Error compiling Cython file,ERROR: Failed building wheel for h5py

发布时间：2024年01月10日

```
pip install versioned-hdf5 pycuda
```

?Collecting versioned-hdf5
? Using cached versioned_hdf5-1.2-py3-none-any.whl
Collecting pycuda
? Using cached pycuda-2022.1.tar.gz (1.7 MB)
? Installing build dependencies ... error
? ERROR: Command errored out with exit status 1:
? ?command: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-36txl654/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'numpy; python_version >= '"'"'3.10'"'"'' 'numpy==1.19.5; python_version >= '"'"'3.8'"'"' and python_version < '"'"'3.10'"'"'' 'numpy==1.15.4; python_version >= '"'"'3.7'"'"' and python_version < '"'"'3.8'"'"'' 'numpy==1.12.1; python_version < '"'"'3.7'"'"''
? ? ? ?cwd: None
? Complete output (2697 lines):

EEEERRRROOOOORRRR

? ERROR: Command errored out with exit status 1: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-zmxq7cr_/numpy_17576782d6ea4f0bab027f02975a5982/setup.py'"'"'; __file__='"'"'/tmp/pip-install-zmxq7cr_/numpy_17576782d6ea4f0bab027f02975a5982/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-pf5ja3g2/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-sylets3s/overlay --compile --install-headers /tmp/pip-build-env-sylets3s/overlay/include/python3.6m/numpy Check the logs for full command output.
? ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/5a/56/4682a5118a234d15aa1c8768a528aac4858c7b04d2674e18d586d3dfda04/pycuda-2021.1.tar.gz#sha256=ab87312d0fc349d9c17294a087bb9615cffcf966ad7b115f5b051008a48dd6ed (from https://pypi.org/simple/pycuda/) (requires-python:~=3.6). Command errored out with exit status 1: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-sylets3s/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'numpy; python_version >= '"'"'3.10'"'"'' 'numpy==1.19.5; python_version >= '"'"'3.8'"'"' and python_version < '"'"'3.10'"'"'' 'numpy==1.15.4; python_version >= '"'"'3.7'"'"' and python_version < '"'"'3.8'"'"'' 'numpy==1.12.1; python_version < '"'"'3.7'"'"'' Check the logs for full command output.
? Using cached pycuda-2020.1-cp36-cp36m-linux_aarch64.whl
Collecting h5py<3
? Using cached h5py-2.10.0.tar.gz (301 kB)
? Preparing metadata (setup.py) ... done
Requirement already satisfied: ndindex>=1.3 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from versioned-hdf5) (1.4)
Requirement already satisfied: numpy in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from versioned-hdf5) (1.19.5)
Collecting decorator>=3.2.0
? Using cached decorator-5.1.1-py3-none-any.whl (9.1 kB)
Collecting appdirs>=1.4.0
? Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Requirement already satisfied: pytools>=2011.2 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from pycuda) (2022.1.12)
Requirement already satisfied: mako in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from pycuda) (1.1.6)
Requirement already satisfied: six in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from h5py<3->versioned-hdf5) (1.16.0)
Requirement already satisfied: sympy in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from ndindex>=1.3->versioned-hdf5) (1.9)
Requirement already satisfied: platformdirs>=2.2.0 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from pytools>=2011.2->pycuda) (2.4.0)
Requirement already satisfied: dataclasses>=0.7 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from pytools>=2011.2->pycuda) (0.8)
Requirement already satisfied: typing-extensions>=4.0 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from pytools>=2011.2->pycuda) (4.1.1)
Requirement already satisfied: MarkupSafe>=0.9.2 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from mako->pycuda) (2.0.1)
Requirement already satisfied: mpmath>=0.19 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from sympy->ndindex>=1.3->versioned-hdf5) (1.3.0)
Building wheels for collected packages: h5py
? Building wheel for h5py (setup.py) ... done
? Created wheel for h5py: filename=h5py-2.10.0-cp36-cp36m-linux_aarch64.whl size=4128945 sha256=69992bedf53b5b098a9f9769c07a6c6a35ec5e15e0c7979cae4e2adbcc5c4813
? Stored in directory: /home/vxking/.cache/pip/wheels/b6/56/20/c89cdcd2d96f5c4bac20ff8dad4477449d70c08abf70f08acf
Successfully built h5py
Installing collected packages: h5py, decorator, appdirs, versioned-hdf5, pycuda
Successfully installed appdirs-1.4.4 decorator-5.1.1 h5py-2.10.0 pycuda-2020.1 versioned-hdf5-1.2

