Laxmikant V. Kalé

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NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions,(More)
We describe Charm++, an object oriented portable parallel programming language based on Cff. Its design philosophy, implementation, sample applications and their performance on various parallel machines are described. Charm++ is an explicitly parallel language consisting of Cft with a few extensions. It provides a clear separation between sequential and(More)
Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also(More)
Processor virtualization is a powerful technique that enables the runtime system to carry out intelligent adaptive optimizations like dynamic resource management. Charm++ is an early language/system that supports processor virtualization. This paper describes Adaptive MPI or AMPI, an MPI implementation and extension, that supports processor virtualization.(More)
Summary form only given. We present a parallel simulator - BigSim - for predicting performance of machines with a very large number of processors. The simulator provides the ability to make performance predictions for machines such as BlueGene/L, based on actual execution of real applications. We present this capability using case-studies of some(More)
2 Summary NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design implemented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decomposition coupled with a multithreaded, message-driven design which is shown to(More)
NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoffelectrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an(More)
Sorting is a commonly used process with a wide breadth of applications in the high performance computing field. Early research in parallel processing has provided us with comprehensive analysis and theory for parallel sorting algorithms. However, modern supercomputers have advanced rapidly in size and changed significantly in architecture, forcing new(More)
dynamics with NAMD on the IBM Blue Gene/L system S. Kumar C. Huang G. Zheng E. Bohm A. Bhatele J. C. Phillips H. Yu L. V. Kalé NAMD (nanoscale molecular dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes, and water molecules. In a biomolecular simulation, the(More)
As high performance clusters continue to grow in size, the mean time between failures shrinks. Thus, the issues of fault tolerance and reliability are becoming one of the challenging factors for application scalability. The traditional disk-based method of dealing with faults is to checkpoint the state of the entire application periodically to reliable(More)