The Engineer (United Kingdom)

The latest version of Raspberry Pi is six times faster than its predecessor and delivers the same amount of power as a standard personal computer. The extremely low price point was the biggest challenge, says Raspberry Pi Foundation founder Eben Upton. The Foundation promotes credit card-sized Raspberry Pi computers as an affordable tool that children can use to learn programming. Priced at about $35, the Raspberry 2 has four times as many processor cores and twice as much memory as its predecessor, and can run the new Windows 10. Upton says the other challenge was moving from a package-on-package system, in which the memory was part of the main system-on-chip, to a discrete system with a separate chip that could provide more memory but that required a more complex way of communicating with the rest of the computer. To read further, please visit http://www.theengineer.co.uk/news/faster-raspberry-pi-brings-low-price-computing-power-to-education/1019814.article.

 

They call it “the Lab-in-a-Box.” According to Nadir Weibel, a research scientist in the Computer Science and Engineering (CSE) department at the University of California, San Diego, inside the box are assorted sensors and software designed to monitor a doctor’s office, particularly during consultations with patients. The goal is to analyze the physician’s behavior and better understand the dynamics of the interactions of the doctor with the electronic medical records and the patients in front of them. The eventual goal is to provide useful input on how to run the medical practice more efficiently. To read further, please visit http://www.calit2.net/newsroom/release.php?id=2491.

The San Diego Supercomputer Center (SDSC) and the University of California, San Diego, is providing data management, visualization and modeling resources, and expertise to a two-month wintertime field campaign to study “atmospheric rivers” and particles of dust, smoke, sea spray, and organic materials called aerosols along the western U.S. coast to better understand variability in the region’s water supply, flood and drought hazards, infrastructure requirements, and optimal reservoir operations. The latest initiative, called the CalWater 2015 project, assembled a team of federal and state agencies plus academic research institutions collaborating in a tightly-coordinated effort involving ground-based observations, air and sea-borne measurements, and advanced weather forecast models.  To read further, please visit http://www.sdsc.edu/News%20Items/PR021115_calwater.html.

Solution for the week of February 16, 2015:

To disable the pictures of the flasks, the line to comment out or remove is line 38 in simulation.c.

The -pg flag can be added to the CFLAGS line in the Makefile to enable compiling for gprof.

Compiling uses the same commands as usual:
"make" to create the object files and executable file
"make clean" to remove the object files and executable file

The command to generate a gmon.out is:
./ideal-gas

To run gprof with the gmon.out file, use the following command:
gprof ideal-gas gmon.out

This reveals that the function taking the longest time is calculateAndPrintSimulationProperties(). This function would be a candidate for parallelism.

 

http://hpcuniversity.org/students/weeklyChallenge/92

UC Irvine and Australian chemists have figured out how to unboil egg whites – an innovation that could dramatically reduce costs for cancer treatments, food production and other segments of the $160 billion global biotechnology industry, according to findings published today in the journal ChemBioChem. “Yes, we have invented a way to unboil a hen egg,” said Gregory Weiss, UCI professor of chemistry and molecular biology & biochemistry. “In our paper, we describe a device for pulling apart tangled proteins and allowing them to refold. We start with egg whites boiled for 20 minutes at 90 degrees Celsius and return a key protein in the egg to working order.” Like many researchers, he has struggled to efficiently produce or recycle valuable molecular proteins that have a wide range of applications but which frequently “misfold” into structurally incorrect shapes when they are formed, rendering them useless. To read further, please visit http://news.uci.edu/press-releases/uci-fellow-chemists-find-a-way-to-unboil-eggs/.

