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MDGRAPE
MDGRAPE-3 is an ultra-high performance petascale supercomputer system developed by the Riken research institute in Japan. It is a special purpose system built for molecular dynamics simulations, especially protein structure prediction. MDGRAPE-3 consists of 201 units of 24 custom MDGRAPE-3 chips (4,824 total), plus additional dual-core Intel Xeon processors (codename "Dempsey") which serve as host machines. In June 2006 Riken announced its completion,Riken press release, Completion of a one-petaflops computer system for simulation of molecular dynamics' achieving the petaFLOPS level of floating point arithmetic performance. This was more than three times faster than the 2006 version of the IBM Blue Gene/L system, which then led the TOP500 list of supercomputers at 0.28 petaFLOPS. Because it's not a general-purpose machine capable of running the LINPACK benchmarks, MDGRAPE-3 does not qualify for the TOP500 list. See also * Supercomputing in Japan * MDGRAPE-4 MDGRAPE-4 is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MDGRAPE-4
MDGRAPE-4 is a supercomputer under development at the RIKEN Quantitative Biology Center (QBiC) in Suita is a city located in northern Osaka Prefecture, Japan. As of October 1, 2016, the city has an estimated population of 378,322 and a population density of 9,880 persons per km². The total area is 36.11 km². The city was founded on April 1, ..., Osaka, Japan. See also * RIKEN MDGRAPE-3 References Riken Supercomputers Supercomputing in Japan molecular dynamics {{compu-book-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Supercomputing In Japan
Japan operates a number of centers for supercomputing which hold world records in speed, with the K computer becoming the world's fastest in June 2011. and Fugaku took the lead in June 2020, and furthered it, as of November 2020, to 3 times faster than number two computer. The K computer's performance was impressive, according to professor Jack Dongarra who maintains the TOP500 list of supercomputers, and it surpassed its next 5 competitors combined. The K computer cost US$10 million a year to operate. Previous records Japan's entry into supercomputing began in the early 1980s. In 1982, Osaka University's LINKS-1 Computer Graphics System used a massively parallel processing architecture, with 514 microprocessors, including 257 Zilog Z8001 control processors and 257 iAPX 86/20 floating-point processors. It was mainly used for rendering realistic 3D computer graphics. It was the world's most powerful computer, as of 1984. The SX-3 supercomputer family was developed by NE ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Petaflops
In computing, floating point operations per second (FLOPS, flops or flop/s) is a measure of computer performance, useful in fields of scientific computations that require floating-point calculations. For such cases, it is a more accurate measure than measuring instructions per second. Floating-point arithmetic Floating-point arithmetic is needed for very large or very small real numbers, or computations that require a large dynamic range. Floating-point representation is similar to scientific notation, except everything is carried out in base two, rather than base ten. The encoding scheme stores the sign, the exponent (in base two for Cray and VAX, base two or ten for IEEE floating point formats, and base 16 for IBM Floating Point Architecture) and the significand (number after the radix point). While several similar formats are in use, the most common is ANSI/IEEE Std. 754-1985. This standard defines the format for 32-bit numbers called ''single precision'', as well as 64- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TOP500
The TOP500 project ranks and details the 500 most powerful non- distributed computer systems in the world. The project was started in 1993 and publishes an updated list of the supercomputers twice a year. The first of these updates always coincides with the International Supercomputing Conference in June, and the second is presented at the ACM/IEEE Supercomputing Conference in November. The project aims to provide a reliable basis for tracking and detecting trends in high-performance computing and bases rankings on HPL, a portable implementation of the high-performance LINPACK benchmark written in Fortran for distributed-memory computers. The 60th TOP500 was published in November 2022. Since June 2022, USA's Frontier is the most powerful supercomputer on TOP500, reaching 1102 petaFlops (1.102 exaFlops) on the LINPACK benchmarks. The United States has by far the highest share of total computing power on the list (nearly 50%), while China currently leads the list in number of s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Supercomputers
A supercomputer is a computer with a high level of performance as compared to a general-purpose computer. The performance of a supercomputer is commonly measured in floating-point operations per second (FLOPS) instead of million instructions per second (MIPS). Since 2017, there have existed supercomputers which can perform over 1017 FLOPS (a hundred quadrillion FLOPS, 100 petaFLOPS or 100 PFLOPS). For comparison, a desktop computer has performance in the range of hundreds of gigaFLOPS (1011) to tens of teraFLOPS (1013). Since November 2017, all of the world's fastest 500 supercomputers run on Linux-based operating systems. Additional research is being conducted in the United States, the European Union, Taiwan, Japan, and China to build faster, more powerful and technologically superior exascale supercomputers. Supercomputers play an important role in the field of computational science, and are used for a wide range of computationally intensive tasks in variou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative erro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative erro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Starting in 1994, the performance of current methods is assessed biannually in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. Protein structure and terminology Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the main chain ab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Supercomputer
A supercomputer is a computer with a high level of performance as compared to a general-purpose computer. The performance of a supercomputer is commonly measured in floating-point operations per second ( FLOPS) instead of million instructions per second (MIPS). Since 2017, there have existed supercomputers which can perform over 1017 FLOPS (a hundred quadrillion FLOPS, 100 petaFLOPS or 100 PFLOPS). For comparison, a desktop computer has performance in the range of hundreds of gigaFLOPS (1011) to tens of teraFLOPS (1013). Since November 2017, all of the world's fastest 500 supercomputers run on Linux-based operating systems. Additional research is being conducted in the United States, the European Union, Taiwan, Japan, and China to build faster, more powerful and technologically superior exascale supercomputers. Supercomputers play an important role in the field of computational science, and are used for a wide range of computationally intensive tasks in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Petascale Computers
Petascale computing refers to computing systems capable of calculating at least 1015 floating point operations per second (1 petaFLOPS). Petascale computing allowed faster processing of traditional supercomputer applications. The first system to reach this milestone was the IBM Roadrunner in 2008. Petascale supercomputers are planned to be succeeded by exascale computers. Definition Floating point operations per second (FLOPS) are one measure of computer performance. FLOPS can be recorded in different measures of precision, however the standard measure (used by the TOP500 supercomputer list) uses 64 bit (double-precision floating-point format) operations per second using the High Performance LINPACK (HPLinpack) benchmark. The metric typically refers to single computing systems, although can be used to measure distributed computing systems for comparison. It can be noted that there are alternative precision measures using the LINPACK benchmarks which are not part of the s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Petascale
Petascale computing refers to computing systems capable of calculating at least 1015 floating point operations per second (1 petaFLOPS). Petascale computing allowed faster processing of traditional supercomputer applications. The first system to reach this milestone was the IBM Roadrunner in 2008. Petascale supercomputers are planned to be succeeded by exascale computers. Definition Floating point operations per second (FLOPS) are one measure of computer performance. FLOPS can be recorded in different measures of precision, however the standard measure (used by the TOP500 supercomputer list) uses 64 bit ( double-precision floating-point format) operations per second using the High Performance LINPACK (HPLinpack) benchmark. The metric typically refers to single computing systems, although can be used to measure distributed computing systems for comparison. It can be noted that there are alternative precision measures using the LINPACK benchmarks which are not part of the stan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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