martin@precision:~/bin/qrefine$ bash config/update_phenix.sh aimnet2 Found developer version of phenix. Phenix location : /opt/phenix/phenix-dev-5480 Phenix conda : /opt/phenix/phenix-dev-5480/conda_base Pytorch/Aimnet2 : true osx-arm64 : false Check above locations/settings. Continue (y/n)?y yes Updating Phenix's conda-base .. Installing pytorch and aimnet2 depedencies .. config/update_phenix.sh: line 112: conda: command not found Collecting git+https://github.com/zubatyuk/aimnet2calc.git Cloning https://github.com/zubatyuk/aimnet2calc.git to /tmp/pip-req-build-uof310rq Running command git clone --filter=blob:none --quiet https://github.com/zubatyuk/aimnet2calc.git /tmp/pip-req-build-uof310rq Resolved https://github.com/zubatyuk/aimnet2calc.git to commit a56ade16193daa0f0d5d89180538e15d94aee659 Preparing metadata (setup.py) ... done Requirement already satisfied: torch<3,>2.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from aimnet2calc==0.0.1) (2.4.1) Collecting torch-cluster Using cached torch_cluster-1.6.3.tar.gz (54 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: numpy in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from aimnet2calc==0.0.1) (1.23.4) Collecting numba Using cached numba-0.60.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB) Requirement already satisfied: ase in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from aimnet2calc==0.0.1) (3.22.1) Requirement already satisfied: requests in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from aimnet2calc==0.0.1) (2.28.1) Requirement already satisfied: fsspec in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (2024.9.0) Requirement already satisfied: nvidia-cuda-runtime-cu12==12.1.105 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (12.1.105) Requirement already satisfied: nvidia-cusolver-cu12==11.4.5.107 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (11.4.5.107) Requirement already satisfied: filelock in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (3.16.1) Requirement already satisfied: nvidia-cuda-nvrtc-cu12==12.1.105 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (12.1.105) Requirement already satisfied: nvidia-cufft-cu12==11.0.2.54 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (11.0.2.54) Requirement already satisfied: nvidia-cusparse-cu12==12.1.0.106 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (12.1.0.106) Requirement already satisfied: nvidia-nvtx-cu12==12.1.105 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (12.1.105) Requirement already satisfied: jinja2 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (3.1.2) Requirement already satisfied: nvidia-cublas-cu12==12.1.3.1 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (12.1.3.1) Requirement already satisfied: nvidia-cuda-cupti-cu12==12.1.105 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (12.1.105) Requirement already satisfied: sympy in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (1.13.3) Requirement already satisfied: nvidia-curand-cu12==10.3.2.106 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (10.3.2.106) Requirement already satisfied: typing-extensions>=4.8.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (4.12.2) Requirement already satisfied: nvidia-nccl-cu12==2.20.5 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (2.20.5) Requirement already satisfied: networkx in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (2.8.8) Requirement already satisfied: nvidia-cudnn-cu12==9.1.0.70 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (9.1.0.70) Requirement already satisfied: triton==3.0.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch<3,>2.0->aimnet2calc==0.0.1) (3.0.0) Requirement already satisfied: nvidia-nvjitlink-cu12 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from nvidia-cusolver-cu12==11.4.5.107->torch<3,>2.0->aimnet2calc==0.0.1) (12.6.77) Requirement already satisfied: matplotlib>=3.1.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from ase->aimnet2calc==0.0.1) (3.6.2) Requirement already satisfied: scipy>=1.1.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from ase->aimnet2calc==0.0.1) (1.9.3) Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from numba->aimnet2calc==0.0.1) (0.43.0) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from requests->aimnet2calc==0.0.1) (1.26.11) Requirement already satisfied: certifi>=2017.4.17 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from requests->aimnet2calc==0.0.1) (2022.9.24) Requirement already satisfied: idna<4,>=2.5 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from requests->aimnet2calc==0.0.1) (3.4) Requirement already satisfied: charset-normalizer<3,>=2 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from requests->aimnet2calc==0.0.1) (2.1.1) Requirement already satisfied: packaging>=20.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (21.3) Requirement already satisfied: python-dateutil>=2.7 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (2.8.2) Requirement already satisfied: pyparsing>=2.2.1 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (3.0.9) Requirement already satisfied: cycler>=0.10 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (0.11.0) Requirement already satisfied: pillow>=6.2.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (9.2.0) Requirement already satisfied: fonttools>=4.22.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (4.38.0) Requirement already satisfied: contourpy>=1.0.1 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (1.0.6) Requirement already satisfied: kiwisolver>=1.0.1 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (1.4.4) Requirement already satisfied: MarkupSafe>=2.