# Installation on MacOS with conda **URL:** \ **Category:** installation\ **Created:** [September 16, 2026, 4:02pm UTC](https://fenicsproject.discourse.group/t/installation-on-macos-with-conda/19827 "2026-09-16T16:02:16Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![TimS](https://avatars.discourse-cdn.com/v4/letter/t/7ea924/32.png) [@TimS](https://fenicsproject.discourse.group/u/TimS)\ **Post date:** [September 16, 2026, 4:02pm UTC](https://fenicsproject.discourse.group/t/installation-on-macos-with-conda/19827/1 "2026-09-16T16:02:16Z")
I have installed conda today using the Anaconda3 distribution from [Download Anaconda Distribution | Anaconda](https://www.anaconda.com/download/) . Here is the conda info: ```auto 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: ```auto xcodebuild -version > Xcode 27.0 > Build version 27A266a ``` ```auto 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: ```auto 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: ```auto 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](https://docs.fenicsproject.org/dolfinx/v0.11.0.post0/python/_downloads/b94ac7be61dc3726ca331afd20f195d2/demo_poisson.py), however I got the following error: ```auto 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 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 : 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: ```auto 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 ```auto 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! ---
**Author:** ![TimS](https://avatars.discourse-cdn.com/v4/letter/t/7ea924/32.png) [@TimS](https://fenicsproject.discourse.group/u/TimS)\ **Post date:** [September 16, 2026, 5:42pm UTC](https://fenicsproject.discourse.group/t/installation-on-macos-with-conda/19827/2 "2026-09-16T17:42:03Z")
Uninstalling Xcode and the Command Line Tools, and then installing only the Command Line Tools Version 26.6 (but not installing Xcode at all) from [Sign In - Apple](https://developer.apple.com/download/all/?q=Command%20Line%20Tools) solved the issue! ---
**Author:** ![ottarhellan](https://avatars.discourse-cdn.com/v4/letter/o/b2d939/32.png) [@ottarhellan](https://fenicsproject.discourse.group/u/ottarhellan)\ **Post date:** [September 16, 2026, 6:14pm UTC](https://fenicsproject.discourse.group/t/installation-on-macos-with-conda/19827/3 "2026-09-16T18:14:26Z")
Great that you figured it out! I had the same issue and got Claude to debug it for me. Here’s Claudes alternate fix that doesn’t require a reinstall, maybe someone else will find it useful. Hit the same error (`ld: dynamic executables or dylibs must link with libSystem.dylib for architecture arm64`) building FFCX forms via CFFI. Turned out `/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk` was symlinked to a beta SDK whose libSystem doesn’t support plain `arm64`. As an alternative to reinstalling CLT, you can just repoint that symlink at an older SDK if one’s still on disk (check `/Library/Developer/CommandLineTools/SDKs/`): ​` sudo ln -sfn MacOSX12.1.sdk /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk ​` Worked for me without touching the Xcode/CLT install at all.