HPC in the News

 

Legislation Introduced to Jumpstart Research Into Exascale Supercomputing
HPCwire

 

U.S. Senator Lamar Alexander (R-Tenn.) and U.S. Rep. Randy Hultgren (R-Ill.), along with U.S. Senator Tammy Baldwin (D-Wis.), today introduced bipartisan legislation that would jumpstart research into exascale supercomputing that they said is “critical to U.S. competitiveness and national security.” The ExaSCALE Computing Leadership Act of 2015 would create research partnerships between industry, universities and U.S. Department of Energy’s national labs to research and develop at least two exascale supercomputer architectures, with the goal of having a fully operational computer system that has reached “exascale” – a measure of speed that is beyond any other system in the world – by 2023. It authorizes funding for these partnerships and requires the department to provide regular status reports to Congress on the progress of the project. To read further, please visit http://www.hpcwire.com/off-the-wire/legislation-introduced-jumpstart-research-exascale-supercomputing/.

30 Under 30: Young Scientists Who Are Changing the World

The Forbes 30 Under 30, is a tally of the brightest stars in 20 different fields under the age of 30. What these young men and women have accomplished in their lifetime is astonishing.Here are just a few examples: Sophie Milam, 26, Chief Engineer at HI-SEAS, designs control systems for so-called tensegrity robots (held together by tension); Elizabeth Beattie, 24, a Ph.D. candidate at the University of Pennsylvania School of Engineering and Applied Science, designed the Titan Arm, an exoskeleton that gives the wearer an extra forty pounds of bicep strength; John Mittermeier, 29, a Ph.D. candidate at Oxford University, is applying big data analytics to conserving endangered species. Three of the 20 fields include Science, Enterprise Technology, and Consumer Technology.To see the full list of 30 Under 30 in all 20 fields, please visit http://www.forbes.com/30under30/#/.

 

XSEDE News from Partners and Friends’

XSEDE Call for Participation

The XSEDE15 Call for Participation, covering all aspects of participation in the conference, is now open. The XSEDE15 Conference, to be held in St. Louis on July 26-30 at the Marriott Renaissance St. Louis Grand Hotel, will showcase the discoveries, innovations, and achievements of those who use, build, and support XSEDE resources and services, as well as those involved in related digital resources endeavors around the world. This year's theme is Scientific Advancements Enabled by Enhanced Cyberinfrastructure.  The annual XSEDE conference is designed to engage and directly benefit diverse communities, including students, educators, researchers, and practitioners across all fields of study and scholarly research with particular emphasis placed on engaging under-represented minorities, women, and people with disabilities. Last year’s XSEDE14 conference saw more than 600 attendees from 49 states and 10 countries. Full papers will be included in the Conference Proceedings and submitted to the ACM Digital Library. XSEDE15 seeks high-quality submissions—including papers, posters, visualizations, and more—in four thematic tracks with due dates as early as March 30.  To find out more information on the Call for Participation and full sponsorship prospectus details, please visit: xsede.org/xsede15, like XSEDE at Facebook.com/XSEDEscience, and follow XSEDE on Twitter (@XSEDEscience). Also follow the hashtag #XSEDE15 for further updates and interaction.

 

             

Call for Papers and Participation

 

Call for Papers: The Science of Cyberinfrastructure: Research, Experience, Applications and Models (SCREAM-15)
June 16, 2015 - Portland, OregonExtended Deadline – February 23, 2015
(in conjunction with HPDC'15)

The SCREAM workshop generally aims to address this gap, and specifically aims to understand, through a combination of experience, application requirements, and conceptual models, how to best to create a conceptual framework for the objective design and assessment of distributed cyberinfrastructure. In other words, it aims to build toward the science of cyberinfrastructure upon what has hitherto been a purely empirical approach to cyberinfrastructure design and practice. The SCREAM Workshop is interested in all areas that will further this objective, in particular the interaction of multiple cyberinfrastructure components and systems (distributed computing, broadly defined), including academic and commercial production systems and research testbeds. For complete information, including topics of interest, please visit https://sites.google.com/site/scream15workshop/home.

