As was raised in the AMCG Fluidity developers meeting, the current configure script doesn't support the default namescheme chosen for VTK libraries in (at least) version 6.2 and 6.3, as used in unstable versions of debian. An example of a workaround method is available here: 32eb490 however this is itself incompatible with the centos packages for VTK 6.1. The intention is to extend the existing autoconf scripts to include all reasonable namings.