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Scalable molecular dynamics with NAMD
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…
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NAMD2: Greater Scalability for Parallel Molecular Dynamics
TLDR
The NAMD2 program is presented, which uses spatial decomposition combined with force decomposition to enhance scalability and modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability.
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CHARM++: a portable concurrent object oriented system based on C++
TLDR
Charm++ is an explicitly parallel language consisting of C++ with a few extensions that provides a clear separation between sequential and parallel objects and helps one write programs that are latency-tolerant.
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NAMD: a Parallel, Object-Oriented Molecular Dynamics Program
TLDR
NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers that uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors.
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Adaptive MPI
TLDR
Adaptive MPI or AMPI is an MPI implementation and extension that supports processor virtualization, which includes a powerful runtime support system that takes advantage of the degree of freedom afforded by allowing it to assign VPs onto processors.
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Toward Exascale Resilience
TLDR
This white paper synthesizes the motivations, observations and research issues considered as determinant of several complimentary experts of HPC in applications, programming models, distributed systems and system management.
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Scalable molecular dynamics on CPU and GPU architectures with NAMD.
TLDR
The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
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NAMD: Biomolecular Simulation on Thousands of Processors
TLDR
This work demonstrates unprecedented scalability in a biomolecular simulation code through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.
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BigSim: a parallel simulator for performance prediction of extremely large parallel machines
TLDR
A parallel simulator - BigSim - for predicting performance of machines with a very large number of processors, based on ideas from parallel discrete event simulation and utilize inherent determinacy of many parallel applications is presented.
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Performance evaluation of adaptive MPI
TLDR
This paper describes AMPI, illustrates its performance benefits through a series of benchmarks, and shows that AMPI is a portable and mature MPI implementation that offers various performance benefits to dynamic applications.
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