BUG: Compatibility Issue for pytensor on macOS 15.4

[astrokang]

Describe the issue:

After updating to macOS 15.4, I encountered a failure when running pymc with pytensor. The error seems to be related to constant folding during graph optimization and LTO (Link Time Optimization) issues during compilation. I don't know. But I have tested that this issue does not occur on macOS 14.x.

Reproduceable code example:

import numpy as np
import pymc as pm
        

def pymc_fitting(x_obs, y_obs, y_err, if_xerr = False, x_err = 0., 
                 if_intrin = True,
                 x_fit_low = None, x_fit_upp = None, 
                 CL_value = 0.90, random_seed = 12):

    """
    Fitting function with pymc

    Parameters:
    
    - x_obs (array): x-axis observed values
    - y_obs (array): y-axis observed values
    - y_err (array): y-axis error values
    - if_xerr (bool): whether consider x-axis error
    - x_err (array): x-axis error values
    - x_fit_low (float): lower limit of x-axis for fitting
    - x_fit_upp (float): upper limit of x-axis for fitting
    - CL_value (float): confidence level value
    - random_seed (int): random seed value

    Returns:

    [x_fit, y_fit_med, [y_fit_low, y_fit_upp]]
    
    - x_fit (array): x-axis fitting values
    - y_fit_med (array): y-axis fitting values
    - y_fit_low (array): y-axis fitting values (lower limit)
    - y_fit_upp (array): y-axis fitting values (upper limit)
    """
    
    # Defime PyMC model and consider linear fitting ("model" Processed implicitly by PyMC)
    with pm.Model() as model:
        
        # Priors for slope and intercept
        k_value = pm.Uniform("slope", lower = -10, upper = 10)
        b_value = pm.Uniform("intercept", lower = -10, upper = 10)

        if not if_xerr:

            x_true_est = x_obs
            
        else:
            
            # Hidden variable for true x values (considering x-axis parameter error)
            x_true_est = pm.Normal("x_true", mu = x_obs, sigma = x_err, shape = len(x_obs))
        
        # Calculate the expected value of y (fitting function)
        y_est = k_value * x_true_est + b_value

        # Whether consider x-axis error
        if if_intrin:

            sigma_scatter = pm.HalfNormal("sigma_scatter", sigma = 1)

        else:

            sigma_scatter = 0
        
        # Observed y error (Implicit likelihood calculation)
        y_obs_likelihood = pm.Normal("y_obs", mu = y_est, sigma = np.sqrt(y_err**2 + sigma_scatter**2), observed = y_obs)
    
        # Sample from the posterior
        trace = pm.sample(5000, return_inferencedata = True, chains = 4, target_accept = 0.99, random_seed = random_seed)


    k_samples = trace.posterior["slope"].values.flatten()
    b_samples = trace.posterior["intercept"].values.flatten()

    if x_fit_low is None:

        x_fit_low = min(x_obs)
        x_fit_upp = max(x_obs)

    x_fit = np.linspace(x_fit_low, x_fit_upp, 1000)
    
    # Calculate the fitted y values for each sample
    y_fit_samples = np.outer(k_samples, x_fit) + b_samples[:, None]
    
    # Calculate the mean and confidence intervals for the fitted y values 
    y_fit_med = np.percentile(y_fit_samples, 50, axis = 0)
    y_fit_low = np.percentile(y_fit_samples, 50 * (1 - CL_value), axis = 0)
    y_fit_upp = np.percentile(y_fit_samples, 50 * (1 + CL_value), axis = 0)
    

    return [x_fit, y_fit_med, [y_fit_low, y_fit_upp]]




# Random seed   
np.random.seed(12)

# True line
k_true = 2
b_true = -5

x_true = np.linspace(0, 10, 50)
y_true = k_true * x_true + b_true

x_plot = np.linspace(-1, 11, 50)
ax_main.plot(x_plot, k_true * x_plot + b_true, label = label_list[0],
             color = 'k', linewidth = 10, linestyle = '-', zorder = 5)

