Sadaf Alam

Research Interests

• Techniques and tools for performance analysis, modeling and prediction of large-scale scientific applications and systems.
• Investigation of future-generation computing architectures and their programming models.
• Benchmarking, characterization and performance evaluation.
• System software for heterogeneous computing platforms.
• Languages and programming paradigms for emerging HPC systems.

Publications

• "Experimental Evaluation of Molecular Dynamics Simulations on Multi-core Systems,", S.R. Alam, P.K. Agarwal, S. Hampton and H. Ong, International Conference on High Performance Computing (HiPC), 2008 [to appear].
• "Early Evaluation of IBM BlueGene/P," S. R. Alam, R. F. Barrett, M. Bast, M. Fahey, J. A. Kuehn, C. McCurdy, J. Rogers, P. C. Roth, R. Sankaran, J.S. Vetter, P. H. Worley, W. Yu, Proceedings of ACM/IEEE Supercomputing Conference (SC08), 2008 [to appear].
• "A Methodology for Developing High Fidelity Communication Models for Large-scale Applications Targeted on Multicore Systems," C. Lively, S.R. Alam, V. Taylor, and J. S. Vetter, 20th International Symposium on Computer Architecture and High Performance Computing, 2008 [to appear].
• "Performance characteristics of bio-molecular simulations on high-end systems with multi-core processors," S.R. Alam, P.K. Agarwal, and J.S. Vetter, Parallel Computing [to appear].
• "Implementation Methodology for Emerging Reconfigurable Systems," P.M. Martin, M.C. Smith, S.R. Alam, and P.K. Agarwal, 51st IEEE International Midwest Symposium on Circuits and Systems (MWSCAS), 2008.
• "Impacts of Multicores on Large-scale Molecular Dynamics Simulations," S.R. Alam, P.K. Agarwal, H. Ong, S. Hampton, and J.S. Vetter, IEEE International Workshop on High Performance Computational Biology (HiCOMB), in conjunction with IPDPS, 2008.
• "Productivity Evaluation on Emerging Architectures," S. R. Alam, J. S. Meredith and J. S. Vetter, Book Chapter in Advances in Computers, 72 (DARPA's HPCS Program: History, Models, Tools, Languages), 2008.
• "Exploring HPCS Languages in Scientific Computing," R. F. Barrett, V. de Almedia, S. R. Alam, D. E. Bernholdt, W. R. Elwasif, J. A. Kuehn, S. W. Poole, and A. G. Shet, Journal of Physics: Conference Series [to appear].
• "Exploring the Performance Potential of Chapel," R.F. Barrett, S.R. Alam, and S. W. Poole, Proc. 50th Cray User Group meeting, 2008.
• "The Cray XT4 Quad-core : A First Look," S.R. Alam, R.F. Barrett, M. Eisenbach, M.R. Fahey, R. Hartman-Baker., J.A. Kuehn, S.W. Poole, R. Sankaran, and P. H. Worley, Proc. 50th Cray User Group meeting, 2008.
• "Throughput Improvement of Molecular Dynamics Simulations Using Reconfigurable Computing," S. R. Alam, P. K. Agarwal, M. C. Smith, J. S. Vetter and D. Caliga, Scalable Computing: Practice and Experience, Vol. 8, No. 4, 2007.
• "Cray XT4: An Early Evaluation for Petascale Scientific Computing," S.R. Alam, R. F. Barrett, M. Fahey, J. A. Kuehn, J. Larkin, R. Sankaran and P. H. Worley, Proceedings of ACM/IEEE Supercomputing Conference (SC07), 2007.
• "Balancing Productivity and Performance on the Cell Broadband Engine," S. R. Alam, J. S. Meredith and J. S. Vetter, IEEE Cluster Conference, 2007.
• "An Exploration of Performance Attributes for Symbolic Modeling of Emerging Processing Devices," S.R. Alam, N. Bhatia and J.S. Vetter, 3rd International High Performance Computing and Communications (HPCC), 2007.
• "Expressing POP with a Global View Using Chapel: Toward a More Productive Ocean Model," R.F. Barrett, S.R. Alam, and S. W. Poole, ORNL Technical Report TM-2007/122, 2007.
• "Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System," S.R. Alam, P.K. Agarwal and J.A. Kuehn, Workshop on progress toward petascale applications in bioinformatics and computational biology at 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007.
• "Sensitivity Analysis of Biomolecular Simulations Using Symbolic Models," S.R. Alam, N. Bhatia and J.S. Vetter, 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007.
• "An Application Specific Memory Characterization Technique for Co-processor Accelerators," S.R. Alam, M.C. Smith, and J.S. Vetter, IEEE International Conference on Application-specific System, Architecture and Processors, 2007.
• "Simulating Biomolecules on the Petascale Supercomputers," P.K. Agarwal, S.R. Alam, and A. Geist, Petascale Computing: Algorithms and Applications (Book Chapter), Chapman & Hall/CRC Computational Science Series, 2007.
• "Using FPGA Devices to Accelerate Biomolecular Simulations," S. R. Alam, P. K. Agarwal, M. C. Smith, J. S. Vetter and D. Caliga, IEEE Computer, Volume 40, Number 3, 2007.
• "Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures," J. S. Meredith, S. R. Alam and J. S. Vetter, IEEE International Workshop on High Performance Computational Biology (HiCOMB), in conjunction with IPDPS, 2007.
