Tools: update run_sim.py to work with absolute paths (by refereing supplied executable path). Begin updating testing scripts.

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.

Test harness has been rewritten to get rid of unnecessary compiles. Also small issue resulting from two active jobs writing into same file has been resolved.

Integrating the test bed I have been working on. Also integrates the bug fix in cuda_valence_angles. Also one little issue in cuda_forces has been resolved.