theano - PyMC3 fails to execute on MacOS Big Sur/ PyCharm

Question

I am attempting to run some simple PyMC3 code in PyCharm on MacOS Big Sur but the execution fails and throws the following error:

Exception: ('Compilation failed (return status=1): ld: library not found for -lSystem. clang-10: error: linker command failed with exit code 1 (use -v to see invocation). ', '[Elemwise{add,no_inplace}(TensorConstant{1.0}, TensorConstant{1.0})]')

I am using PyCharm 2020.3.2. I am able to install pymc3 (version 3.8) and theano (1.0.4) into the environment. Code I am attempting to run follows:

import numpy as np
import scipy.stats as stats
import matplotlib.pyplot as plt
import pymc3 as pm

np.random.seed(123)
n_experiments = 4
theta_real = 0.35
data = stats.bernoulli.rvs(p=theta_real, size=n_experiments)

with pm.Model() as our_first_model:
    theta = pm.Beta('theta', alpha=1, beta=1)
    y = pm.Bernoulli('y', p=theta, observed=data)
    start = pm.find_MAP()
    step = pm.Metropolis()
    trace = pm.sample(1000, step=step, start=start)
    burnin = 100
    chain = trace[burnin:]
    pm.traceplot(chain, lines={'theta':theta_real});

I disabled Apple System Integrity Protection on some speculation that maybe Apple hiding /usr/include might be the source of the problem; it made no difference. No clue how else to fix this.

Answer 1

From the information in comments it seems like your anaconda is broken. Update anaconda and try again.

If that doesn't work, try to install PyMC3 in the system Python not the Anaconda one. This will use the system clang and not the Anaconda clang.