Author Archive Andrew Knotts

ByAndrew Knotts

Survey of Scientific Computing Coming Aug. 7th – 11th

CACDS is pleased to announce a 5-day, hands-on workshop in various aspects of High performance Computing hosted right here at the University of Houston.  The workshop will be hosted in Room 200 in Philip G. Hoffman Hall (PGH).  Among the topics that will be discussed are: Linux, Python, OpenMP, OpenMP, Machine Learning, R-Language, and much more!  Please make sure you register to join us for this free event!

Register here: https://www.cacds.uh.edu/education/summer-training/

 

ByAndrew Knotts

Dr. Pengzhi Zhang Featured in the Biophysical Journal

Our own Dr. Zhang was featured on the cover of the Biophysical Journal.  Zhang, who earned his Ph.D. from UH now works as a research scientist at CACDS.

Congratulations to Dr. Zhang and keep up the good work!

ByAndrew Knotts

Dr. Prosperetti Wins International Acclaim

Our own Director, Dr. Andrea Prosperetti, is now an international winner of the Cataldo Agostinelli e Angiola Gili Agostinelli International Prize.  This prize is given by the Academia dei Lincei in Rome, Italy.  This organization was founded in 1603 and one of its early members was Galileo Galilei.  This honor, bestowed on Dr. Prosperetti, will be added to his resume alongside others like Distinguished Professor of mechanical engineering at UH, the Berkhoff Professor of applied physics at the University of Twente, and elected member of the National Academy of Engineering.

We are very proud to have this amazing scientist at the head of our proud organization, and look forward to his continued work!

You can read the Cullen College of Engineering article HERE

ByAndrew Knotts

XSEDE HPC Summer Bootcamp June 6-9!

CACDS is pleased to be hosting XSEDE’s Summer Bootcamp from June 6-9, 2017 in PGH 200.

This 4 day event will include MPI, OpenMP, OpenACC and accelerators. This event will be presented using the Wide Area Classroom(WAC) training platform and will conclude with a special hybrid exercise contest that will challenge the students to apply their skills over the following 3 weeks and be awarded the Fourth Annual XSEDE Summer Boot Camp Championship Trophy.  In addition, an XSEDE Badge will be available to those who complete the Challenge.

Register Herehttps://www.xsede.org/web/xup/course-calendar/-/training-user/class/559/session/1278 

The agenda is as follows:

Tuesday June 6
10:00 Welcome
10:15 Computing Environment
10:45 Intro to Parallel Computing
11:30 Intro to OpenMP
12:30 Lunch break
1:30 Exercise 1     (zip folder of all exercises) 
2:15 More OpenMP
3:30 Exercise 2
4:00 Adjourn
Wednesday June 7
10:00 Intro to OpenACC
11:00 Exercise 1
11:30 Introduction to OpenACC (cont.)
12:00 Lunch break
1:00 Exercise 2
1:45 Introduction to OpenACC (cont.)
2:00 Using OpenACC with CUDA Libraries
2:30 Advanced OpenACC
3:00 OpenMP 4.0 Sneak Peek
4:00 Adjourn
Thursday June 8
10:00 Introduction to MPI
12:00 Lunch break
1:00 Intro exercises
2:10 Intro exercises review
2:15 Scalable Programming: Laplace code
2:45 Laplace Exercise
4:00 Adjourn
Friday June 9
10:00 Laplace Exercise (Cont)
11:30 Laplace Solution
12:00 Lunch break
1:00 Advanced MPI
2:00 Outro to Parallel Computing
3:00 Parallel Tools
3:20 Hybrid Computing
3:40 Hybrid Competition
4:00 Adjourn

 

ByAndrew Knotts

XSEDE Big Data Workshop May 18-19

Thursday and Friday, May 18-19, 2017 from 10am-4pm in PGH 200

CACDS has worked with XSEDE (Extreme Science and Engineering Discovery Environment) and Pittsburgh Supercomputing Center (PSC) to host intriguing and informative Big Data Workshops. These workshops have attracted many people from around the Houston community, such as researchers from MD Anderson Cancer Center, Baylor College of Medicine, as well as students, postdocs, and faculty from Chemistry, Biology, Computer Science, and Electrical Engineering. CACDS will be hosting the 2-day long Big Data workshop hosted by XSEDE and we look forward to seeing everyone in PGH 200 for this event.

