NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Visualizing the Performance of Parallel Programs
IEEE Software
Performance Evaluation of the Quadrics Interconnection Network
Cluster Computing
Converse: An Interoperable Framework for Parallel Programming
IPPS '96 Proceedings of the 10th International Parallel Processing Symposium
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
SvPablo: A Multi-Language Architecture-Independent Performance Analysis System
ICPP '99 Proceedings of the 1999 International Conference on Parallel Processing
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Tools and strategies for debugging distributed stream processing applications
Software—Practice & Experience
Visualizing large-scale streaming applications
Information Visualization
Programming heterogeneous clusters with accelerators using object-based programming
Scientific Programming
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
Avoiding hot-spots on two-level direct networks
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
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Some of the most challenging applications to parallelize scalably are the ones that present a relatively small amount of computation per iteration. Multiple interacting performance challenges must be identified and solved to attain high parallel efficiency in such cases. We present case studies involving NAMD, a parallel classic molecular dynamics application for large biomolecular systems, and CPAIMD, Car-Parrinello ab initio molecular dynamics application, and efforts to scale them to large number of processors. Both applications are implemented in Charm++, and the performance analysis was carried out using Projections, the performance visualization/analysis tool associated with Charm++. We showcase a series of optimizations facilitated by Projections. The resultant performance of NAMD led to a Gordon Bell award at SC 2002 with unprecedented speedup on 3000 processors with teraflops level peak performance. We also explore the techniques for applying the performance visualization/analysis tool on future generation extreme-scale parallel machines and discuss the scalability issues with Projections.