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Pystan2 environment for linux machines
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| conda create -n stan2 python=3.7 --yes | |
| conda activate stan2 | |
| conda install -c anaconda gcc_linux-64 gxx_linux-64 --yes | |
| ## FOR MAC: | |
| # conda install -c anaconda clang_osx-64 clangxx_osx-64 --yes | |
| conda install -c conda-forge numpy pandas scipy cython ipython jupyterlab matplotlib freetype --yes | |
| python -m pip install --upgrade pip | |
| pip install pystan==2.19.0.0 | |
| conda install -c conda-forge arviz --yes | |
| python -c "import pystan; import arviz" |
Pystan environment for the Upcoming course: Principled Modelling in Stan. NOTE: have to fix Python=3.7 to fix this issue in matplotlib (imported by arviz) and then have to force pip to install pystan==2.19
When running on M1 Mac:
conda install -c anaconda clang_osx-64 clangxx_osx-64 --yes~ conda install -c anaconda clang_osx-64 clangxx_osx-64 --yes
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/tommylees/miniconda3/envs/stan2
added / updated specs:
- clang_osx-64
- clangxx_osx-64
The following packages will be downloaded:
package | build
---------------------------|-----------------
cctools-927.0.2 | h5ba7a2e_4 1.7 MB anaconda
clang-10.0.0 |default_hf57f61e_0 24.2 MB anaconda
clang_osx-64-10.0.0 | h05bbb7f_0 15 KB anaconda
clangxx-10.0.0 |default_hf57f61e_0 123 KB anaconda
clangxx_osx-64-10.0.0 | h05bbb7f_1 18 KB anaconda
compiler-rt-10.0.0 | h47ead80_0 77 KB anaconda
compiler-rt_osx-64-10.0.0 | hbcc88fd_0 3.1 MB anaconda
ld64-450.3 | h3c32e8a_4 1.2 MB anaconda
libllvm10-10.0.1 | h76017ad_5 20.4 MB anaconda
llvm-openmp-10.0.0 | h28b9765_0 270 KB anaconda
tapi-1000.10.8 | ha1b3eb9_0 4.9 MB anaconda
------------------------------------------------------------
Total: 56.0 MB
The following NEW packages will be INSTALLED:
cctools anaconda/osx-64::cctools-927.0.2-h5ba7a2e_4
clang anaconda/osx-64::clang-10.0.0-default_hf57f61e_0
clang_osx-64 anaconda/osx-64::clang_osx-64-10.0.0-h05bbb7f_0
clangxx anaconda/osx-64::clangxx-10.0.0-default_hf57f61e_0
clangxx_osx-64 anaconda/osx-64::clangxx_osx-64-10.0.0-h05bbb7f_1
compiler-rt anaconda/osx-64::compiler-rt-10.0.0-h47ead80_0
compiler-rt_osx-64 anaconda/noarch::compiler-rt_osx-64-10.0.0-hbcc88fd_0
ld64 anaconda/osx-64::ld64-450.3-h3c32e8a_4
libllvm10 anaconda/osx-64::libllvm10-10.0.1-h76017ad_5
llvm-openmp anaconda/osx-64::llvm-openmp-10.0.0-h28b9765_0
tapi anaconda/osx-64::tapi-1000.10.8-ha1b3eb9_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2021.10.26~ --> anaconda::ca-certificates-2020.10.14-0
certifi pkgs/main::certifi-2021.10.8-py37hecd~ --> anaconda::certifi-2020.6.20-py37_0
Downloading and Extracting Packages
compiler-rt-10.0.0 | 77 KB | ################################################################################### | 100%
libllvm10-10.0.1 | 20.4 MB | ################################################################################### | 100%
ld64-450.3 | 1.2 MB | ################################################################################### | 100%
clangxx-10.0.0 | 123 KB | ################################################################################### | 100%
compiler-rt_osx-64-1 | 3.1 MB | ################################################################################### | 100%
llvm-openmp-10.0.0 | 270 KB | ################################################################################### | 100%
cctools-927.0.2 | 1.7 MB | ################################################################################### | 100%
clang-10.0.0 | 24.2 MB | ################################################################################### | 100%
clangxx_osx-64-10.0. | 18 KB | ################################################################################### | 100%
tapi-1000.10.8 | 4.9 MB | ################################################################################### | 100%
clang_osx-64-10.0.0 | 15 KB | ################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
objc[16431]: Class AMSupportURLConnectionDelegate is implemented in both /usr/lib/libamsupport.dylib (0x1e99eb678) and /Library/Apple/System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x1042202c8). One of the two will be used. Which one is undefined.