# Observed data
x_err = np.random.uniform(0.2, 0.6, size = len(x_true))
x_obs = x_true + np.random.normal(size = len(x_true)) * x_err

intrin_sig = 2        # Intrinsic scatter
y_err = np.random.uniform(1, 3, size = len(x_true))
y_obs = y_true + np.random.normal(size = len(x_true)) * np.sqrt(y_err**2 + intrin_sig**2)


# pymc fitting
# interval_list = [x_fit, y_fit_mean, [y_fit_low, y_fit_upp]]
interval_list = pymc_fitting(x_obs, y_obs, y_err, if_xerr = True, x_err = x_err, 
                             CL_value = 0.90, random_seed = 12)

Error message:

ERROR (pytensor.graph.rewriting.basic): Rewrite failure due to: constant_folding
ERROR (pytensor.graph.rewriting.basic): node: ExpandDims{axis=0}(2)
ERROR (pytensor.graph.rewriting.basic): TRACEBACK:
ERROR (pytensor.graph.rewriting.basic): Traceback (most recent call last):
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/graph/rewriting/basic.py", line 1916, in process_node
    replacements = node_rewriter.transform(fgraph, node)
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/graph/rewriting/basic.py", line 1086, in transform
    return self.fn(fgraph, node)
           ~~~~~~~^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/tensor/rewriting/basic.py", line 1173, in constant_folding
    return unconditional_constant_folding.transform(fgraph, node)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/graph/rewriting/basic.py", line 1086, in transform
    return self.fn(fgraph, node)
           ~~~~~~~^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/tensor/rewriting/basic.py", line 1122, in unconditional_constant_folding
    thunk = node.op.make_thunk(node, storage_map, compute_map, no_recycling=[])
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/link/c/op.py", line 119, in make_thunk
    return self.make_c_thunk(node, storage_map, compute_map, no_recycling)
           ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/link/c/op.py", line 84, in make_c_thunk
    outputs = cl.make_thunk(
        input_storage=node_input_storage, output_storage=node_output_storage
    )
  File "/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/link/c/basic.py", line 1185, in make_thunk
...
ld: -lto_library library filename must be 'libLTO.dylib'
clang++: error: linker command failed with exit code 1 (use -v to see invocation)


Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?87be159b-d347-49e3-8226-abc1672dda64) or open in a [text editor](command:workbench.action.openLargeOutput?87be159b-d347-49e3-8226-abc1672dda64). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

You can find the C code in this temporary file: [/var/folders/ch/qk2fyfsd5f75z607yqb892200000gn/T/pytensor_compilation_error_xiy08s1v](https://file+.vscode-resource.vscode-cdn.net/var/folders/ch/qk2fyfsd5f75z607yqb892200000gn/T/pytensor_compilation_error_xiy08s1v)
library to_library is not found.

......

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
File ~/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/link/c/lazylinker_c.py:66
     65         if version != actual_version:
---> 66             raise ImportError(
     67                 "Version check of the existing lazylinker compiled file."
     68                 f" Looking for version {version}, but found {actual_version}. "
     69                 f"Extra debug information: force_compile={force_compile}, _need_reload={_need_reload}"
     70             )
     71 except ImportError:

ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.3, but found None. Extra debug information: force_compile=False, _need_reload=True

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
File ~/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/link/c/lazylinker_c.py:87
     86     if version != actual_version:
---> 87         raise ImportError(
     88             "Version check of the existing lazylinker compiled file."
     89             f" Looking for version {version}, but found {actual_version}. "
     90             f"Extra debug information: force_compile={force_compile}, _need_reload={_need_reload}"
     91         )
     92 except ImportError:
     93     # It is useless to try to compile if there isn't any
...
CompileError: Compilation failed (return status=1):
/Users/dendrophile/miniconda3/envs/pymc_env/bin/clang++ -dynamiclib -g -Wno-c++11-narrowing -fno-exceptions -fno-unwind-tables -fno-asynchronous-unwind-tables -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -fPIC -undefined dynamic_lookup -ld64 -I/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/numpy/_core/include -I/Users/dendrophile/miniconda3/envs/pymc_env/include/python3.13 -I/Users/dendrophile/miniconda3/envs/pymc_env/lib/python3.13/site-packages/pytensor/link/c/c_code -L/Users/dendrophile/miniconda3/envs/pymc_env/lib -fvisibility=hidden -o /Users/dendrophile/.pytensor/compiledir_macOS-15.4-arm64-arm-64bit-Mach-O-arm-3.13.2-64/lazylinker_ext/lazylinker_ext.so /Users/dendrophile/.pytensor/compiledir_macOS-15.4-arm64-arm-64bit-Mach-O-arm-3.13.2-64/lazylinker_ext/mod.cpp
ld: -lto_library library filename must be 'libLTO.dylib'
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...