Third Call for Papers: 2nd INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY (AlCoB 2015)
August 4-6, 015 – Mexico City, Mexico
Submission Deadline – March 2, 2015 

AlCoB aims at promoting and displaying excellent research using string and graph algorithms and combinatorial optimization to deal with problems in biological sequence analysis, genome rearrangement, evolutionary trees, and structure prediction. The conference will address several of the current challenges in computational biology by investigating algorithms aimed at: 1) assembling sequence reads into a complete genome, 2) identifying gene structures in thegenome, 3) recognizing regulatory motifs, 4) aligning nucleotides and comparing genomes, 5) reconstructing regulatory networks of genes, and 6) inferring the evolutionary phylogeny of species. For more information and scope of topics, please visit http://grammars.grlmc.com/alcob2015/.

Call for Papers Extended: 2015 11th International Conference on Natural Computation (ICNC 2015) and 2015 12th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD 2015)
August 15-17, 2015 - Zhangjiajie, China
Extended Paper Submission Deadline – March 15, 2015 

ICNC-FSKD is a premier international forum for scientists and researchers to present the state of the art of data mining and intelligent methods inspired from nature, particularly biological, linguistic, and physical systems, with applications to computers, circuits, systems, control, robotics, communications, and more. This is an exciting and emerging interdisciplinary area in which a wide range of theory and methodologies are being investigated and developed to tackle complex and challenging problems. The registration fee of US-D410 includes proceedings, lunches, dinners, banquet, coffee breaks, and all technical sessions. For more information, visit the conference web page:  http://icnc-fskd.hnu.edu.cn/.

Cy-Tera & LinkSCEEM-2  HPC Production Access Call for Proposals
Proposal Deadline – April 1, 2015

LinkSCEEM aims at the establishment of a high performance computing (HPC) eco-system in the Eastern Mediterranean region by integrating and coordinating regional computational resources. The Cy-Tera facility is the first multi-Tflop/s HPC facility in Cyprus, serving the needs of the regional scientific community by supporting applications in many fields of great scientific and/or societal importance. LinkSCEEM and Cy-Tera invite scientists from the Eastern Mediterranean region to their seventh joint call for production access to HPC resources. This call invites applications for computing resources in order to carry out projects which have high scientific quality and impact. Allocation will be for 1 year starting from 1st June 2015. This call runs in parallel to the rolling call for Preparatory Access. More information can be found at http://linksceem.eu/ls2/user-resources/how-to-apply/howto-apply-production.html

Call for Papers: The Society of Motion Picture and Television Engineers (SMPTE)|
October 26-29, 2015 – Hollywood, California
Abstract Deadline – June 26, 2015

 

The Society of Motion Picture and Television Engineers (SMPTE), the worldwide leader in motion-imaging standards and education for the communications, media, entertainment, and technology industries, is seeking proposals for technical papers for the SMPTE 2015 Annual Technical Conference & Exhibition. The proposed papers must be informational and address technical theory, research, innovation, application, or practice specific to any of the evolving technologies associated with the media technology industry. A complete and more specific listing of possible topics is available at https://www.smpte.org/ATC with instructions on submitting a paper proposal, along with more details about SMPTE 2015. Further information about SMPTE is available online at https://www.smpte.org/.

 

Upcoming Conferences, Workshops and Webinars

 

SDSC's WorDS Center of Excellence 2015 Quarterly Briefings
March 3, 2015, 3:00 - 5:00pm – La Jolla, California

Workflows for Data Science (WorDS) Provides Workflow Solutions for Industry and Academia

•    Are you interested in learning new computational tools and techniques for your scientific computing and data science applications?

•    Interested in saving time, optimizing and scaling up your computations to produce results faster or communicating your research results more effectively?

WorDS will help you focus on scientific questions and the end-to-end process, from data generation to journal publication or preparing for clinical trials. For registration and details, please visit http://words.sdsc.edu/events.

