Unable to install Firedrake on Mac

[huisophiewang]

Hi,
I'm having some difficulties installing Firedrake. It looks like petsc configuration failed. I'm installing it on a Macbook M3 Pro with macOS 14. I've attached the log files here. Any help would be appreciated! Thank you!
firedrake-install.log
configure.log

[connorjward]

You are failing to build chaco. It isn't essential for Firedrake to function so can you try running

export PETSC_CONFIGURE_OPTIONS=--download-chaco=no

before calling firedrake-install? Hopefully that will skip the build of chaco.

@JDBetteridge any insights as to why there are errors like:

submain/balance.c:254:18: warning: passing arguments to 'make_term_props' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
                make_term_props(graph, subnvtxs, loc2glob, assignment,

[JDBetteridge]

Chaco is (currently) a hard dependency, but the issue @Ig-dolci has linked contains the solution.

[Ig-dolci]

That is a petsc issue. So, perhaps trying to install without Chaco can be a plausible option.

[huisophiewang]

I added "--download-chaco-commit=HEAD" to chaco configuration (assuming that's the suggestion of the post referred to by @Ig-dolci), it still has the same error.

I can potentially switch to other operations systems such as Linux or Windows. What would be the recommended operation system to run firedrake?
configure.log

[connorjward]

If all goes to plan we should have updated our PETSc fork by the end of the day, which should resolve these issues ideally. Firedrake also works well on Linux or using the Windows Subsystem for Linux (WSL) on Windows.

[huisophiewang]

Thank you! Please let me know when PETSc is updated and what I need to do to.

[connorjward]

Sorry for not notifying you sooner. We did update PETSc today. If you delete your previous virtual environment and run firedrake-install again hopefully things will work for you this time.

[huisophiewang]

It still has the same Chaco error. Is there some way for me to check and make sure that I am installing the latest fixed version?

[connorjward]

Sorry it seems like PETSc have not yet fixed the Chaco build problems (https://gitlab.com/petsc/petsc/-/issues/1557). We will try to fix this ASAP next week.

[javjrg]

Hi, I have the same error. Are there some solution for this problem?

Thanks a lot for help

[connorjward]

Sorry it seems like PETSc have not yet fixed the Chaco build problems (https://gitlab.com/petsc/petsc/-/issues/1557). We will try to fix this ASAP next week.

[huisophiewang]

Is there any update about the Chaco problem?

[connorjward]

There appears to have been no progress made by PETSc on this. We may however have a workaround. A very helpful user (@lrtfm) on Slack said:

If you prefer not to downgrade your Xcode, here are some alternative ways to overcome the issues.
Edit the script firedrake-install at line786:

firedrake/scripts/firedrake-install

Line 786 in 1bbd9df

petsc_options.add("--CFLAGS=-Wno-implicit-function-declaration")

            petsc_options.add("--CFLAGS=-Wno-implicit-function-declaration")

to

            petsc_options.add("--CFLAGS=-Wno-implicit-function-declaration -Wno-int-conversion -Wno-deprecated-non-prototype -Wno-implicit-int")

to overcome the issue for now.
Here, -Wno-deprecated-non-prototype -Wno-implicit-int for chaco, and -Wno-int-conversion for openblas.

2. If you encounter an error with Cython when compiling Cython code in Firedrake, you may need to apply the following patch to Firedrake.

diff --git a/setup.py b/setup.py
index fae92d9a7..cb21b3bff 100644
--- a/setup.py
+++ b/setup.py
@@ -68,11 +68,13 @@ link_args = ["-L%s/lib" % d for d in dirs] + ["-Wl,-rpath,%s/lib" % d for d in d
 libspatialindex_so = Path(rtree.core.rt._name).absolute()
 link_args += [str(libspatialindex_so)]
 link_args += ["-Wl,-rpath,%s" % libspatialindex_so.parent]
+extra_compile_args = ["-Wno-incompatible-function-pointer-types"]
 
 extensions = [Extension("firedrake.cython.{}".format(ext),
                         sources=[os.path.join("firedrake", "cython", "{}.pyx".format(ext))],
                         include_dirs=include_dirs,
                         libraries=libs,
+                        extra_compile_args=extra_compile_args,
                         extra_link_args=link_args,
                         cython_compile_time_env=cython_compile_time_env) for (ext, libs) in cythonfiles]
 if 'CC' not in env:

[lrtfm]

There appears to be a segmentation fault issue with MUMPS in the current PETSc version on MacOS (arm64) when running in parallel, see here.