PyMC version information:

Environment
• macOS version: 15.4
• Python version: 3.13 (inside Conda environment)
• pytensor version: (latest from conda-forge)
• pymc version: 5.21.1

Context for the issue:

I have successfully run my code just a week before, but now it has failed, just after I updated my macOS to 15.4 yesterday. Tested on macOS 14 (inside a VM) and everything worked fine, confirming that the issue is specific to macOS 15.4.

[welcome]

]
🎉 Welcome to PyMC! 🎉 We're really excited to have your input into the project! 💖

If you haven't done so already, please make sure you check out our Contributing Guidelines and Code of Conduct.

[astrokang]

Revise: pytensor version: 2.28.3 (latest for PyMC from conda-forge)

[ricardoV94]

CC @maresb @lucianopaz

[lingjie00]

Facing this issue as well, I suspect it's related to command line tool v16.3.

Interestingly, this issue only seems to happen within VSCode environment and does not affect when I run in terminal.

Previously it was working on VSCode terminal, but now it failed even in VSCode terminal. mmm

UPDATE:
So I think somehow it's related to the exectuables in conda, I changed the order of PATH and now it works in VSCode terminal as well

# failing PATH
/opt/homebrew/Caskroom/miniforge/base/envs/pymc/bin:/opt/homebrew/Caskroom/miniforge/base/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/ling/Library/Application Support/Code/User/globalStorage/github.copilot-chat/debugCommand

# working PATH
/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/ling/Library/Application Support/Code/User/globalStorage/github.copilot-chat/debugCommand:/opt/homebrew/Caskroom/miniforge/base/envs/pymc/bin:/opt/homebrew/Caskroom/miniforge/base/condabin

[astrokang]

THX! @lingjie00

I have also tested the solutions following @lingjie00 's suggestions. For now, I think PyMC/PyTensor compilation failures on macOS 15.4 were caused by using conda-installed clang++ instead of the system compiler. The conda version created incompatible LTO library links.

So one of my suggested solution (simpler) is as follows:

# Problematic path in conda environment
(pymc_env) $ which clang++
/Users/USER/miniconda3/envs/pymc_env/bin/clang++  ❌

# Remove conda's compiler toolchain
conda remove --force clang clangxx -n pymc_env

# Verification
(pymc_env) $ which clang++
/usr/bin/clang++  ✅

Key Fix: Forcing the environment to use macOS system compilers instead of conda's versions resolves LTO linking issues.

This solution worked consistently across VSCode and terminal after PATH adjustments! 😃

[ricardoV94]

Reopening because users will keep seeing this problem

[ricardoV94]

@maresb do you know if there's any open issue on conda related to clang?

[maresb]

I had a look and I didn't find any recent relevant issues around conda. I did find this SO post by @corneliusroemer and this Discourse thread about this same issue.

I see that libLTO.dylib is provided by the llvmdev conda-forge package, so I wonder if this is a missing dependency? It's bad to mix conda-forge and system packages like in the current workaround.

I don't use Mac, so I don't have any good way to test myself. Would anyone else be able to test if installing llvmdev is another viable workaround?

[astrokang]

THX for @maresb's reply and suggestions.

I have tried, as you advised, installing llvmdev. However, it doesn't work for solving the problem. 🤔 So, up till now, conda remove --force clang clangxx -n pymc_env seems to be the only one simplest way, at least for me.

[maresb]

Thanks @astrokang for the quick answer!

