Cannot install the library

[jmlipman]

Hi,

I tried to pip install TopologyLayer, as well as doing "python setup.py install --record files.txt". In both cases, I get an extremely long error. These are the very last lines:

` from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/options/conv.h:61:24: note: candidate: ‘decltype ((torch::nn::detail::ConvNdOptions)this) torch::nn::detail::ConvNdOptions::padding(const int&) [with long unsigned int D = 1; decltype ((torch::nn::detail::ConvNdOptions)this) = torch::nn::detail::ConvNdOptions<1>&]’
61 | TORCH_ARG(padding_t, padding) = 0;
| ^~~~~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/arg.h:7:15: note: in definition of macro ‘TORCH_ARG’
7 | inline auto name(const T& new_##name) -> decltype(this) { / NOLINT /
| ^~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/options/conv.h:61:24: note: candidate expects 1 argument, 0 provided
61 | TORCH_ARG(padding_t, padding) = 0;
| ^~~~~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/arg.h:7:15: note: in definition of macro ‘TORCH_ARG’
7 | inline auto name(const T& new_##name) -> decltype(this) { / NOLINT /
| ^~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/options/conv.h:61:24: note: candidate: ‘decltype ((torch::nn::detail::ConvNdOptions)this) torch::nn::detail::ConvNdOptions::padding(int&&) [with long unsigned int D = 1; decltype ((torch::nn::detail::ConvNdOptions)this) = torch::nn::detail::ConvNdOptions<1>&]’
61 | TORCH_ARG(padding_t, padding) = 0;
| ^~~~~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/arg.h:11:15: note: in definition of macro ‘TORCH_ARG’
11 | inline auto name(T&& new_##name) -> decltype(this) { / NOLINT */
| ^~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/options/conv.h:61:24: note: candidate expects 1 argument, 0 provided
61 | TORCH_ARG(padding_t, padding) = 0;
| ^~~~~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/arg.h:11:15: note: in definition of macro ‘TORCH_ARG’
11 | inline auto name(T&& new_##name) -> decltype(this) { / NOLINT */
| ^~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/conv.h:3,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional.h:4,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:4,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/options/conv.h:64:18: note: candidate: ‘decltype(auto) torch::nn::detail::ConvNdOptions::padding(std::initializer_list) [with long unsigned int D = 1]’
64 | decltype(auto) padding(std::initializer_list<int64_t> il) {
| ^~~~~~~
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/options/conv.h:64:18: note: candidate expects 1 argument, 0 provided
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules.h:20,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:7,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h: In instantiation of ‘void torch::nn::ConvNdImpl<D, Derived>::reset_parameters() [with long unsigned int D = 1; Derived = torch::nn::ConvTranspose1dImpl]’:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:101:5: required from ‘void torch::nn::ConvNdImpl<D, Derived>::reset() [with long unsigned int D = 1; Derived = torch::nn::ConvTranspose1dImpl]’
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:33:8: required from here
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:105:27: error: cannot convert ‘const torch::enumtype::kFanIn’ to ‘int’
105 | init::kaiming_uniform_(
| ~~~~~~~~~~~~~~~~~~~~~~^
| |
| const torch::enumtype::kFanIn
106 | weight,
| ~~~~~~~
107 | /a=/std::sqrt(5)); // NOLINT(cppcoreguidelines-avoid-magic-numbers)
| ~~~~~~~~~~~~~~~~~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:5,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/init.h:99:17: note: initializing argument 3 of ‘at::Tensor torch::nn::init::kaiming_uniform_(at::Tensor, double, int, int)’
99 | FanModeType mode = torch::kFanIn,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules.h:20,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:7,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h: In instantiation of ‘void torch::nn::ConvNdImpl<D, Derived>::reset_parameters() [with long unsigned int D = 3; Derived = torch::nn::Conv3dImpl]’:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:101:5: required from ‘void torch::nn::ConvNdImpl<D, Derived>::reset() [with long unsigned int D = 3; Derived = torch::nn::Conv3dImpl]’
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:33:8: required from here
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:105:27: error: cannot convert ‘const torch::enumtype::kFanIn’ to ‘int’
105 | init::kaiming_uniform_(
| ~~~~~~~~~~~~~~~~~~~~~~^
| |
| const torch::enumtype::kFanIn
106 | weight,
| ~~~~~~~
107 | /a=/std::sqrt(5)); // NOLINT(cppcoreguidelines-avoid-magic-numbers)
| ~~~~~~~~~~~~~~~~~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:5,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/init.h:99:17: note: initializing argument 3 of ‘at::Tensor torch::nn::init::kaiming_uniform_(at::Tensor, double, int, int)’
