NACC Applications

xcelerit SDK is a software development kit (SDK) that boosts the performance of processing-intensive software. It allows applications to easily leverage the full processing power of workstations with multi-core CPUs from AMD® and Intel®, or GPUs from Nvidia® and AMD®. It can also exploit all the processing power available in a heterogeneous cluster (e.g. combination of CPUs and GPUs). Only a single source code is needed to exploit all different architectures. Access requires registration with xcelerit.

 

R + gputools: Version: 0.21, Published: 2010-05-25, Authors: Josh Buckner, Mark Seligman, Justin Wilson. Software licensed under GPL3. R is the most popular open source statistical environment in the biomedical research community. Gputools accelerates many computational functions of R, such as R dist function, R hclust function, Pearson and Kendall correlation coefficients, and the Granger test ('granger.test' in the R MSBVAR package). Deploy on NACC using GPU-enabled appliance (Debian 5). Price: 12 Compute Units/hr.

 

GPU-BLAST: Vouzis, P. D. and N. V. Sahinidis, "GPU-BLAST: Using graphics processors to accelerate protein sequence alignment," Bioinformatics, 2010 (accepted). Using a general-purpose graphics processing unit (GPU), Carnegie Melon researchers developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST (www.ncbi.nlm.nih.gov). In comparison to the sequential NCBI-BLAST, GPU-BLAST is nearly four times faster, while producing identical results. Deploy on NACC using GPU-enabled appliance (CentOS 5.4). Price: 12 Compute Units/hr.

 

GPU NAMD: NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. This implementation accelerates runtimes 7.2x with GPU-enabled appliance. Deploy on GPU-enabled NACC appliance. To use this software, you must accept the license terms and download software from here. Price: 12 Compute Units/hr.

 

The GPU accelerated version of PMEMD 11, supports both explicit solvent PME simulations in all three canonical ensembles (NVE, NVT and NPT) and implicit solvent Generalized Born simulations. It has been designed to support as many of the standard PMEMD v11 features as possible. For limitations, click here Price: 12 Compute Units/hr..

Scott L. Grand; Andreas W. Goetz; Dong Xu; Duncan Poole & Ross C. Walker "Acceleration of amber generalized born calculations using nvidia graphics processing units." (in preparation), 2010 Scott L. Grand; Andreas W. Goetz; Dong Xu; Duncan Poole & Ross C. Walker "Achieving high performance in amber PME simulations using graphics processing units without compromising accuracy." (in preparation), 2010