installation failure on Mac 'ERROR: Failed building wheel for h5py'

[jkingslake]

I am installing on mac 13.2.1 (22D68).

It seems to fail when trying to install h5py. I tried installing h5py with homebrew separately, but that did not seem to help.

This issue seems to be the same, but it is unclear if it was resolved.

Log files are attached.

Any help would be much appreciated.

firedrake-install.log
PETSC log files:
configure.log
make.log

[connorjward]

I notice two things:

• You are using the system Python. This is known to cause problems. Please use a homebrew-installed Python version instead.
• I'm seeing a number of warnings like:

  ld: warning: dylib (/Users/jkingslake/firedrake/src/petsc/default/lib/libmpi.dylib) was built for newer macOS version (10.15) than being linked (10.9))
  

  This surprises me because 10.9 is really quite an old version to be cropping up here. Is your firedrake-install freshly downloaded? And is your xcode installation up to date?

[jkingslake]

Thanks so much for taking a look so quickly!

System Python

I was aware of this issue and tried to avoid it, but I didnt find much online about how to determine if I am using the system python. I ran brew install python prior to this installation and that all seemed to work. How do I tell if I am using the system python? How do I ensure that I am using the homebrew version for the installation?

newer macOS version...

I downloaded the install script a few weeks ago. Should i get a more recent one?

I did update xcode while dealing with another issue with this installation. I can try doing that again if you think it will help.

[jkingslake]

update: I am trying adding export PATH="/usr/local/opt/python/libexec/bin:$PATH" to .zshrc as suggested here

[jkingslake]

The installation is now working! 🥳 !

Two things I did to solve this are:

1. At this stage I had already installed python with homebrew using brew install python, it just wasnt using this version yet. To correct this I added
   export PATH="/usr/local/opt/python/libexec/bin:$PATH"
   to .zshrc, as suggested here. This ensures that the homebrew-installed version of python is the default python you get when you type python into the terminal. I think adding the same line to .bash_profile will work the same way if your terminal is set up to use bash.
2. I download the latest firedrake installation script using
   wget https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
   Then ran it.

In case they are useful to anyone, here are the firedrake and petsc log files from the successful installation:
firedrake-install.log
configure.log
make.log

Note, prior to this I was having an issue with a fortran compiler, so I followed the advice here and reinstalled the xcode command line tools.

Thanks @connorjward for the help!

[jkingslake]

I wrote down the steps I followed to install firedrake and icepack on my 2018 macbook air here, in case it is useful to anyone.

@connorjward, I wonder if it would be useful to include some of these steps in the docs. Maybe around here. Maybe in the form of FAQs? I would be happy to contribute a PR if it can be useful for the next person trying to tackle this installation.

[connorjward]

Thanks @jkingslake. It would be nice to include some of this in the installation instructions. Specifically I think it would be good to mention:

• One should use $(brew --prefix)/bin/python3 to make sure you're using the right Python. I think this is better than telling users to modify their PATH.
• Add some instructions for updating xcode. I know a number of users hit this.
• Maybe it would be useful to mention that users should always try to download a fresh install script as we frequently modify it.

This sort of thing might be good to add to the flowchart we already have: https://firedrakeproject.org/download.html#debugging-install-problems.

[hwoo749]

Hiya,

I have successfully downloaded firedrake, and I have been following your instructions @jkingslake on how to install icepack, which have been very helpful - I think I have installed it correctly but I am struggling to activate the virtual environment.
I get this message:

harrietwoodward@Harriets-MacBook-Air ~ % source firedrake/bin/activate
(firedrake) harrietwoodward@Harriets-MacBook-Air ~ % cd $VIRTUAL_ENV/src/icepack
cd: no such file or directory: /Users/harrietwoodward/firedrake/src/icepack

The path to icepack is as follows:

How do I go about activating the icepack virtual environment? I tried cd $VIRTUAL_ENV/firedrake/bin/firedrake/src/icepack
but this gave me the same error message of no such file or directory. Any help would be greatly appreciated!

[connorjward]

Your icepack is installed into firedrake/bin/firedrake/src/icepack. It should actually be firedrake/src/icepack. I think you should be able to simply run pip install git+https://github.com/icepack/icepack.git#egg=icepack to have it installed correctly.

[hwoo749]

Hi there, thank you for the quick reply. :))

I ran that command, and this installed icepack in this path:

How do I go about activating the virtual environment from this path?

[ReubenHill]

I think you should be able to do it with $ source /harrietwoodward/firedrake/bin/activate

[hwoo749]

Hiya, I think I've got it sorted! Thank you for your help. :))

I ran the tests and got this message - apparently they should be fine though right? Only warnings, no errors.

===================================== test session starts ======================================
platform darwin -- Python 3.11.3, pytest-7.3.1, pluggy-1.0.0
rootdir: /Users/harrietwoodward/firedrake/bin/firedrake/src/icepack
plugins: nbval-0.10.0, mpi-0.1, xdist-3.2.1, anyio-3.6.2
collecting ... firedrake:WARNING OMP_NUM_THREADS is not set or is set to a value greater than 1, we suggest setting OMP_NUM_THREADS=1 to improve performance
collected 4 items

test/ice_shelf_test.py log(error) ~= 1.90382 * log(dx) -28.0289
log(error) ~= 2.91626 * log(dx) -42.3439
log(error) ~= 3.92242 * log(dx) -56.6201
.log(error) ~= 1.90382 * log(dx) -28.0289
log(error) ~= 2.91626 * log(dx) -42.3439
log(error) ~= 3.91985 * log(dx) -56.5973
.log(error) ~= 2.4978 * log(dx) -45.7326
..

======================================= warnings summary =======================================
test/ice_shelf_test.py::test_diagnostic_solver_convergence[icepack]
test/ice_shelf_test.py::test_diagnostic_solver_convergence[icepack]
/Users/harrietwoodward/firedrake/src/loopy/loopy/target/c/compyte/dtypes.py:184: DeprecationWarning: np.bool8 is a deprecated alias for np.bool_. (Deprecated NumPy 1.24)
reg.get_or_register_dtype("bool", np.bool8)

test/ice_shelf_test.py: 12248 warnings
/Users/harrietwoodward/firedrake/src/ufl/ufl/core/expr.py:276: DeprecationWarning: Expr.ufl_domain() is deprecated, please use extract_unique_domain(expr) instead.
warnings.warn("Expr.ufl_domain() is deprecated, please "

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================== 4 passed, 12250 warnings in 572.51s (0:09:32) =========================

[ReubenHill]

You can surpress firedrake:WARNING OMP_NUM_THREADS is not set or is set to a value greater than 1, we suggest setting OMP_NUM_THREADS=1 to improve performance by doing what it says: $ export OMP_NUM_THREADS = 1 (add this to your bashrc to avoid needing to do it regularly).

The others you don't need to worry about.