99 | FanModeType mode = torch::kFanIn,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules.h:20,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:7,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h: In instantiation of ‘void torch::nn::ConvNdImpl<D, Derived>::reset_parameters() [with long unsigned int D = 2; Derived = torch::nn::Conv2dImpl]’:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:101:5: required from ‘void torch::nn::ConvNdImpl<D, Derived>::reset() [with long unsigned int D = 2; Derived = torch::nn::Conv2dImpl]’
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:33:8: required from here
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:105:27: error: cannot convert ‘const torch::enumtype::kFanIn’ to ‘int’
105 | init::kaiming_uniform_(
| ~~~~~~~~~~~~~~~~~~~~~~^
| |
| const torch::enumtype::kFanIn
106 | weight,
| ~~~~~~~
107 | /a=/std::sqrt(5)); // NOLINT(cppcoreguidelines-avoid-magic-numbers)
| ~~~~~~~~~~~~~~~~~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:5,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/init.h:99:17: note: initializing argument 3 of ‘at::Tensor torch::nn::init::kaiming_uniform_(at::Tensor, double, int, int)’
99 | FanModeType mode = torch::kFanIn,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules.h:20,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:7,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h: In instantiation of ‘void torch::nn::ConvNdImpl<D, Derived>::reset_parameters() [with long unsigned int D = 1; Derived = torch::nn::Conv1dImpl]’:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:101:5: required from ‘void torch::nn::ConvNdImpl<D, Derived>::reset() [with long unsigned int D = 1; Derived = torch::nn::Conv1dImpl]’
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:33:8: required from here
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/modules/conv.h:105:27: error: cannot convert ‘const torch::enumtype::kFanIn’ to ‘int’
105 | init::kaiming_uniform_(
| ~~~~~~~~~~~~~~~~~~~~~~^
| |
| const torch::enumtype::kFanIn
106 | weight,
| ~~~~~~~
107 | /a=/std::sqrt(5)); // NOLINT(cppcoreguidelines-avoid-magic-numbers)
| ~~~~~~~~~~~~~~~~~~~
In file included from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn.h:5,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/all.h:16,
from /xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/extension.h:5,
from /zhome/72/3/199765/delete/TopologyLayer/topologylayer/functional/persistence/pybind.cpp:1:
/xxxx/envs/bricks/lib/python3.10/site-packages/torch/include/torch/csrc/api/include/torch/nn/init.h:99:17: note: initializing argument 3 of ‘at::Tensor torch::nn::init::kaiming_uniform_(at::Tensor, double, int, int)’
99 | FanModeType mode = torch::kFanIn,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
ninja: build stopped: subcommand failed.
Traceback (most recent call last):
File "/xxxx/envs/bricks/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2107, in _run_ninja_build
subprocess.run(
File "/appl9/python/3.10.12/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/zhome/72/3/199765/delete/TopologyLayer/setup.py", line 11, in
setup(name='topologylayer',
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/init.py", line 107, in setup
return distutils.core.setup(**attrs)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/command/install.py", line 80, in run
self.do_egg_install()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/command/install.py", line 129, in do_egg_install
self.run_command('bdist_egg')
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/command/bdist_egg.py", line 164, in run
cmd = self.call_command('install_lib', warn_dir=0)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/command/bdist_egg.py", line 150, in call_command
self.run_command(cmdname)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/command/install_lib.py", line 11, in run
self.build()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/command/install_lib.py", line 111, in build
self.run_command('build_ext')
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 84, in run
_build_ext.run(self)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
self.build_extensions()
File "/xxxx/envs/bricks/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 870, in build_extensions
build_ext.build_extensions(self)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
self._build_extensions_serial()
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
self.build_extension(ext)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 246, in build_extension
_build_ext.build_extension(self, ext)
File "/xxxx/envs/bricks/lib/python3.10/site-packages/Cython/Distutils/build_ext.py", line 135, in build_extension
super(build_ext, self).build_extension(ext)
File "/appl9/python/3.10.12/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 548, in build_extension
objects = self.compiler.compile(
File "/xxxx/envs/bricks/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 683, in unix_wrap_ninja_compile
_write_ninja_file_and_compile_objects(
File "/xxxx/envs/bricks/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1783, in _write_ninja_file_and_compile_objects
_run_ninja_build(
File "/xxxx/envs/bricks/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2123, in _run_ninja_build
raise RuntimeError(message) from e
RuntimeError: Error compiling objects for extension
`

