Unable to install on Mac M1 (original) (raw)

I have tried install pymc through conda and via pip/setuptools/github and I get the same error when I run this example code:

import numpy as np
import pymc as pm

X = np.random.normal(size=100)
y = np.random.normal(X) * 1.2

with pm.Model() as linear_model:
    weights = pm.Normal("weights", mu=0, sigma=1)
    noise = pm.Gamma("noise", alpha=2, beta=1)
    y_observed = pm.Normal(
        "y_observed",
        mu=X @ weights,
        sigma=noise,
        observed=y,
    )

    prior = pm.sample_prior_predictive()
    posterior = pm.sample()
    posterior_pred = pm.sample_posterior_predictive(posterior)

The error message is (truncated here):

ERROR (aesara.graph.opt): Optimization failure due to: constant_folding
ERROR (aesara.graph.opt): node: InplaceDimShuffle{}(TensorConstant{(1,) of 100})
ERROR (aesara.graph.opt): TRACEBACK:
ERROR (aesara.graph.opt): Traceback (most recent call last):
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/graph/opt.py", line 1850, in process_node
    replacements = lopt.transform(fgraph, node)
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/graph/opt.py", line 1055, in transform
    return self.fn(fgraph, node)
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/tensor/basic_opt.py", line 2954, in constant_folding
    thunk = node.op.make_thunk(node, storage_map, compute_map, no_recycling=[])
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/op.py", line 131, in make_thunk
    return self.make_c_thunk(node, storage_map, compute_map, no_recycling)
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/op.py", line 96, in make_c_thunk
    outputs = cl.make_thunk(
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/basic.py", line 1198, in make_thunk
    cthunk, module, in_storage, out_storage, error_storage = self.__compile__(
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/basic.py", line 1133, in __compile__
    thunk, module = self.cthunk_factory(
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/basic.py", line 1629, in cthunk_factory
    module = get_module_cache().module_from_key(key=key, lnk=self)
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/cmodule.py", line 1216, in module_from_key
    module = lnk.compile_cmodule(location)
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/basic.py", line 1538, in compile_cmodule
    module = c_compiler.compile_str(
  File "/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/cmodule.py", line 2575, in compile_str
    raise CompileError(
aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
/usr/bin/clang++ -dynamiclib -g -O3 -fno-math-errno -Wno-unused-label -Wno-unused-variable -Wno-write-strings -Wno-c++11-narrowing -fno-exceptions -fno-unwind-tables -fno-asynchronous-unwind-tables -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -m64 -fPIC -undefined dynamic_lookup -I/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/numpy/core/include -I/Users/robertarbon/opt/miniconda3/envs/pymc/include/python3.9 -I/Users/robertarbon/opt/miniconda3/envs/pymc/lib/python3.9/site-packages/aesara/link/c/c_code -L/Users/robertarbon/opt/miniconda3/envs/pymc/lib -fvisibility=hidden -o /Users/robertarbon/.aesara/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.9.0-64/tmpvw4knnhk/mba10987274f369529454d4a60996746c3927712a0b1b3928446a3c275151e2ee.so /Users/robertarbon/.aesara/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.9.0-64/tmpvw4knnhk/mod.cpp
In file included from /Users/robertarbon/.aesara/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.9.0-64/tmpvw4knnhk/mod.cpp:1:
In file included from /Users/robertarbon/opt/miniconda3/envs/pymc/include/python3.9/Python.h:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:64:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:93:16: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]
        unsigned char   *_base;
...
...

My hardware:

OS: Mac 12.1

I’ve install pymc from github (output below from conda list):
pymc 4.0.0b6 dev_0 <develop>

My CPATH is set to:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/

However if i run:

(pymc) ➜  include xcrun --show-sdk-path
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk

It’s also a bit weird that the .aesara directory created for compilation is:

/.aesara/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.9.0-64

Note: I also I installed my whole workspace/account from a previous M1 which in turn was installed from a previous intel machine (probably running 10.6 but I can’t remember exact version).

I’ve also tried running pymc3 but that also fails but with a different error.

Any help greatly appreciated!

Thanks.

UPDATE

I created a soft-link to the current MacOS SDK (12.3) from MacOSX10.15.sdk and it works, i.e.:

(pymc) ➜  SDKs ll
total 0
lrwxr-xr-x  1 root  wheel    14B 18 May 10:23 MacOSX.sdk -> MacOSX12.3.sdk
drwxr-xr-x@ 7 root  wheel   224B 13 Jan 20:18 MacOSX10.14.sdk
lrwxr-xr-x  1 root  wheel    14B 18 May 13:19 MacOSX10.15.sdk -> MacOSX12.3.sdk
drwxr-xr-x@ 7 root  wheel   224B 13 Jan 20:18 MacOSX11.0.sdk
drwxr-xr-x  7 root  wheel   224B 18 May 10:23 MacOSX11.3.sdk
lrwxr-xr-x  1 root  wheel    14B 18 May 10:22 MacOSX11.sdk -> MacOSX11.3.sdk
drwxr-xr-x  7 root  wheel   224B 22 Jul  2021 MacOSX12.0.sdk
drwxr-xr-x  7 root  wheel   224B 19 Nov 22:25 MacOSX12.1.sdk
drwxr-xr-x  7 root  wheel   224B 18 May 10:24 MacOSX12.3.sdk
lrwxr-xr-x  1 root  wheel    14B 18 May 10:22 MacOSX12.sdk -> MacOSX12.3.sdk

This doesn’t seem like the optimum solution - so any help is still appreciated.