1. Great things happened at the International Conference for High Performance Computing,
Networking, Storage and Analysis (SC16) in Salt Lake City, Utah, held on November
12-18, 2016. CSRC students and faculty shared their research
project results, and CSRC was selected to participate together
with 13 other universities from the U.S. and other countries in
the student cluster competition.
SC16 programs and activities included a strong technical
meeting and associated workshops (with peer-reviewed
publications), as well as an industrial exhibit where attendees
visited research, education, and vendor booths. SC is where new
advances in computing technologies are showcased, advances
in research are presented, educational institutions feature their
programs. It was the primary annual gathering for researchers,
developers, and commercial companies involved in high-end
supercomputing, big data, and high speed networks. Last year,
the meeting attendance at SC15 was nearly 13,000 attendees,
and over 340 exhibitors, including several CSRC faculty and
students in presenting several research projects or participating
in student programs.
There is a tradition at SC meetings where researchers not only
submit and attend technical presentations, but many of the universities and national research
laboratories host research booths, which are included as part of the technical exhibits. These
booths are used to promote research being conducted, arrange meetings, interact with attendees,
and to disseminate information about undergraduate and graduate studies programs. The key
goals of this CSRC research booth include:
• Raising awareness within the HPC community about the quality of research and education
at SDSU and increasing awareness of High-end computing within the SDSU community.
• Introducing CSRC graduate programs to professors, attendees from other universities
who might be in a position to refer undergraduates to our program, and vendors who
might support the program or Ph.D. students.
• Increasing the level of participation by CSRC,
Colleges of Sciences and Engineering, and SDSU
faculty, research and student communities.
• Mentoring SDSU students.
• Serving as a gathering place for SDSU alumni and
for local San Diego vendors to drop by and talk about
SDSU.
SCisameetingwherestudentsareverystronglyencouraged
to participate, as either paper or poster presenters (there is
Eunsil Baik, a 2012 CSRC Ph.D. graduate, is now Senior
Data Scientist at Microsoft Corporation in Seattle,
Washington. After receiving her Ph.D, she moved to
Hawthorne, CA to conduct research at ReResearch. From there
to the Bay Area, she worked as a data scientist in Cablevision,
and finally returning to the state of Washington with a new
position at Microsoft. Congratulations Eunsil! Your pursuit
of opportunities and perseverance is an inspiration for our
graduate students and faculty.
SDSU
Computational Science
Graduate Programs:
PhD. in Computational Science
Master Degree in Computational Science
Contact the CSRC or Be Placed on
the Mailing List:
Computational Science
Research Center
GMCS Building, Room 206
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-1245
Telephone: (619) 594-3430
csrc@mail.sdsu.edu
Give to the Computational Science
Research Center for the Graduate
Student Research Projects Fund:
Donations to the CSRC can be made in the
following ways:
By check made out to:
The SDSU Campanile Foundation
or through credit card by contacting the
Computational Science Research Center
GMCS Building, Room 206
College of Sciences
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-1245
Telephone: (619) 594-3430
csrc@mail.sdsu.edu
Executive Board
Director
Jose E. Castillo, PhD
Associate Directors
Andrew Cooksy, PhD
Satchi Venkataraman, PhD
Paul Paolini, PhD
Computer Support Coordinator
James Otto, PhD
Business Developer
Ezra Bejar, PhD
COMPUTATIONAL SCIENCE
ODYSSEY is published bi-annually by the
Computational Science Research Center
for the faculty, friends and supporters of San
Diego State University.
Your comments, suggestions and bulletin
submissions are welcome. Please call Parisa
Plant at (619) 594-2260 or e-mail: parisa.
plant@sdsu.edu
Ezra Bejar Editor-in-Chief
Parisa Plant Editor/Publication
Diana Prout Graphic Designer
CSRC Alumni Spotlight
O D Y S S E YO D Y S S E Y
C O M P U TAT I O N A L S C I E N C E
Director
Jose E. Castillo, PhD
Advisory Board
John Newsam, Chair
Tioga Research, Inc.
Gary Fogel
Natural Selection, Inc.
Mark E. Pflieger
Cortech Solutions, Inc.
Anton Zajac
ESET Foundation
Bill Bartling
California Dept. of Conservation
Bob Parker
SPAWAR
Scott Kahn
Illumina, Inc.
Victor Pereyra
Stanford University
Antonio Redondo
Los Alamos National Laboratory
FA L L
2016
S C 1 6 C o n f e r e n c e c o n t i n u e d o n P a g e 3
In This Issue
SC16 Article .....................................Page 1
Director’s Corner & Newsworthy .Page 2
SC16 Article continued...................Page 3
Alumni & LANL Testimonies.........Page 4
CSRC at the International Conference
for High Performance Computing, Networking, Storage and Analysis (SC16)
THE
CSRC doctoral student Priscilla Kelly shares her experience
while interning at Los Alamos National Laboratory in New
Mexico... “Overall, I really enjoyed my trip at LANL this past
summer. I had two projects to work on: Developing a test suite
for interoperability among GPU languages in C with CUDA,
OpenCL, and OpenACC, then optimizing code for parallel
high performance computing by reducing memory access and
adding high level OpenMP directives. My mentors were Bob
Robey and Joe Schoonover. The LANL staff was extremely thoughtful and patient.
They critiqued my resume and helped review my poster at the summer symposium.