/numpyos.o" failed with exit status 1
? ? ? ----------------------------------------
? ERROR: Command errored out with exit status 1: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ave3wem2/numpy_0e74cd4e72304665b95f75398289883d/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ave3wem2/numpy_0e74cd4e72304665b95f75398289883d/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-mcan4ucj/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-ynurdtr8/normal --compile --install-headers /tmp/pip-build-env-ynurdtr8/normal/include/python3.6m/numpy Check the logs for full command output.
? ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/15/fb/86d26128a5ea42d20f402109e76a63e59845d73171887a08a43a28b847dc/h5py-3.0.0.tar.gz#sha256=7d3803be1b530c68c2955faba726dc0f591079b68941a0c0269b5384a42ab519 (from https://pypi.org/simple/h5py/) (requires-python:>=3.6). Command errored out with exit status 1: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-ynurdtr8/normal --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'Cython>=0.29; python_version < "3.8"' pkgconfig 'numpy==1.17.5; python_version == "3.8"' 'numpy==1.12; python_version == "3.6"' 'Cython>=0.29.14; python_version >= "3.8"' 'numpy==1.14.5; python_version == "3.7"' 'numpy==1.19.3; python_version >= "3.9"' Check the logs for full command output.
? Using cached h5py-2.10.0.tar.gz (301 kB)
? Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy>=1.7 in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from h5py) (1.19.5)
Requirement already satisfied: six in /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages (from h5py) (1.16.0)
Building wheels for collected packages: h5py
? Building wheel for h5py (setup.py) ... error
? ERROR: Command errored out with exit status 1:
? ?command: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ngtjaq98/h5py_f1eb7e5ee9e5428782b9db46943ec3a9/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ngtjaq98/h5py_f1eb7e5ee9e5428782b9db46943ec3a9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-nf16jhi_
? ? ? ?cwd: /tmp/pip-install-ngtjaq98/h5py_f1eb7e5ee9e5428782b9db46943ec3a9/
? Complete output (496 lines):
? running bdist_wheel
? running build
? running build_py
? creating build
? creating build/lib.linux-aarch64-3.6
? creating build/lib.linux-aarch64-3.6/h5py
? copying h5py/__init__.py -> build/lib.linux-aarch64-3.6/h5py
? copying h5py/highlevel.py -> build/lib.linux-aarch64-3.6/h5py
? copying h5py/version.py -> build/lib.linux-aarch64-3.6/h5py
? copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-3.6/h5py
? copying h5py/ipy_completer.py -> build/lib.linux-aarch64-3.6/h5py
? creating build/lib.linux-aarch64-3.6/h5py/_hl
? copying h5py/_hl/files.py -> build/lib.linux-aarch64-3.6/h5py/_hl

..........................

Error compiling Cython file:
? ? ------------------------------------------------------------
? ? ...
? ? # License: ?Standard 3-clause BSD; see "license.txt" for full license terms
? ? # ? ? ? ? ? and contributor agreement.
? ??
? ? from defs cimport *
? ??
? ? from _objects cimport class ObjectID
? ? ? ? ? ? ? ? ? ? ? ? ? ^
? ? ------------------------------------------------------------
? ??
? ? h5py/h5t.pxd:12:22: Expected an identifier
? ??
? ? Error compiling Cython file:

......

? ? File "/home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
? ? ? raise CompileError(None, pyx_file)
? Cython.Compiler.Errors.CompileError: /tmp/pip-install-ngtjaq98/h5py_f1eb7e5ee9e5428782b9db46943ec3a9/h5py/_conv.pyx
? ----------------------------------------
? ERROR: Failed building wheel for h5py
? Running setup.py clean for h5py
Failed to build h5py
Installing collected packages: h5py
? ? Running setup.py install for h5py ... error
? ? ERROR: Command errored out with exit status 1:
? ? ?command: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ngtjaq98/h5py_f1eb7e5ee9e5428782b9db46943ec3a9/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ngtjaq98/h5py_f1eb7e5ee9e5428782b9db46943ec3a9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-gvesuuce/install-record.txt --single-version-externally-managed --compile --install-headers /home/vxking/archiconda3/envs/mmdeploy/include/python3.6m/h5py
? ? ? ? ?cwd: /tmp/pip-install-ngtjaq98/h5py_f1eb7e5ee9e5428782b9db46943ec3a9/
? ? Complete output (497 lines):
? ? running install
? ? running build
? ? running build_py
? ? creating build
? ? creating build/lib.linux-aarch64-3.6
? ? creating build/lib.linux-aarch64-3.6/h5py
? ? copying h5py/__init__.py -> build/lib.linux-aarch64-3.6/h5

