Parallel computer distributed memory

This completes the outline of FAMUSAMM. The algorithm has been implemented in the MD simulation program EGO VIII [48] in a sequential and a parallelized version the latter has been implemented and tested on a number of distributed memory parallel computers, e.g., IBM SP2, Cray T3E, Parsytec CC and ethernet-linked workstation clusters running PVM or MPI. 

The complexity analysis shows that the load is evenly balanced among processors and therefore we should expect speedup close to P and efficiency close to 100%. There are however few extra terms in the expression of the time complexity (first order terms in TV), that exist because of the need to compute the next available row in the force matrix. These row allocations can be computed ahead of time and this overhead can be minimized. This is done in the next algorithm. Note that, the communication complexity is the worst case for all interconnection topologies, since simple broadcast and gather on distributed memory parallel systems are assumed. 

Y. Hwang, R. Das, F. H. Saltz, M. Hadoscek and B. R. Brooks, Parallelizing molecular dynamics programs for distributed-memory machines , IEEE Computational Science and Engineering, Vol 2, no 2, 18-29, 1995. 

M. Rame and M. Delshad. A compositional reservoir simulator on distributed memory parallel computers. In Proceedings Volume, pages 89-100. 13th SPE Reservoir Simulation Symp (San Antonio, TX, 2/12-2/15), 1995. 

Bernardo DN, Ding YB, Kroghjespersen K, Levy RM (1995) Evaluating polarizable potentials on distributed-memory parallel computers - program-development and applications. J Comput Chem 16(9) 1141-1152... 

Beckers JVL, Lowe CP, DeLee SW (1998) An iterative PPPM method for simulating Coulombic systems on distributed memory parallel computers, Mol Simul, 20 369—383... 

The four-index transformation is a good test case for parallel algorithm development of electronic structure calculations, because it has O(N ) operations, a low computation to data transfer ratio and is a compact piece of code. Distributed-memory algorithms were presented for a number of standard QC methods by Whiteside and co-workers Li52 special emphasis on the integral transformation. Details of their implementation on a 32-processor Intel hypercube were provided. 

Rendell et al. compared three previously reported algorithms to the fourth-order triple excitation energy component in MBPT." The authors investigated the implementation of these algorithms on current Intel distributed-memory parallel computers. The algorithms had been developed for shared-... 

Sato, Tanaka, and Yao also reported a parallel implementation of the AMBER MD module.The target machine, the APIOOO distributed-memory parallel computer developed at Fujitsu, consisted of up to 1024 processor elements connected with three different networks. To obtain a higher degree of parallelism and better load balance between processors, a particle division method was developed to randomly allocate particles to processors. Experiments showed that a problem with 41,095 atoms can be processed 226 times faster with a 512-processor APIOOO than by a single processor. 

Distributed Computing An environment in which various tasks and resources are distributed among different computing systems (possibly from diiferent vendors) also used to refer to parallel computing on a distributed-memory architecture. 

Distributed Memory Memory that is apportioned to a specific node of a parallel computing system. A given node can directly access the memory on that node only. 

R. J. Harrison and R. A. Kendall, Theor. Chim. Acta, 79, 337 (1991). A Parallel Version of ARGOS A Distributed Memory Model for Shared Memory UNIX Computers. 

L. A. Covick and M. K. Sando,/ Comput. Chem., 11,1151 (1990). Four-Index Transformation on Distributed-Memory Parallel Computers. 

T. R. Furlam and H. F. King,/. Comput. Chem., submitted for publication. Implementation of a Parallel Direct SCF Algorithm on a Distributed Memory Computer. 

S. E. DeBolt and P. A. Kollman, /. Comput. Chem., 14, 312 (1993). AMBERCUBE MD, Parallelization of AMBER S Molecular Dynamics Module for Distributed-Memory Hypercube Computers. 

D. Brown, J. H. R. Clarke, M. Okuda, and T. Yamazaik, Comput. Phys. Commun., 74, 67 (1993). A Domain Decomposition Parallelization Strategy for Molecular Dynamics Simulations on Distributed Memory Machines. 

Quantum Mechanical Reactive Scattering Using a High-Performance Distributed-Memory Parallel Computer. 

Studies of Electron-Molecule Collisions on Distributed-Memory Parallel Computers. 

C. Winstead, P. G. Hipes, M. A. P. Lima, and V. McKoy,/. Chem. Phys., 94, 5455 (1991). Studies of Electron Collisions with Polyatomic Molecules Using Distributed-Memory Parallel Computers. 

J. V. L. Beckers, C. P. Lowe, and S. W. D. Leeuw, An Iterative PPPM Method for Simulating Coulombic Systems on Distributed Memory Parallel Computers, Mol. Simul., 20 (1998), 369-383. 

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