 ^~~
  src/shapelet_transform.cpp:316:116: error: ‘num_shapelet_samples’ not specified in enclosing ‘parallel’
    316 |             auto shapelet_times = torch::linspace(0, length.detach().item(), num_shapelet_samples, length.options());
        |                                                                                                                    ^
  src/shapelet_transform.cpp:310:17: error: enclosing ‘parallel’
    310 |         #pragma omp parallel for default(none) \
        |                 ^~~
  src/shapelet_transform.cpp:360:66: error: ‘num_samples’ not specified in enclosing ‘parallel’
    360 |             std::tie(discrepancy, index) = detail::continuous_min(times[0], times[-1] - length, min_fn, num_samples);
        |                                            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  src/shapelet_transform.cpp:310:17: error: enclosing ‘parallel’
    310 |         #pragma omp parallel for default(none) \
        |                 ^~~
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for torchshapelets

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