.............

warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared
? ??
? ? Error compiling Cython file:
? ? ------------------------------------------------------------
? ? ...
? ? # License: ?Standard 3-clause BSD; see "license.txt" for full license terms
? ? # ? ? ? ? ? and contributor agreement.
? ??
? ? from defs cimport *
? ??
? ? from _objects cimport class ObjectID
? ? ? ? ? ? ? ? ? ? ? ? ? ^
? ? ------------------------------------------------------------
? ??
? ? h5py/h5t.pxd:12:22: Expected an identifier
? ??
? ? Error compiling Cython file:
? ? ------------------------------------------------------------
? ? ...
? ? ? ? Low-level type-conversion routines.
? ? """
? ??
? ? from h5 import get_config
? ? from h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
? ? from h5t cimport H5PY_OBJ, typewrap, py_create, TypeID
? ? ^
? ? ----------------------------------------------------

pip3 show Cython

pip3 install 'Cython<3'

pip list
Package ? ? ? ? ? Version ? Editable project location
----------------- --------- ------------------------------------
addict ? ? ? ? ? ?2.4.0
cycler ? ? ? ? ? ?0.11.0
Cython ? ? ? ? ? ?3.0.6
dataclasses ? ? ? 0.8
flatbuffers ? ? ? 23.5.26
kiwisolver ? ? ? ?1.3.1
Mako ? ? ? ? ? ? ?1.1.6
MarkupSafe ? ? ? ?2.0.1
matplotlib ? ? ? ?3.3.4
mmcv ? ? ? ? ? ? ?2.0.0 ? ? /home/vxking/mmdeploy_ws/mmcv
mmengine ? ? ? ? ?0.4.0
mpmath ? ? ? ? ? ?1.3.0
ndindex ? ? ? ? ? 1.4
numpy ? ? ? ? ? ? 1.19.5
onnx ? ? ? ? ? ? ?1.10.0
onnxruntime-gpu ? 1.10.0
opencv-python ? ? 4.8.1.78
packaging ? ? ? ? 21.3
Pillow ? ? ? ? ? ?8.4.0
pip ? ? ? ? ? ? ? 21.3.1
platformdirs ? ? ?2.4.0
protobuf ? ? ? ? ?3.19.6
pyparsing ? ? ? ? 3.1.1
python-dateutil ? 2.8.2
pytools ? ? ? ? ? 2022.1.12
PyYAML ? ? ? ? ? ?6.0.1
setuptools ? ? ? ?58.0.4
six ? ? ? ? ? ? ? 1.16.0
sympy ? ? ? ? ? ? 1.9
tensorrt ? ? ? ? ?8.2.1.8
termcolor ? ? ? ? 1.1.0
torch ? ? ? ? ? ? 1.10.0
torchvision ? ? ? 0.11.1 ? ?/home/vxking/mmdeploy_ws/torchvision
typing_extensions 4.1.1
wheel ? ? ? ? ? ? 0.37.1
yapf ? ? ? ? ? ? ?0.32.0
?

