Pande VS, Joerg C, Yu Grosberg A, Tanaka T. Enumerations of the Hamiltonian walks on a cubic sublattice. J Phys A 1994;27: 6231--6236.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....each other. The Cilk program is based on serial code by R. Sargent of MIT s Media Laboratory. Thread length was enhanced by serializing the bottom 7 levels of the search tree. pfold is a protein folding program that finds hamiltonian paths in a three dimensional grid using backtrack search [83]. Written by Chris Joerg of MIT s Laboratory for Computer Science and V. Pande of MIT s Center for Material Sciences and Engineering, pfold was the first program to enumerate all hamiltonian paths in a 3#4#4grid. We timed the enumeration of all paths starting with a certain sequence. ray is a ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....with the gcc compiler, and the runtime system runs identically on all platforms. Many bugs in the Cilk compiler were fixed, and the runtime system has been simplified. To date, prototype applications developed in Cilk include graphics rendering (ray tracing and radiosity) protein folding [24], backtracking search, N body simulation, and dense and sparse matrix computations. Our largest application e#ort so far is a series of chess programs. One of our programs, #Socrates [18] finished second place in the 1995 ICCA World Computer Chess Championship in Hong Kong running on the ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....in this release is a debugging tool called the Nondeterminator [14, 10] which can help Cilk programmers to localize data race bugs in their code. 1.3. ABOUT THIS MANUAL 5 To date, prototype applications developed in Cilk include graphics rendering (ray tracing and radiosity) protein folding [26], backtracking search, N body simulation, and dense and sparse matrix computations. Our largest application effort is a series of chess programs. One of our programs, Socrates [19] finished second place in the 1995 ICCA World Computer Chess Championship in Hong Kong running on the 1824 node ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....This research was supported in part by the Advanced Research Projects Agency (ARPA) under Grants N00014 94 1 0985 and N00014 92 J 1310. Robert Blumofe was supported in part by an ARPA High Performance Computing Graduate Fellowship. include graphics rendering, backtrack search, protein folding [37], and the Socrates chess program [25] which won second prize at the 1995 ICCA World Computer Chess Championship running on the 1824 node Intel Paragon at Sandia National Labs. Like all runtime systems for Cilk, Cilk NOW schedules threads using a provably efficient algorithm based on the technique ....

....using a work stealing scheduler. This scheduler delivers performance that can be predicted accurately with a simple abstract model [6, 8] Moreover this simple model can be adapted to the case of heterogeneous processors and networks [32] Recently, we ran a Cilk protein folding application pfold [37] using Cilk NOW on a network of about 50 Sun SPARCstations connected by shared 10 Mb s Ethernet to solve a large scale protein folding problem. The program ran for 9 days, surviving several machine crashes and reboots, utilizing 6566 processor hours of otherwise idle cycles, with no ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....version. Also included in this release is a debugging tool, called the Nondeterminator [13] which helps Cilk programmers to localize determinacy race bugs in their code. To date, prototype applications developed in Cilk include graphics rendering, pro 4 CHAPTER 1. INTRODUCTION tein folding [25], backtracking search, N body simulation, and dense and sparse matrix computations. Our largest application effort is a series of chess programs. The previous program, Socrates [18] finished second place (before Deep Thought) in the 1995 ICCA World Computer Chess Championship in Hong Kong ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....parallel thread in Cilk 4 is typically less than 3 times the cost of an ordinary C procedure call, so Cilk programs scale down to run on one processor with nearly the efficiency of analogous C programs. To date, prototype applications developed in Cilk include graphics rendering, protein folding [16], backtracking search, N body simulation, and dense matrix computations. Our largest application is the Socrates chess program [11] which won second place out of a field of 24 systems in the 1995 ICCA World Computer Chess Championship in Hong Kong running on the 1824 node Intel Paragon at Sandia ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....that are present in the process version. Also included in this release is a debugging tool, called the Nondeterminator [12] which helps Cilk programmers to localize determinacy race bugs in their code. To date, prototype applications developed in Cilk include graphics rendering, protein folding [24], backtracking search, N body simulation, and dense and sparse ma3 trix computations. Our largest application effort is a series of chess programs. The previous program, Socrates [17] finished second place (before Deep Thought) in the 1995 ICCA World Computer Chess Championship in Hong Kong ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....parallel thread in Cilk 4 is typically less than 3 times the cost of an ordinary C procedure call, so Cilk programs scale down to run on one processor with nearly the efficiency of analogous C programs. To date, prototype applications developed in Cilk include graphics rendering, protein folding [16], backtracking search, N body simulation, and dense matrix computations. Our largest application is the Socrates chess program [11] which won second place out of a field of 24 systems in the 1995 ICCA World Computer Chess Championship in Hong Kong running on the 1824 node Intel Paragon at Sandia ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....low overhead, software implementation. A key principle in the Cilk development methodology is that the runtime mechanisms and language features are closely tied to the development of practical applications. To date, major applications developed in Cilk include graphics rendering, protein folding [PJGT] backtracking search, N body simulation, and the Socrates chess program [JK94] which won 3rd place in the 1994 ACM ICCC (International Computer Chess Championship) and recently won 2nd place in the 1995 ICCC. 1.3 The Cilk Model of Multithreaded Computation A Cilk program consists of a ....

Vijay S. Pande, Chris Joerg, Alexander Yu. Grosberg, and Toyoichi Tanaka. Enumeration of the hamiltonian walks on a cubic sublattice. To appear in Journal of Physics A.