• "On the Path to Enable Multi-scale Biomolecular Simulations on PetaFLOPS Supercomputer with Multi-core Processors," S. R. Alam and Pratul K. Agarwal, IEEE International Workshop on High Performance Computational Biology (HiCOMB), in conjunction with IPDPS, 2007.
• "An Evaluation of the ORNL XT3," S. R. Alam, R. F. Barrett, M. R. Fahey, J. A. Kuehn, O. E. Messer, R. T. Mills, P. C. Roth, J. S. Vetter and P. H. Worley, International Journal of High Performance Computing Applications, in press.
• "Symbolic Performance Modeling of HPCS Applications," S. R. Alam, N. Bhatia, and J. S. Vetter, Cyberinfrastructure Technology Watch, Volume 2, Number 4B, 2006.
• "Biomolecular Simulations on Petascale: Promises and Challenges," P. K. Agarwal and S. R. Alam, Journal of Physics: Conference Series, Volume 46, 2006.
• "Characterization of Scientific Workloads on Systems with Multi-core Processors," S. R. Alam, R. F. Barrett, J. A. Kuehn, P. C. Roth and J. S. Vetter, IEEE International Symposium on Workload Characterization, 2006.
• "Investigation of Benchmark Suites for High-Performance Reconfigurable Computing Platforms," M. C. Smith, S. R. Alam and J. S. Vetter, 9th Annual Military and Aerospace Applications of Programmable Devices & Technologies (MAPLD) International Conference, 2006.
• "Hierarchical Model Validation of Symbolic Performance Models of Scientific Applications," S. R. Alam and J. S. Vetter, Euro-Par Conference, 2006.
• "An Analysis of System Balance Requirements for Scientific Applications," S. R. Alam and J. S. Vetter, Proc. 35th International Conference on Parallel Processing, 2006.
• "Performance Modeling of Emerging HPC Architecture," N. Bhatia, S. R. Alam and J. S. Vetter, Proc. DOD High Performance Computing Modernization Program UGC, 2006.
• "Cray XD1 Experiences and Comparisons with other FPGA-based Supercomputer Systems," O. Storaasli, S. R. Alam and M. Smith, Cray User Group (CUG) Conference, 2006.
• "Scientific Applications Performance on the Cray Multi-threaded Architecture (MTA-II)," S. R. Alam, R. Barrett, C. McCurdy, P. Roth and J. S. Vetter, Eldorado Workshop at the Cray User Group (CUG) Conference, 2006.
• "Early Evaluation of the Cray XT3", J. S. Vetter, S. R. Alam, T. Dunigan, M. Fahey, P. Roth and P. Worley, 20th IEEE International Parallel & Distributed Processing Symposium (IPDPS), 2006.
• "A Framework to Develop Symbolic Performance Models of Parallel Applications", S. R. Alam, and J. S. Vetter, 5th International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS 2006).
• "Performance Characterization of Biomolecular Molecular Dynamics Algorithms on Massively-Parallel Supercomputers", S. R. Alam, J. S. Vetter, P. K. Agarwal and Al Geist, Proc. of ACM SIGPLAN Symp. on Principles and Practice of Parallel Programming, 2006.
• "A High Performance Programming Model for Large-Scale Molecular Dynamics Calculations on Reconfigurable Supercomputers", L. Cordova, S. Alam, M. Smith and J. Vetter, 9th Annual Workshop on High Performance Embedded Computing (HPEC), 2005.
• "Sparse Matrix-Vector Multiplication Kernel on a Reconfigurable Computer", S. Akella, S. Alam, R. Barrett, R. Mills, M. Smith and J. Vetter, HPEC, 2005.
• "Scientific Computing Beyond CPUs: FPGA implementations of common scientific kernels", M. Smith, J. Vetter and S. Alam, 2005 MAPLD International Conference.
• "Performance and Scalability Analysis of Cray X1 Loop Vectorization and Multistreaming". S. Alam and J.S. Vetter. Proceedings International Conference on Computational Science, Part I. Springer-Verlag Lecture Notes in Computer Science 3514, 2005.
• "Early Evaluation of the Cray XT3 at ORNL", J. Vetter, S. Alam, R. Barrett, T. Dunigan, Jr., M. Fahey, J. Kuehn, J. White III, and P. Worley. Proc. Cray User Group Conference, USA, 2005.
• "Comparative Analysis of Interprocess Communication on the X1, XD1, and XT3", P. Worley, S. Alam, T. Dunigan, Jr., M. Fahey, J. Vetter and J. White III. Proc. Cray User Group Conference, USA, 2005.
• "Early Evaluation of the Cray XD1", M. Fahey, S. Alam, T. Dunigan, Jr., N. Hathaway, R. Studham, J. Vetter, and P. Worley Proc. Cray User Group Conference, USA, 2005.
• "A Methodology for Simulating Scientific Supercomputing Systems". S.Alam and R.N. Ibbett. Summer Computer Simulation Conference, USA, 2004.
• "Performance Evaluation of Local Communications: A Case-study". S. Alam, R.N. Ibbett and F. Mallet. 15th International Conference on Parallel and Distributed Computing and Systems, USA, November 2003.
• "Simulation of a Computer Architecture for Quantum Chromodynamics Calculations". S. Alam, R.N. Ibbett and F. Mallet, Crossroads, The ACM Student Magazine, Interdisciplinary Computer Science, Issue 9.3, Spring 2003, pp. 18-23.
• "An Extensible Clock mechanism for Computer Architecture Simulations". F. Mallet, R.N. Ibbett and S. Alam. 13th International Conference on Modeling and Simulation, USA, May 2002, Vol. I, pp. 225-230.