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from jinja2->torch<3,>2.0->aimnet2calc==0.0.1) (2.1.1) Requirement already satisfied: mpmath<1.4,>=1.1.0 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from sympy->torch<3,>2.0->aimnet2calc==0.0.1) (1.3.0) Requirement already satisfied: six>=1.5 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=3.1.0->ase->aimnet2calc==0.0.1) (1.16.0) Building wheels for collected packages: aimnet2calc, torch-cluster Building wheel for aimnet2calc (setup.py) ... done Created wheel for aimnet2calc: filename=aimnet2calc-0.0.1-py3-none-any.whl size=10881 sha256=9652191cd1ec1d5b23b59bdb5d71551a7c31e8dd0d6ffc0a85edfce39ba0d828 Stored in directory: /tmp/pip-ephem-wheel-cache-li1n7vhn/wheels/a8/00/5c/4ec981c6ab624543e282cdef6ba81f352885af71687dca05bf Building wheel for torch-cluster (setup.py) ... error error: subprocess-exited-with-error × python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [45 lines of output] running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-39 creating build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/radius.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/grid.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/fps.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/nearest.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/__init__.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/testing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/knn.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/graclus.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/sampler.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/typing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/rw.py -> build/lib.linux-x86_64-cpython-39/torch_cluster running egg_info writing torch_cluster.egg-info/PKG-INFO writing dependency_links to torch_cluster.egg-info/dependency_links.txt writing requirements to torch_cluster.egg-info/requires.txt writing top-level names to torch_cluster.egg-info/top_level.txt reading manifest file 'torch_cluster.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*' found under directory 'test' adding license file 'LICENSE' writing manifest file 'torch_cluster.egg-info/SOURCES.txt' running build_ext building 'torch_cluster._fps_cpu' extension creating build/temp.linux-x86_64-cpython-39 creating build/temp.linux-x86_64-cpython-39/csrc creating build/temp.linux-x86_64-cpython-39/csrc/cpu gcc -pthread -B /__w/1/phenix/conda_base/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -DWITH_PYTHON -Icsrc -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/TH -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/THC -I/__w/1/phenix/conda_base/include/python3.9 -c csrc/cpu/fps_cpu.cpp -o build/temp.linux-x86_64-cpython-39/csrc/cpu/fps_cpu.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_fps_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++17 In file included from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/Device.h:4, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/python.h:8, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/extension.h:9, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/torch.h:6, from csrc/cpu/../extensions.h:2, from csrc/cpu/fps_cpu.h:3, from csrc/cpu/fps_cpu.cpp:1: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for torch-cluster Running setup.py clean for torch-cluster Successfully built aimnet2calc Failed to build torch-cluster Installing collected packages: numba, torch-cluster, aimnet2calc Running setup.py install for torch-cluster ... error error: subprocess-exited-with-error × Running setup.py install for torch-cluster did not run successfully. │ exit code: 1 ╰─> [47 lines of output] running install /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.linux-x86_64-cpython-39 creating build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/radius.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/grid.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/fps.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/nearest.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/__init__.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/testing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/knn.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/graclus.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/sampler.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/typing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/rw.py -> build/lib.linux-x86_64-cpython-39/torch_cluster running egg_info writing torch_cluster.egg-info/PKG-INFO writing dependency_links to torch_cluster.egg-info/dependency_links.txt writing requirements to torch_cluster.egg-info/requires.txt writing top-level names to torch_cluster.egg-info/top_level.txt reading manifest file 'torch_cluster.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*' found under directory 'test' adding license file 'LICENSE' writing manifest file 'torch_cluster.egg-info/SOURCES.txt' running build_ext building 'torch_cluster._fps_cpu' extension creating build/temp.linux-x86_64-cpython-39 creating build/temp.linux-x86_64-cpython-39/csrc creating build/temp.linux-x86_64-cpython-39/csrc/cpu gcc -pthread -B /__w/1/phenix/conda_base/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -DWITH_PYTHON -Icsrc -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/TH -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/THC -I/__w/1/phenix/conda_base/include/python3.9 -c csrc/cpu/fps_cpu.cpp -o build/temp.linux-x86_64-cpython-39/csrc/cpu/fps_cpu.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_fps_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++17 In file included from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/Device.h:4, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/python.h:8, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/extension.h:9, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/torch.h:6, from csrc/cpu/../extensions.h:2, from csrc/cpu/fps_cpu.h:3, from csrc/cpu/fps_cpu.cpp:1: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure × Encountered error while trying to install package. ╰─> torch-cluster note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure. martin@precision:~/bin/qrefine$ qrefine.python -m pip install torch-cluster Collecting torch-cluster Using cached torch_cluster-1.6.3.tar.gz (54 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: scipy in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from torch-cluster) (1.9.3) Requirement already satisfied: numpy<1.26.0,>=1.18.5 in /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages (from scipy->torch-cluster) (1.23.4) Building wheels for collected packages: torch-cluster Building wheel for torch-cluster (setup.py) ... error error: subprocess-exited-with-error × python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [45 lines of output] running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-39 creating build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/radius.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/grid.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/fps.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/nearest.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/__init__.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/testing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/knn.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/graclus.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/sampler.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/typing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/rw.py -> build/lib.linux-x86_64-cpython-39/torch_cluster running egg_info writing torch_cluster.egg-info/PKG-INFO writing dependency_links to torch_cluster.egg-info/dependency_links.txt writing requirements to torch_cluster.egg-info/requires.txt writing top-level names to torch_cluster.egg-info/top_level.txt reading manifest file 'torch_cluster.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*' found under directory 'test' adding license file 'LICENSE' writing manifest file 'torch_cluster.egg-info/SOURCES.txt' running build_ext building 'torch_cluster._fps_cpu' extension creating build/temp.linux-x86_64-cpython-39 creating build/temp.linux-x86_64-cpython-39/csrc creating build/temp.linux-x86_64-cpython-39/csrc/cpu gcc -pthread -B /__w/1/phenix/conda_base/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -DWITH_PYTHON -Icsrc -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/TH -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/THC -I/__w/1/phenix/conda_base/include/python3.9 -c csrc/cpu/fps_cpu.cpp -o build/temp.linux-x86_64-cpython-39/csrc/cpu/fps_cpu.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_fps_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++17 In file included from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/Device.h:4, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/python.h:8, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/extension.h:9, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/torch.h:6, from csrc/cpu/../extensions.h:2, from csrc/cpu/fps_cpu.h:3, from csrc/cpu/fps_cpu.cpp:1: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for torch-cluster Running setup.py clean for torch-cluster Failed to build torch-cluster Installing collected packages: torch-cluster Running setup.py install for torch-cluster ... error error: subprocess-exited-with-error × Running setup.py install for torch-cluster did not run successfully. │ exit code: 1 ╰─> [47 lines of output] running install /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.linux-x86_64-cpython-39 creating build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/radius.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/grid.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/fps.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/nearest.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/__init__.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/testing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/knn.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/graclus.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/sampler.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/typing.py -> build/lib.linux-x86_64-cpython-39/torch_cluster copying torch_cluster/rw.py -> build/lib.linux-x86_64-cpython-39/torch_cluster running egg_info writing torch_cluster.egg-info/PKG-INFO writing dependency_links to torch_cluster.egg-info/dependency_links.txt writing requirements to torch_cluster.egg-info/requires.txt writing top-level names to torch_cluster.egg-info/top_level.txt reading manifest file 'torch_cluster.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*' found under directory 'test' adding license file 'LICENSE' writing manifest file 'torch_cluster.egg-info/SOURCES.txt' running build_ext building 'torch_cluster._fps_cpu' extension creating build/temp.linux-x86_64-cpython-39 creating build/temp.linux-x86_64-cpython-39/csrc creating build/temp.linux-x86_64-cpython-39/csrc/cpu gcc -pthread -B /__w/1/phenix/conda_base/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -O2 -isystem /__w/1/phenix/conda_base/include -fPIC -DWITH_PYTHON -Icsrc -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/TH -I/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/THC -I/__w/1/phenix/conda_base/include/python3.9 -c csrc/cpu/fps_cpu.cpp -o build/temp.linux-x86_64-cpython-39/csrc/cpu/fps_cpu.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_fps_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++17 In file included from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/Device.h:4, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/python.h:8, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/extension.h:9, from /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/torch.h:6, from csrc/cpu/../extensions.h:2, from csrc/cpu/fps_cpu.h:3, from csrc/cpu/fps_cpu.cpp:1: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure × Encountered error while trying to install package. ╰─> torch-cluster note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure. martin@precision:~/bin/qrefine$ which qrefine.python /opt/phenix/phenix-dev-5480/build/bin/qrefine.python