ImportError, theano compilation failure with conda main channel packages

[mfenner1]

In short, this works:

conda create --name pymc3 -c conda-forge pymc3
conda activate pymc3
python -c 'import pymc3'

and this doesn't

conda create --name pymc3  pymc3
conda activate pymc3
python -c 'import pymc3'

This question is, what has to happen in the main conda channel for the build to succeed? Is there a simple set of conda installs that will yield a working pymc3 environment (without resorting to conda-forge)?

Completely understand if this is out of scope for the main development crew. If there's interest, I'd spend some time digging into making a main-channel compatible solution.

Best,
Mark

Using a fresh conda environment, importing any version of pymc3 fails.

After:

conda create --name pymc3 pymc3
conda activate pymc3
python

import pymc3

yields:

You can find the C code in this temporary file: /var/folders/3y/xr2qnjvs0fbgwy9j5fdf39zc0000gn/T/theano_compilation_error_ufu6mdv_
Traceback (most recent call last):
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/gof/lazylinker_c.py", line 81, in <module>
    actual_version, force_compile, _need_reload))
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/gof/lazylinker_c.py", line 105, in <module>
    actual_version, force_compile, _need_reload))
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/pymc3/__init__.py", line 5, in <module>
    from .distributions import *
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/pymc3/distributions/__init__.py", line 1, in <module>
    from . import timeseries
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/pymc3/distributions/timeseries.py", line 1, in <module>
    import theano.tensor as tt
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/__init__.py", line 110, in <module>
    from theano.compile import (
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/compile/__init__.py", line 12, in <module>
    from theano.compile.mode import *
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/compile/mode.py", line 11, in <module>
    import theano.gof.vm
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/gof/vm.py", line 674, in <module>
    from . import lazylinker_c
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/gof/lazylinker_c.py", line 140, in <module>
    preargs=args)
  File "/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/gof/cmodule.py", line 2391, in compile_str
    (status, compile_stderr.replace('\n', '. ')))
Exception: Compilation failed (return status=1): ld: file not found: @rpath/libc++abi.1.dylib for architecture x86_64. clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation). 
>>> 
(pymc3)

Contents of temporary compilation file are here:

theano_compilation_error.txt

The failed compilation command from the bottom of that file is

/Users/mfenner/anaconda3/envs/pymc3/bin/clang++ -dynamiclib -g 
     -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION 
     -m64 -fPIC -undefined dynamic_lookup 
     -I/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/numpy/core/include 
     -I/Users/mfenner/anaconda3/envs/pymc3/include/python3.7m 
     -I/Users/mfenner/anaconda3/envs/pymc3/lib/python3.7/site-packages/theano/gof/c_code 
     -L/Users/mfenner/anaconda3/envs/pymc3/lib 
     -fvisibility=hidden 
     -o /Users/mfenner/.theano/compiledir_Darwin-15.6.0-x86_64-i386-64bit-i386-3.7.4-64/lazylinker_ext/lazylinker_ext.so 
     /Users/mfenner/.theano/compiledir_Darwin-15.6.0-x86_64-i386-64bit-i386-3.7.4-64/lazylinker_ext/mod.cppld: file not found: @rpath/libc++abi.1.dylib for architecture x86_64

Since this is likely a missing system file (c++ library) in a certain spot, I have the same behavior with versions 3.2, 3.3, 3.4.1, 3.5, and 3.6. Likewise, this isn't a bug with pymc3 as much as the packaging and system libraries. The major set of packages that installing via -c conda-forge added was a conda managed clang suite.

• PyMC3 Version: 3.6
• Theano Version: 1.0.3
• Python Version: 3.7.4
• Operating system: OSX

% uname -a
Darwin Marks-MacBook-Air.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64

• How did you install PyMC3: (as above)

[junpenglao]

Thanks for reporting, but the top two code snippets are identical?

[mfenner1]

DOH! My fault. Updated. (The second was supposed to be without a -c argument ... that is, using conda's main package channel).

[ricardoV94]

Closing as this seems pretty stale