HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. We installed HiPhy a while back but could not get it to run correctly in MPI mode. It took a while to puzzle out all the problems, turned out we needed to recompile from scratch, but as the source relied on cmake this required us to remove our old version and upgrade to cmake 2.8. In addition the source required GLIBCXX_3.4.15 which required gcc4.6 to be referenced. Once that was done the compile was simple:
cmake -DINSTALL_PREFIX=/opt/exp_soft/<dest> .
make MPI (or MP2)
make install
Don't leave off the final '.' in the cmake command above!
To run this as MPI requires the use of the mpirun facility:
mpirun -machinefile ${PBS_NODEFILE} HYPHYMPI data.bf
And depending on the directives the appropriate resources are assigned:
