sPuReMD: enable debug builds. Fix compilation issues when optimizations disabled (-O0). Fix graph coloring data structure management.

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.

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.

sPuReMD: fix SuperLU build and code. Fix ILU_PAR (compute factors separately). Move diagonal preconditioner computation. Refactor precondition computations. General code clean-up.