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Life in a Drop: Ohio Supercomputer Helps Prove Hydration’s Role in Protein Folding

Jul 14, 2016 | It’s perhaps fitting that in the middle of the summer, when water management is a common challenge, that a paper in the Proceeding of the National Academy of Sciences (PNAS) offers more proof that life as we know it can’t occur without water. Using Ohio Supercomputing Center resources, researchers have shown the critical role water plays in actively guiding protein folding and movement. “For a long time, scientists have been trying to figure out how water interacts with proteins... 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... Read more…

A Celebration of Women in HPC

Jul 7, 2016 | Why are there not more women in HPC? This was the simple question that led to the formation of the Women in HPC (WHPC) network nearly three years ago. Under the direction of founder Dr. Toni Collis of the Edinburgh Parallel Computing Centre (EPCC), the organization has been gaining momentum and making a name for itself since its inaugural Women in HPC workshop at SC14. At ISC 2016 in Frankfurt, Germany, WHPC expanded its program to three events: its fourth international Women in High Performance Computing (WHPC) workshop; a BOF on women in HPC; and a networking luncheon. The BOF (June 21) and the workshop (June 23) shared the theme of addressing the gender gap in HPC. Women in HPC has found that women make up between 5 and 17 percent of HPC users, researchers and conference attendees. Read more…

PNNL’s CENATE Quickly Winning Industry Support and Collaboration

Jul 6, 2016 | Getting to the root of how things work has informed and progressed all aspects of scientific discovery. As computers and applications grow in complexity, seemingly poised to enter a new phase beyond the limits of Moore’s Law and CMOS technology, enlightening how they work best is paramount. With new resources from a growing list of industry partners, the Center for Advanced Technology Evaluation – known as CENATE – a computing proving ground at Pacific Northwest National Laboratory supported by the U.S. Department of Energy’s Office of Advanced Scientific Computing Research, is rapidly expanding its capabilities to assist the high-performance computing community. 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. Read more…

Genomic Sequencing at Children’s Mercy: Saving Time to Save Lives

Jul 1, 2016 | Genomic sequencing – that is, rapid sequencing – is instrumental to diagnosing and treating critically ill patients, and managing the high data volumes involved in genomics is essential to the process. Children’s Mercy Hospital in Kansas City, MO, (354 beds, not-for-profit, treating children from birth through the age of 21) operates what it says is the world’s first whole genome sequencing center in a pediatric setting, where physicians, clinical laboratory scientists, molecular geneticists, bioinformaticians and software engineers work to sequence and analyze rare inherited diseases. 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. Read more…

XSEDE16 Program Emphasizes Inclusion, Says Chair Kelly Gaither

Jun 29, 2016 | Ahead of XSEDE16, which takes place in Miami from July 17-21, HPCwire reached out to conference chair Dr. Kelly Gaither to get the inside track on this year's program, her work in scientific visualization and her commitment to increasing diversity in HPC. Gaither serves as the director of Visualization at the Texas Advanced Computing Center at The University of Texas at Austin. She has over 30 refereed publications in fields ranging from computational mechanics to supercomputing applications to scientific visualization. Over the past ten years, she has actively participated in conferences related to her field and has given numerous invited talks. Read more…

Profile of a Data Science Pioneer

Jun 28, 2016 | As he approaches retirement, Reagan Moore reflects on SRB, iRODS, and the ongoing challenge of helping scientists manage their data. In 1994, Reagan Moore managed the production computing systems at the San Diego Supercomputer Center (SDSC), a job that entailed running and maintaining huge Cray computing systems as well as networking, archival storage, security, job scheduling, and visualization systems. At the time, research was evolving from analyses done by individuals on single computers into a collaborative activity using distributed, interconnected and heterogeneous resources. Read more…

Thomas Sterling’s ISC 2016 Closing Keynote

Jun 23, 2016 | Capturing the sparkle, wit, and selective skewering in Thomas Sterling’s annual closing ISC keynote is challenging. This year was his 13th, which perhaps conveys the engaging manner and substantive content he delivers. Like many in the room, Sterling is an HPC pioneer as well as the director of CREST, the Center for Research in Extreme Scale Technologies, Indiana University. In his ISC talk, Sterling holds up a mirror to the HPC world, shares what he sees, and invites all to look in as well and see what they may. Read more…