A) Install MPI.
B) Make sure that the mpi compilers (mpicc?) are in the path visible to SCons; if they don't install to the standard place that the normal user can see, then you can try going into rosetta_source/tools/build and copying the file "site.settings.topsail" to the file "site.settings"; this causes SCons to look in more places for compilers.
C) add "extras=mpi" to your compile command line:
scons bin mode=release extras=mpi
run.sh
#$ -N relax
#$ -P eer-775-aa
#$ -l h_rt=60:00:00
#$ -cwd
#$ -o script1.log
#$ -e script1.err
#$ -pe default 8
module load compilers/gcc/4.4.2 mpi/openmpi/1.4.3_gcc
mpirun -np 64 /soft/rosetta-3.2/source-10/bin/relax.mpi.linuxgccrelease @relax.flags
