High-Performance Parallelization

Hauser, J., T. Ludewig, T. Gollnick, R. Winkelmann, R. Williams, J. Muylaert, and M. Spil. 1999. A pure Java parallel flow solver. AIAA Paper No.99-0549. Hauser, J., T. Ludewig, R. Williams, R. Winkelmann, T. Gollnick, S. Brunett, and J. Muylaert. 2000. A test suite for high-performance parallel Java. Advances Engineering Software 31(8-9) 687-96. 

The large computational demands indicate that a special care must be given to searching for accurate, robust and efficient numerical methods, which are capable to exploit the power of high-performance (parallel) computers. 

The high-performance parallel direct MP2 algorithm P2. R, S, M, and N denote shells of atomic orbitals. Occupied orbitals, i, can be processed in batches, I, to reduce the storage requirement. Distributed indices are underlined. R, S pairs are distributed either statically or dynamically as explained in the text. 

Nieplocha J, Foster I, Kendall RA (1998) Chemlo high performance parallel I/o for computational chemistry applications. Int J High Perform C 12(3) 345-363. doi 10.1177/109434209801200304... 

LAMMPS. Another message-passing MD code is LAMMPS [33] used for high-performance parallelized molecular dynamics calculations. The current version (version 17) is compatible with both AMBER and CHARMM. 

Brewer EA et al. Proteus a high-performance parallel-architecture simulator. Cambridge, MA Massachusetts Institute of Technology. Laboratory for Computer Science 1991. 

Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L., Skeel, R.D., Schul-ten, K. NAMD - A parallel, object-oriented molecular dynamics program. Int. J. Supercomputing Applications and High Performance Computing 10 (1996) 251-268. 

K. Schulten. NAMD—a parallel, object-oriented molecular dynamics program. Inti. J. Supercomput. Applies. High Performance Computing, 10 251-268, 1996. 

W. T. Rankin and J. A. Board, Jr., A Portable Distributed Implementation of the Parallel Multipole Tree Algorithm, Proceedings, Fourth IEEE International Symposium on High Performance Distributed Computing, IEEE Computer Society Press (1995), pp. 17-22. 

Rankin, W., Board, J. A portable distributed implementation of the parallel multipole tree algorithm. IEEE Symposium on High Performance Distributed Computing. Duke University Technical Report 95-002. 

Clark, T., Hanxleden, R., McCammon, J., Scott, L. Parallelizing molecular dynamics using spatial decomposition. In Proceedings of the scalable high performance computing conference. May 23-25, 1994, Knoxville, Tennessee. IEEE Computer Society Press, Los Alamitos, California, 1994. 

NWChem is part of the Molecular Science Software Suite (MS ) which has been recognized by R D Magazine as one of the 100 most technologically signihcant new products and processes of 1999. The other elements of MS are Ecce, which is a problem-solving environment, and ParSoft, which is the underlying libraries and tools for parallel communication and high-performance input/output. All of the MS components are available publicly. 

Parallel to the development of mass spectrometric instrumentation and methodologies, the improvements of separation techniques, such as gas chromatography (GC), high performance liquid chromatography (HPLC) and capillary electrophoresis (CE), and of their coupling with MS allowed the study of complex mixtures, that are generally encountered in most studies. 

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