Package ? ? ? ? ? Version ? Editable project location
----------------- --------- ------------------------------------
addict ? ? ? ? ? ?2.4.0
cycler ? ? ? ? ? ?0.11.0
Cython ? ? ? ? ? ?0.29.36
dataclasses ? ? ? 0.8
flatbuffers ? ? ? 23.5.26
kiwisolver ? ? ? ?1.3.1
Mako ? ? ? ? ? ? ?1.1.6
MarkupSafe ? ? ? ?2.0.1
matplotlib ? ? ? ?3.3.4
mmcv ? ? ? ? ? ? ?2.0.0 ? ? /home/vxking/mmdeploy_ws/mmcv
mmengine ? ? ? ? ?0.4.0
mpmath ? ? ? ? ? ?1.3.0
ndindex ? ? ? ? ? 1.4
numpy ? ? ? ? ? ? 1.19.5
onnx ? ? ? ? ? ? ?1.10.0
onnxruntime-gpu ? 1.10.0
opencv-python ? ? 4.8.1.78
packaging ? ? ? ? 21.3
Pillow ? ? ? ? ? ?8.4.0
pip ? ? ? ? ? ? ? 21.3.1
platformdirs ? ? ?2.4.0
protobuf ? ? ? ? ?3.19.6
pyparsing ? ? ? ? 3.1.1
python-dateutil ? 2.8.2
pytools ? ? ? ? ? 2022.1.12
PyYAML ? ? ? ? ? ?6.0.1
setuptools ? ? ? ?58.0.4
six ? ? ? ? ? ? ? 1.16.0
style ? ? ? ? ? ? 1.1.0
sympy ? ? ? ? ? ? 1.9
tensorrt ? ? ? ? ?8.2.1.8
termcolor ? ? ? ? 1.1.0
torch ? ? ? ? ? ? 1.10.0
torchvision ? ? ? 0.11.1 ? ?/home/vxking/mmdeploy_ws/torchvision
typing_extensions 4.1.1
update ? ? ? ? ? ?0.0.1
wheel ? ? ? ? ? ? 0.37.1
yapf ? ? ? ? ? ? ?0.32.0

///

pip install versioned-hdf5 pycuda
Collecting versioned-hdf5
? Using cached versioned_hdf5-1.2-py3-none-any.whl
Collecting pycuda
? Using cached pycuda-2022.1.tar.gz (1.7 MB)
? Installing build dependencies ... error
? ERROR: Command errored out with exit status 1:
? ?command: /home/vxking/archiconda3/envs/mmdeploy/bin/python3.6 /home/vxking/archiconda3/envs/mmdeploy/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-36txl654/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'numpy; python_version >= '"'"'3.10'"'"'' 'numpy==1.19.5; python_version >= '"'"'3.8'"'"' and python_version < '"'"'3.10'"'"'' 'numpy==1.15.4; python_version >= '"'"'3.7'"'"' and python_version < '"'"'3.8'"'"'' 'numpy==1.12.1; python_version < '"'"'3.7'"'"''
? ? ? ?cwd: None
? Complete output (2697 lines):
? Ignoring numpy: markers 'python_version >= "3.10"' don't match your environment
? Ignoring numpy: markers 'python_version >= "3.8" and python_version < "3.10"' don't match your environment
? Ignoring numpy: markers 'python_version >= "3.7" and python_version < "3.8"' don't match your environment
.......

?sudo apt-get update
$ sudo apt-get install libhdf5-serial-dev hdf5-tools libhdf5-dev zlib1g-dev zip libjpeg8-dev liblapack-dev libblas-dev gfortran
$ sudo apt-get install python3-pip
$ sudo pip3 install -U pip testresources setuptools
$ sudo ln -s /usr/include/locale.h /usr/include/xlocale.h
$ pip3 install Cython==0.29.36
$ pip3 install pkgconfig
$ git clone https://github.com/h5py/h5py.git
$ git checkout 3.1.0
$ git cherry-pick 3bf862daa4ebeb2eeaf3a0491e05f5415c1818e4
$ H5PY_SETUP_REQUIRES=0 pip3 install . --no-deps --no-build-isolation
$ sudo pip3 install -U numpy==1.19.4 future mock keras_preprocessing keras_applications gast==0.2.1 protobuf pybind11 packaging
$ sudo pip3 install --extra-index-url https://developer.download.nvidia.com/compute/redist/jp/v461 tensorflow

sudo pip3 install --extra-index-url https://developer.download.nvidia.com/compute/redist/jp/v461 tensorflow

apt-get update
apt-get install -y python3-pip pkg-config
apt-get install -y libhdf5-serial-dev hdf5-tools libhdf5-dev zlib1g-dev zip libjpeg8-dev liblapack-dev libblas-dev gfortran
ln -s /usr/include/locale.h /usr/include/xlocale.h
pip3 install --verbose 'protobuf<4' 'Cython<3'
wget --no-check-certificate https://developer.download.nvidia.com/compute/redist/jp/v461/tensorflow/tensorflow-2.7.0+nv22.1-cp36-cp36m-linux_aarch64.whl
pip3 install --verbose tensorflow-2.7.0+nv22.1-cp36-cp36m-linux_aarch64.whl?

stdout? ?

pip3 install --verbose h5py

?stderr instead of stdout

pip3 install --verbose h5py 2>&1 | tee log.txt

文章来源:https://blog.csdn.net/vxgu86/article/details/134836607
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