I have installed conda today using the Anaconda3 distribution from Download Anaconda Distribution | Anaconda . Here is the conda info:
active environment : base
active env location : /opt/anaconda3
shell level : 1
user config file : /Users/[redacted]/.condarc
populated config files : /opt/anaconda3/.condarc
/opt/anaconda3/condarc.d/anaconda-auth.yml
/Users/[redacted]/.condarc
conda version : 26.7.2
conda-build version : 26.5.0
python version : 3.14.6.final.0
solver : libmamba (default)
virtual packages : __archspec=1=m3
__conda=26.7.2=0
__osx=26.6.2=0
__unix=0=0
base environment : /opt/anaconda3 (writable)
conda av data dir : /opt/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/osx-arm64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-arm64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/anaconda3/pkgs
/Users/[redacted]/.conda/pkgs
notices cache : /Users/[redacted]/Library/Caches/conda/notices
envs directories : /opt/anaconda3/envs
/Users/[redacted]/.conda/envs
temporary directory : /var/folders/6f/7rqfnkm544vctrrxvscx5ndh0000gp/T
platform : osx-arm64
user-agent : conda/26.7.2 requests/2.34.2 CPython/3.14.6 Darwin/25.6.0 OSX/26.6.2 solver/libmamba conda-libmamba-solver/26.7.0 libmambapy/2.3.2 aau/0.8.1 c/. s/. e/.
UID:GID : 502:20
netrc file : None
offline mode : False
I have Xcode and the Command Line Tools installed:
xcodebuild -version
> Xcode 27.0
> Build version 27A266a
clang -v
> Apple clang version 21.0.0 (clang-2100.3.34.2)
> Target: arm64-apple-darwin25.6.0
> Thread model: posix
> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
I then installed dolfinx as described on the fenicsproject page:
conda create -n test
conda activate test
conda install -c conda-forge fenics-dolfinx mpich pyvista
This installed fenics-dolfinx version 0.11 and related packages:
pip3 list
[...]
fenics-basix 0.11.0
fenics-dolfinx 0.11.0
fenics-ffcx 0.11.0
fenics-ufl 2026.1.0
[...]
I then tried running the demo_poisson.py script from https://docs.fenicsproject.org/dolfinx/v0.11.0.post0/python/_downloads/b94ac7be61dc3726ca331afd20f195d2/demo_poisson.py, however I got the following error:
ld: warning: duplicate -rpath '/opt/anaconda3/envs/test/lib' ignored
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libm.tbd, malformed file
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libm.tbd:4:20: error: unknown architecture
arm64e.x1-macos, arm64e.x1-maccatalyst ]
^~~~~~~~~~~~~~~
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd, malformed file
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd:4:20: error: unknown architecture
arm64e.x1-macos, arm64e.x1-maccatalyst ]
^~~~~~~~~~~~~~~
ld: dynamic executables or dylibs must link with libSystem.dylib for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Traceback (most recent call last):
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/compilers/C/unix.py", line 413, in link
self.call(linker + ld_args)
~~~~~~~~~^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/compilers/C/base.py", line 1177, in call
subprocess.check_call(cmd, env=macos.inject_ver(env), **kwargs)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/subprocess.py", line 420, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['clang', '-bundle', '-undefined', 'dynamic_lookup', '-Wl,-rpath,/opt/anaconda3/envs/test/lib', '-L/opt/anaconda3/envs/test/lib', '-Wl,-rpath,/opt/anaconda3/envs/test/lib', '-L/opt/anaconda3/envs/test/lib', './libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.o', '-lm', '-o', './libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.cpython-314-darwin.so']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/cffi/ffiplatform.py", line 48, in _build
dist.run_command('build_ext')
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/dist.py", line 1106, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1047, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/command/build_ext.py", line 95, in run
_build_ext.run(self)
~~~~~~~~~~~~~~^^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/command/build_ext.py", line 382, in run
self.build_extensions()
~~~~~~~~~~~~~~~~~~~~~^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/command/build_ext.py", line 498, in build_extensions
self._build_extensions_serial()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/command/build_ext.py", line 524, in _build_extensions_serial
self.build_extension(ext)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/command/build_ext.py", line 260, in build_extension
_build_ext.build_extension(self, ext)
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/command/build_ext.py", line 609, in build_extension
self.compiler.link_shared_object(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
objects,
^^^^^^^^
...<8 lines>...
target_lang=language,
^^^^^^^^^^^^^^^^^^^^^
)
^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/compilers/C/base.py", line 822, in link_shared_object
self.link(
~~~~~~~~~^
Compiler.SHARED_OBJECT,
^^^^^^^^^^^^^^^^^^^^^^^
...<11 lines>...
