Purpose-Built Supercomputing

By Michael Feldman

July 9, 2008

In HPC, there has always been a tension between general-purpose and special-purpose architectures. That tension reflects two facets of the market: to apply HPC to more application domains and more users, and to increase performance for the most demanding applications. With a sort of schizophrenic behavior, HPC exploits Moore’s Law’s for all it’s worth, and then, unsatisfied, tries to find a way to beat it.

In the early days of supercomputing, special-purpose silicon dominated the industry, exemplified by the custom-built vector machines from Cray and NEC. But by the 1990s, the “attack of the killer micros” ushered in the era of general-purpose CPUs, specifically the x86 franchise. Because of the favorable hardware and software economics offered by general-purpose hardware, many people thought this model would go on forever. Now there are some indications it won’t.

By incorporating a few thousand souped-up game chips into its design, the IBM Roadrunner demonstrated how a far and how fast an architecture can leap over its brethren. Using the latest Cell processors, IBM was able to reach a petaflop in Linpack performance before any of the competition, not to mention the company’s own PowerPC-based Blue Gene. Today there are plans afoot to build other high-end supercomputers using the latest GPU chips from NVIDIA. And although both Cell and GPU processors are specialized, they are derived from chips that are used in commodity gaming systems. Thus they retain some of the volume production advantages of general-purpose CPUs, if not the software advantages.

But to squeeze even more application performance from silicon, one must resort to true custom designs. Perhaps the most extreme example of this approach is Japan’s latest MDGRAPE supercomputer built by RIKEN. The system was not built for general-purpose computing. It was designed specifically to perform molecular dynamics simulations, especially for protein structure prediction and the development of new drugs. Using 4808 custom MDGRAPE-3 processors, that machine reportedly achieved a petaflop two years before the IBM Roadrunner did. But since it wasn’t a Linpack petaflop it didn’t count in the TOP500 supercomputer tally.

At the end of 2008, a U.S. based firm, D.E. Shaw and Company, is scheduled to complete the development of another custom-built supercomputer for molecular dynamics (MD). The project is headed by David E. Shaw, a computer scientist who made his fortune on Wall Street as a quantitative trader. The new MD machine, called “Anton” (after the legendary microbiologist Anton van Leeuwenhoek), incorporates 512 custom-built ASICs hooked together by a high-speed communication network. The system is designed to execute millisecond-scale MD simulations.

The millisecond scale is the important feature since it represents at least a thousand-fold increase in the timescale of MD simulations currently being carried out on supercomputers. It will allow researchers to get a much better sense of protein folding behavior and other biochemical interactions. Specifically, it should give scientists a much more powerful tool for understanding disease mechanisms and for developing new drugs.

But will a custom-built design be worth it, even for specific applications with a lot of science and potentially, commercial worth, riding on the results? In an ACM article which describes Anton, the researchers offer their rationalization for the approach:

A natural question is whether a specialized machine for molecular simulation can gain a significant performance advantage over general-purpose hardware. After all, history is littered with the corpses of specialized machines, spanning a huge gamut from Lisp machines to database accelerators. Performance and transistor count gains predicted by Moore’s law, together with the economies of scale behind the development of commodity processors, have driven a history of general-purpose microprocessors outpacing special-purpose solutions. Any plan to build specialized hardware must account for the expected exponential growth in the capabilities of general-purpose hardware.

We concluded that special-purpose hardware is warranted in this case because it leads to a much greater improvement in absolute performance than the expected speedup predicted by Moore’s law over our development time period, and because we are currently at the cusp of simulating timescales of great biological significance. We expect Anton to run simulations over 1000 times faster than was possible when we began this project. Assuming that transistor densities continue to double every 18 months and that these increases translate into proportionally faster processors and communication links, one would expect approximately a tenfold improvement in commodity solutions over the five-year development time of our machine (from conceptualization to bring-up). We therefore expect that a specialized solution will be able to access biologically critical millisecond timescales significantly sooner than commodity hardware.

A custom-built approach is also being undertaken by researchers at Berkeley Lab who are designing a multi-petaflop supercomputer for next generation climate modeling. In this case though, they’re attempting to exploit commodity technology from the embedded computing space. Because of power and hardware limitations, the Berkeley guys believe it will not even be possible to construct practical general-purpose machines as computing approaches the exascale level. If true, special-purpose architectures will not just be an alternative approach, it will be the only way forward.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first planned U.S. exascale computer. Intel also provided a glimpse of Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutting for the Expo Hall opening is Monday at 6:45pm, with the Read more…

By Tiffany Trader

SC19’s HPC Impact Showcase Chair: AI + HPC a ‘Speed Train’

November 16, 2019

This year’s chair of the HPC Impact Showcase at the SC19 conference in Denver is Lori Diachin, who has spent her career at the spearhead of HPC. Currently deputy director for the U.S. Department of Energy’s (DOE) Read more…

By Doug Black

Microsoft Azure Adds Graphcore’s IPU

November 15, 2019

Graphcore, the U.K. AI chip developer, is expanding collaboration with Microsoft to offer its intelligent processing units on the Azure cloud, making Microsoft the first large public cloud vendor to offer the IPU designe Read more…

By George Leopold

At SC19: What Is UrgentHPC and Why Is It Needed?

November 14, 2019

The UrgentHPC workshop, taking place Sunday (Nov. 17) at SC19, is focused on using HPC and real-time data for urgent decision making in response to disasters such as wildfires, flooding, health emergencies, and accidents. We chat with organizer Nick Brown, research fellow at EPCC, University of Edinburgh, to learn more. Read more…

By Tiffany Trader

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

IBM Accelerated Insights

Data Management – The Key to a Successful AI Project

 

Five characteristics of an awesome AI data infrastructure

[Attend the IBM LSF & HPC User Group Meeting at SC19 in Denver on November 19!]

AI is powered by data

While neural networks seem to get all the glory, data is the unsung hero of AI projects – data lies at the heart of everything from model training to tuning to selection to validation. Read more…

China’s Tencent Server Design Will Use AMD Rome

November 13, 2019

Tencent, the Chinese cloud giant, said it would use AMD’s newest Epyc processor in its internally-designed server. The design win adds further momentum to AMD’s bid to erode rival Intel Corp.’s dominance of the glo Read more…

By George Leopold

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first plann Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutt Read more…

By Tiffany Trader

SC19’s HPC Impact Showcase Chair: AI + HPC a ‘Speed Train’

November 16, 2019

This year’s chair of the HPC Impact Showcase at the SC19 conference in Denver is Lori Diachin, who has spent her career at the spearhead of HPC. Currently Read more…

By Doug Black

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Intel AI Summit: New ‘Keem Bay’ Edge VPU, AI Product Roadmap

November 12, 2019

At its AI Summit today in San Francisco, Intel touted a raft of AI training and inference hardware for deployments ranging from cloud to edge and designed to support organizations at various points of their AI journeys. The company revealed its Movidius Myriad Vision Processing Unit (VPU)... Read more…

By Doug Black

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quant Read more…

By John Russell

Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale. That’s the conclusion drawn by the scientists and researchers of Europe’s NEXTGenIO project, an initiative funded by the European Commission’s Horizon 2020 program to explore this new... Read more…

By Jan Rowell

MLPerf Releases First Inference Benchmark Results; Nvidia Touts its Showing

November 6, 2019

MLPerf.org, the young AI-benchmarking consortium, today issued the first round of results for its inference test suite. Among organizations with submissions wer Read more…

By John Russell

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This