Is the error message still ld: -lto_library library filename must be 'libLTO.dylib'?

[astrokang]

Yes, the same problem again @maresb :

ERROR (pytensor.graph.rewriting.basic): Rewrite failure due to: constant_folding
ERROR (pytensor.graph.rewriting.basic): node: ExpandDims{axis=0}(2)
ERROR (pytensor.graph.rewriting.basic): TRACEBACK:
ERROR (pytensor.graph.rewriting.basic): Traceback (most recent call last):
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/graph/rewriting/basic.py", line 1922, in process_node
    replacements = node_rewriter.transform(fgraph, node)
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/graph/rewriting/basic.py", line 1086, in transform
    return self.fn(fgraph, node)
           ~~~~~~~^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/tensor/rewriting/basic.py", line 1173, in constant_folding
    return unconditional_constant_folding.transform(fgraph, node)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/graph/rewriting/basic.py", line 1086, in transform
    return self.fn(fgraph, node)
           ~~~~~~~^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/tensor/rewriting/basic.py", line 1122, in unconditional_constant_folding
    thunk = node.op.make_thunk(node, storage_map, compute_map, no_recycling=[])
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/link/c/op.py", line 119, in make_thunk
    return self.make_c_thunk(node, storage_map, compute_map, no_recycling)
           ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/link/c/op.py", line 84, in make_c_thunk
    outputs = cl.make_thunk(
        input_storage=node_input_storage, output_storage=node_output_storage
    )
  File "/Users/dendrophile/miniconda3/envs/test_env/lib/python3.13/site-packages/pytensor/link/c/basic.py", line 1185, in make_thunk
...
ld: -lto_library library filename must be 'libLTO.dylib'
clang++: error: linker command failed with exit code 1 (use -v to see invocation)


Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?88723952-b902-481c-a630-4dca737229b6) or open in a [text editor](command:workbench.action.openLargeOutput?88723952-b902-481c-a630-4dca737229b6). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

You can find the C code in this temporary file: [/var/folders/ch/qk2fyfsd5f75z607yqb892200000gn/T/pytensor_compilation_error_ujd0relt](https://file+.vscode-resource.vscode-cdn.net/var/folders/ch/qk2fyfsd5f75z607yqb892200000gn/T/pytensor_compilation_error_ujd0relt)
library to_library is not found.

......

Here is my setup workflow:

conda create -c conda-forge -n test_env "pymc>=5"   
conda activate test_env
conda install -c conda-forge nutpie blackjax numpyro astropy notebook llvmdev

and the setup details within the conda environmen:

name: test_env
channels:
  - conda-forge
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
dependencies:
  - absl-py=2.2.0=pyhd8ed1ab_0
  - accelerate=1.5.2=pyhd8ed1ab_0
  - adwaita-icon-theme=48.0=unix_0
  - aiobotocore=2.21.1=pyhd8ed1ab_0
  - aiohappyeyeballs=2.6.1=pyhd8ed1ab_0
  - aiohttp=3.11.16=py313ha9b7d5b_0
  - aioitertools=0.12.0=pyhd8ed1ab_1
  - aiosignal=1.3.2=pyhd8ed1ab_0
  - anyio=4.9.0=pyh29332c3_0
  - appnope=0.1.4=pyhd8ed1ab_1
  - argon2-cffi=23.1.0=pyhd8ed1ab_1
  - argon2-cffi-bindings=21.2.0=py313h20a7fcf_5
  - arrow=1.3.0=pyhd8ed1ab_1
  - arviz=0.21.0=pyhd8ed1ab_0
  - astropy=7.0.1=pyhd8ed1ab_0
  - astropy-base=7.0.1=py313h61b28de_0
  - astropy-iers-data=0.2025.3.31.0.36.18=pyhd8ed1ab_0
  - asttokens=3.0.0=pyhd8ed1ab_1
  - async-lru=2.0.5=pyh29332c3_0
  - atk-1.0=2.38.0=hd03087b_2
  - attrs=25.3.0=pyh71513ae_0
  - aws-c-auth=0.8.7=h771b9f8_1
  - aws-c-cal=0.8.7=hf78e982_1
  - aws-c-common=0.12.1=h5505292_0
  - aws-c-compression=0.3.1=h2da6199_3
  - aws-c-event-stream=0.5.4=hc8cef5c_3
  - aws-c-http=0.9.5=h7ae4978_0
  - aws-c-io=0.17.0=hda12475_8
  - aws-c-mqtt=0.12.2=hd618802_3
  - aws-c-s3=0.7.13=hb321cbc_3
  - aws-c-sdkutils=0.2.3=h2da6199_3
  - aws-checksums=0.2.3=h2da6199_3
  - aws-crt-cpp=0.31.1=hf6bcbf0_1
  - aws-sdk-cpp=1.11.510=hbf97231_4
  - azure-core-cpp=1.14.0=hd50102c_0
  - azure-identity-cpp=1.10.0=hc602bab_0
  - azure-storage-blobs-cpp=12.13.0=h7585a09_1
  - azure-storage-common-cpp=12.8.0=h9ca1f76_1
  - azure-storage-files-datalake-cpp=12.12.0=hcdd55da_1
  - babel=2.17.0=pyhd8ed1ab_0
  - beautifulsoup4=4.13.3=pyha770c72_0
  - blackjax=1.2.4=pyhd8ed1ab_1
  - blas=2.131=openblas
  - blas-devel=3.9.0=31_h11c0a38_openblas
  - bleach=6.2.0=pyh29332c3_4
  - bleach-with-css=6.2.0=h82add2a_4
  - botocore=1.37.1=pyge310_1234567_0
  - bottleneck=1.4.2=py313hde99e4e_0
  - bqplot=0.12.43=pyhd8ed1ab_1
  - brotli=1.1.0=hd74edd7_2
  - brotli-bin=1.1.0=hd74edd7_2
  - brotli-python=1.1.0=py313h3579c5c_2
  - bzip2=1.0.8=h99b78c6_7
  - c-ares=1.34.4=h5505292_0
  - ca-certificates=2025.1.31=hf0a4a13_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cachetools=5.5.2=pyhd8ed1ab_0
  - cairo=1.18.4=h6a3b0d2_0
  - cctools_osx-arm64=1010.6=h3b4f5d3_6
  - certifi=2025.1.31=pyhd8ed1ab_0
  - cffi=1.17.1=py313hc845a76_0
  - charset-normalizer=3.4.1=pyhd8ed1ab_0
  - chex=0.1.88=pyhd8ed1ab_1
  - clang=18.1.8=default_h474c9e2_8
  - clang-18=18.1.8=default_hf90f093_8
  - clang_impl_osx-arm64=18.1.8=h2ae9ea5_24
  - clang_osx-arm64=18.1.8=h07b0088_24
  - clangxx=18.1.8=default_h1ffe849_8
  - clangxx_impl_osx-arm64=18.1.8=h555f467_24
  - clangxx_osx-arm64=18.1.8=h07b0088_24
  - click=8.1.8=pyh707e725_0
  - cloudpickle=3.1.1=pyhd8ed1ab_0
  - colorama=0.4.6=pyhd8ed1ab_1
  - comm=0.2.2=pyhd8ed1ab_1
  - compiler-rt=18.1.8=h856b3c1_1
  - compiler-rt_osx-arm64=18.1.8=h832e737_1
  - cons=0.4.6=pyhd8ed1ab_1
  - contourpy=1.3.1=py313h0ebd0e5_0
  - cpython=3.13.2=py313hd8ed1ab_101
  - cycler=0.12.1=pyhd8ed1ab_1
  - dask-core=2025.3.0=pyhd8ed1ab_0
  - debugpy=1.8.13=py313h928ef07_0
  - decorator=5.2.1=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - epoxy=1.5.10=h1c322ee_1
  - etils=1.12.2=pyhd8ed1ab_0
  - etuples=0.3.9=pyhd8ed1ab_1
  - exceptiongroup=1.2.2=pyhd8ed1ab_1
  - executing=2.1.0=pyhd8ed1ab_1
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