Build info:
avogadro build (needs EIGEN2, doesn’t work with EIGEN3 !)
==================
Requirements
— CMake 2.6.0 or later (2.8.0 recommended)
–> module load cmake
— Qt 4.5.0 or later (4.5.3 recommended)
–> module load qt
— OpenBabel 2.2.2 or later (development version from
http://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk is recommended)
–> module load openbabel

— Eigen 2.0.3 or later (2.0.9 recommended)

(get openbabel via module load openbabel)

cmake ../ -DCMAKE_INSTALL_PREFIX=/software/avogadro/1.1.0 -DEIGEN2_INCLUDE_DIR=/software/eigen/2.0.17/include
make -j2
make install

openbabel build
======================
Requirements
============
— CMake 2.4.8 or later
–> module load cmake

— Eigen 2.0.3 or later (optional)

–> eigen install, only include files.
because cmake for openbabel points to
/software/eigen/2.0.17/include/Eigen/src/Core/util/Macros.h

but eigen include path is this:
/software/eigen/2.0.17/include/eigen2/Eigen/src/Core/util/Macros.h

had to create softlink in
/software/eigen/2.0.17/include/:
ln -s eigen2/Eigen .

— libxml2 (optional)
–> was found
— zlib (optional)
was found
— wxWidgets 2.8 (optional, needed to build GUI)

—-> module load wxGTK

cmake ../ -DCMAKE_INSTALL_PREFIX=/software/openbabel/2.3.2 -DEIGEN2_INCLUDE_DIR=/software/eigen/2.0.17/include

(this complains that EIGEN3 can’t be found, but make completes anyway, obgui opens when gcc-4.7.2 is default compiler)

make -j2
make install