Using Multilisp for Solving Constraint Satisfaction Problems: An Application to Nucleic Acid 3D Structure Determination

This paper describes and evaluates a parallel program for determining the threedimensional structure of nucleic acids. A parallel constraint satisfaction algorithm is used to search a discrete space of shapes. Using two realistic data sets, we compare a previous sequential version of the program written in Miranda to the new sequential and parallel versions written in C, Scheme, and Multilisp, and explain how these new versions were designed to attain good absolute performance. Critical issues were: the performance of floating-point operations, garbage collection, load balancing, and contention for shared data. We found that speedup was dependent on the data set. For the first data set, nearly linear speedup was observed for up to 64 processors whereas for the second the speedup was limited to a factor of 16.