....was itself inspired in part by the research reported here. The per processor overhead of the Cilk implementation, compared with a native C implementation, is typically at most 15 percent on various applications that we have programmed. To date, our applications include a protein folding program [19], which was the first program to find the number of hamiltonian paths in a 4 Theta 4 Theta 3 grid, and a parallel chess playing program Socrates, which won third prize at the 1994 ACM International Computer Chess Championship. Acknowledgments Thanks to Bruce Maggs of Carnegie Mellon, who ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 1994. To appear.

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Vijay S. Pande, Chris Joerg, Alexander Yu. Grosberg, and Toyoichi Tanaka. Enumeration of the hamiltonian walks on a cubic sublattice. To appear in Journal of Physcs A.

....importantly, Socrates employs a linguistic layer to help the programmer express the program independently of the scheduler. Separating the system greatly simplified the implementation of Socrates, and allowed us to implement several other parallel applications including a protein folding program [PJG 94] which was the first program to find the number of Hamiltonian paths in a 4 Theta 4 Theta 3 grid, and some smaller programs such as the doubly recursive Fibonacci routine, a backtracking search to solve the problem of determining how many ways there are to place n queens on an n by n chess ....

Vijay S. Pande, Chris Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumeration of the Hamiltonian walks on a cubic sublattice. Journal of Physics A., 1994. (To appear.)

....employed. While the enumeration of maximally compact conformations is much more feasible than, for example, all conformations of chain with a given length N , exhaustive enumerations of even maximally compact conformations of chains longer than N = 27 requires a great deal of computing power [Pande et al. 1994a] while 36mers can be easily enumerated on a massively parallel supercomputer (128 node CM 5) and the maximally compact 48 mer conformations have also been enumerated, but required 2 CPU weeks on the CM 5) Thus, 27mers have become a canonical model for folding and design studies. Recently, it ....

.... the evolutionary like optimization of proteins, Shakhnovich and Gutin Monte Carlo annealed sequences with the criteria that the sequence minimized the energy of a particular target conformation [Shakhnovich and Gutin, 1993] Another incarnation of the same idea is the so called Imprinting Model [Pande et al. 1994c] Interestingly, as soon as these models were suggested, a prediction was made as to which kind of correlations should exist in protein sequences, and those correlations were indeed immediately found [Pande et al. 1994b] see section 7.6 for more details) Later in this work, we shall discuss ....

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Pande, V. S., C. Joerg, A. Yu. Grosberg, and T. Tanaka. 1994. Enumerations of the Hamiltonian Walks on a Cubic Sublattice. J. Phys. A27:6231.

....of placing N queens on a N Theta N chessboard so that no two queens attack each other. The Cilk program is based on serial code by R. Sargent of the MIT Media Laboratory. Thread length was enhanced by serializing the bottom 7 levels of the search tree. ffl pfold is a protein folding program [35] written in conjunction with V. Pande of MIT s Center for Material Sciences and Engineering. This program finds hamiltonian paths in a threedimensional grid using backtrack search. It was the first program to enumerate all hamiltonian paths in a 3 Theta 4 Theta 4 grid. We timed the enumeration ....

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....the chosen processor. This work stealing scheduling strategy tends to provide good load balancing without requiring excessive communication [KZ93, RSAU91, ZO94] We wrote several applications in PCM, including a ray tracer based on the serial POVRAY program [POV93] and a protein folding code [PJGT94] which is still being used to investigate various models of protein formation. The PCM system performed well on these applications, achieving nearly linear speedup without adding significant overhead. This initial system showed us that we could easily build a powerful multithreaded system. The ....

....description given to us by Pande. For the rest of this section we will be concerned mainly with the implementation of this problem using PCM, focusing on the routine that enumerates all possible paths. More details on the algorithms used and the results obtained with this program are given in [PJGT94] At its heart, this program is a search program that finds all possible unique paths that visit each node of the cube exactly once. This algorithm works by incrementally building up paths through the cube until complete paths are reached. The function Figure 2 9: A Folded Polymer Count Entries ....

[Article contains additional citation context not shown here]

Vijay S. Pande, Christopher F. Joerg, Alexander Yu Grosberg, and Toyoichi Tanaka. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

....on serial code by R. Sargent of the MIT Media Laboratory. Thread length was enhanced by serializing the bottom 7 levels of the search tree. ffl pfold(x,y,z) is a protein folding program that finds hamiltonian paths in a three dimensional grid of size x Theta y Theta z using backtrack search [38]. Written by Chris Joerg of MIT s Laboratory for Computer Science and V. Pande of MIT s Center for Material Sciences and Engineering, pfold was the first program to enumerate all hamiltonian paths in a 3 Theta 4 Theta 4 grid. For our experiments, we timed the enumeration of all paths starting ....

Pande, V. S., Joerg, C. F., Grosberg, A. Y., and Tanaka, T. Enumerations of the hamiltonian walks on a cubic sublattice. Journal of Physics A, 27, 1994.

No context found.

Pande VS, Joerg C, Yu Grosberg A, Tanaka T. Enumerations of the Hamiltonian walks on a cubic sublattice. J Phys A 1994;27: 6231--6236.

No context found.

Pande, V., Grosberg, A., Joerg, C., & Tanaka, T. (1994). Enumeration of the hamiltonian walks on a cubic sublattice. J. Phys. A: Math. Gen. 27, 6231--6236.

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