Can't make conda environment on Intel Mac (Tahoe 26.3.1a)

[rwest]

Bug Description

When creating a new conda environment from environment.yml using conda env create, the solver hangs indefinitely (observed >47 minutes with no resolution).

conda env create -f environment.yml -n rmg_env18 -v
Channels:
 - conda-forge
 - rmg
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: |

The trigger for needing a fresh environment was the recent addition of pysidt-rmg to the dependencies.

How To Reproduce

1. On macOS 26 (Tahoe) with an Intel (osx-64) machine, clone RMG-Py at or near commit 3.3.0-605-g17990e8ee
2. Run conda env create -f environment.yml -n rmg_env_new
3. Observe that the solver never completes

Expected Behavior

The conda environment should resolve and install within a few minutes, as it does on CI (macOS runners on GitHub Actions).

Workaround

Rather than creating a fresh environment, I activated my previous environment (rmg_env17, Python 3.11.14) and installed the missing package directly:

conda install -c rmg pysidt-rmg

This succeeded, for me, and my environment is working.

But it leaves our installation method for others with a similar setup broken.

Installation Information

• OS: macOS 26.3.1 alpha (ProductVersionExtra: (a), Darwin 25.3.0) — Intel x86_64 (osx-64 platform)
• Installation method: Source install from environment.yml via Miniconda3
• conda version: 26.1.1
  • solver: libmamba (default)
  • conda-libmamba-solver: 25.4.0
  • libmamba / libmambapy: 2.1.1
• RMG-Py: 3.3.0-605-g17990e8ee (from git describe --tags on main)
• RMG-database: 3.3.0-22-g2c90c6985

Key packages in the working rmg_env17 environment (Python 3.11.14, osx-64):

Package	Version	Channel
python	3.11.14	conda-forge
cython	3.0.12	conda-forge
numpy	1.26.4	conda-forge
scipy	1.16.0	conda-forge
rdkit	2025.09.5	conda-forge
openbabel	3.1.1	conda-forge
matplotlib	3.10.8	conda-forge
mopac	23.1.2	conda-forge
pydas	1.0.4	rmg
pydqed	1.0.4	rmg
pysidt-rmg	1.2.0	rmg

Additional Context

Hypothesis (from Claude Code, not verified): The hang is likely caused by the __osx virtual package being set to 26.3.1 (macOS Tahoe alpha). The libmamba solver may be spending a very long time trying to satisfy package constraints in conda-forge and the rmg channel that were authored before macOS 26 existed — for example, packages that specify an upper bound on __osx or that pin osx_is_app_ext. This would explain why CI on macOS (GitHub Actions runners on Sequoia/15.x) passed without issue. Other Intel Mac users on stable macOS releases may not hit this at all.

I note that updating conda itself didn't help (conda update -n base -c defaults conda upgraded from 26.1.0 to 26.1.1 but 26.3.2 appears to be the newest, which may require a newer Python in the base environment, which would mean reinstalling Miniconda entirely).

[rwest]

Some follow-up diagnostics after posting this issue. (these notes drafted by Claude)

What I tried:

1. CONDA_OVERRIDE_OSX=14.0 conda env create -f environment.yml -n rmg_env18 (libmamba solver) — killed after 12 minutes, no resolution
2. CONDA_OVERRIDE_OSX=13.0 conda env create -f environment.yml -n rmg_env18 --solver=classic — killed after 15 minutes, no resolution

What this rules out:

• The __osx=26.3.1 virtual package is probably not the main cause — overriding it to 14.0 or 13.0 made no difference.
• It's not a libmamba-vs-classic issue — both solvers hang equally.
• pysidt-rmg itself is not the source of complexity. When installed into an existing environment it only pulled in dill and multiprocess, both trivial packages.

What the CI logs reveal:

Inspecting the GitHub Actions log for the macos-15-intel job, the CI runner also takes 1588 seconds (26 minutes) to resolve the environment — so a fresh solve from environment.yml is slow everywhere, not just on macOS 26.

The key difference between CI and my local setup is the solver version:

Component	Local	CI
libmamba	2.1.1	2.6.0
conda-libmamba-solver	25.4.0	26.4.0

CI also uses mamba env create (not conda env create) and injects a python=3.11 pin before solving.

