sPuReMD: complete preconditioner application using level scheduling with permutations based on graph coloring.

sPuReMD: fix Jacobi iteration synchronization issues and change inner SpMV thread scheduling policy to guided for load balancing.

sPuReMD: expand domain-based QEq matrix cut-off and add control file parameter. Update control file.

sPuReMD: fix incorrect thread parallelism inside bonded force routines. Update default value of CFLAGS in autotools.

sPuReMD: refactor tri solve level sched memory management. Change OpenMP thread scheduling policy to static. Modify logging output format.

sPuReMD: fix diagonal preconditioner computation and level scheduling application. Modify preconditioner logic to compute and cache sparsity-based info. Update run script.

Just removing now unnecessary printfs that clutter the code

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.

sPuReMD: refactor preconditioning using control file parameters. Add ILUT_PAR precondioner method. Fix control file parsing bugs.

sPuReMD: begin refactoring data structures from array of structs to struct or arrays (sparse_matrix).

Add minor checks to PG-PuReMD and PuReMD. Major refactoring of sPuReMD: backport much of PuReMD code and add CUSTOM geo format.

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.