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I have an M1 MacBook. I have installed python 3.9.1 using pyenv, and have pip3 version 21.0.1. I have installed homebrew and hdf5 1.12.0_1 via brew install hdf5.

When I type

pip3 install h5py

I get the error:

Requirement already satisfied: numpy>=1.19.3 in /Users/.../.pyenv/versions/3.9.1/lib/python3.9/site-packages (from h5py) (1.20.0)
Building wheels for collected packages: h5py
  Building wheel for h5py (PEP 517) ... error

  Loading library to get build settings and version: libhdf5.dylib
  error: Unable to load dependency HDF5, make sure HDF5 is installed properly
  error: dlopen(libhdf5.dylib, 6): image not found
  ----------------------------------------
  ERROR: Failed building wheel for h5py

I saw that libhdf5.dylib is present in /opt/homebrew/opt/hdf5/lib, so I tried export LDFLAGS="-L/opt/homebrew/opt/hdf5/lib" and export CPPFLAGS="-L/opt/homebrew/opt/hdf5/include" beforehand but they don't help.

How can I install h5py?

I am actually installing h5py as a requirement to install Keras.

Thanks!

Racing Tadpole
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  • I'm not a Mac guy, so of limited help. However, I saw a similar question about installing Python packages on Mac M1. He did NOT use pip to install packages. Instead, he used macports, like this: `sudo port install package_name`. Good luck – kcw78 Mar 22 '21 at 13:29

3 Answers3

80

This works for me:

$ brew install hdf5
$ export HDF5_DIR="$(brew --prefix hdf5)"
$ pip install --no-binary=h5py h5py
David Pärsson
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user15990707
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  • https://docs.h5py.org/en/latest/build.html#custom-installation for more info – Pieter Meiresone Jan 04 '22 at 14:33
  • Happy to hear this worked for others. This failed for me however with 6 compilation errors (h5py version 2.10.0--Keras compatability). – ephsmith Mar 07 '22 at 21:54
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    it might not be 1.12.0_4 anymore. For me it was 1.13.0. Update accordingly – Scaraux Mar 22 '22 at 18:18
  • Assigning a version tracker with `VERSION=$(brew list --versions hdf5 | cut -d' ' -f2)` after installing hdf5 allows you to select the right directory as in `export HDF5_DIR=/opt/homebrew/Cellar/hdf5/$VERSION` – Jona Engel Mar 24 '22 at 15:56
  • `export HDF5_DIR=$(brew --prefix hdf5)` is a much simpler way to get the directory. – David Pärsson Mar 31 '22 at 11:58
  • I also had to export the include directory: ```bash export HDF5_DIR="$(brew --prefix hdf5)" export CPATH=$(brew --prefix)/include:${CPATH} ``` – patzm May 09 '22 at 16:52
  • This works for me on a brand new M1 Mac, and got me on the path to installing Tensorflow which is NOT easy on the M1 Mac. I had to `pip install tensor flow-metal` followed by `pip install tensorflow-macos`. BUT when I did this, tensorflow-macos installation would fail building the HDF5 stuff. And your post worked and then I got my Tensorflow demo running. – Paul Z May 10 '22 at 22:47
  • It cannot hep. Here is the issue "error: dlopen(/usr/local/opt/hdf5/lib/libhdf5.dylib, 0x0006): tried: '/usr/local/opt/hdf5/lib/libhdf5.dylib' (mach-o file, but is an incompatible architecture (have (x86_64)," – GoingMyWay Mar 23 '23 at 04:49
15

Try to install h5py using conda. Works for me.

conda install h5py
Vasantharajan Charangan
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    Easy and straightforward solution. Works on my Apple M1 Mac Mini. Thanks! – RandomWalker Jan 27 '22 at 22:09
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    worked on a MacBook with M1 – MichaelHuelsen Feb 05 '22 at 20:58
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    Happy that Anaconda is there for us M1 folks. They do a pretty good job of getting everything working. Sadly, I can't use Anaconda for every project. – ephsmith Mar 07 '22 at 21:55
  • This works great. I'm not even using Anaconda (and the environment I used this for still is not). This installed h5py and libs onto the system and satisfied the requirement for all my python.org/pip managed environments for tables and other packages as well. I wanted to avoid getting into homebrew on this system, and this was perfect! – Zim May 11 '23 at 11:28
0

Here are some steps you can follow to install hdf5 on macOS M1.

Step 0 (optional): Uninstall hdf5 with brew if you have installed.

brew uninstal hdf5 --ignore-dependencies

Step 1: Install hdf5 with brew.

arch -arm64 brew install hdf5

Step 2: Find the directory of hdf5 and hdf5.h.

sudo find / -iname "*hdf5.h*" # use sudo if possible

On my laptop, the output is

/usr/local/include/hdf5.h
/usr/local/Cellar/hdf5/1.12.2_2/include/hdf5.h
/usr/local/Cellar/opencv/4.7.0_2/include/opencv4/opencv2/flann/hdf5.h
/usr/local/Cellar/vtk/9.2.6/include/vtk-9.2/vtk_hdf5.h
/System/Volumes/Data/usr/local/include/hdf5.h
/System/Volumes/Data/usr/local/Cellar/hdf5/1.12.2_2/include/hdf5.h
/System/Volumes/Data/usr/local/Cellar/opencv/4.7.0_2/include/opencv4/opencv2/flann/hdf5.h
/System/Volumes/Data/usr/local/Cellar/vtk/9.2.6/include/vtk-9.2/vtk_hdf5.h

Step 3: Set CPATH and HDF5_DIR.

export CPATH=$CPATH:/usr/local/include/:/usr/local/Cellar/hdf5/1.12.2_2/include

and

export HDF5_DIR=/usr/local/Cellar/hdf5/1.12.2_2

Note that on your laptop, these directories can be different.

Step 4: Install hdf5 with pip.

arch -arm64 pip3.9 install hdf5

It then successfully completes the installation.

halfer
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GoingMyWay
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