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Gazing into Computational Biology’s Crystal Ball

Aug 23, 2016 |

Sorting out computational biology’s future is tricky. It likely won’t be singular. First-principle, mechanistic simulation has so far proven challenging but could eventually become game changing. Meanwhile pattern recognition and matching in massive ‘omics’ datasets have been extremely productive and likely to remain dominant at present. Now, an MIT professor and colleagues write that two Read more…

ARM Unveils Scalable Vector Extension for HPC at Hot Chips

Aug 22, 2016 |

ARM and Fujitsu today announced a scalable vector extension (SVE) to the ARMv8-A architecture intended to enhance ARM capabilities in HPC workloads. Fujitsu is the lead silicon partner in the effort (so far) and will use ARM with SVE technology in its post K computer, Japan’s next flagship supercomputer planned for the 2020 timeframe. This is an important incremental step for ARM, which seeks to push more aggressively into mainstream and HPC server markets.

Container Testing Reveals ‘Memory Pressure’ on Apps

Aug 18, 2016 |

With early adopters of application container technology completing early testing in multi-tenant settings, potential performance issues are beginning to surface. Among them, according to hyper-scaler LinkedIn, is a Linux kernel feature called “control groups” used with most containers to assign resources. In an analysis based on several months of “pressure testing,” Zhenyun Zhuang, a software Read more…

Think Fast – Is Neuromorphic Computing Set to Leap Forward?

Aug 15, 2016 |

Steadily advancing neuromorphic computing technology has created high expectations for this fundamentally different approach to computing. Its strengths – like the human brain it attempts to mimic – are pattern recognition (space and time) and inference reasoning. Advocates say it will also be possible to compute at much lower power than current paradigms. At ISC Read more…

Intel to Acquire AI Startup Nervana Systems

Aug 9, 2016 |

If we needed another sign that Intel is serious about mining AI market opportunities, it came today when the chip company announced it had inked a “definitive agreement” to acquire artificial intelligence and deep learning company Nervana Systems. Financial terms haven’t been disclosed yet, but a source familiar with the deal told Recode it’s worth more Read more…

MPI Is Not Perfect … Yet

Aug 3, 2016 |

The Message Passing Interface (MPI) is the standard definition of a communication API that has underpinned traditional HPC for decades. The message passing programming represents distributed-memory hardware architectures using processes that send messages to each other. When first standardised in 1993-4, MPI was a major step forward from the many proprietary, system-dependent, and semantically different message-passing libraries that came before it.

FlyElephant 2.0 Is Now Available

Jul 28, 2016 |

July 28 — The FlyElephant team is happy to announce the release of the platform FlyElephant 2.0, with following updates: internal expert community, collaboration on projects, public tasks, Docker and Jupyter support, a new file storage system and work with HPC clusters. FlyElephant is a platform for data scientists, engineers and scientists, which provides a ready-computing infrastructure for Read more…

MIT’s Multicore Swarm Architecture Advances Ordered Parallelism

Jul 21, 2016 |

A relatively new architecture explicitly designed for parallelism – Swarm – based on work at MIT has shown promise for substantially speeding up classes of applications (graphs, for example) and decreasing the programming burden to achieve parallelism. The work, recounted in a recent paper, Unlocking Ordered Parallelism with the Swarm Architecture, bucks conventional wisdom and Read more…

RISC-V Startup Aims to Democratize Custom Silicon

Jul 13, 2016 |

Momentum for open source hardware made a significant advance this week with the launch of startup SiFive and its open source chip platforms based on the RISC-V instruction set architecture. The founders of the fabless semiconductor company — Krste Asanovic, Andrew Waterman, and Yunsup Lee — invented the free and open RISC-V ISA at the University of California, Berkeley, six years ago. The progression of RISC-V and the launch of SiFive opens the door to a new way of chip building that skirts prohibitive licensing costs and lowers the barrier to entry…

ISC Workshop Tackles the Co-development Challenge

Jul 12, 2016 |

The long percolating discussion over ‘co-development’ and how best it should be undertaken has gained new urgency in the race towards exascale computing. At a workshop held at ISC2016 last month – Form Follows Function: Do algorithms and applications challenge or drag behind the hardware evolution? – several distinguished panelists offered varying viewpoints. Yesterday, session organizer Tobias Weinzierl posted a summary synopsis of the workshop discussion on arXiv.org. Weinzierl (Durham University) and co-organizer Michael Bader (Technische Universität München) are active participants in the ExaHyPE project (An Exascale Hyperbolic PDE (partial differential equation) Engine, funded by EU’s Horizon 2020 program).

