There is a compatibility issue affecting some Ubuntu 9.10 users, and probably anyone using CUDA 2.3 with gcc-4.4. Symptom: errors about “__sync_fetch_and_add” being undefined. Solution 1: make gcc-4.3 the default gcc (http://pascalg.wordpress.com/2010/01/14/cuda-on-ubuntu-9-10linux-mint-helena/) Solution 2: make another gcc (e.g. gcc-4.3) the default just for nvcc. Do this by making a directory (e.g. $HOME/.theano/nvcc-bindir) and installing two symlinks in it: one called gcc pointing to gcc-4.3 (or lower) and one called g++ pointing to g++-4.3 (or lower). Then add compiler_bindir = /path/to/nvcc-bindir to the [nvcc] section of your .theanorc (libdoc_config).
.theanorc file should be under the folder $HOME. If there is no such file, then create a new one.