Install issue while building h5py (pyproject.toml) #2035
Comments
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There's no pre-built package for ARM Macs yet (#2008), so pip is trying to build h5py from source, and failing to find HDF5. See also #1810, where there's a suggestion of how to make it work if you use Homebrew. |
Thanks but still not work. I try this one, unfortunately got same errors. |
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What was the exact command? Where is the HDF5 library installed on that computer? |
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Not installed on my mac. just try to install |
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I tried these command $ pip install --no-binary=h5py h5py $ HDF5_DIR=/path/to/hdf5 pip install --no-binary=h5py h5py $ HDF5_VERSION=X.Y.Z pip install --no-binary=h5py h5py $ CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/path/to/parallel-hdf5 pip install --no-binary=h5py h5py Just did all of that I can see |
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The last command, the "mpicc", is not applicable to your case. If I understand correctly: (1) you installed HDF5 library on your Mac; (2) tried to install h5py using the "HDF5_DIR=..." pip command, and still got an error? What was the error? |
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To be clear, you need HDF5 installed before you can build h5py from source. Where the docs have |
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By default, if using formula On an m1 (arm) mac, arm homebrew's default path for hdf5 will be On an x86 mac (or using x86 brew on an arm mac), the path will be |
most forums had a different export path, this worked for me. |
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It works with this tutorial on my m1 machine try it yourself. Solution here |
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my 2c here (also see #2052 and #2053): just do yourself a favor and build hdf5 from source with something like, and then you can safely install h5py like this: Otherwise, the conda build is pretty solid and resolves all of this efficiently.
This is not the "system" python --- macos comes with pyhon2 (soon to be removed) and python3 (3.8) via xcode. |
Thank you! Everything works for me) |
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I am going to close this because #2065 is merged which will build wheels for the next release and this issue can currently be fixed by installing hdf5 and a compiler on the user's machine. |
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Great thank you so much. |
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This work for me: Almost 2nd option will resolve the issue. |
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I don't even know what hdf5 is, but why don't you guys make a Mac release and spare us all the pain? I'm building a docker container on my Mac, so several of the options here are even more complicated for me. I'm pretty sure we don't need HDFS access at all, but HDF5 is unfortunately a transitive dependency that I have to live with. Please make a Mac build if you are such a low level library. Thanks! |
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Try building your Docker image from the conda, miniconda, or mamba base images? Then you would have h5py for the arm64 (my guess for your Mac) architecture. P.S. HDF5 is https://www.hdfgroup.org/solutions/hdf5 |
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Thanks for the suggestion. I will try that next. But this seems to have worked: |
Hi, I was install h5py command by
pip3 install h5pyBut I got error like this.
$ pip3 install h5py DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 Collecting h5py Using cached h5py-3.6.0.tar.gz (384 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: numpy>=1.14.5 in /opt/homebrew/lib/python3.9/site-packages (from h5py) (1.22.0) Building wheels for collected packages: h5py Building wheel for h5py (pyproject.toml) ... error ERROR: Command errored out with exit status 1: command: /opt/homebrew/opt/python@3.9/bin/python3.9 /opt/homebrew/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/tmppozhj8tz cwd: /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae Complete output (123 lines): running bdist_wheel running build running build_py creating build creating build/lib.macosx-12-arm64-3.9 creating build/lib.macosx-12-arm64-3.9/h5py copying h5py/h5py_warnings.py -> build/lib.macosx-12-arm64-3.9/h5py copying h5py/version.py -> build/lib.macosx-12-arm64-3.9/h5py copying h5py/__init__.py -> build/lib.macosx-12-arm64-3.9/h5py copying h5py/ipy_completer.py -> build/lib.macosx-12-arm64-3.9/h5py creating build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/files.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/compat.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/__init__.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/selections.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/dataset.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/vds.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/selections2.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/group.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/datatype.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/attrs.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/dims.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/base.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl copying h5py/_hl/filters.py -> build/lib.macosx-12-arm64-3.9/h5py/_hl creating build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_attribute_create.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_file_image.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/conftest.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_h5f.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_group.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_errors.