This workshop will focus on topics such as Hadoop and Spark and will be presented using the Wide Area Classroom(WAC) training platform.

ByAndrew Knotts

Dr. Lars Grabow wins Award for Research Excellence

Dr. Lars Grabow has won the 2017 Research and Scholarship Excellence Award at the Assistant Professor level.  Dr. Grabow is also going to be featured on the cover of the September issue of Chem Cat Chem.  The graphic on the cover was developed by our own Dr. Martin Huarte-Espinosa.  The image shows the charge density difference in the transition state of methane activation over a single crystal Pd(100) surface as obtained from electronic structure simulations.

CACDS would like to congratulate Dr. Grabow on both of these honors and we look forward to even more in the future!

ByAndrew Knotts

New ON DEMAND CACDS Courses

Do you have an issue involving High Performance Computing?  Do you need explanations about Python, MATLAB, Cuda, or other programs?  Do you just want to know more about the exciting world of High Performance Computing?  Well great news!  Help is only a knock, phone call, or email away.

The Center for Advanced Computing and Data Systems is proud to announce the addition of On Demand Courses to our already extensive list of training opportunities.  With On Demand Courses, all you have to do is get in touch with a member of our Technical Team, and they will guide you through whatever issue you are having.  You can send them an email, make a phone call, or drop by our new offices in the Multi-Disciplinary Research and Engineering Building (MREB Suite 205).

You can get in touch with the Technical Team RIGHT HERE!

We look forward to helping you out with any questions you have!  Just drop us a line!

ByAndrew Knotts

Electrical and Physical Characterization of Nano- and Non-Linear Devices for Future Computing

March 28, 2017 from 12-1pm in PGH 216

Presenter: R. Stan Williams, Quantum Science Research Laboratory at Hewlett-Packard

With the end of Moore’s Law in sight, there is a great deal of angst in the information technology community over how computing can keep pace now that data is being generated and accumulated at an exponential rate.  One solution is to perform exponentially more computation per unit of energy expended in a computer.  This may very well require the exploitation of nonlinear dynamical systems to encode and process information in unconventional ways.  Both nanoscale structures and neurons can display pathologically nonlinear responses such as chaos to a small stimulus, and in many ways the former can be used to emulate the latter.  After a brief introduction to a couple of nonlinear electronic devices, i.e. passive or synaptic memristors and locally active or axonic memristors, I will describe the electronic and physical characterization tools and techniques that we have developed to characterize these systems.  Standard electronic test and measurement systems are largely incapable of providing the appropriate time and/or frequency dependent information required to quantitatively characterize and model memristors.  We have built flexible high-speed systems that enable us to watch the electronic switching in highly nonlinear systems in real-time from 10’s of picoseconds to minutes.  This type of data is critical to construct compact models for both the switching and the reliability of dynamical devices.  We base our models, as much as possible, on the actual physical mechanisms that occur inside the devices as they operate.  For this purpose, we have worked with both the Advanced Light Source at LBNL and the Stanford Synchrotron Radiation Laboratory to utilize the technique of Scanning Transmission X-ray Microscopy to examine functioning memristors in situ and in operando under controlled temperature and electrical bias conditions.  We have imaged the structure and chemical composition of different conductance states of devices in order to determine what and how atoms move inside solid state devices as they are switching electrically under an external bias, whether that switching occurs via a phase transition or through drift, diffusion and thermophoresis of atomic species like oxygen.  The electrical and mechanistic information come together in the compact device models that we supply to circuit architects so that they can faithfully and predictively simulate a wide range of circuits before they commit to a design that will be fabricated.

