Here are a couple different ways that I invoke runtests:

#
#serial, 2d_Poisson
#
~/Trilinos/development-branch/Trilinos/commonTools/test/utilities/runtests
--trilinos-dir=/home/jhu/Trilinos/development-branch/Trilinos --comm=serial
--build-dir=/home/jhu/Trilinos/development-branch/sandbox-mpi
--category=2d_Poisson
--output-dir=/home/jhu/Trilinos/development-branch/sandbox-mpi/packages/ml/test

#
#parallel, 3d_Poisson
#
~/Trilinos/development-branch/Trilinos/commonTools/test/utilities/runtests
--trilinos-dir=/home/jhu/Trilinos/development-branch/Trilinos --comm=mpi
--build-dir=/home/jhu/Trilinos/development-branch/sandbox-mpi
--category=3d_Poisson_parallel
--output-dir=/home/jhu/Trilinos/development-branch/sandbox-mpi/packages/ml/test
