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322
NAMD: biomolecular simulation on thousands of processors
- In Supercomputing
, 2002
"... Abstract 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 cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with ..."
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Cited by 113 (33 self)
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Abstract 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 cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained 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.
Anton: A Special-Purpose Machine for Molecular Dynamics Simulation
- in Proc. 34th International Symposium on Computer Architecture (ISCA’07
, 2007
"... The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry and medicine. A wide range of biologic ..."
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Cited by 65 (8 self)
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The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry and medicine. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond—about three orders of magnitude beyond the duration of the longest current MD simulations. In this paper, we describe a massively parallel machine called Anton, which should be capable of executing millisecondscale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication
ACHIEVING HIGH PERFORMANCE ON EXTREMELY LARGE PARALLEL MACHINES: PERFORMANCE PREDICTION AND LOAD BALANCING
, 2005
"... Parallel machines with an extremely large number of processors (at least tens of thousands processors) are now in operation. For example, the IBM BlueGene/L machine with 128K processors is currently being deployed. It is going to be a significant challenge for application developers to write paralle ..."
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Cited by 51 (8 self)
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Parallel machines with an extremely large number of processors (at least tens of thousands processors) are now in operation. For example, the IBM BlueGene/L machine with 128K processors is currently being deployed. It is going to be a significant challenge for application developers to write parallel programs in order to exploit the enormous compute power available and manually scale their applications on such machines. Solving these problems involves finding suitable parallel programming models for such machines and addressing issues like load imbalance. In this thesis, we explore Charm++ programming model and its migratable objects for programming such machines and dynamic load balancing techniques to help parallel applications to easily scale on a large number of processors. We also present a parallel simulator that is capable of predicting parallel performance to help analysis and tuning of the parallel performance and facilitate the development of new load balancing techniques, even before such machines are built. We evaluate the idea of virtualization and its usefulness in helping a programmer to write applications with high degree of parallelism. We demonstrate it by developing several mini-applications with millionway parallelism. We show that Charm++ and AMPI (an extension to MPI) with migratable objects and
Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms
"... NAMD † is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique used now by most scalable programs for biomolecular simulations, including Blue Matter and Desmond developed by IBM and D. E. Shaw respectively. NAMD ..."
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Cited by 48 (32 self)
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NAMD † is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique used now by most scalable programs for biomolecular simulations, including Blue Matter and Desmond developed by IBM and D. E. Shaw respectively. NAMD is developed using CHARM++ and benefits from its adaptive communication-computation overlap and dynamic load balancing. This paper focuses on new scalability challenges in biomolecular simulations: using much larger machines and simulating molecular systems with millions of atoms. We describe new techniques we have developed to overcome these challenges. Since our approach involves automatic adaptive runtime optimizations, one interesting issue involves harmful interaction between multiple adaptive strategies, and how to deal with them. Unlike most other molecular dynamics programs, NAMD runs on a wide variety of platforms ranging from commodity clusters to supercomputers. It also scales to large machines: we present results for up to 65,536 processors on IBM’s Blue Gene/L and 8,192 processors on Cray XT3/XT4 in addition to results on NCSA’s Abe, SDSC’s DataStar and TACC’s LoneStar cluster, to demonstrate efficient portability. Since our IPDPS’06 paper two years ago, two new highly scalable programs named Desmond and Blue Matter have emerged, which we compare with NAMD in this paper. 1
Adapting a Message-Driven Parallel Application to GPU-Accelerated Clusters
- in International Conference on High Performance Computing, Networking, Storage and Analysis, 2008. SC 2008
, 2008
"... ‡ The authors contributed equally. § To whom correspondence should be addressed. Abstract—Graphics processing units (GPUs) have become an attractive option for accelerating scientific computations as a result of advances in the performance and flexibility of GPU hardware, and due to the availability ..."
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Cited by 46 (5 self)
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‡ The authors contributed equally. § To whom correspondence should be addressed. Abstract—Graphics processing units (GPUs) have become an attractive option for accelerating scientific computations as a result of advances in the performance and flexibility of GPU hardware, and due to the availability of GPU software development tools targeting general purpose and scientific computation. However, effective use of GPUs in clusters presents a number of application development and system integration challenges. We describe strategies for the decomposition and scheduling of computation among CPU cores and GPUs, and techniques for overlapping communication and CPU computation with GPU kernel execution. We report the adaptation of these techniques to NAMD, a widely-used parallel molecular dynamics simulation package, and present performance results for a 64-core 64-GPU cluster. I.