ByAndrew Knotts

Visualization of simulation results in Virtual and Augmented Reality Seminar

The Center for Advanced Computing and Data Systems will be hosting a seminar that will be given by Dr. Uwe Woessner in PGH 216 from 12-1 p.m. on April 6, 2017.

Abstract:

Virtual environments provide an ideal environment for engineering teams or research groups to analyze and discuss complex simulation results. Not only the 3D vision and surround view but most important the intuitive interaction with the data enable an efficient analysis and communication of simulation results. Collaborative virtual environments provide similar functionality but extend the reach to remote sites and Augmented Reality allows a direct comparison of simulation results with live experiments. All these technologies will be presented by means of examples from engineering, forensics, urban planning and more.

About the Presenter: 

Since 2004, Uwe Woessner is heading the visualization department at the High Performance Computing Center Stuttgart (HLRS).
He received his PhD. in Mechanical Engineering from the University of Stuttgart in 2009. Since 1996 he is working in the Collaborative Research Center “Rapid Prototyping” established at the University of Stuttgart in the field of VR based virtual and augmented prototyping. He is guest professor and guest lecturer at the IFOER and ITE, TU-Vienna, Austria and at HSR, Rapperswil, Switzerland. He is also Co-founder of VirCinity GmbH.
He received international Awards such as the 2003 HPC Challenge and 2006 HPC Bandwidth Challenge.
His current research interests include collaborative virtual environments for scientific visualization, Augmented Reality, 3D user interfaces and interaction techniques for computational steering.
He is in the committee of several VR and 3D User Interface related conferences such as IEEE VR, IEEE Vis, EuroVR, GI VRAR.

ByAndrew Knotts

Journal of Geophysical Research

The Journal of Geophysical Research has published an article that features Center for Advanced Computing and Data Systems support and resources.  The article details Remote sensing evidence of decadal changes in major tropospheric ozone precursors over East Asia.  The research outlined in the article was, in part, obtained by using the Opuntia Cluster and advanced CACDS support.

The paper’s abstract explains the research that was completed:

Recent regulatory policies in East Asia reduce ozone precursors, but these changes are spatially and temporally nonuniform. This study investigates variations in the long-term trends of tropospheric NO2, HCHO, and HCHO/NO2 ratios to diagnose ozone sensitivity to changes in NOx and volatile organic compound using the Ozone Monitoring Instrument (OMI). Using an adaptive-degree polynomial filter, we identify extremums of time series of NO2 to determine when and how NO2 change. Due to the regulations in China, trends which were predominantly upward turned downward. The years undergoing these changes primarily happened in 2011 and 2012. OMI column densities, however, suggest that NOxsources in South Korea, the Pearl River Delta (PRD), Taiwan, and Japan have not consistently decreased. Specifically, as Chinese exports of NO2 started subsiding, increasing trends in NO2 columns over several Korean cities, including Seoul, become evident. To quantify the changes in NOx emissions from summertime 2010 to 2014, we conduct a 3D-Var inverse modeling using a regional model with MIX-Asia inventory and estimate NOx emissions (in 2010 and 2014) for the PRD (1.6 and 1.5 Gg/d), the Yangtze River Delta (3.9 and 3.0 Gg/d), north China (15.6 and 14.3 Gg/d), South Korea (1.6 and 1.5 Gg/d), and Japan (2.7 and 2.6 Gg/d). OMI HCHO shows upward trends in East Asia resulting from anthropogenic effects; however, the magnitudes are negative in the PRD, Japan, North Korea, and Taiwan. OMI HCHO/NO2 ratios reveal that while South Korea, Japan, and the south of China have undergone toward more NOx-sensitive regime, areas around the Bohai Sea have become more NOx saturated.

The full text can be found by visiting: http://onlinelibrary.wiley.com/doi/10.1002/2016JD025663/full