target_lang,
^^^^^^^^^^^^
)
^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/setuptools/_distutils/compilers/C/unix.py", line 415, in link
raise LinkError(msg)
distutils.compilers.C.errors.LinkError: Command '['clang', '-bundle', '-undefined', 'dynamic_lookup', '-Wl,-rpath,/opt/anaconda3/envs/test/lib', '-L/opt/anaconda3/envs/test/lib', '-Wl,-rpath,/opt/anaconda3/envs/test/lib', '-L/opt/anaconda3/envs/test/lib', './libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.o', '-lm', '-o', './libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.cpython-314-darwin.so']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/[redacted]/git/shapeopt-3d-navierstokes/numerics/demo_poisson.py", line 159, in <module>
problem = LinearProblem(
a,
...<3 lines>...
petsc_options={"ksp_type": "preonly", "pc_type": "lu", "ksp_error_if_not_converged": True},
)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/dolfinx/fem/petsc.py", line 790, in __init__
self._a = _create_form(
~~~~~~~~~~~~^
a,
^^
...<3 lines>...
entity_maps=entity_maps,
^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/dolfinx/fem/forms.py", line 476, in form
return _create_form(form)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/dolfinx/fem/forms.py", line 468, in _create_form
return _form(form)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/dolfinx/fem/forms.py", line 384, in _form
ufcx_form, module, code = jit.ffcx_jit(
~~~~~~~~~~~~^
comm, form, form_compiler_options=form_compiler_options, jit_options=jit_options
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/dolfinx/jit.py", line 61, in mpi_jit
return local_jit(*args, **kwargs)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/dolfinx/jit.py", line 221, in ffcx_jit
r = ffcx.codegeneration.jit.compile_forms([ufl_object], options=p_ffcx, **p_jit)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/ffcx/codegeneration/jit.py", line 244, in compile_forms
raise e
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/ffcx/codegeneration/jit.py", line 224, in compile_forms
impl = _compile_objects(
decl,
...<9 lines>...
visualise=visualise,
)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/ffcx/codegeneration/jit.py", line 400, in _compile_objects
ffibuilder.compile(tmpdir=cache_dir, verbose=True, debug=cffi_debug)
~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/cffi/api.py", line 720, in compile
return recompile(self, module_name, source, tmpdir=tmpdir,
target=target, source_extension=source_extension,
compiler_verbose=verbose, debug=debug, **kwds)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/cffi/recompiler.py", line 1569, in recompile
outputfilename = ffiplatform.compile('.', ext,
compiler_verbose, debug)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/cffi/ffiplatform.py", line 20, in compile
outputfilename = _build(tmpdir, ext, compiler_verbose, debug)
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/cffi/ffiplatform.py", line 54, in _build
raise VerificationError('%s: %s' % (e.__class__.__name__, e))
cffi.VerificationError: LinkError: Command '['clang', '-bundle', '-undefined', 'dynamic_lookup', '-Wl,-rpath,/opt/anaconda3/envs/test/lib', '-L/opt/anaconda3/envs/test/lib', '-Wl,-rpath,/opt/anaconda3/envs/test/lib', '-L/opt/anaconda3/envs/test/lib', './libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.o', '-lm', '-o', './libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.cpython-314-darwin.so']' returned non-zero exit status 1.
Exception ignored while calling deallocator <function LinearProblem.__del__ at 0x115b74b40>:
Traceback (most recent call last):
File "/opt/anaconda3/envs/test/lib/python3.14/site-packages/dolfinx/fem/petsc.py", line 882, in __del__
lambda obj: obj is not None, (self._solver, self._A, self._b, self._x, self._P_mat)
AttributeError: 'LinearProblem' object has no attribute '_solver'
Abort(808576911): Fatal error in internal_Finalize: Other MPI error, error stack:
internal_Finalize(50)...........: MPI_Finalize failed
MPII_Finalize(421)..............:
MPID_Finalize(711)..............:
MPIDI_OFI_mpi_finalize_hook(861):
flush_send_queue(830)...........:
MPIDI_NM_progress(108)..........:
MPIDI_OFI_handle_cq_error(593)..: OFI poll failed (default nic=utun4: Input/output error)
Inside the environment, I observe that a different clang than the system clang is used:
clang -v
> clang version 23.1.1
> Target: arm64-apple-darwin25.6.0
> Thread model: posix
> InstalledDir: /opt/anaconda3/envs/test/bin
> Configuration file: /opt/anaconda3/envs/test/bin/arm64-apple-darwin-clang.cfg
I have tried reinstalling and/or downgrading clang, however nothing seems to work.
Manual compilation of the cffi with the clang in the environment does not work (same error). Compilation using the system clang (see above) by changing directory to ~/.cache/fenics and running
mv libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.c.failed libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.c
clang -bundle -undefined dynamic_lookup -Wl,-rpath,/opt/anaconda3/envs/test/lib -L/opt/anaconda3/envs/test/lib -Wl,-rpath,/opt/anaconda3/envs/test/lib -L/opt/anaconda3/envs/test/lib ./libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.o -lm -o ./libffcx_forms_812eb41c7947a5841f4fccab85cd4e6b90e48ecf.cpython-314-darwin.so
works (no errors and the .so file is generated), but the error persists when rerunning python3 demo_poisson.py.
Help would be greatly appreciated!