Scaling applications to massively parallel machines using projections performance analysis tool
- In Future Generation Computer Systems Special Issue on: Large-Scale System Performance Modeling and Analysis
, 2005
"... 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 invo ..."
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Cited by 41 (23 self)
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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 will showcase a series of optimizations facilitated by Projections. The resultant performance of NAMD led to a Gordon Bell award at SC2002 with unprecedented speedup on 3,000 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. 1
Simulation-based performance prediction for large parallel machines
- International Journal of Parallel Programming
, 2005
"... We present a performance prediction environment for large scale computers such as the Blue Gene machine. It consists of a parallel simulator, BigSim, for predicting per-formance of machines with a very large number of proces-sors, and BigNetSim, which incorporates a pluggable mod-ule of a detailed c ..."
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Cited by 39 (11 self)
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We present a performance prediction environment for large scale computers such as the Blue Gene machine. It consists of a parallel simulator, BigSim, for predicting per-formance of machines with a very large number of proces-sors, and BigNetSim, which incorporates a pluggable mod-ule of a detailed contention-based network model. The sim-ulators provide the ability to make performance predictions for very large machines such as Blue Gene/L. We illustrate the utility of our simulators using validation and predic-tion studies of several applications using smaller numbers of processors for simulations. 1
Algorithmic challenges in computational molecular biophysics
- Journal of Computational Physics
, 1999
"... A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and recent descriptions of algorithmic work in long ..."
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Cited by 38 (3 self)
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A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and recent descriptions of algorithmic work in long-time integration for molecular dynamics; fast electrostatic evaluation; crystallographic refinement approaches; and implementation of large, computation-intensive programs on modern architectures. Expected future developments of the field are also discussed. c ○ 1999 Academic Press Key Words: biomolecular simulations; molecular dynamics; long-time integration; fast electrostatics; crystallographic refinement; high-performance platforms.
Microscopic kinetics of DNA translocation through synthetic nanopores
- Biophys. J
"... ABSTRACT We have previously demonstrated that a nanometer-diameter pore in a nanometer-thick metal-oxidesemiconductor-compatible membrane can be used as a molecular sensor for detecting DNA. The prospects for using this type of device for sequencing DNA are avidly being pursued. The key attribute of ..."
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Cited by 37 (11 self)
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ABSTRACT We have previously demonstrated that a nanometer-diameter pore in a nanometer-thick metal-oxidesemiconductor-compatible membrane can be used as a molecular sensor for detecting DNA. The prospects for using this type of device for sequencing DNA are avidly being pursued. The key attribute of the sensor is the electric field-induced (voltage-driven) translocation of the DNA molecule in an electrolytic solution across the membrane through the nanopore. To complement ongoing experimental studies developing such pores and measuring signals in response to the presence of DNA, we conducted molecular dynamics simulations of DNA translocation through the nanopore. A typical simulated system included a patch of a silicon nitride membrane dividing water solution of potassium chloride into two compartments connected by the nanopore. External electrical fields induced capturing of the DNA molecules by the pore from the solution and subsequent translocation. Molecular dynamics simulations suggest that 20-basepair segments of double-stranded DNA can transit a nanopore of 2.2 3 2.6 nm 2 cross section in a few microseconds at typical electrical fields. Hydrophobic interactions between DNA bases and the pore surface can slow down translocation of single-stranded DNA and might favor unzipping of doublestranded DNA inside the pore. DNA occluding the pore mouth blocks the electrolytic current through the pore; these current blockades were found to have the same magnitude as the blockade observed when DNA transits the pore. The feasibility of using molecular dynamics simulations to relate the level of the blocked ionic current to the sequence of DNA was investigated.
Scaling molecular dynamics to 3000 processors with projections: A performance analysis case study
- In Terascale Performance Analysis Workshop, International Conference on Computational Science(ICCS
, 2003
"... Abstract. 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 a case ..."
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Cited by 35 (13 self)
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Abstract. 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 a case study involving NAMD, a parallel molecular dynamics application, and efforts to scale it to run on 3000 processors with Tera-FLOPS level performance. NAMD is implemented in Charm++, and the performance analysis was carried out using “projections”, the performance visualization/analysis tool associated with Charm++. We will showcase a series of optimizations facilitated by projections. The resultant performance of NAMD led to a Gordon Bell award at SC2002. 1
