I've edited this post as I've broken the problem down to something smaller than a thesis. I can run the following command in the cmd window:
lualatex file.tex
with the following script no problem:
\documentclass{article}
\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{compat=1.8}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{float}
\usepackage[hang,small,bf]{caption}
\usepackage{color}
%\usetikzlibrary{external}
%\tikzexternalize
\begin{document}
The golden-crowned sifaka is a medium-sized lemur characterized by mostly white fur, prominent furry ears and a golden-orange crown.
\begin{figure}
\input{sdof.tex}
\caption{This is the caption}
\end{figure}
\begin{figure}
\input{strain.tikz}
\caption{This is the caption}
\end{figure}
\end{document}
But when I uncomment the
\usetikzlibrary{external}
\tikzexternalize
lines and use the following:
lualatex --shell-escape -interaction=nonstopmode file.tex
it compiles the first figure into file-figure0.pdf no problem but when it gets to teh second, there are problems and it gives a fatal error
sdof.tex is a simple diagram i drew myself in inkscape and the second strain.tikz is matlab2tikz output of lots of data points from a test.
_(blind guess here). – JLDiaz Jun 30 '13 at 12:54t_figs/OReilly_Gerard_Thesis-figure2.logto check whether there is any hint to your problem? – Alexander Jun 30 '13 at 15:55