PyStan + Anaconda installation instructions


#1

It would be good to add to the PyStan installation instructions, that after installing Anaconda from the installation package, it’s recommended to run
conda update --all
Without this Anaconda 4.4.0 (released in May 31) + Ubuntu 16.04, gives a cryptic error.
After this both
conda install pystan (installing PyStan 2.14)
and
pip install pystan (installing PyStan 2.16)
worked just fine for me.

Aki


#2

Anaconda finally updated their libgcc to 5.2.

This problem originates from the incompatible ABI between gcc 4.x and <5.2. The default gcc compiler for Ubuntu is >5.2. This is fine and everything works.
Then one installs Anaconda, which comes without gcc, but it has libgcc installed(numba or some other package needs it). libgcc comes with libstdc++ which is used if any C++ code is compiled with Anaconda. libgcc used to be 4.8 which meant that one could compile C++ code, but could not import anything compiled.

Now if one updates their libgcc this problem goes away.

conda update libgcc 

ps. I do not recommend using Anaconda, instead use conda virtual environment. It is clean and easy to maintain. One can even install R /R-studio in conda-env (channel r or conda-forge).

conda create -n stan_env python=3.6 numpy cython pandas matplotlib scipy pystan jupyter notebook
source activate stan_env
# to list conda environments
conda-env list

#3

Is there some other conda than the one which is part of Anaconda or Miniconda?

Aki


#4

No. It is the same. I usually only download miniconda. If one needs Anaconda:

conda install Anaconda

#5

Anaconda finally updated their libgcc to 5.2.

Is this system specific? libgcc on Mac is still 4.8.5, and I’m getting a long list of warnings when compiling stan file.

And like @avehtari mentioned, conda installs PyStan 2.14, so probably shouldn’t included pystan in the installed list if you want the latest version.


#6

It might be. I have not tested.

If it is only warnings, then no need to worry about it. It is normal.

Adding -c conda-forge to the installation line should give you the latest PyStan release (on unix and osx, have to fix this for Windows).

OT. On windows one needs M2W64 toolchain + libpython