Efficient Parallel Execution of Sequence Similarity Analysis Via Dynamic Load Balancing
نویسندگان
چکیده
We present a parallel approach to analyzing sequence similarity in a set of genomes that employs dynamic load balancing to address the variation in execution time for genes of different lengths and complexity, the variation in processor power in different nodes of the computer cluster, and the variation in other load on the nodes. Our approach executes using MPI on a cluster of computers. We provide experimental results to demonstrate the effectiveness of using our approach in conjunction with NCBI BLAST.
منابع مشابه
A novel dynamic load balancing scheme for parallel systems
Adaptive mesh refinement (AMR) is a type of multiscale algorithm that achieves high resolution in localized regions of dynamic, multidimensional numerical simulations. One of the key issues related to AMR is dynamic load balancing (DLB), which allows large-scale adaptive applications to run efficiently on parallel systems. In this paper, we present an efficient DLB scheme for structured AMR (SA...
متن کاملParallel Global Aircraft Configuration Design Space Exploration
– The preliminary design space exploration for large, interdisciplinary engineering problems is often a difficult and time-consuming task. General techniques are needed that efficiently and methodically search the design space. This work focuses on the use of parallel load balancing techniques integrated with a global optimizer to reduce the computational time of the design space exploration. T...
متن کاملRandom Seeking: A General, Efficient, and Informed Randomized Scheme for Dynamic Load Balancing
We propose a completely general, informed randomized dynamic load balancing method called random seeking (RS) suitable for parallel algorithms with characteristics found in many search algorithms used in artificial intelligence and operations research and many divide-and-conquer algorithms. In it, source processors randomly seek out sink processors for load balancing by flinging “probe” message...
متن کاملDynamic Load Balancing in a Message Passing Virtual Parallel Machine Dynamic Load Balancing in a Message Passing Virtual Parallel Machine
In this paper we will look into the problem of dynamic balancing of tasks in a het-erogenous parallel computing environment. The parallel programs are assumed to be executed in the Single Program Multiple Data (SPMD) style. The criteria for re-balancing the load are discussed; the eeect of data movement required in the load balancing is considered; and novel algorithms of dynamic load balancing...
متن کاملEfficiency of Dynamic Load Balancing Based on Permanent Cells for Parallel Molecular Dynamics Simulation
This paper addresses a dynamic load balancing method of domain decomposition for 3-dimensional Molecular Dynamics on parallel computers. In order to reduce interprocessor communication overhead, we are introducing a concept of permanent cells to the dynamic load balancing method. Molecular Dynamics simulations on a parallel computer T3E prove that the proposed method using load balancing much i...
متن کامل