A new load-balancing strategy for the solution of dynamical large-tree-search problems using a hierarchical approach

We describe a new load-balancing strategy, applied here to the protein structure prediction problem, for improving the efficiency of the hierarchical approach when dealing with coarse-grained problems associated with large tree searches. Unlike other load-balancing strategies that reassign load from the heavily loaded processors to the lightly loaded or idle ones, the proposed strategy changes the virtual communication tree among the processors as the computational tree changes. The strategy incurs minimal overhead and is scalable.

[1]  Thomas L. Casavant,et al.  A Taxonomy of Scheduling in General-Purpose Distributed Computing Systems , 1988, IEEE Trans. Software Eng..

[2]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[3]  Vipin Kumar,et al.  Parallel depth first search. Part I. Implementation , 1987, International Journal of Parallel Programming.

[4]  Alexander H. G. Rinnooy Kan,et al.  Stochastic methods for global optimization , 1984 .

[5]  Panos M. Pardalos,et al.  Parallel Processing of Discrete Optimization Problems , 1995 .

[6]  George L. Nemhauser,et al.  The Traveling Salesman Problem: A Survey , 1968, Oper. Res..

[7]  Greg L. Hura,et al.  Solution X-ray scattering as a probe of hydration-dependent structuring of aqueous solutions , 1999 .

[8]  George Cybenko,et al.  Dynamic Load Balancing for Distributed Memory Multiprocessors , 1989, J. Parallel Distributed Comput..

[9]  Teodor Gabriel Crainic,et al.  Branch-and-bound parallelization strategies applied to a depot location and container fleet management problem , 2000, Parallel Comput..

[10]  Teodor Gabriel Crainic,et al.  PARALLEL BRANCH-AND-BOUND ALGORITHMS: SURVEY AND SYNTHESIS , 1993 .

[11]  Katherine Yelick,et al.  Randomized load balancing for tree-structured computation , 1994, Proceedings of IEEE Scalable High Performance Computing Conference.

[12]  Laxmikant V. Kalé,et al.  Run-Time Support for Adaptive Load Balancing , 2000, IPDPS Workshops.

[13]  C. Levinthal.  Are there pathways for protein folding , 1968 .

[14]  Francis C. M. Lau,et al.  An analytical comparison of nearest neighbor algorithms for load balancing in parallel computers , 1995, Proceedings of 9th International Parallel Processing Symposium.

[15]  Richard H. Byrd,et al.  A Global Optimization Strategy for Predicting -helical Protein Tertiary Structure , 2000, Comput. Chem..

[16]  Richard H. Byrd,et al.  A Hierarchical Approach for Parallelization of a Global Optimization Method for Protein Structure Prediction , 1999, Euro-Par.

[17]  Reinhard Lüling,et al.  Solving the traveling salesman problem with a distributed branch-and-bound algorithm on a 1024 processor network , 1995, Proceedings of 9th International Parallel Processing Symposium.

[18]  Geoffrey C. Fox,et al.  Hierarchical Scheduling of Dynamic Parallel Computaion on Hypercube Multicomputers , 1994, J. Parallel Distributed Comput..

[19]  Vipin Kumar,et al.  Parallel depth first search. Part II. Analysis , 1987, International Journal of Parallel Programming.

[20]  P. Argos,et al.  Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence. , 1995, Critical reviews in biochemistry and molecular biology.

[21]  L. G. Mitten.  Branch-and-Bound Methods: General Formulation and Properties , 1970, Oper. Res..

[22]  Silvia A. Crivelli,et al.  Task Parallelism: What a Tool Can Provide and What Should Be Left to the User , 1996, Euro-Par, Vol. I.

[23]  Cauligi S. Raghavendra,et al.  A Dynamic Load-Balancing Policy With a Central Job Dispatcher (LBC) , 1992, IEEE Trans. Software Eng..

[24]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[25]  Vipin Kumar,et al.  Floorplan optimization on multiprocessors , 1989, Proceedings 1989 IEEE International Conference on Computer Design: VLSI in Computers and Processors.

[26]  Rainer Pollak.  A Hierarchical Load Balancing Environment for Parallel and Distributed Supercomputer , 1995 .

[27]  Silvia A. Crivelli,et al.  The PMESC Programming Library for Distributed-Memory MIMD Computers , 1999, J. Parallel Distributed Comput..

[28]  Bernard Gendron,et al.  Parallel Branch-and-Branch Algorithms: Survey and Synthesis , 1994, Oper. Res..

[29]  Laxmikant V. Kalé,et al.  Chare Kernel - a Runtime Support System for Parallel Computations , 1991, J. Parallel Distributed Comput..

[30]  Edward D. Lazowska,et al.  A Comparison of Receiver-Initiated and Sender-Initiated Adaptive Load Sharing , 1986, Perform. Evaluation.

[31]  H. Scheraga,et al.  Conformational Energy Calculations on Polypeptides and Proteins , 1994 .

[32]  Brett W. Bader,et al.  A physical approach to protein structure prediction. , 2002, Biophysical Journal.

[33]  Udi Manber,et al.  DIB—a distributed implementation of backtracking , 1987, TOPL.

[34]  R. Lathrop.  The protein threading problem with sequence amino acid interaction preferences is NP-complete. , 1994, Protein engineering.

[35]  Z. Hafidi,et al.  Load Balancing and Parallel Tree Search: The MPIDA* Algorithm , 1995, PARCO.

[36]  Laxmikant V. Kalé,et al.  A load balancing strategy for prioritized execution of tasks , 1993, [1993] Proceedings Seventh International Parallel Processing Symposium.