OLCF Researchers Scale R to Tackle Big Science Data Sets

Jul 6, 2016 |

Sometimes lost in the discussion around big data is the fact that big science has long generated huge data sets. “In fact, large-scale simulations that run on leadership-class supercomputers work at such high speeds and resolution that they generate unprecedented amounts of data. The size of these datasets—ranging from a few gigabytes to hundreds of Read more…

Trinity Wrestles with Knights Landing Programming Challenge with COE

Jul 5, 2016 |

Seventy-one years ago, on July 16, 1945, an incredible explosion lit up the New Mexico night sky. This was the Trinity Test, the world’s first nuclear detonation, and it marked the beginning of the Nuclear Age. It also ushered in the age of supercomputers, which essentially began with weapons science at Los Alamos National Laboratory (LANL). Now a new Trinity, a next generation Cray XC supercomputer is about to take center stage to help the national security labs achieve their primary mission – to provide the nation with a safe, secure and effective nuclear deterrent.

Third Annual JuliaCon Concludes

Jul 1, 2016 |

CAMBRIDGE, Mass., July 1 — “Julia is a great tool.” That’s what Nobel Laureate Thomas J. Sargent told 250 engineers, computer scientists, programmers, and data scientists during the third annual JuliaCon held at MIT’s Computer Science and Artificial Intelligence Labs. This year’s JuliaCon was the biggest yet, and featured presentations describing how Julia is being used Read more…

Compilers and More: OpenACC to OpenMP (and back again)

Jun 29, 2016 |

In the last year or so, I’ve had several academic researchers ask me whether I thought it was a good idea for them to develop a tool to automatically convert OpenACC programs to OpenMP 4 and vice versa. In each case, the motivation was that some systems had OpenMP 4 compilers (x86 plus Intel Xeon Phi Knights Corner) and others had OpenACC (x86 plus NVIDIA GPU or AMD GPU), and someone wanting to run a program across both would need two slightly different programs. In each case, the proposed research sounded like a more-or-less mechanical translation process, something more like a sophisticated awk script, and that’s doomed from the start. I will explain below in more detail how I came to this conclusion.

HPE Tackles Phi, Debuts Mfg. Solution and New HPC Software Environment

Jun 20, 2016 |

Hewlett Packard Enterprise (HPE), now about eight months into its transition as a separate entity, retained the prestige of fielding the most systems of any vendor on the Top500 list announced at the ISC2016. HPE had 127 systems (25.4 percent) though the number was down from 155 just six months ago. Other ISC news included Read more…

NVIDIA Debuts PCIe-based P100; Broadens Aim at CPU Dominance

Jun 19, 2016 |

NVIDIA seems to be mounting a vigorous effort to dethrone the CPU as the leader of the processor pack for HPC and demanding datacenter workloads. That’s a tall order. Introduction at ISC 2016 of a PCIe-based version of is new Tesla P100 card is one element in the strategy. It should ease the upgrade path Read more…

Heading into ISC16, OpenHPC Releases Latest Stack with 60-plus Packages

Jun 16, 2016 |

SC15 was sort of a muted launch party for OpenHPC – the nascent effort to develop a ‘plug-and-play’ software framework for HPC. There seemed to be widespread agreement the idea had merit, not a lot of knowledge of details, and some wariness because Intel was a founding member and vocal advocate. Next week, ISC16 will mark the next milestone for OpenHPC, which has since grown into a full-fledged Linux Foundation Collaborative Project and today released version 1.0.1 of OpenHPC (build and test tools).

OpenACC Adds Support for OpenPOWER; Touts Growing Traction

Jun 13, 2016 |

In a show of strength leading up to ISC the OpenACC standards group today announced its first OpenPOWER implementation, the addition of three new members – University of Illinois, Brookhaven National Laboratory, and Stony Brook University – and details of its expanding 2016 training schedule. Michael Wolfe, technical director of OpenACC, also talked with HPCwire about thorny compiler challenges still remaining as…

IBM Launches Apache Spark Development Environment

Jun 8, 2016 |

IBM, which has bet big on Apache Spark as a kind of analytics operating system ($300 million investment), yesterday announced the first cloud-based development environment for near real-time, high performance analytics using Apache Spark and a variety of tools from IBM and others. According to IBM the new set of capabilities, available on IBM Bluemix Read more…

Exiting Intel, James Reinders Offers a Brief Personal Retrospective

Jun 6, 2016 |

You may have heard that Intel has encouraged “long timers” (like me) to consider early retirement. Well, the offer was convincing for me. After 10,001 days at Intel, it is time for me to start the next phase of my life. I’ve accepted the “ERP offer” (early retirement) with my last day being June 24, 2016 (exactly 10,000 days after my start date). I’ll be in the office as much as needed to help transitions and wrap things up. Let me know if you need/want anything from me as I finish up.