In addition to the previously mentioned patches, if you intend to use MUMPS in parallel, you may want to consider using the latest version of PETSc like so:

python3 firedrake-install --package-branch petsc Firedrake_20240312.0

[javjrg]

Thanks a lot for your support and time, I followed the instruction but when I tried to update using

firedrake-update

I have the following error:

Running /Users/javjrg/firedrake/bin/firedrake-update
BLAS config is {'BLAS': '/Users/javjrg/firedrake/src/petsc/default', 'OPENBLAS': '/Users/javjrg/firedrake/src/petsc/default', 'LDFLAGS': '-L/opt/homebrew/opt/gcc/lib/gcc/13'}
Configuration saved to /Users/javjrg/firedrake/.configuration.json
Updating the git repository for firedrake
Creating firedrake-update script.
Running ../bin/firedrake-update --no-update-script
Installing command line tools...
Checking brew doctor...
Installing required packages via homebrew...
Required package 'gcc' is already installed via Homebrew.
Required package 'autoconf' is already installed via Homebrew.
Required package 'make' is already installed via Homebrew.
Required package 'automake' is already installed via Homebrew.
Required package 'cmake' is already installed via Homebrew.
Required package 'libtool' is already installed via Homebrew.
Required package 'boost' is already installed via Homebrew.
BLAS config is {'BLAS': '/Users/javjrg/firedrake/src/petsc/default', 'OPENBLAS': '/Users/javjrg/firedrake/src/petsc/default', 'LDFLAGS': '-L/opt/homebrew/opt/gcc/lib/gcc/13'}
Configuration saved to /Users/javjrg/firedrake/.configuration.json
Finding dependencies of PyOP2

Finding dependencies of firedrake

Updating the git repository for petsc
Traceback (most recent call last):
  File "/Users/javjrg/firedrake/src/../bin/firedrake-update", line 1964, in <module>
    update_petsc = git_update("petsc", deps["petsc"])
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/javjrg/firedrake/src/../bin/firedrake-update", line 982, in git_update
    check_call(["git", "pull", "--recurse-submodules"])
  File "/Users/javjrg/firedrake/src/../bin/firedrake-update", line 674, in check_call
    log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode())
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['git', 'pull', '--recurse-submodules']' returned non-zero exit status 1.


Update log saved in /Users/javjrg/firedrake/firedrake-update.log

Can someone help me with that?

firedrake-update.log

[connorjward]

This says that you cannot run the command git pull inside of firedrake/src/petsc. Do you have unstashed changes? You can cd $VIRTUAL_ENV/src/petsc then git status to see if that's the case. You should be able to run git pull from that directory without error.

[javjrg]

Thanks for your answer. It looks like you've resolved the issue with the branch. To update, I used:

git checkout firedrake

Then, I was able to update without any problems. Finally, I ran the tests with:

cd $VIRTUAL_ENV/src/firedrake
pytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection"

And I received the following output:

================================================================================================ test session starts =================================================================================================
platform darwin -- Python 3.11.9, pytest-8.1.1, pluggy-1.4.0
rootdir: /Users/javjrg/firedrake/src/firedrake
configfile: setup.cfg
plugins: anyio-4.3.0, mpi-0.1, xdist-3.5.0, nbval-0.11.0
collected 3517 items / 3490 deselected / 1 skipped / 27 selected                                                                                                                                                     

tests/regression/test_dg_advection.py ....                                                                                                                                                                     [ 14%]
tests/regression/test_poisson_strong_bcs.py .................                                                                                                                                                  [ 77%]
tests/regression/test_poisson_strong_bcs_nitsche.py ....                                                                                                                                                       [ 92%]
tests/regression/test_stokes_mini.py ..                                                                                                                                                                        [100%]

================================================================================================== warnings summary ==================================================================================================
../fiat/FIAT/__init__.py:5
  /Users/javjrg/firedrake/src/fiat/FIAT/__init__.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    import pkg_resources

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================================================================== 27 passed, 1 skipped, 3490 deselected, 1 warning in 96.82s (0:01:36) ========================================================================
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
There is one unused database option. It is:
Option left: name:-k value: poisson_strong or stokes_mini or dg_advection source: command line

It seems like everything is now in order. Thanks again for your time.

[Ig-dolci]

There appears to be a segmentation fault issue with MUMPS in the current PETSc version on MacOS (arm64) when running in parallel, see here.

In addition to the previously mentioned patches, if you intend to use MUMPS in parallel, you may want to consider using the latest version of PETSc like so:

python3 firedrake-install --package-branch petsc Firedrake_20240312.0

I also opened an issue in PETSc for the errors with MUMPS.