We present performance results on a Windows cluster with up to 768 cores using MPI and two variants of threading - CCR and TPL. CCR (Concurrency and Coordination Runtime) presents a message based interface while TPL (Task Parallel Library) allows for loops to be automatically parallelized. MPI is used between the cluster nodes (up to 32) and either threading or MPI for parallelism on the 24 cores of each node. We use a simple matrix multiplication kernel as well as a significant bioinformatics gene clustering application. We find that the two threading models offer similar performance with MPI outperforming both at low levels of parallelism but threading much better when the grain size (problem size per process) is small. We find better performance on Intel compared to AMD on comparable 24 core systems. We develop simple models for the performance of the clustering code.

BACKGROUND: Human immunodeficiency virus (HIV) research involves ongoing, repetitious sequencing of the HIV genome and the massive accumulation of associated investigational data. As a result, the storage of annotated DNA and/or protein sequences, as well as information retrieval, have become increasingly difficult tasks, with scientists extracting less information from their collected data than they should. OBJECTIVES: Our objective was to design and develop a software package to aid researchers in the storage, analysis and exploration of their HIV-associated data. RESULTS: HIVbase contains familiar, easy-to-use interfaces and functionality for integrating many types of disparate data. The software contains tools that allow for the mass import of raw genetic data, eliminate repetitious sequence translations, have the ability to identify automatically and store HIV regions of interest from nucleic acid or protein sequences, allow for the export of data in commonly used analysis-ready formats, and for unique querying approaches.