Hypothesis (from Claude Code, not verified): The indefinite hang locally — versus a slow-but-successful solve on CI — is most likely due to bugs in libmamba 2.1.1 that were fixed by 2.6.0. The next thing to try is upgrading libmamba in the base environment. I'll try that tomorrow.

Possible longer-term fix?:

Even on CI a fresh solve takes 26 minutes, which is uncomfortably long. Shipping a conda-lock lockfile alongside environment.yml could make fresh installs fast and reproducible for everyone — users install from a pre-solved lockfile with no solver run required:

conda-lock install --name rmg_env conda-lock.yml

[calvinp0]

Hi @rwest,

I just wanted to add here that for our ARC install and RMG installation in our CI and Dockerfile we noticed that if we set the python version in the command line, it improved the solve time.

For example

mamba env create -f environment.yml python=3.9

From my understanding, and as Claude pointed out, pinning the python version reduced the backtracking, and that the python version would take precedence before any package version is considered. Now, I don't fully understand the complete idea of why this helps but it did improve the solve time.

Here in our ARC PR, I mentioned it: ReactionMechanismGenerator/ARC#867 (comment)
Although, I am aware this was in relation to Micromamba but since Mamba and Micromamba are the same org, I believe they would follow the same rules.

[rwest]

Thanks @calvinp0, that was a very helpful direction to follow.
A few notes I've discovered so far.

1. the conda env create -f environment.yml route (and mamba equivalent) ignores any additional command line specifications like the python version.
2. the work-around (as done behind the scenes by the setup-miniconda action in our CI) is to patch the environment.yml file before installing from it, so the python=3.11 pin is inside the dependencies list.
3. there's a newer preferred route to drop the env word and just do conda create -f environment.yml which will take additional commands, like your example conda env create -f environment.yml python=3.11 documented here.
4. ...but, that was introduced very recently in conda 26.3.0 (2026-03-30) and the newest version I can get by running conda update -n base -c conda-forge conda is 26.1.1.
5. ...but explicitly forcing the newer conda via conda install -n base -c conda-forge conda=26.3 does work (so dumb that the method they tell you to use to update it doesn't actually update it)
6. With this newest conda (I got 26.3.2) the command conda create --file environment.yml -n rmg_env18 python=3.11 does not immediately crash. Update: it solved in only a couple of minues! I seem to have at environment!

So, what worked for me:

conda deactivate
conda install -n base -c conda-forge conda=26.3
conda create --file environment.yml -n rmg_env18 python=3.11
conda activate rmg_env18

Thoughts on what we should recommend in our installation instructions?
It's more steps for the user, but patching the environment.yml to include python=3.11 inside it is likely to work with older conda versions. Or we could guide people through getting a newer conda, and start telling everyone to use conda create --file... instead of conda env create --file... ?

Unfortunately there'll be another comment after this describing how the environment doesn't work

[rwest]

More bad news:

When I did make in the new environment it crashed with

building 'rmgpy.rmgobject' extension
clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/rwest/miniconda3/envs/rmg_env18/include -fPIC -O2 -isystem /Users/rwest/miniconda3/envs/rmg_env18/include -I/Users/rwest/miniconda3/envs/rmg_env18/lib/python3.11/site-packages/numpy/core/include -I/Users/rwest/miniconda3/envs/rmg_env18/include/python3.11 -c rmgpy/rmgobject.c -o build/temp.macosx-11.0-x86_64-cpython-311/rmgpy/rmgobject.o
clang: error: invalid version number in 'MACOSX_DEPLOYMENT_TARGET=11.0'
error: command '/usr/bin/clang' failed with exit code 1

I suspected polluted environment variables, so I started a new terminal, reactivated the new conda environment, and ran make clean.
but that now says /Users/rwest/miniconda3/envs/rmg_env18/bin/python: No module named pip.
Apparently pip is not in our environment.yml. So I conda install pip and run make clean then make still crashes.

