A review of High Performance Computing foundations for scientists
---
paper_title: Essentials Of Computational Chemistry Theories And Models

paper_content:

Thank you very much for downloading essentials of computational chemistry theories and models. Maybe you have knowledge that, people have search hundreds times for their chosen books like this essentials of computational chemistry theories and models, but end up in harmful downloads. Rather than reading a good book with a cup of coffee in the afternoon, instead they juggled with some malicious bugs inside their laptop.
---
paper_title: 369 Tflop-s molecular dynamics simulations on the petaflop hybrid supercomputer ‘Roadrunner’

paper_content:

We describe the implementation of a short-range parallel molecular dynamics (MD) code, SPaSM, on the heterogeneous general-purpose Roadrunner supercomputer. Each Roadrunner ‘TriBlade’ compute node consists of two AMD Opteron dual-core microprocessors and four IBM PowerXCell 8i enhanced Cell microprocessors (each consisting of one PPU and eight SPU cores), so that there are four MPI ranks per node, each with one Opteron and one Cell. We will briefly describe the Roadrunner architecture and some of the initial hybrid programming approaches that have been taken, focusing on the SPaSM application as a case study. An initial ‘evolutionary’ port, in which the existing legacy code runs with minor modifications on the Opterons and the Cells are only used to compute interatomic forces, achieves roughly a 2× speedup over the unaccelerated code. On the other hand, our ‘revolutionary’ implementation adopts a Cell-centric view, with data structures optimized for, and living on, the Cells. The Opterons are mainly used to direct inter-rank communication and perform I-O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard–Jones pair potential benchmark reached a peak of 369 Tflop-s double-precision floating-point performance on the full Roadrunner system (27.7p of peak), nearly 10× faster than the unaccelerated (Opteron-only) version. Copyright © 2009 John Wiley & Sons, Ltd.
---
paper_title: Spending Moore's dividend

paper_content:

Multicore computers shift the burden of software performance from chip designers and processor architects to software developers.
---
paper_title: Giant Magnetoresistance of (001)Fe/(001)Cr Magnetic Superlattices

paper_content:

We have studied the magnetoresistance of (001)Fe/(001)Cr superlattices prepared by molecularbeam epitaxy. A huge magnetoresistance is found in superlattices with thin Cr layers: For example, with ${t}_{\mathrm{Cr}}=9$ \AA{}, at $T=4.2$ K, the resistivity is lowered by almost a factor of 2 in a magnetic field of 2 T. We ascribe this giant magnetoresistance to spin-dependent transmission of the conduction electrons between Fe layers through Cr layers.
---
paper_title: Future hard disk drive systems

paper_content:

Abstract This paper briefly reviews the evolution of today's hard disk drive with the additional intention of orienting the reader to the overall mechanical and electrical architecture. The modern hard disk drive is a miracle of storage capacity and function together with remarkable economy of design. This paper presents a personal view of future customer requirements and the anticipated design evolution of the components. There are critical decisions and great challenges ahead for the key technologies of heads, media, head–disk interface, mechanics, and electronics.
---
paper_title: Utilizing high performance computing for chemistry: parallel computational chemistry.

paper_content:

Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.
---
paper_title: Scientific data management in the coming decade

paper_content:

Scientific instruments and computer simulations are creating vast data stores that require new scientific methods to analyze and organize the data. Data volumes are approximately doubling each year. Since these new instruments have extraordinary precision, the data quality is also rapidly improving. Analyzing this data to find the subtle effects missed by previous studies requires algorithms that can simultaneously deal with huge datasets and that can find very subtle effects --- finding both needles in the haystack and finding very small haystacks that were undetected in previous measurements.
---
paper_title: Introduction to High Performance Computing for Scientists and Engineers

paper_content:

Written by high performance computing (HPC) experts, Introduction to High Performance Computing for Scientists and Engineers provides a solid introduction to current mainstream computer architecture, dominant parallel programming models, and useful optimization strategies for scientific HPC. From working in a scientific computing center, the authors gained a unique perspective on the requirements and attitudes of users as well as manufacturers of parallel computers. The text first introduces the architecture of modern cache-based microprocessors and discusses their inherent performance limitations, before describing general optimization strategies for serial code on cache-based architectures. It next covers shared- and distributed-memory parallel computer architectures and the most relevant network topologies. After discussing parallel computing on a theoretical level, the authors show how to avoid or ameliorate typical performance problems connected with OpenMP. They then present cache-coherent nonuniform memory access (ccNUMA) optimization techniques, examine distributed-memory parallel programming with message passing interface (MPI), and explain how to write efficient MPI code. The final chapter focuses on hybrid programming with MPI and OpenMP. Users of high performance computers often have no idea what factors limit time to solution and whether it makes sense to think about optimization at all. This book facilitates an intuitive understanding of performance limitations without relying on heavy computer science knowledge. It also prepares readers for studying more advanced literature.
---
paper_title: An optimal multimedia object allocation solution in multi-powermode storage systems

paper_content:

