With the huge amount of data involved in experiments at Brookhaven National Laboratory, extremely powerful computers are needed to conduct research in many areas of science. Brookhaven has a vast amount of computing power available to help researchers solve data-intensive problems.
The Brookhaven Computational Science Center (CSC) brings together researchers in biology, chemistry, physics and medicine with applied mathematicians and computer scientists to take advantage of the new opportunities for scientific discovery made possible by modern computers. In support of this, the center has a close alliance with applied mathematicians and computer scientists at Stony Brook University and Columbia University. The CSC is a key resource of the New York Center for Computational Sciences, a joint venture between Brookhaven National Laboratory and Stony Brook University's Institute for Advanced Computational Science.
At the CSC, computer clusters running the Linux operating system – typically containing 100 to 200 processors – are currently available for performing scientific calculations for Brookhaven researchers and their collaborators.
The HPC Code center is a central resource where domain scientists can bring their codes, or ideas for codes, and have those parallelized efficiently on High Performance Computing platforms. The HPC Code center ports, tunes, runs and maintains BNL used application codes on BlueGene/Q, clusters with accelerators, general linux clusters, and leadership facilities.
To submit a request for the HPC code center, please fill our online web form. One of our staff will contact you about your proposed project. Please contact Nicholas D'Imperio (firstname.lastname@example.org) if you have any questions.
Supported by a $26-million grant from New York State, Brookhaven Lab and Stony Brook University host IBM Blue Gene/P machines known collectively as New York Blue. New York Blue is the centerpiece for the New York Center for Computational Sciences, which fosters research collaborations among research institutions, universities and companies throughout New York State. Brookhaven Lab is among the academic and industrial users of the facility that perform research in a wide variety of sciences, including biology, medicine, materials science, nanoscience, renewable energy, finance and technology.
The Blue Gene/P has one rack and can run threaded codes.
The CSC also hosts two Blue Gene/Q research supercomputers: a 1-rack IBM Blue Gene/Q for general purpose research that boasts 16 cores per compute node, links together 16384 processors, runs threaded code, has total peak performance of 200 teraflop, and placed fifth on the June 2012 Graph 500 benchmark list; and a 2-rack IBM Blue Gene/Q for use by the BNL Riken Research Center..
Computational Science Center Seminar
"From Metadynamics to Dynamics"
Presented by Prof. Michele Parrinello, Dept. of Chemistry and Applied Biosciences, ETH Zurich & Universita della Svizzera Italiana Lugano,, Switzerland
10:45 am, Bldg. 735, 2nd floor seminar room
Wednesday, March 19, 2014, 10:45 am
Hosted by: Robert Harrison
Metadynamics is a commonly used and successful enhanced sampling method in atomistic simulations, with applications that range from nanotechnology to biophysics, By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. A statistical analysis of the distribution of transition times allows us to verify a posteriori the accuracy of our calculations. We apply our method to a number of examples of increasing complexity. We find excellent agreement between our calculations and the results of long unbiased molecular dynamics simulations whenever the latter are feasible. We will show applications to the average escape time of a ligand from a protein, which is an important parameter in a drug design strategy and to the calculation of homogeneous nucleation rates.
Computational Science Center Seminar
"QUANTUM-CLASSICAL SCIENCE FOR THE PLASMA-MATERIAL INTERFACE"
Presented by Predrag Krstic, Institute for Advanced Computational Science
11 am, Bldg. 463B, John Dunn Seminar Room 157
Tuesday, April 1, 2014, 11:00 am
Hosted by: Robert Harrison
Plasma-Material Interface (PMI) mixes materials of the two worlds, creating a dynamical surface which is one of the most challenging areas of multidisciplinary science, with many fundamental processes and synergies. We present the experimentally validated atomistic theory and computation for studying the dynamics of the creation and evolution of the PMI under irradiation by atoms and molecules at carbon, lithiated carbon and tungsten, as well as the emerging elastic and inelastic processes, in particular retention and sputtering chemistry. Recent work with lithium coatings deposited on a variety of metallic and graphitic surfaces, in a number of tokamak fusion machines around the world, has provided evidence of the sensitive dependence plasma behavior has on these ultra-thin deposited films. Our computer simulations, done in collaboration with Japanese and French scientists, and validated by in-situ experiments at Purdue University and at NSTX of PPPL have elucidated roles of lithium in carbon walls to the recycling of the plasma hydrogen. We performed quantum-classical atomistic calculations on many thousands of random trajectories to clarify the interplay of lithium and oxygen in amorphous carbon. We show that the presence of oxygen in the surface plays the key role in the increased uptake chemistry and suppression of erosion, while lithium has a decisive role in achieving high concentrations of oxygen in the upper layers of the surface upon bombardment by deuterium. D atoms preferentially bind with O and C-O when there is a comparable amount of oxygen to Li at surface. This finding explains a number of previously puzzling laboratory and reactor-based experimental results obtained over the last decade, having ramifications that go well beyond fusion.