PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into MPI-only code. Fix and backport numerous bugs (void pointer arithmetic and dereferences, etc.). Update code to match new data structures. Begin merging changes from OpenMP code (sPuReMD) for preconditioning work.

The MPI-Not-GPU version is able to run through all benchmarks with decent agreement with the other versions now. The test harness has been modified to allow testing between the three functional versions.
Also added a README file in the test_harness directory about how to use the harness. Finally, I have saved one copy of the output from the previous test run to sim_output_082516.txt, for future comparison.