Visualization Tutorial Webinar
March 6, 2015 - La Jolla, California and virtually
Registration Deadline – March 2, 2015

Amit Chourasia from SDSC is offering a beginning data visualization tutorial entitled, “Scientific Visualization: Concept, Execution and Ubiquitous Access.” It’s being offered both at SDSC and as a webcast.  I think it might be a worthwhile experience particularly if there were a site that wanted to act as a satellite site and host a group to learn together. The advantage of a satellite site is threefold.  First, the attendees can view the webinar on a large screen and keep their laptops free for doing the hands-on exercises. Secondly, an on-site facilitator can field questions and (maybe) answer some of them (or present them to Amit through the ReadyTalk interface).  Third, the attendees meet other folks who are just starting to learn how to visualize and share data. More information can be found at http://www.sdsc.edu/Events/gordonviz2015/index.html.

Open Gris Forum – 43
March 25-27, 2015 – Crystal City, Virginia

OGF 43 will be co-located with the GENI Engineering Conference 22 (GEC22) and US Ignite Application Summit that will be held March 23-26, 2015 at the Hilton Crystal City Hotel at Washington Reagan National Airport in Crystal City, Virginia near Washington DC, USA. The OGF group meetings will run from Wednesday through Friday and will highlight mutual topics between the networking, security, applications and API design communities. All OGF groups are encouraged to meet at this event, which will also include Global Lambda Integrated Facility Technical Work Group Meetings. OGF 43 encourages participation in and will be helping to plan a variety of hands-on developer-oriented events at this meeting in cooperation with GEC22, and with the organizers of the Cloud Standards Customer Council at the nearby Object Management Group Technical Meeting in Reston, Virginia, continuing our long series of events in cooperation with the Cloud Plugfest organization. For more information and to register, please visit https://www.ogf.org/dokuwiki/doku.php/events/ogf-43.

PRACEdays15 Conference
May 26 = 20, 2015 – Dublin Ireland

The PRACEdays15 conference programme is packed with high-level international keynote speakers, including a talk by RIST, Japan, and many parallel sessions dealing with different HPC topics in science and industry. One of the main highlights of the conference will be a keynote speech by Masahiro Seki, president of the Research Organization for Information Science and Technology (RIST), Japan. Further information, the conference schedule, and a registration link can be found here: http://www.prace-ri.eu/pracedays15/.

 

Research News From Around the World

 

New Computation Method at Cornell Helps Identify Functional DNA

Cornell University scientists have created a computational method to identify biologically significant DNA in the human genome. The method combines two techniques to pinpoint signals of selective pressure in DNA--one that looks for divergence and another that looks for mutations in DNA between individual humans. The new method clusters functionally similar markers in the genome into groups, and subsequently estimates the probability of whether a group is contributing to the fitness of the species based on associated patterns of divergence and genomic polymorphisms. Researchers generated a fitness consequence (fitCons) score that predicts which genetic material might be under selective pressure and therefore biologically significant. Compared to conventional techniques, fitCons scores demonstrated a much greater power to predict which genetic material regulates the expression of genes. To read further, please v9w95 http://www.news.cornell.edu/stories/2015/01/new-computation-method-helps-identify-functional-dna.
               

Student Engagement and Opportunities 

The XSEDE Scholars Program
Application Deadline:  March 31, 2015
Acceptance Notification: April 10, 2015

The XSEDE Scholars Program (XSP) is a program for U.S. students from underrepresented groups in the area of computational sciences.  As a Scholar, you will learn more about high performance computing and XSEDE resources, network with cutting-edge researchers and professional leaders, and belong to a cohort of student peers to establish a community of academic leaders. In particular, the focus is on the following underrepresented groups: African Americans, Hispanics, Native Americans, and women. For complete information and application details, please visit https://docs.google.com/forms/d/1gnmb9su5WX7OQUO3K0FgpQeOzy-ymMsU28sslNJvfIA/viewform

More Students Earning STEM Degrees, Report Shows
U.S. News & World Report

The prevalence of science, technology, engineering, and mathematics (STEM) degrees increased between 2004 and 2014 at the bachelor's, master's and doctoral levels, according to a National Student Clearinghouse report. Although both men and women increasingly are choosing STEM degrees, "in terms of the shares of degrees earned within individual disciplines, women are gaining ground in some STEM areas, while losing ground in others," says Clearinghouse executive research director Doug Shapiro. Overall, 40 percent of bachelor's degrees earned by men and 29 percent of those earned by women are now in STEM fields, according to the report. In addition, 58 percent of the degrees earned by men at the doctoral level and 33 percent of the degrees earned by women at the doctoral level are in STEM fields.," Shapiro says. For more information, please visit http://www.usnews.com/news/articles/2015/01/27/more-students-earning-degrees-in-stem-fields-report-shows.

The San Diego Supercomputer Center Announces Its Summer Program

Summer 2015 will be a great summer filled with fun and learning at the San Diego Supercomputer Center on the campus of the University of California, San Diego. With over 20 workshops to choose from, summer offerings include animation creation, programming arduino apps, android app development, physics, cinematic art, ocean science and much more! Workshops are open to students in middle and high school but please see each individual workshop description, as some workshops are specific to high school students only. We look forward to seeing you this summer! To view their summer line up, please visit http://education.sdsc.edu/studenttech/?page_id=570

Summer 2015 Clemson University Research Experience for Undergraduates: Collaborative Data Visualization Applications
Applications Deadline - March 31 2015

Clemson University is accepting applications for participation inthe REU Site: Research Experience for Undergraduates in Collaborative Data Visualization Applications for summer 2015. Eligible students include all undergraduate students, enrolled in an undergraduate university/college with an interest in visualization. For complete information, please visit http://citi.clemson.edu/viz/reu/. For questions, please contact  Vetria Byrd (vlbyrd@clemson.edu).

These Middle School Girls Had An Idea That Could Help Alzheimer's Patients Remember Loved Ones

Huffington Post

 

After 12-year-old Annie Gainer learned her grandfather had developed Alzheimer's, it took only a year for an especially precious part of his memory to slip away -- one that left him unable to remember her name. "We made him a scrapbook. He has 36 grandkids but he can only remember his children’s names," Annie told The Huffington Post. "He can’t associate that me and my brothers are my mother’s kids."  Determined to help others living with Alzheimer's, Annie and six of classmates at St. Catherine of Alexandria in the Chicago suburb of Oak Lawn put their heads together to conceive a facial recognition concept smartphone app for the annual Verizon Innovative App Challenge. "We didn’t do it for the money or the prize," Annie said. "We just want to get it created to help Alzheimer's patients." To read further, please visit http://www.huffingtonpost.com/2015/02/05/verizon-alzheimers-app_n_6617290.html?utm_hp_ref=girls-in-stem&utm_content=buffer97f92&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer.

 

Computational Science News of Interest
 

New Search Engine Lets Users Look for Relevant Results Faster

Researchers at the Helsinki Institute for Information Technology believe they have developed technology that will make Web searches more efficient. The new search engine is designed to show related keywords and topics to help those who do not know exactly what they are looking for or how to formulate a query to find it. The SciNet search engine features a topic radar to display the range of keywords and topics, and how they are related to each other. The relevance is tied to its distance from the center point of the radar, with the most related being closest to the center. Users would indicate what information is most useful by moving the words around the keyword cloud. To read further, please visit http://www.aalto.fi/en/current/news/2015-01-27/.

 

Social Media and HPC
 

FTC Says Internet-Connected Devices Pose Big Risks
The New York Times

Internet-connected devices present serious data security and privacy risks, according to a U.S. Federal Trade Commission (FTC) report released on Tuesday, which urged organizations to make data protection a top priority. Although the report acknowledges the potential benefits for users of smart devices, it notes the technology also generates enormous amounts of personal data that could be misused or obtained by hackers. The report also says organizations should develop new ways to communicate their data collection and handling practices. However, the FTC does not have the power to enforce these regulations, and it has urged Congress to enact a baseline federal consumer privacy law, although such legislation is unlikely to pass in a Republican-controlled Congress. To read further, please visit http://bits.blogs.nytimes.com/2015/01/27/f-t-c-calls-for-strong-data-and-privacy-protection-with-connected-devices/?_r=0,