I tried make build to see if that's any easier than the full make install. The output is simpler and shorter and I think points to the problem.

make build
python setup.py build_ext --inplace
Deduplicated LDFLAGS from '-Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib' to '-Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib'
Deduplicated LDSHARED from 'clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib' to 'clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib'
Deduplicated BLDSHARED from 'clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib' to 'clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib'
Deduplicated PY_LDFLAGS from '-Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib -Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib' to '-Wl,-rpath,/Users/rwest/miniconda3/envs/rmg_env18/lib -L/Users/rwest/miniconda3/envs/rmg_env18/lib'
Compiling rmgpy/rmgobject.pyx because it changed.
Compiling rmgpy/kinetics/arrhenius.pyx because it changed.
Compiling rmgpy/kinetics/chebyshev.pyx because it changed.
Compiling rmgpy/kinetics/kineticsdata.pyx because it changed.
Compiling rmgpy/kinetics/falloff.pyx because it changed.
Compiling rmgpy/kinetics/model.pyx because it changed.
Compiling rmgpy/kinetics/tunneling.pyx because it changed.
Compiling rmgpy/kinetics/surface.pyx because it changed.
Compiling rmgpy/kinetics/uncertainties.pyx because it changed.
Compiling rmgpy/molecule/atomtype.py because it changed.
Compiling rmgpy/molecule/element.py because it changed.
Compiling rmgpy/molecule/graph.pyx because it changed.
Compiling rmgpy/molecule/group.py because it changed.
Compiling rmgpy/molecule/molecule.py because it changed.
Compiling rmgpy/molecule/symmetry.py because it changed.
Compiling rmgpy/molecule/vf2.pyx because it changed.
Compiling rmgpy/molecule/converter.py because it changed.
Compiling rmgpy/molecule/translator.py because it changed.
Compiling rmgpy/molecule/util.py because it changed.
Compiling rmgpy/molecule/inchi.py because it changed.
Compiling rmgpy/molecule/resonance.py because it changed.
Compiling rmgpy/molecule/pathfinder.py because it changed.
Compiling rmgpy/molecule/kekulize.pyx because it changed.
Compiling rmgpy/pdep/collision.pyx because it changed.
Compiling rmgpy/pdep/configuration.pyx because it changed.
Compiling rmgpy/pdep/me.pyx because it changed.
Compiling rmgpy/pdep/msc.pyx because it changed.
Compiling rmgpy/pdep/reaction.pyx because it changed.
Compiling rmgpy/pdep/rs.pyx because it changed.
Compiling rmgpy/pdep/cse.pyx because it changed.
Compiling rmgpy/statmech/conformer.pyx because it changed.
Compiling rmgpy/statmech/mode.pyx because it changed.
Compiling rmgpy/statmech/rotation.pyx because it changed.
Compiling rmgpy/statmech/schrodinger.pyx because it changed.
Compiling rmgpy/statmech/torsion.pyx because it changed.
Compiling rmgpy/statmech/translation.pyx because it changed.
Compiling rmgpy/statmech/vibration.pyx because it changed.
Compiling rmgpy/thermo/thermodata.pyx because it changed.
Compiling rmgpy/thermo/model.pyx because it changed.
Compiling rmgpy/thermo/nasa.pyx because it changed.
Compiling rmgpy/thermo/wilhoit.pyx because it changed.
Compiling rmgpy/constants.py because it changed.
Compiling rmgpy/quantity.py because it changed.
Compiling rmgpy/reaction.py because it changed.
Compiling rmgpy/species.py because it changed.
Compiling rmgpy/chemkin.pyx because it changed.
Compiling rmgpy/solver/base.pyx because it changed.
Compiling rmgpy/solver/simple.pyx because it changed.
Compiling rmgpy/solver/liquid.pyx because it changed.
