Stan.jl Setup

2018-07-25 Julia Andrew B. Collier

I’m busy preparing a poster about Stan.jl for JuliaCon 2018. Getting set up is pretty simple, although there are some minor details that I thought I’d document.

Installing CmdStan

The Stan.jl uses the CmdStan command line client for interacting with Stan. This is what I did to install CmdStan on my Ubuntu 18.04 system.

  1. Download the source distribution.

    $ wget -P /tmp/ https://github.com/stan-dev/cmdstan/releases/download/v2.17.1/cmdstan-2.17.1.tar.gz
  2. Unpack it under /opt/.

    $ cd /opt
    $ sudo tar -zxvf /tmp/cmdstan-2.17.1.tar.gz
    $ cd cmdstan-2.17.1
  3. Build.

    $ sudo make build

Since the distribution was unpacked under /opt/ it was read only for non-root users. As a result I had a minor issue actually running my first Stan model because in the process Stan tried to create the precompiled header model_header.hpp.gch under /opt/ which, of course, resulted in a permission denied error. Quick fix for this: apply the changes from this pull request and rebuild. Sorted!

Upon success you can clean up the download.

$ rm /tmp/cmdstan-2.17.1.tar.gz

Julia Initialisation

There are a couple of ways to tell Julia where to find stanc. You can either set an environment variable (this should ideally be appended to the end of ~/.bashrc so that it is applied to each session).

export CMDSTAN_HOME=/opt/cmdstan-2.17.1/

Alternatively, if you don’t want to clutter up your shell namespace you can define it in your personal Julia initialisation file, ~/.juliarc.jl:

const CmdStanDir = "/opt/cmdstan-2.17.1/";

I prefer the second approach.

Install the Package

Now fire up Julia then install and load the Stan.jl package.

julia> Pkg.add("Stan")
julia> using Stan

Find links to pertinent documentation in the package repository.

Next: Chairing a Conference Session.
Previous: What's New in R 3.5.0?.