All posts by Soumik

HPC day 2015

ARC hosted their second annual HPC day on April 6th at the Inn at Virginia Tech! For the agenda, the poster session winners, and for more information please click here.

Click here to view pictures of this event.

Amyloid Beta Peptide

Alzheimers disease is a disease that causes loss of brain functions that are involved in memory, communication, and thought. The amyloid β-peptide (Aβ has been identified as the core component of protein aggregates in the brain of Alzheimer's patients. The pathway by which Aβ leaves the cell membrane and self-associates is largely a mystery.

The lab of Dr. David Bevan, a faculty member of in the Biochemistry department at Virginia Tech, studies this peptide, with a focus on the association of Aβ with membranes. It is thought that small aggregates of Aβ cause toxicity by disrupting cell membranes. Preventing the formation of these aggregates is an approach that is being studied as way to treat Alzheimer's disease. Experimental work has identified the dietary compounds that may bind to Aβ and inhibit the damaging effects of this peptide.

Part of the challenge is understanding what happens on the molecular level, and it is difficult to apply experimental techniques to find out this mechanism. "It is thought that the onset and the progression of Alzheimer's are due to the aggregation of this particular peptide, and we are trying to understand the molecular mechanisms of the development of the disease," explains Dr. Bevan.

"But with computational methods, we can see at the atomistic level the kinds of interaction and so on. This may lead to changes in the structure of amyloid beta peptide as well as factors that increase the propensity to aggregate."

Computational simulations focus on understanding this effect with the goal of designing effective small molecule inhibitors of Aβ aggregation. The simulations are based on experiments using both in vitro and in vivo studies.

The research in Dr. Bevan' laboratory is focused on molecular modeling as an approach to studying protein structure and function. During the period from January 2011 until May 2012, his lab used 6,000,000 CPU hours on Advanced Research Computing System's (ARC's) now-retired System X supercomputer.

On March 20, 2013, ARC launched a new large-scale machine, BlueRidge, which is comprised of 318 Intel Sandy Bridge nodes. With a total of 5,088 cores and 20 TB of memory, BlueRidge is ARC's largest research computing system to date. Having access to Blue Ridge will help expand Dr. Bevan's research going forward.

He hopes that in some point, his lab will begin to try to simulate the process of protein folding, which takes anywhere from milliseconds to a second depending on the size of the protein and the nature of its folding habit.

"I think with Blue Ridge, we will be able to do that, again by working with fairly small proteins or peptides, especially those that have very distinct protein structure folds, we can simulate the process when they go from extended form into the folded form."

Recently, Dr. Bevan won the award for outstanding dissertation adviser in Science Technology, Engineering, and Mathematics. In addition, his graduate students, Justin Lemkul, a 2012 doctoral degree recipient in Biochemistry, and Nikki Lewis-Huff, a Ph.D. candidate in Bioinformatics and Computational Biology, have received several awards. Anne Brown, another graduate student from his lab, has been accepted into the College of Agriculture and Life Sciences Graduate Teaching Program.

He said that he tries to provide just enough mentoring to his students so they are able to develop their own ideas but do not get totally lost somewhere. "Giving them free reign, so they can conceive and develop their own ideas is important, because they are more enthusiastic about something they have thought about, and they want to see if they can actually perform it, in our case in simulations. When they have generated hypothesis, they want to develop that hypothesis further,"said Dr. Bevan

Other research projects in the Bevan lab are described on the Bevan Lab web site.



Gas-surface interactions are everywhere

Even as you read this, molecules of gas are colliding with your skin and the walls around you. These kinds of interactions between gases and surfaces are important in many different fields. For example, consider an important problem in the life sciences: respiration. Breathing itself is a process that involves a gas-surface interaction.

As oxygen molecules sprint around the atmosphere, eventually they will end up in your blood stream. Somewhere along the way they have interacted with the surfaces of your lungs and passed into your blood stream. This is what Diego Troya, an associate professor of Chemistry at Virginia Tech, is interested in. His lab is trying to understand the interactions between gases and surfaces.

 As oxygen molecules sprint around the atmosphere, eventually they will end up in your blood stream. Somewhere along the way they have interacted with the surfaces of your lungs and passed into your blood stream. This is what Diego Troya, an associate professor of Chemistry at Virginia Tech, is interested in. His lab is trying to understand the interactions between gases and surfaces.

His lab is trying to carry out simulations of the molecular dynamics of collisions between the gases of the low-Earth orbit atmosphere and models of the polymers that are used as thermal blankets or protective paints on the spacecraft surface. These simulations will provide valuable information about the microscopic reaction mechanisms of erosion processes that cannot be determined from in-orbit or ground-based experiments.

His lab is also studying the adsorption of chemical-warfare agents on surfaces. Recent news has reported the use of substances like Sarin as a warfare agent. This gas is a nerve agent that deactivates the enzyme that controls muscle relaxation, and can be fatal in large concentrations.