objc[16431]: Class AMSupportURLSession is implemented in both /usr/lib/libamsupport.dylib (0x1e99eb6c8) and /Library/Apple/System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x104220318). One of the two will be used. Which one is undefined.
objc[16437]: Class AMSupportURLConnectionDelegate is implemented in both /usr/lib/libamsupport.dylib (0x1e99eb678) and /Library/Apple/System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x10442c2c8). One of the two will be used. Which one is undefined.
objc[16437]: Class AMSupportURLSession is implemented in both /usr/lib/libamsupport.dylib (0x1e99eb6c8) and /Library/Apple/System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x10442c318). One of the two will be used. Which one is undefined.When running: sm = pystan.StanModel(model_code=schools_code)
Get the error:
INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_19a09b474d1901f191444eaf8a6b8ce2 NOW.
---------------------------------------------------------------------------
DistutilsExecError Traceback (most recent call last)
~/miniconda3/envs/stan2/lib/python3.7/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
117 self.spawn(compiler_so + cc_args + [src, '-o', obj] +
--> 118 extra_postargs)
119 except DistutilsExecError as msg:
~/miniconda3/envs/stan2/lib/python3.7/distutils/ccompiler.py in spawn(self, cmd)
909 def spawn(self, cmd):
--> 910 spawn(cmd, dry_run=self.dry_run)
911
~/miniconda3/envs/stan2/lib/python3.7/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
35 if os.name == 'posix':
---> 36 _spawn_posix(cmd, search_path, dry_run=dry_run)
37 elif os.name == 'nt':
~/miniconda3/envs/stan2/lib/python3.7/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
158 "command %r failed with exit status %d"
--> 159 % (cmd, exit_status))
160 elif os.WIFSTOPPED(status):
DistutilsExecError: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 254
During handling of the above exception, another exception occurred:
CompileError Traceback (most recent call last)
<ipython-input-2-25aa85272b50> in <module>
24 'sigma': [15, 10, 16, 11, 9, 11, 10, 18]}
25
---> 26 sm = pystan.StanModel(model_code=schools_code)
27 fit = sm.sampling(data=schools_dat, iter=1000, chains=4)
~/miniconda3/envs/stan2/lib/python3.7/site-packages/pystan/model.py in __init__(self, file, charset, model_name, model_code, stanc_ret, include_paths, boost_lib, eigen_lib, verbose, obfuscate_model_name, extra_compile_args)
347
348 try:
--> 349 build_extension.run()
350 finally:
351 if redirect_stderr:
~/miniconda3/envs/stan2/lib/python3.7/distutils/command/build_ext.py in run(self)
338
339 # Now actually compile and link everything.
--> 340 self.build_extensions()
341
342 def check_extensions_list(self, extensions):
~/miniconda3/envs/stan2/lib/python3.7/distutils/command/build_ext.py in build_extensions(self)
447 self._build_extensions_parallel()
448 else:
--> 449 self._build_extensions_serial()
450
451 def _build_extensions_parallel(self):
~/miniconda3/envs/stan2/lib/python3.7/distutils/command/build_ext.py in _build_extensions_serial(self)
472 for ext in self.extensions:
473 with self._filter_build_errors(ext):
--> 474 self.build_extension(ext)
475
476 @contextlib.contextmanager
~/miniconda3/envs/stan2/lib/python3.7/distutils/command/build_ext.py in build_extension(self, ext)
532 debug=self.debug,
533 extra_postargs=extra_args,
--> 534 depends=ext.depends)
535
536 # XXX outdated variable, kept here in case third-part code
~/miniconda3/envs/stan2/lib/python3.7/distutils/ccompiler.py in compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
572 except KeyError:
573 continue
--> 574 self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
575
576 # Return *all* object filenames, not just the ones we just built.
~/miniconda3/envs/stan2/lib/python3.7/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
118 extra_postargs)
119 except DistutilsExecError as msg:
--> 120 raise CompileError(msg)
121
122 def create_static_lib(self, objects, output_libname,
CompileError: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 254
Error when trying to create environment on M1 Mac:
conda create -n stan2 python=3.7 --yes
conda activate stan2
## FOR MAC:
conda install -c anaconda clang_osx-64 clangxx_osx-64 --yes
conda install -c conda-forge numpy pandas scipy cython ipython jupyterlab matplotlib freetype --yes
python -m pip install --upgrade pip
pip install pystan==2.19.0.0
conda install -c conda-forge arviz --yes
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Weird matplotlib errors:
SO Answer Here
matplotlib/matplotlib#12601
FIX: force python to
python=3.7