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_slicing.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_h5pl.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_attrs.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/__init__.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_attrs_data.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_h5t.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_big_endian_file.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_h5p.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_h5o.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_datatype.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/common.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_dataset.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_file.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_selections.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_dtype.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_h5.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_file2.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_completions.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_filters.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_base.py -> build/lib.macosx-12-arm64-3.9/h5py/tests copying h5py/tests/test_objects.py -> build/lib.macosx-12-arm64-3.9/h5py/tests creating build/lib.macosx-12-arm64-3.9/h5py/tests/data_files copying h5py/tests/data_files/__init__.py -> build/lib.macosx-12-arm64-3.9/h5py/tests/data_files creating build/lib.macosx-12-arm64-3.9/h5py/tests/test_vds copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-12-arm64-3.9/h5py/tests/test_vds copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-12-arm64-3.9/h5py/tests/test_vds copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-12-arm64-3.9/h5py/tests/test_vds copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-12-arm64-3.9/h5py/tests/test_vds copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.macosx-12-arm64-3.9/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.macosx-12-arm64-3.9/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.macosx-12-arm64-3.9/h5py/tests/data_files running build_ext Loading library to get build settings and version: libhdf5.dylib ******************************************************************************** Summary of the h5py configuration HDF5 include dirs: [] HDF5 library dirs: [] HDF5 Version: (1, 12, 1) MPI Enabled: False ROS3 VFD Enabled: False Rebuild Required: True ******************************************************************************** Executing api_gen rebuild of defs Executing cythonize() [ 1/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/_conv.pyx [ 2/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/_errors.pyx [ 3/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/_objects.pyx [ 4/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/_proxy.pyx [ 5/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/_selector.pyx [ 6/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/defs.pyx [ 7/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5.pyx [ 8/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5a.pyx [ 9/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5ac.pyx [10/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5d.pyx [11/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5ds.pyx [12/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5f.pyx [13/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5fd.pyx [14/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5g.pyx [15/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5i.pyx [16/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5l.pyx [17/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5o.pyx [18/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5p.pyx [19/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5pl.pyx [20/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5r.pyx [21/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5s.pyx [22/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5t.pyx [23/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/h5z.pyx [24/24] Cythonizing /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/utils.pyx creating build/temp.macosx-12-arm64-3.9 creating build/temp.macosx-12-arm64-3.9/private creating build/temp.macosx-12-arm64-3.9/private/var creating build/temp.macosx-12-arm64-3.9/private/var/folders creating build/temp.macosx-12-arm64-3.9/private/var/folders/01 creating build/temp.macosx-12-arm64-3.9/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn creating build/temp.macosx-12-arm64-3.9/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T creating build/temp.macosx-12-arm64-3.9/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c creating build/temp.macosx-12-arm64-3.9/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae creating build/temp.macosx-12-arm64-3.9/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -DH5_USE_18_API -DNPY_NO_DEPRECATED_API=0 -I./h5py -I/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/lzf -I/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/lzf/lzf -I/opt/homebrew/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/include -I/opt/homebrew/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/defs.c -o build/temp.macosx-12-arm64-3.9/private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/defs.o In file included from /private/var/folders/01/5f5ftlvn2w7c9prxbs4410780000gn/T/pip-install-kxj8kd1c/h5py_72dcad2fa1ef4e7b9d05c4c92c290dae/h5py/defs.c:734: ./h5py/api_compat.h:27:10: fatal error: 'hdf5.h' file not found #include "hdf5.h" ^~~~~~~~ 1 error generated. error: command '/usr/bin/clang' failed with exit code 1 ---------------------------------------- ERROR: Failed building wheel for h5py Failed to build h5py ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projectsI don't know why dose happen so please help me. thank u 😄
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