Invited Talks and Posters

• "Performance Evaluation of the Cray XT3 Configured with Dual-Core Opteron Processors," S. R. Alam, R. F. Barrett and J. S. Vetter, ACM SIGPLAN Symp. on Principles and Practice of Parallel Programming, 2007.
• "Simulating Molecular Machines of Life on Reconfigurable Computers," SRC Annual User Group Meeting, 2006.
• "A task-based Development Model for Accelerating Large-scale Scientific Applications on FPGA-based Reconfigurable Computing Platforms,. Reconfigurable Systems Summer Institute, 2006.
• "New Frontiers for Scientific Applications: Capabilities and Challenges of Heterogeneous Processing Devices," S. R. Alam and M. C. Smith, Poster Session for Women Scientists at the Oak Ridge National Laboratory, 2006.
• "Early Evaluation of the Cray XT3," J. S. Vetter, S. R. Alam, T. H. Dunigan, Jr., M. R. Fahey, P. C. Roth, P. H. Worley, poster session, Supercomputing 2005.
• "ORNL Experience with the Watson Blue Gene (BGW) Consortium Day,. Blue Gene/L Consortium Meting at Supercomputing Conference, 2005.
• "Power-Efficient Scientific Computing with a Gigaflops-Scale Accelerator", S. Alam, Poster Session for Women Scientists at the Oak Ridge National Laboratory, 2005.
• "HASE: A Toolset for Modelling Massively-Parallel Computers: Parameterised Simulation Model of the QCDOC Machine". S. Alam, Informatics Jamboree, University of Edinburgh, 2002.