Use of these subtances in the battlefield also results in contamination of equipment and other materials like sand that might inadvertently get shipped back to the United States. In the Troya lab, modeling work is used to find out how this agent sticks to common surfaces so that more efficient decontamination trategies can be developed. Because nerve agents like Sarin are extremely toxic, studies in a laboratory setting are challenging. Therefore, computational simulations can fill the experimental void and help to get a complete picture of the surface chemistry of this gas.

Because the lab is engaged in research of the interactions of gas moleculs with extended surfaces, Dr. Troya's lab uses over a million CPU hours a year. In the spring of 2013, Troya's lab started using BlueRidge, Virginia Tech Advanced Research Center's new supercomputer, and his lab has benefitted tremendously from this resource. Blueridge provides the type of cutting-edge research equipment that provides results very quickly, and it has been an incredible gift for their laboratory. "BlueRidge is many times faster than the prior computer we used to operate. A lot of problems that we couldn’t tackle before Blueridge hav now become tractable," said Prof. Troya.

Since the lab is using this state-of-the-art equipment, the researchers have to be properly trained to exploit its capabilities. In his laboratory, Dr. Troya is a hands-on adviser to his graduate students (Angela Edwards, Robert Chapleski, and Jacky Chan). He always tries to work with them individually, and it is not rare to find him sitting with them as they learn to write computer programs or analyze the result of the simulations.

Fall 2014 NLI Short Courses

In Fall of 2014, the Interdisciplinary Center for Applied Mathematics (ICAM) and ARC will offer a three-session short course on Parallel Computing with MATLAB as a part of the Virginia Tech Network Learning Initiatives (NLI) curriculum. The course will be taught by Dr. Eugene Cliff of ICAM in conjunction with Advanced Research Computing. Users can enroll through NLI here. Click here for course descriptions and registration information.

BlueRidge – Our new supercomputing cluster

In March 2013, Virginia Tech's Advanced Research Computing (ARC) released BlueRidge, providing faculty, staff, and students with the largest computing asset to date as measured by memory and number of cores. This Cray CS-300 cluster ranked number 402 on the November 2012 Top500 list, the industry-standard ranking of the world's 500 fastest supercomputers, with a score of 86.3 teraflops, or 86.3 trillion floating point operations per second. This is more than eight times the computing power provided by System X, which put Virginia Tech on the supercomputing map in 2003.

BlueRidge, which was purchased through funding provided by Virginia Tech and the State of Virginia, is composed of 318 nodes (individual computers) each outfitted with two octa-core Intel Sandy Bridge central processing units (CPUs) and 64 gigabytes (GB) of memory. In addition, five nodes are equipped with 128 GB of memory for jobs that are especially memory intensive. The systemwide totals of 5,088 cores and 20.4 terabytes (TB) of memory are two and a half times as many cores and four times the memory of any other system at Virginia Tech. BlueRidge is also the first Sandy Bridge cluster at Virginia Tech, an important distinction as Sandy Bridge CPUs have the ability to do twice the number of double precision computations in a single cycle as their Intel Westmere predecessors.

The large number of cores available on BlueRidge will allow Virginia Tech researchers to run massively-parallel simulations, allowing them to tackle more complicated problems more quickly than they have before. And the system's huge memory footprint will enable faculty to investigate the kinds of big data subjects that are increasingly the focus of attention in computationally-intensive arenas.

In addition, ARC is currently working on the addition of two Intel Xeon Phi coprocessors on 130 of the 318 nodes (260 Xeon Phi cards in all), with expected release of those nodes in Fall 2013. This architecture (also known as Many-Integrated-Core or MIC) is considered a significant development in high-performance computing, providing accelerated capability reminiscent of GPUs, but more integration with CPUs and compatibility with existing CPU programming paradigms (C/C++, Fortran, etc).

BlueRidge, the NSF-funded HokieSpeed CPU-GPU cluster, and the shared-memory system HokieOne provide researchers with a variety of options to address specific computing requirements arising from an array of research areas. All of these systems are housed in the university's cooled, access-restricted machine room in the Corporate Research Center and maintained by ARC, a unit within the Office of the Vice President of Information Technology devoted to maintaining, advancing, and providing support to large-scale research computing systems in the university.

Name BlueRidge
Vendor/Model Cray CS-300
Key Features, Uses Large-scale computation
Login Node
blueridge1 or blueridge2
Available March 2013
Operating System CentOS Linux 6
Theoretical CPU Peak (TeraFlops) 105.8
Nodes 318
Cores 5,088
Cores/Node 16
CPU Model Intel Sandy Bridge
CPU Speed 2.60 GHz
Memory Size 20.4 TB
Memory/Core 4 GB*
Memory/Node 64 GB*
Interconnect QDR InfiniBand
Notes Requires Allocation
*5 nodes have 128 GB (8 GB/core)

More information about BlueRidge can be found at the links below.