Given a set of multimedia objects R=lo1, o2, …, okr each of which has a set of multiple versions oi.v=lAi.0, Ai.1, …, Ai.mr, i=1, 2, …, k, there is a problem of distributing these objects in a server system so that user requests for accessing specified multimedia objects can be fulfilled with the minimum energy consumption and without significant degrading of the system performance. This paper considers the allocation problem of multimedia objects in multi-powermode storage systems, where the objects are distributed among multi-powermode storages based on the access pattern to the objects. We design an underlying infrastructure of storage system and propose a dynamic multimedia object allocation policy based on the designed infrastructure, which integrate and prove the optimality of the proposed policy. Copyright © 2010 John Wiley & Sons, Ltd.
---
paper_title: Spending Moore's dividend

paper_content:

Multicore computers shift the burden of software performance from chip designers and processor architects to software developers.
---
paper_title: The impact of multicore on math software

paper_content:

Power consumption and heat dissipation issues are pushing the microprocessors industry towards multicore design patterns. Given the cubic dependence between core frequency and power consumption, multicore technologies leverage the idea that doubling the number of cores and halving the cores frequency gives roughly the same performance reducing the power consumption by a factor of four. With the number of cores on multicore chips expected to reach tens in a few years, efficient implementations of numerical libraries using shared memory programming models is of high interest. The current message passing paradigm used in ScaLAPACK and elsewhere introduces unnecessary memory overhead and memory copy operations, which degrade performance, along with the making it harder to schedule operations that could be done in parallel. Limiting the use of shared memory to fork-join parallelism (perhaps with OpenMP) or to its use within the BLAS does not address all these issues.
---
paper_title: Utilizing high performance computing for chemistry: parallel computational chemistry.

paper_content:

Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.
---
paper_title: The impact of IBM Cell technology on the programming paradigm in the context of computer systems for climate and weather models

paper_content:

The call for ever-increasing model resolutions and physical processes in climate and weather models demands a continual increase in computing power. The IBM Cell processor's order-of-magnitude peak performance increase over conventional processors makes it very attractive to fulfill this requirement. However, the Cell's characteristics, 256 kB local memory per SPE and the new low-level communication mechanism, make it very challenging to port an application. As a trial, we selected the solar radiation component of the NASA GEOS-5 climate model, which: (1) is representative of column-physics components (half of the total computational time), (2) has an extremely high computational intensity: the ratio of computational load to main memory transfers, and (3) exhibits embarrassingly parallel column computations. In this paper, we converted the baseline code (single-precision Fortran) to C and ported it to an IBM BladeCenter QS20. For performance, we manually SIMDize four independent columns and include several unrolling optimizations. Our results show that when compared with the baseline implementation running on one core of Intel's Xeon Woodcrest, Dempsey, and Itanium2, the Cell is approximately 8.8x, 11.6x, and 12.8x faster, respectively. Our preliminary analysis shows that the Cell can also accelerate the dynamics component (∼25p total computational time). We believe these dramatic performance improvements make the Cell processor very competitive as an accelerator. Copyright © 2009 John Wiley & Sons, Ltd.
---
paper_title: octopus: a tool for the application of time-dependent density functional theory

paper_content:

We report on the background, current status, and current lines of development of the octopus project. This program materializes the main equations of density-functional theory in the ground state, and of time-dependent density-functional theory for dynamical effects. The focus is nowadays placed on the optical (i.e. electronic) linear response properties of nanostructures and biomolecules, and on the non-linear response to high-intensity fields of finite systems, with particular attention to the coupled ionic-electronic motion (i.e. photo-chemical processes). In addition, we are currently extending the code to the treatment of periodic systems (both to one-dimensional chains, two-dimensional slabs, or fully periodic solids), magnetic properties (ground state properties and excitations), and to the field of quantum-mechanical transport or “molecular electronics.” In this communication, we concentrate on the development of the methodology: we review the essential numerical schemes used in the code, and report on the most recent implementations, with special attention to the introduction of adaptive coordinates, to the extension of our real-space technique to tackle periodic systems, and on large-scale parallelization. More information on the code, as well as the code itself, can be found at http://www.tddft.org/programs/octopus/. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
---
paper_title: The Future of Microprocessors

paper_content:

