Publications

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Performance Characterization of Molecular Dynamics Techniques for Biomolecular Simulations, Alam, S. R., Agarwal Pratul, Geist Al, and Vetter Jeffrey S. , ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPOPP), New York City, (2006)
Characterizing Applications on the MTA2 Multithreading Architecture, Alam, S. R., Barrett Richard, McCurdy Collin, Roth Philip C., and Vetter Jeffrey S. , 48th Cray User Group meeting (CUG 2006), Lugano, Switzerland, (2006)
Characterization of Scientific Workloads on Systems with Multi-Core Processors, Alam, S. R., Barrett Richard F., Kuehn Jeffery A., Roth Philip C., and Vetter Jeffrey S. , IEEE International Symposium on Workload Characterization (IISWC), San Jose, California, (2006)
Symbolic Performance Modeling of HPCS Applications, Alam, S. R., Bhatia Nikhil, and Vetter Jeffrey S. , Cyberinfrastructure Technology Watch, Volume 2, Issue 4B, (2006)
A Framework to Develop Symbolic Performance Models of Parallel Applications, Alam, S. R., and Vetter Jeffrey S. , 5th International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS 2006), Rhodes Island, Greece, (2006)
Hierarchical Model Validation of Symbolic Performance Models of Scientific Kernels (Distinguished Paper), Alam, S. R., and Vetter Jeffrey S. , Euro-Par, Dresden, (2006)
An Analysis of System Balance Requirements for Scientific Applications, Alam, S. R., and Vetter Jeffrey S. , 35th International Conference on Parallel Processing (ICPP), Columbus, (2006)
Using FPGA Devices to Accelerate Biomolecular Simulations, Alam, S. R., Agarwal Pratul K., Smith Melissa C., Vetter Jeffrey S., and Caliga David , IEEE Computer, Volume 40, Issue 2, p.66-73, (2007)
An Exploration of Performance Attributes for Symbolic Modeling of Emerging Processing Devices, Alam, S. R., Bhatia Nikhil, and Vetter Jeffrey S. , 3rd International High Performance Computation Conference (HPCC), Volume 4782, (2007)
Sensitivity Analysis of Biomolecular Simulations using Symbolic Models, Alam, S. R., Bhatia Nikhil, and Vetter Jeffrey S. , 7th International Conf. on BioInformatics & BioEngineering, Boston, (2007)
Balancing Productivity and Performance on the Cell Broadband Engine, Alam, S. R., Meredith Jeremy S., and Vetter Jeffrey S. , IEEE Annual International Conference on Cluster Computing, Houston, (2007)
An Application Specific Memory Characterization Technique for Co-processor Accelerators, Alam, S. R., Smith M. C., and Vetter Jeffrey S. , IEEE 18th International Conference on Application-specific Systems, Architectures and Processors, (2007)
Performance characteristics of biomolecular simulations on high-end systems with multi-core processors, Alam, S. R., Agarwal PK, and Vetter Jeffrey S. , Parallel Computing, Volume 34, Issue 11, p.640-651, (2008)
Impact of Multicores on Large-scale Molecular Dynamics Simulations, Alam, S. R., Agarwal Pratul, Ong H., Hampton S., and Vetter Jeffrey S. , IEEE International Workshop on High Performance Computational Biology (HiCOMB), in conjunction with IPDPS, p.1-7, (2008)
Early Evaluation of IBM BlueGene/P, Alam, S. R., Barrett R. F., Fahey M. R., and Kuehn J. A. , Proceedings of the ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis (SC08), November, Los Alamitos, CA, (2008)