Twitter Can Predict Rates of Coronary Heart Disease, According to Penn Research

University of Pennsylvania researchers have demonstrated that Twitter can serve as a dashboard indicator of a community’s psychological well-being and can predict rates of heart disease. The researchers note Twitter can capture more information about heart disease risk than many traditional factors combined because it also characterizes the psychological atmosphere of a community. For example, they found expressions of negative emotions such as anger, stress, and fatigue in a county’s tweets were associated with higher heart disease risk, while positive emotions such as excitement and optimism were associated with lower risk. The researchers collected a set of public tweets made between 2009 and 2010 and used established emotional dictionaries, as well as automatically generated clusters of words reflecting behaviors and attitudes, to analyze a random sample of tweets from individuals who had made their locations available. To read further, please visit http://www.upenn.edu/pennnews/news/twitter-can-predict-rates-coronary-heart-disease-according-penn-research.

San Diego Supercomputer Center High School Volunteer Summer 2015  Internship Opportunities at the University of California, San Diego 

San Diego Supercomputer Center, UC San Diego 
June 22 – August 14, 2015 (eight weeks)

For the sixth year, SDSC launches an exciting volunteer internship program for high school students entitled Research Experience for High School Students (REHS). As part of this program, students will be paired with an SDSC mentor and will work as part of a research team dedicated to a particular area of computational research.

Please browse the research opportunities at http://education.sdsc.edu/studenttech/?page_id=657.

 

SUMMARY:


This problem challenges you to use the GNU gprof utility to identify a function in a program that takes the longest time to run, thereby making it a candidate for parallelism.

 

QUESTION:


This challenge problem is based on the serial (non-parallel) version of the ideal gas model described in a previous challenge problem. It is recommended that you familiarize yourself with this problem first:

http://hpcuniversity.org/students/weeklyChallenge/89/

As part of this challenge, no documentation is provided to you about using the GNU gprof utility, but this can be easily found via a Web search.

First, download the starter code and comment out or remove the code that prints the picture of the flasks at each time step.

Next, compile the program with the relevant flag for gprof added to the Makefile.

Then, run the program to generate a gmon.out file.

Finally, use gprof and the gmon.out file to identify which function takes the most time to run.

 

SOLUTION:
 Will be posted February 23, 2015

 

LINK:
http://hpcuniversity.org/students/weeklyChallenge/92http://hpcuniversity.org/students/weeklyChallenge/92/

Summer 2015 will be a great summer filled with fun and learning at the San Diego Supercomputer Center on the campus of the University of California, San Diego. With over 20 workshops to choose from, summer offerings include animation creation, programming arduino apps, android app development, physics, cinematic art, ocean science and much more! Workshops are open to students in middle and high school but please see each individual workshop description, as some workshops are specific to high school students only. We look forward to seeing you this summer!

To view their summer line up, please visit http://education.sdsc.edu/studenttech/?page_id=570.

March 17-19, 2015 - Clemson University, South Carolina
Submission Deadline – February 27, 2015

Professionals involved in operating and supporting campus shared research computing infrastructure are invited to share their experiences in 10-minute lightning talks during a workshop on Advancing Research Computing on Campuses. For more information and specific Lightning Talk topics, please visit http://citi.clemson.edu/arcc/.

We are looking for faculty/staff interested in teaching on-line semester courses on high-end HPC issues that can be offered to graduate students at multiple institutions across the country.  The objective is to offer high-end HPC courses not normally available at most campuses.  Participating students earn graduate credit at their own institution. We welcome a broad range of topics including extreme scale computing, big data, scientific visualization, and domain science issues in HPC. We pay the faculty member a stipend, and provide funding for a TA.  We cover costs for video-taping of presentations.  We recruit faculty from institutions across the country to engage their students in taking these courses. For more information, please visit https://conferences.xsede.org/xsede15.