The performance of microprocessors that power modern computers has continued to increase exponentially over the years for two main reasons. First, the transistors that are the heart of the circuits in all processors and memory chips have simply become faster over time on a course described by Moore’s law,1 and this directly affects the performance of processors built with those transistors. Moreover, actual processor performance has increased faster than Moore’s law would predict,2 because processor designers have been able to harness the increasing numbers of transistors available on modern chips to extract more parallelism from software. This is depicted in figure 1 for Intel’s processors.
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paper_title: Cramming More Components Onto Integrated Circuits

paper_content:

The future of integrated electronics is the future of electronics itself. The advantages of integration will bring about a proliferation of electronics, pushing this science into many new areas. Integrated circuits will lead to such wonders as home computers—or at least terminals connected to a central computer—automatic controls for automobiles, and personal portable communications equipment. The electronic wristwatch needs only a display to be feasible today. But the biggest potential lies in the production of large systems. In telephone communications, integrated circuits in digital filters will separate channels on multiplex equipment. Integrated circuits will also switch telephone circuits and perform data processing. Computers will be more powerful, and will be organized in completely different ways. For example, memories built of integrated electronics may be distributed throughout the machine instead of being concentrated in a central unit. In addition, the improved reliability made possible by integrated circuits will allow the construction of larger processing units. Machines similar to those in existence today will be built at lower costs and with faster turnaround.
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paper_title: N-body simulation for self-gravitating collisional systems with a new SIMD instruction set extension to the x86 architecture, Advanced Vector eXtensions

paper_content:

We present a high-performance N-body code for self-gravitating collisional systems accelerated with the aid of a new SIMD instruction set extension of the x86 architecture: Advanced Vector eXtensions (AVX), an enhanced version of the Streaming SIMD Extensions (SSE). With one processor core of Intel Core i7-2600 processor (8 MB cache and 3.40 GHz) based on Sandy Bridge micro-architecture, we implemented a fourth-order Hermite scheme with individual timestep scheme (Makino and Aarseth, 1992), and achieved the performance of 20 giga floating point number operations per second (GFLOPS) for double-precision accuracy, which is two times and five times higher than that of the previously developed code implemented with the SSE instructions (Nitadori et al., 2006b), and that of a code implemented without any explicit use of SIMD instructions with the same processor core, respectively. We have parallelized the code by using so-called NINJA scheme (Nitadori et al., 2006a), and achieved 90 GFLOPS for a system containing more than N = 8192 particles with 8 MPI processes on four cores. We expect to achieve about 10 tera FLOPS (TFLOPS) for a self-gravitating collisional system with N 105 on massively parallel systems with at most 800 cores with Sandy Bridge micro-architecture. This performance will be comparable to that of Graphic Processing Unit (GPU) cluster systems, such as the one with about 200 Tesla C1070 GPUs (Spurzem et al., 2010). This paper offers an alternative to collisional N-body simulations with GRAPEs and GPUs.
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paper_title: octopus: a first-principles tool for excited electron-ion dynamics.

paper_content:

We present a computer package aimed at the simulation of the electron–ion dynamics of finite systems, both in one and three dimensions, under the influence of time-dependent electromagnetic fields. The electronic degrees of freedom are treated quantum mechanically within the time-dependent Kohn–Sham formalism, while the ions are handled classically. All quantities are expanded in a regular mesh in real space, and the simulations are performed in real time. Although not optimized for that purpose, the program is also able to obtain static properties like ground-state geometries, or static polarizabilities. The method employed proved quite reliable and general, and has been successfully used to calculate linear and non-linear absorption spectra, harmonic spectra, laser induced fragmentation, etc. of a variety of systems, from small clusters to medium sized quantum dots.  2002 Elsevier Science B.V. All rights reserved.
---
paper_title: Introduction to High Performance Computing for Scientists and Engineers

paper_content:

Written by high performance computing (HPC) experts, Introduction to High Performance Computing for Scientists and Engineers provides a solid introduction to current mainstream computer architecture, dominant parallel programming models, and useful optimization strategies for scientific HPC. From working in a scientific computing center, the authors gained a unique perspective on the requirements and attitudes of users as well as manufacturers of parallel computers. The text first introduces the architecture of modern cache-based microprocessors and discusses their inherent performance limitations, before describing general optimization strategies for serial code on cache-based architectures. It next covers shared- and distributed-memory parallel computer architectures and the most relevant network topologies. After discussing parallel computing on a theoretical level, the authors show how to avoid or ameliorate typical performance problems connected with OpenMP. They then present cache-coherent nonuniform memory access (ccNUMA) optimization techniques, examine distributed-memory parallel programming with message passing interface (MPI), and explain how to write efficient MPI code. The final chapter focuses on hybrid programming with MPI and OpenMP. Users of high performance computers often have no idea what factors limit time to solution and whether it makes sense to think about optimization at all. This book facilitates an intuitive understanding of performance limitations without relying on heavy computer science knowledge. It also prepares readers for studying more advanced literature.
---
paper_title: 369 Tflop-s molecular dynamics simulations on the petaflop hybrid supercomputer ‘Roadrunner’

paper_content:

We describe the implementation of a short-range parallel molecular dynamics (MD) code, SPaSM, on the heterogeneous general-purpose Roadrunner supercomputer. Each Roadrunner ‘TriBlade’ compute node consists of two AMD Opteron dual-core microprocessors and four IBM PowerXCell 8i enhanced Cell microprocessors (each consisting of one PPU and eight SPU cores), so that there are four MPI ranks per node, each with one Opteron and one Cell. We will briefly describe the Roadrunner architecture and some of the initial hybrid programming approaches that have been taken, focusing on the SPaSM application as a case study. An initial ‘evolutionary’ port, in which the existing legacy code runs with minor modifications on the Opterons and the Cells are only used to compute interatomic forces, achieves roughly a 2× speedup over the unaccelerated code. On the other hand, our ‘revolutionary’ implementation adopts a Cell-centric view, with data structures optimized for, and living on, the Cells. The Opterons are mainly used to direct inter-rank communication and perform I-O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard–Jones pair potential benchmark reached a peak of 369 Tflop-s double-precision floating-point performance on the full Roadrunner system (27.7p of peak), nearly 10× faster than the unaccelerated (Opteron-only) version. Copyright © 2009 John Wiley & Sons, Ltd.
---
paper_title: Lattice Boltzmann simulation optimization on leading multicore platforms

paper_content:

We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of search-based performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to a lattice Boltzmann application (LBMHD) that historically has made poor use of scalar microprocessors due to its complex data structures and memory access patterns. We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Clovertown, AMD Opteron X2, Sun Niagara!, STI Cell, as well as the single core Intel Itanium.2. Rather than hand-tuning LBMHD for each system, we develop a code generator that allows us identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our auto- tuned LBMHD application achieves up to a 14times improvement compared with the original code. Additionally, we present detailed analysis of each optimization, which reveal surprising hardware bottlenecks and software challenges for future multicore systems and applications.
---
paper_title: Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

paper_content:

Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.
---
paper_title: Utilizing high performance computing for chemistry: parallel computational chemistry.

paper_content:

Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.
---
paper_title: The Future of Microprocessors

paper_content:

The performance of microprocessors that power modern computers has continued to increase exponentially over the years for two main reasons. First, the transistors that are the heart of the circuits in all processors and memory chips have simply become faster over time on a course described by Moore’s law,1 and this directly affects the performance of processors built with those transistors. Moreover, actual processor performance has increased faster than Moore’s law would predict,2 because processor designers have been able to harness the increasing numbers of transistors available on modern chips to extract more parallelism from software. This is depicted in figure 1 for Intel’s processors.
---
paper_title: Proton Transfer 200 Years after von Grotthuss: Insights from Ab Initio Simulations

paper_content:

In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly conttibuted to the improvement of our undetstanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the -many-body interactions by solving the electronic structure problem 'on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advawes. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited state proton transfer in solution, phase transitions in ice, and pratonated water networis in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
---
paper_title: Introduction to High Performance Computing for Scientists and Engineers

paper_content:

Written by high performance computing (HPC) experts, Introduction to High Performance Computing for Scientists and Engineers provides a solid introduction to current mainstream computer architecture, dominant parallel programming models, and useful optimization strategies for scientific HPC. From working in a scientific computing center, the authors gained a unique perspective on the requirements and attitudes of users as well as manufacturers of parallel computers. The text first introduces the architecture of modern cache-based microprocessors and discusses their inherent performance limitations, before describing general optimization strategies for serial code on cache-based architectures. It next covers shared- and distributed-memory parallel computer architectures and the most relevant network topologies. After discussing parallel computing on a theoretical level, the authors show how to avoid or ameliorate typical performance problems connected with OpenMP. They then present cache-coherent nonuniform memory access (ccNUMA) optimization techniques, examine distributed-memory parallel programming with message passing interface (MPI), and explain how to write efficient MPI code. The final chapter focuses on hybrid programming with MPI and OpenMP. Users of high performance computers often have no idea what factors limit time to solution and whether it makes sense to think about optimization at all. This book facilitates an intuitive understanding of performance limitations without relying on heavy computer science knowledge. It also prepares readers for studying more advanced literature.
---
paper_title: 369 Tflop-s molecular dynamics simulations on the petaflop hybrid supercomputer ‘Roadrunner’

paper_content:

We describe the implementation of a short-range parallel molecular dynamics (MD) code, SPaSM, on the heterogeneous general-purpose Roadrunner supercomputer. Each Roadrunner ‘TriBlade’ compute node consists of two AMD Opteron dual-core microprocessors and four IBM PowerXCell 8i enhanced Cell microprocessors (each consisting of one PPU and eight SPU cores), so that there are four MPI ranks per node, each with one Opteron and one Cell. We will briefly describe the Roadrunner architecture and some of the initial hybrid programming approaches that have been taken, focusing on the SPaSM application as a case study. An initial ‘evolutionary’ port, in which the existing legacy code runs with minor modifications on the Opterons and the Cells are only used to compute interatomic forces, achieves roughly a 2× speedup over the unaccelerated code. On the other hand, our ‘revolutionary’ implementation adopts a Cell-centric view, with data structures optimized for, and living on, the Cells. The Opterons are mainly used to direct inter-rank communication and perform I-O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard–Jones pair potential benchmark reached a peak of 369 Tflop-s double-precision floating-point performance on the full Roadrunner system (27.7p of peak), nearly 10× faster than the unaccelerated (Opteron-only) version. Copyright © 2009 John Wiley & Sons, Ltd.
---
paper_title: Spending Moore's dividend

paper_content:

Multicore computers shift the burden of software performance from chip designers and processor architects to software developers.
---
paper_title: The Case for Energy-Proportional Computing

paper_content:

Energy-proportional designs would enable large energy savings in servers, potentially doubling their efficiency in real-life use. Achieving energy proportionality will require significant improvements in the energy usage profile of every system component, particularly the memory and disk subsystems.
---
paper_title: The impact of multicore on math software

paper_content:

Power consumption and heat dissipation issues are pushing the microprocessors industry towards multicore design patterns. Given the cubic dependence between core frequency and power consumption, multicore technologies leverage the idea that doubling the number of cores and halving the cores frequency gives roughly the same performance reducing the power consumption by a factor of four. With the number of cores on multicore chips expected to reach tens in a few years, efficient implementations of numerical libraries using shared memory programming models is of high interest. The current message passing paradigm used in ScaLAPACK and elsewhere introduces unnecessary memory overhead and memory copy operations, which degrade performance, along with the making it harder to schedule operations that could be done in parallel. Limiting the use of shared memory to fork-join parallelism (perhaps with OpenMP) or to its use within the BLAS does not address all these issues.
---
paper_title: The impact of IBM Cell technology on the programming paradigm in the context of computer systems for climate and weather models

paper_content:

The call for ever-increasing model resolutions and physical processes in climate and weather models demands a continual increase in computing power. The IBM Cell processor's order-of-magnitude peak performance increase over conventional processors makes it very attractive to fulfill this requirement. However, the Cell's characteristics, 256 kB local memory per SPE and the new low-level communication mechanism, make it very challenging to port an application. As a trial, we selected the solar radiation component of the NASA GEOS-5 climate model, which: (1) is representative of column-physics components (half of the total computational time), (2) has an extremely high computational intensity: the ratio of computational load to main memory transfers, and (3) exhibits embarrassingly parallel column computations. In this paper, we converted the baseline code (single-precision Fortran) to C and ported it to an IBM BladeCenter QS20. For performance, we manually SIMDize four independent columns and include several unrolling optimizations. Our results show that when compared with the baseline implementation running on one core of Intel's Xeon Woodcrest, Dempsey, and Itanium2, the Cell is approximately 8.8x, 11.6x, and 12.8x faster, respectively. Our preliminary analysis shows that the Cell can also accelerate the dynamics component (∼25p total computational time). We believe these dramatic performance improvements make the Cell processor very competitive as an accelerator. Copyright © 2009 John Wiley & Sons, Ltd.
---
paper_title: Millisecond-scale molecular dynamics simulations on Anton

paper_content:

Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first time the simulation of biological molecules at an atomic level of detail for periods on the order of a millisecond---about two orders of magnitude beyond the previous state of the art. Anton is now running simulations on a timescale at which many critically important, but poorly understood phenomena are known to occur, allowing the observation of aspects of protein dynamics that were previously inaccessible to both computational and experimental study. Here, we report Anton's performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations. We also discuss the manner in which novel algorithms have been coordinated with Anton's co-designed, application-specific hardware to achieve these results.
---
paper_title: The Future of Microprocessors

paper_content:

The performance of microprocessors that power modern computers has continued to increase exponentially over the years for two main reasons. First, the transistors that are the heart of the circuits in all processors and memory chips have simply become faster over time on a course described by Moore’s law,1 and this directly affects the performance of processors built with those transistors. Moreover, actual processor performance has increased faster than Moore’s law would predict,2 because processor designers have been able to harness the increasing numbers of transistors available on modern chips to extract more parallelism from software. This is depicted in figure 1 for Intel’s processors.
---
paper_title: JANUS: an FPGA-based System for High Performance Scientific Computing

paper_content:

Janus is a modular, massively parallel, and reconfigurable FPGA-based computing system. Each Janus module has one computational core and one host. Janus is tailored to, but not limited to, the needs of a class of hard scientific applications characterized by regular code structure, unconventional data-manipulation requirements, and a few Megabits database. The authors discuss this configurable system's architecture and focus on its use for Monte Carlo simulations of statistical mechanics, as Janus performs impressively on this class of application.
---
paper_title: Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

paper_content:

Discovering the functional mechanisms of biological systems frequently requires information that challenges the spatial and temporal resolution limits of current experimental techniques. Recent dramatic methodological advances have made all-atom molecular dynamics (MD) simulations an ever more
---
paper_title: Introduction to High Performance Computing for Scientists and Engineers

paper_content:

Written by high performance computing (HPC) experts, Introduction to High Performance Computing for Scientists and Engineers provides a solid introduction to current mainstream computer architecture, dominant parallel programming models, and useful optimization strategies for scientific HPC. From working in a scientific computing center, the authors gained a unique perspective on the requirements and attitudes of users as well as manufacturers of parallel computers. The text first introduces the architecture of modern cache-based microprocessors and discusses their inherent performance limitations, before describing general optimization strategies for serial code on cache-based architectures. It next covers shared- and distributed-memory parallel computer architectures and the most relevant network topologies. After discussing parallel computing on a theoretical level, the authors show how to avoid or ameliorate typical performance problems connected with OpenMP. They then present cache-coherent nonuniform memory access (ccNUMA) optimization techniques, examine distributed-memory parallel programming with message passing interface (MPI), and explain how to write efficient MPI code. The final chapter focuses on hybrid programming with MPI and OpenMP. Users of high performance computers often have no idea what factors limit time to solution and whether it makes sense to think about optimization at all. This book facilitates an intuitive understanding of performance limitations without relying on heavy computer science knowledge. It also prepares readers for studying more advanced literature.
---
paper_title: 369 Tflop-s molecular dynamics simulations on the petaflop hybrid supercomputer ‘Roadrunner’

paper_content:

We describe the implementation of a short-range parallel molecular dynamics (MD) code, SPaSM, on the heterogeneous general-purpose Roadrunner supercomputer. Each Roadrunner ‘TriBlade’ compute node consists of two AMD Opteron dual-core microprocessors and four IBM PowerXCell 8i enhanced Cell microprocessors (each consisting of one PPU and eight SPU cores), so that there are four MPI ranks per node, each with one Opteron and one Cell. We will briefly describe the Roadrunner architecture and some of the initial hybrid programming approaches that have been taken, focusing on the SPaSM application as a case study. An initial ‘evolutionary’ port, in which the existing legacy code runs with minor modifications on the Opterons and the Cells are only used to compute interatomic forces, achieves roughly a 2× speedup over the unaccelerated code. On the other hand, our ‘revolutionary’ implementation adopts a Cell-centric view, with data structures optimized for, and living on, the Cells. The Opterons are mainly used to direct inter-rank communication and perform I-O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard–Jones pair potential benchmark reached a peak of 369 Tflop-s double-precision floating-point performance on the full Roadrunner system (27.7p of peak), nearly 10× faster than the unaccelerated (Opteron-only) version. Copyright © 2009 John Wiley & Sons, Ltd.
---
paper_title: Extending Amdahl's Law for Energy-Efficient Computing in the Many-Core Era

paper_content:

An updated take on Amdahl's analytical model uses modern design constraints to analyze many-core design alternatives. The revised models provide computer architects with a better understanding of many-core design types, enabling them to make more informed tradeoffs.
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paper_title: The LINPACK Benchmark : past , present and future

paper_content:

SUMMARY This paper describes the LINPACK Benchmark and some of its variations commonly used to assess the performance of computer systems. Aside from the LINPACK Benchmark suite, the TOP500 and the HPL codes are presented. The latter is frequently used to obtained results for TOP500 submissions. Information is also given on how to interpret the results of the benchmark and how the results fit into the performance evaluation process. Copyright c � 2003 John Wiley & Sons, Ltd.
---
paper_title: Spending Moore's dividend

paper_content:

Multicore computers shift the burden of software performance from chip designers and processor architects to software developers.
---
paper_title: Giant Magnetoresistance of (001)Fe/(001)Cr Magnetic Superlattices

paper_content:

We have studied the magnetoresistance of (001)Fe/(001)Cr superlattices prepared by molecularbeam epitaxy. A huge magnetoresistance is found in superlattices with thin Cr layers: For example, with ${t}_{\mathrm{Cr}}=9$ \AA{}, at $T=4.2$ K, the resistivity is lowered by almost a factor of 2 in a magnetic field of 2 T. We ascribe this giant magnetoresistance to spin-dependent transmission of the conduction electrons between Fe layers through Cr layers.
---
paper_title: Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

paper_content:

Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.
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paper_title: Scientific data management in the coming decade

paper_content:

Scientific instruments and computer simulations are creating vast data stores that require new scientific methods to analyze and organize the data. Data volumes are approximately doubling each year. Since these new instruments have extraordinary precision, the data quality is also rapidly improving. Analyzing this data to find the subtle effects missed by previous studies requires algorithms that can simultaneously deal with huge datasets and that can find very subtle effects --- finding both needles in the haystack and finding very small haystacks that were undetected in previous measurements.
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paper_title: Computer simulation study of the structural stability and materials properties of DNA-intercalated layered double hydroxides.

paper_content:

The intercalation of DNA into layered double hydroxides (LDHs) has various applications, including drug delivery for gene therapy and origins of life studies. The nanoscale dimensions of the interlayer region make the exact conformation of the intercalated DNA difficult to elucidate experimentally. We use molecular dynamics techniques, performed on high performance supercomputing grids, to carry out large-scale simulations of double stranded, linear and plasmid DNA up to 480 base pairs in length intercalated within a magnesium-aluminum LDH. Currently only limited experimental data have been reported for these systems. Our models are found to be in agreement with experimental observations, according to which hydration is a crucial factor in determining the structural stability of DNA. Phosphate backbone groups are found to align with aluminum lattice positions. At elevated temperatures and pressures, relevant to origins of life studies which maintain that the earliest life forms originated around deep ocean hydrothermal vents, the structural stability of LDH-intercalated DNA is substantially enhanced as compared to DNA in bulk water. We also discuss how the materials properties of the LDH are modified due to DNA intercalation.
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paper_title: Grid Computing: Techniques and Applications

paper_content:

Designed for senior undergraduate and first-year graduate students, this classroom-tested book shows professors how to teach this subject in a practical way. It encompasses the varied and interconnected aspects of Grid computing, including how to design a system infrastructure and Grid portal. The text covers job submission and scheduling, Grid security, Grid computing services and software tools, graphical user interfaces, workflow editors, and Grid-enabling applications. It also contains programming assignments and multiple-choice questions and answers. The authors Web site offers various instructional resources, including slides and links to software for the programming assignments.
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paper_title: Introduction to High Performance Computing for Scientists and Engineers

paper_content:

Written by high performance computing (HPC) experts, Introduction to High Performance Computing for Scientists and Engineers provides a solid introduction to current mainstream computer architecture, dominant parallel programming models, and useful optimization strategies for scientific HPC. From working in a scientific computing center, the authors gained a unique perspective on the requirements and attitudes of users as well as manufacturers of parallel computers. The text first introduces the architecture of modern cache-based microprocessors and discusses their inherent performance limitations, before describing general optimization strategies for serial code on cache-based architectures. It next covers shared- and distributed-memory parallel computer architectures and the most relevant network topologies. After discussing parallel computing on a theoretical level, the authors show how to avoid or ameliorate typical performance problems connected with OpenMP. They then present cache-coherent nonuniform memory access (ccNUMA) optimization techniques, examine distributed-memory parallel programming with message passing interface (MPI), and explain how to write efficient MPI code. The final chapter focuses on hybrid programming with MPI and OpenMP. Users of high performance computers often have no idea what factors limit time to solution and whether it makes sense to think about optimization at all. This book facilitates an intuitive understanding of performance limitations without relying on heavy computer science knowledge. It also prepares readers for studying more advanced literature.
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paper_title: 369 Tflop-s molecular dynamics simulations on the petaflop hybrid supercomputer ‘Roadrunner’

paper_content:

We describe the implementation of a short-range parallel molecular dynamics (MD) code, SPaSM, on the heterogeneous general-purpose Roadrunner supercomputer. Each Roadrunner ‘TriBlade’ compute node consists of two AMD Opteron dual-core microprocessors and four IBM PowerXCell 8i enhanced Cell microprocessors (each consisting of one PPU and eight SPU cores), so that there are four MPI ranks per node, each with one Opteron and one Cell. We will briefly describe the Roadrunner architecture and some of the initial hybrid programming approaches that have been taken, focusing on the SPaSM application as a case study. An initial ‘evolutionary’ port, in which the existing legacy code runs with minor modifications on the Opterons and the Cells are only used to compute interatomic forces, achieves roughly a 2× speedup over the unaccelerated code. On the other hand, our ‘revolutionary’ implementation adopts a Cell-centric view, with data structures optimized for, and living on, the Cells. The Opterons are mainly used to direct inter-rank communication and perform I-O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard–Jones pair potential benchmark reached a peak of 369 Tflop-s double-precision floating-point performance on the full Roadrunner system (27.7p of peak), nearly 10× faster than the unaccelerated (Opteron-only) version. Copyright © 2009 John Wiley & Sons, Ltd.
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paper_title: An optimal multimedia object allocation solution in multi-powermode storage systems

paper_content:

Given a set of multimedia objects R=lo1, o2, …, okr each of which has a set of multiple versions oi.v=lAi.0, Ai.1, …, Ai.mr, i=1, 2, …, k, there is a problem of distributing these objects in a server system so that user requests for accessing specified multimedia objects can be fulfilled with the minimum energy consumption and without significant degrading of the system performance. This paper considers the allocation problem of multimedia objects in multi-powermode storage systems, where the objects are distributed among multi-powermode storages based on the access pattern to the objects. We design an underlying infrastructure of storage system and propose a dynamic multimedia object allocation policy based on the designed infrastructure, which integrate and prove the optimality of the proposed policy. Copyright © 2010 John Wiley & Sons, Ltd.
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Title: A Review of High Performance Computing Foundations for Scientists

Section 1: Introduction
Description 1: Introduce the importance and role of scientific computer simulation, and provide an overview of High Performance Computing (HPC) and its application.

Section 2: Hardware basics
Description 2: Describe the basic components of a computer, including memory, Control Unit, Arithmetic Logic Unit (ALU), and how these components work together. Discuss memory hierarchy in detail.

Section 3: Beyond the Von Neumann paradigm
Description 3: Explain the limitations of the traditional Von Neumann architecture and discuss modern improvements and alternatives such as integration, clock-rate increase, superscalarity, multicore architecture, multithreading, SIMD instructions, out-of-order execution, and simplified instruction sets.

Section 4: Parallel computers
Description 4: Discuss the architecture and design of parallel computers, including shared-memory and distributed-memory systems, the importance of network topology, and different types of parallel supercomputers.

Section 5: Hybrid and heterogeneous models
Description 5: Describe the construction and benefits of hybrid and heterogeneous machines that combine different kinds of processors such as CPUs, GPUs, and special-purpose chips. Include a discussion on the advantages and challenges of these models.

Section 6: Distributed computing
Description 6: Explain newer forms of high-performance computing like grid computing, volunteer computing, and cloud computing. Discuss how these distributed computing methods work, their benefits and drawbacks.

Section 7: Intrinsic limitations to accuracy and efficiency
Description 7: Examine the issues related to accuracy and execution time in scientific calculations. Discuss machine precision errors, soft errors, algorithm-specific errors, and the implications of Amdahl's Law and Gustafson's Law on parallel computing.