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HPC & Life Sciences
19 Sep 2013 | | Contributor(s):: Thomas Cheatham
Biomolecular simulation provides a means to explore biomolecular structure, dynamics and interactions on timescales from femptoseconds to milliseconds on available high performance computing computational resources. Since the first protein simulations in ~1975, atomistic molecular dynamics (MD)...
HPC Software Engineering: "Do as I say, not as I do"
19 Sep 2013 | | Contributor(s):: Erik Lindahl
Most scientific software projects started as a quick hack on somebody's laptop, but before you know it there might be dozens of future students and postdocs involved. However, unlike 30 years ago, today few of us are only one supercomputer from a single vendor providing a single compiler. Many...
Introduction to Directive Based Programming
13 Sep 2013 | | Contributor(s):: John Urbanic
OpenMP, and now OpenACC, have become standard ways of doing multi-core and GPGPU parallelization. One of the main reasons for their adoption is that they allow the preservation of an existing serial code base while performing gradual parallelization on a code. This directive based approach allows...
Modern GPU Programming with CUDA and Thrust
12 Sep 2013 | | Contributor(s):: Gilles Civario
Today's GPUs are massively parallel devices which provide programmers with TeraFlops supercomputing performance. But programming these devices and exploiting their fantastic potential is not always easy and might discourage application developers. CUDA for example is too often seen as a very low...
10 Sep 2013 | | Contributor(s):: John Urbanic
Astrophysics: How to simulate the most catastrophic events in the universe
09 Sep 2013 | | Contributor(s):: Luciano Rezzolla
Quantum Chromodynamics on a space-time lattice – building up the femto universe of atomic nuclei on a computer
09 Sep 2013 | | Contributor(s):: Akira Ukawa
Everyone knows that all atoms are made of atomic nuclei and electrons around them, and that atomic nuclei are made of protons and neutrons bound by pions. Every scientist would know that protons and neutrons in turn are made of quarks, and are bound by gluons. Not every scientist may know,...
HPC & the Inventor's dilemma: Abandoning 15 years of Molecular Simulation Work to Move to GPUs
06 Sep 2013 | | Contributor(s):: Erik Lindahl
Alternate Title:Parallel molecular dynamics - how we evolved from 10 cores to heterogeneous GPU acceleration and petascale parallelizationMolecular dynamics has come a long way the last 20 years; what was once a small esoteric technique in theoretical physics is now a standard tool of molecular...
Introductory Parallel CPU Programming
23 Aug 2013 | | Contributor(s):: Mark Bull
Keynote: The Data and Compute-Driven Transformation of Modern Science
22 Aug 2013 | | Contributor(s):: Ed Seidel
Modern science is undergoing a profound transformation as it aims to tackle the complex problems of the 21st Century. It is becoming highly collaborative; problems as diverse as climate change, renewable energy, or the origin of gamma-ray bursts require understanding processes that no single...
International HPC Summer School 2013
21 Aug 2013 |
The U.S. National Science Foundation's Extreme Science and Engineering Discovery Environment (XSEDE) project, the European Union Seventh Framework Program's Partnership for Advanced Computing in Europe (PRACE), and RIKEN Advanced Institute for Computational Science (AICS) have collaborated to...
Advanced Parallel CPU Programming Part 2: Fundamentals of OmpSs
21 Aug 2013 | | Contributor(s):: Xavier Teruel
Tasking and Synchronization --> Data Sharing Attributes, Dependence Model, Other Tasking Directives Clauses, Taskwait, Synchronization, Outlined Task Syntax;Memory Regions, Nesting and Dependences --> Memory regions and dependences, Nested tasks and dependences, Using dependence sentinels;...