M2Mac Pystan Compile error

Interfaces PyStan
1

I got some errors when I run below pystan code.

import pystan
import matplotlib.pyplot as plt
import numpy as np

OneVar_code = """
data {
        int<lower=0> J;
        real y[J];
}
parameters {
        real<lower=-1000, upper=1000> mu;
        real<lower=0, upper=1000> sigma;
}
transformed parameters {
}
model {
        y ~ normal(mu, sigma);
}
"""

LData =  [ 44, 44, 56, 59, 44, 44, 63, 60, 34, 58,

           55, 50, 32, 61, 47, 25, 38, 47, 30, 42]

OneVar_dat = { 'J' : len(LData), 'y': LData }
sm = pystan.StanModel(model_code=OneVar_code)
fit = sm.sampling(data=OneVar_dat, iter=5000, chains=4, n_jobs=1)
print(fit)

Here is some errors I got.

DistutilsExecError                        Traceback (most recent call last)
File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/unixccompiler.py:185, in UnixCCompiler._compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    184 try:
--> 185     self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs)
    186 except DistutilsExecError as msg:

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/ccompiler.py:1041, in CCompiler.spawn(self, cmd, **kwargs)
   1040 def spawn(self, cmd, **kwargs):
-> 1041     spawn(cmd, dry_run=self.dry_run, **kwargs)

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/spawn.py:70, in spawn(cmd, search_path, verbose, dry_run, env)
     69     cmd = cmd[0]
---> 70 raise DistutilsExecError(
     71     "command {!r} failed with exit code {}".format(cmd, exitcode)
     72 )

DistutilsExecError: command '/Users/username/opt/anaconda3/envs/testenviroment/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 254

During handling of the above exception, another exception occurred:

CompileError                              Traceback (most recent call last)
Cell In[7], line 40
     35 LData =  [ 44, 44, 56, 59, 44, 44, 63, 60, 34, 58,
     36 
     37            55, 50, 32, 61, 47, 25, 38, 47, 30, 42]
     39 OneVar_dat = { 'J' : len(LData), 'y': LData }
---> 40 sm = pystan.StanModel(model_code=OneVar_code)
     41 fit = sm.sampling(data=OneVar_dat, iter=5000, chains=4, n_jobs=1)
     42 print(fit)

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/pystan/model.py:378, in StanModel.__init__(self, file, charset, model_name, model_code, stanc_ret, include_paths, boost_lib, eigen_lib, verbose, obfuscate_model_name, extra_compile_args, allow_undefined, include_dirs, includes)
    375     orig_stderr = pystan.misc._redirect_stderr()
    377 try:
--> 378     build_extension.run()
    379 finally:
    380     if redirect_stderr:
    381         # restore stderr

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py:345, in build_ext.run(self)
    342     self.compiler.set_link_objects(self.link_objects)
    344 # Now actually compile and link everything.
--> 345 self.build_extensions()

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py:467, in build_ext.build_extensions(self)
    465     self._build_extensions_parallel()
    466 else:
--> 467     self._build_extensions_serial()

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py:493, in build_ext._build_extensions_serial(self)
    491 for ext in self.extensions:
    492     with self._filter_build_errors(ext):
--> 493         self.build_extension(ext)

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py:548, in build_ext.build_extension(self, ext)
    545 for undef in ext.undef_macros:
    546     macros.append((undef,))
--> 548 objects = self.compiler.compile(
    549     sources,
    550     output_dir=self.build_temp,
    551     macros=macros,
    552     include_dirs=ext.include_dirs,
    553     debug=self.debug,
    554     extra_postargs=extra_args,
    555     depends=ext.depends,
    556 )
    558 # XXX outdated variable, kept here in case third-part code
    559 # needs it.
    560 self._built_objects = objects[:]

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/ccompiler.py:600, in CCompiler.compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
    598     except KeyError:
    599         continue
--> 600     self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
    602 # Return *all* object filenames, not just the ones we just built.
    603 return objects

File ~/opt/anaconda3/envs/testenviroment/lib/python3.8/site-packages/setuptools/_distutils/unixccompiler.py:187, in UnixCCompiler._compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    185     self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs)
    186 except DistutilsExecError as msg:
--> 187     raise CompileError(msg)

CompileError: command '/Users/username/opt/anaconda3/envs/testenviroment/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 254

My python and other module or package are latest.
If you have some solutions for this, could you let me know? Thanks in advance.

2

I’m guessing this is related to an incompatibility with libc++ 16 which we recently fixed. It’s hard to be super sure without a full error from the compiler, but I’m not sure how you can get that out of pystan

A similar issue was reported here

Since it looks like you’re using conda, you can try to manually install an older libcxx (conda install "libcxx<16"), otherwise, we plan on releasing a 2.32.1 release early next week which will include the fix for this.

3

I recommend upgrading to pystan 3.x or cmdstanpy.

Pystan 2.x is not supported any more and will not get any fixes.