Python version: 3.10.12
OS: AlmaLinux 9.4
Other packages:
asttokens==2.4.1
connected-components-3d==3.18.0
contourpy==1.2.1
cycler==0.12.1
Cython==3.0.11
decorator==5.1.1
distlib==0.3.7
exceptiongroup==1.2.2
executing==2.0.1
filelock==3.12.2
fonttools==4.53.1
fsspec==2024.6.1
gudhi==3.10.1
h5py==3.11.0
imageio==2.35.1
ipython==8.26.0
jedi==0.19.1
jinja2==3.1.4
joblib==1.4.2
kiwisolver==1.4.5
lazy-loader==0.4
MarkupSafe==2.1.5
matplotlib==3.9.2
matplotlib-inline==0.1.7
MedPy==0.5.2
monai==1.3.2
mpmath==1.3.0
networkx==3.3
nibabel==5.2.1
numpy==1.26.4
nvidia-cublas-cu12==12.1.3.1
nvidia-cuda-cupti-cu12==12.1.105
nvidia-cuda-nvrtc-cu12==12.1.105
nvidia-cuda-runtime-cu12==12.1.105
nvidia-cudnn-cu12==8.9.2.26
nvidia-cufft-cu12==11.0.2.54
nvidia-curand-cu12==10.3.2.106
nvidia-cusolver-cu12==11.4.5.107
nvidia-cusparse-cu12==12.1.0.106
nvidia-nccl-cu12==2.20.5
nvidia-nvjitlink-cu12==12.6.20
nvidia-nvtx-cu12==12.1.105
opencv-python==4.10.0.84
packaging==24.1
pandas==2.2.2
parso==0.8.4
pexpect==4.9.0
pillow==10.4.0
platformdirs==3.9.1
POT==0.9.4
prompt-toolkit==3.0.47
ptyprocess==0.7.0
pure-eval==0.2.3
pygments==2.18.0
pyparsing==3.1.4
python-dateutil==2.9.0.post0
pytz==2024.1
PyYAML==6.0.2
scikit-image==0.24.0
scikit-learn==1.5.1
scipy==1.14.1
SimpleITK==2.3.1
six==1.16.0
stack-data==0.6.3
sympy==1.13.2
threadpoolctl==3.5.0
tifffile==2024.8.24
torch==2.3.1
torchaudio==2.3.1
torchvision==0.18.1
traitlets==5.14.3
triton==2.3.1
typing-extensions==4.12.2
tzdata==2024.1
UNKNOWN==0.0.0
virtualenv==20.24.1
wcwidth==0.2.13

[Yanzi-S]

I also have this problem, have you solved it? Thanks!

[jmlipman]

No :(