Compiling rmgpy/solver/mbSampled.pyx because it changed.
Compiling rmgpy/solver/surface.pyx because it changed.
[ 1/51] Cythonizing rmgpy/chemkin.pyx
[ 2/51] Cythonizing rmgpy/constants.py
[ 3/51] Cythonizing rmgpy/kinetics/arrhenius.pyx
[ 4/51] Cythonizing rmgpy/kinetics/chebyshev.pyx
[ 5/51] Cythonizing rmgpy/kinetics/falloff.pyx
[ 6/51] Cythonizing rmgpy/kinetics/kineticsdata.pyx
[ 7/51] Cythonizing rmgpy/kinetics/model.pyx
[ 8/51] Cythonizing rmgpy/kinetics/surface.pyx
[ 9/51] Cythonizing rmgpy/kinetics/tunneling.pyx
[10/51] Cythonizing rmgpy/kinetics/uncertainties.pyx
[11/51] Cythonizing rmgpy/molecule/atomtype.py
[12/51] Cythonizing rmgpy/molecule/converter.py
[13/51] Cythonizing rmgpy/molecule/element.py
[14/51] Cythonizing rmgpy/molecule/graph.pyx
[15/51] Cythonizing rmgpy/molecule/group.py
[16/51] Cythonizing rmgpy/molecule/inchi.py
[17/51] Cythonizing rmgpy/molecule/kekulize.pyx
[18/51] Cythonizing rmgpy/molecule/molecule.py
[19/51] Cythonizing rmgpy/molecule/pathfinder.py
[20/51] Cythonizing rmgpy/molecule/resonance.py
[21/51] Cythonizing rmgpy/molecule/symmetry.py
[22/51] Cythonizing rmgpy/molecule/translator.py
[23/51] Cythonizing rmgpy/molecule/util.py
[24/51] Cythonizing rmgpy/molecule/vf2.pyx
[25/51] Cythonizing rmgpy/pdep/collision.pyx
[26/51] Cythonizing rmgpy/pdep/configuration.pyx
[27/51] Cythonizing rmgpy/pdep/cse.pyx
[28/51] Cythonizing rmgpy/pdep/me.pyx
[29/51] Cythonizing rmgpy/pdep/msc.pyx
[30/51] Cythonizing rmgpy/pdep/reaction.pyx
[31/51] Cythonizing rmgpy/pdep/rs.pyx
[32/51] Cythonizing rmgpy/quantity.py
[33/51] Cythonizing rmgpy/reaction.py
[34/51] Cythonizing rmgpy/rmgobject.pyx
[35/51] Cythonizing rmgpy/solver/base.pyx
[36/51] Cythonizing rmgpy/solver/liquid.pyx
[37/51] Cythonizing rmgpy/solver/mbSampled.pyx
[38/51] Cythonizing rmgpy/solver/simple.pyx
[39/51] Cythonizing rmgpy/solver/surface.pyx
warning: rmgpy/solver/surface.pyx:408:61: Unreachable code
[40/51] Cythonizing rmgpy/species.py
[41/51] Cythonizing rmgpy/statmech/conformer.pyx
[42/51] Cythonizing rmgpy/statmech/mode.pyx
[43/51] Cythonizing rmgpy/statmech/rotation.pyx
[44/51] Cythonizing rmgpy/statmech/schrodinger.pyx
[45/51] Cythonizing rmgpy/statmech/torsion.pyx
[46/51] Cythonizing rmgpy/statmech/translation.pyx
[47/51] Cythonizing rmgpy/statmech/vibration.pyx
[48/51] Cythonizing rmgpy/thermo/model.pyx
[49/51] Cythonizing rmgpy/thermo/nasa.pyx
[50/51] Cythonizing rmgpy/thermo/thermodata.pyx
[51/51] Cythonizing rmgpy/thermo/wilhoit.pyx
/Users/rwest/miniconda3/envs/rmg_env18/lib/python3.11/site-packages/setuptools/dist.py:334: InformationOnly: Normalizing '4.0.0.rc1' to '4.0.0rc1'
  self.metadata.version = self._normalize_version(self.metadata.version)
running build_ext
building 'rmgpy.rmgobject' extension
creating build/temp.macosx-11.0-x86_64-cpython-311/rmgpy
clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/rwest/miniconda3/envs/rmg_env18/include -fPIC -O2 -isystem /Users/rwest/miniconda3/envs/rmg_env18/include -I/Users/rwest/miniconda3/envs/rmg_env18/lib/python3.11/site-packages/numpy/core/include -I/Users/rwest/miniconda3/envs/rmg_env18/include/python3.11 -c rmgpy/rmgobject.c -o build/temp.macosx-11.0-x86_64-cpython-311/rmgpy/rmgobject.o
clang: error: invalid version number in 'MACOSX_DEPLOYMENT_TARGET=11.0'
error: command '/usr/bin/clang' failed with exit code 1
make: *** [build] Error 1

[rwest]

Turns out my clang compiler was too old (Apple clang version 11.0.0 (clang-1100.0.33.16), installed in 2019). Nuking and reinstalling the MacOS X developer tools solved it:

sudo rm -rf /Library/Developer/CommandLineTools
xcode-select --install