Here, we will learn how to install and configure xolotl. There are two ways to install xolotl, based on your level of expertise:

Method	Download a MATLAB toolbox	Use git
Who should do this	Everyone	Developers, advanced users
Ease	Very easy	Some configuration needed
OS support	All common OSes	Probably won't work on Windows

Installing using a MATLAB toolbox

xolotl is available as a MATLAB toolbox. Click here to download it, and drag the downloaded file onto your MATLAB terminal to install it. You should get a popup that looks like this:

Click on the "Install" button and you should be all set!

Install using git

If you are comfortable with git, you can clone all the code and dependencies yourself:

git clone https://github.com/sg-s/srinivas.gs_mtools
git clone https://github.com/sg-s/puppeteer
git clone https://github.com/sg-s/xolotl
git clone https://github.com/sg-s/cpplab

You will have to manually set your MATLAB paths. Make sure you add the main folder for puppeteer, cpplab, and xolotl, and all subfolders of srinivas.gs_mtools/src.

Updating

In most cases, xolotl can update itself to the latest version using ::

xolotl.update()

If you installed using git, xolotl will attempt to do a git pull and update itself. If you installed it as a MATLAB toolbox, xolotl will delete the old toolbox, download the new one, and install that.

Uninstalling

If you installed xolotl as a MATLAB toolbox, you can easily uninstall it using:

xolotl.uninstall()

Note that this doesn't do anything if you installed using git, or if you manually downloaded the files and linked them.

Compilers on GNU/Linux

There are a couple of quirks specific to using the MEX compiler on Linux machines.

• MATLAB can be particular about the version of g++ it works with. For best results, use the compiler version recommended by MATLAB.
• In addition, it's best to point MATLAB towards the system compiler, rather than one installed through distributions like Anaconda.
• On certain Linux distributions, MEX cannot identify the installed g++ compiler, even when it exists on your path (e.g. which g++ in the terminal works fine). The error looks something like this

  >> !which g++
  /bin/g++
  >> !g++ -dumpversion
  8.1.0
  >> mex -setup C++
  Error using mex
  No supported compiler was found.

MATLAB recommends changing your path so that you default to an older version of g++. This is not strictly necessary. MATLAB can still compile using MEX with newer versions of g++ in most cases. Generally, downgrading to an older version of g++ doesn't solve this problem.

There is a relatively simply fix however. Credit goes to GitHub user bonanza123 for figuring it out.

• First, download the proper version of gcc/g++ as normal. If you use a package manager, there are generally legacy versions under gcc-VERSION where VERSION is the version number (e.g. 6). You can also find them here.
• Second, change the mex_LANG_glnxa64.xml specification file, where LANG is either C or C++. This is typically found at ~/.matlab/R2018a/mex_C_glnxa64.xml (where R2018a is the MATLAB version and we're looking for the C language file).
• Replace all references to $GCC with the path to the soft-link to your gcc compiler (e.g. /usr/bin/gcc-6). If you don't have a soft-link to your compiler set up (i.e. which gcc doesn't tell you the path to the link), then you have to set one up.
• Repeat this process for the mex_C++_glnxa64.xml file. It should be in the same location as the C-specific file. Sometimes MATLAB doesn't generate the C++ .xml file, causing a lot of errors. If it doesn't exist, copy the C-specific version of the file, rename it to mex_C++_glnxa64.xml and replace all references to gcc with g++ so that MATLAB is forced to use the correct compiler.

The problem is fixed if you see something like this in MATLAB:

  >> mex.getCompilerConfigurations('C++')
  ans =

  CompilerConfiguration with properties:

             Name: 'g++'
     Manufacturer: 'GNU'
         Language: 'C++'
          Version: ''
         Location: '/usr/bin/g++-6'
        ShortName: 'g++'
         Priority: 'A'
          Details: [1×1 mex.CompilerConfigurationDetails]
       LinkerName: ''
    LinkerVersion: ''
           MexOpt: '/home/alec/.matlab/R2018a/mex_C++_glnxa64.xml'