I would be happy to work with them again in the future.”
Neelam Patel, a CSRC master’s student, says, “It was
a great experience... The lab is located in the small
town of Los Alamos, NM. The Parallel Computing Summer
Research Internship (PCSRI) was a great way to learn about
high performance computing (HPC) for those with little or
no experience in the field. During the internship, we worked
on large-scale scientific codes and were able to run code on
some of the newest architectures that would otherwise not be
available to us. In the process, we gained experience in dealing with HPC systems
and programming methods. The PCSRI mentors were very knowledgeable in their
respective fields and there was much to learn from them. This research experience
enhanced both my knowledge and interest in HPC.”
Dr. Mary Thomas and the CSRC Student Cluster Team
Stephanie Lauber is a doctoral student in CSRC and has the following testimony:
“This summer at Los Alamos I was able to apply parallel programming skills
learned at SDSU and reinforce these skills through crash courses provided by the
summer internship to work on a Coupled Cluster Doubles (CCD) code created by a
fellow student. At the end of the summer, the students were encouraged to showcase
their work at the annual summer school student symposium where we were able
to speak with other students and staff members from different departments lab
wide. The environment within the summer program allowed us to develop our
computational skills, learn to talk to students across different disciplines and get an
inside look at life inside a national lab. I would highly recommend this program to
any 1st or 2nd year CSRC student as a way to gain experience in a lab setting while
also continuing to improve the skills we gain through classes at SDSU and CGU.”
Los Alamos National Laboratory (LANL) offered three student internships to
CSRC students in 2016. LANL has a competitive educational program providing
students with relevant research experience, while they are pursuing a graduate
degree. This year LANL selected the following three CSRC students out of a total
of nine internships in the nation. Please see their testimonies below...
Los Alamos National Lab - Internship Program

2. Dear Friends,
Welcome back to the 2016 Fall semester! The CSRC is excited to have 45 Doctoral and 15 Master’s students
in the Computational Science Program. We offer congratulations to Priscilla Kelly on obtaining her Master’s
degree in the spring of 2016. She has enrolled in our doctoral program for this semester. Congratulations
also to our doctoral summer 2016 graduates: Vincent Berardi, Kimberly Leung, Seethal Paluri and Julia
Ross. In total, since the program’s inception, CSRC has graduated 54 Doctoral and 55 Master’s students.
Director’s Corner - Paul Paolini
a doctoral showcase program), to apply for an ACM SIGHPC
travel grant (http://www.sighpc.org/resources/travel), or
to apply for an award to attend as a student volunteer (SV,
http://sc16.supercomputing.org/studentssc/). The SV awards
are highly visible, competitive and subject to review and can
be listed in a students’ resume, and travel expense awards
(housing, food, conference fees). Participation is also a lot
of fun for the students: Including dinners, reception job
fairs, and educational events
are held just for the students.
The CSRC strongly encourages
student participation by actively
supporting them to apply for
student positions, to submit
presentations, and to participate
in booth activities. Each year
SDSU has had several students
who have won these competitive
awards. This year, three SDSU
students were selected: Sumukh
Manjunanth, Manuel Valera,
and Angel Velazco. The CSRC
welcomes participation by all
SDSU students, and provides
support to them in several areas:
• Providing information on how to participate in the
technical program such as submitting papers and posters,
or participating in the doctoral research showcase.
• Helping students apply for SV awards by providing
informational email announcements, guiding them
throughout the application process, and providing letters
of support in conjunction with supervising faculty.
• Mentoring the students on how to attend and participate
in these meetings by an in-depth experience of attending
and participating in an international scientific meeting.
• Giving students the opportunity to be involved at an even
deeper level by spending time in our booth, where they
provide information about the program and SDSU to a
general public audience.
SC16 Conference continued from Page 1
Dr. Jose Castillo was interviewed by the Daily Aztec in relation to how the NIH funding of health disparities research will
benefit SDSU. This endowment is part of a group of external research grants funded by public and private organizations for
the 2015-16 fiscal year. Castillo states, “The reason why the NIH grant is a very good grant is because at the end in 10 or 20
years, we (will) have generated 20 million.” “The money stays here (at SDSU) and it doesn’t disappear. You just continue
using that money,” says Castillo.
Coming this Fall of 2017-- Master’s Degree in Computational Science with Emphasis in Data Science.
Associated faculty member, Dr. Satish Sharma, Engineering Sciences, received a $469,555 grant from the Department of
Defense, Office of Naval Research, to continue his work on “Quasi-Far-Field System Upgrade for Millimeter Wave (mmw)
Frequency Expansion.” An important project with many applications in wireless communications.
Best wishes to CSRC Professor Calvin Johnson, Physics, who has been awarded a $95,000 grant from the US Department
of Energy for his work on “Nuclear Structure and Transitions: Computational Studies and Resources.”
CSRC graduate student, Priscilla Kelly just published in the October issue of Nature Physics: McLeod,A, et al, “Nanotextured
Phase Coexistence in the Correlated Insulator V203,” Nature Physics, 2016, DOI: 10.1038/nphys3882.
Professor Barbara Bailey, Statistics, who is an associated faculty at CSRC, received funding from the NSF STATMOS
(https://lnkd.in/bi5kSqi) to support her work and travel of doctoral student, Colette Smirniotis, in Computational Statistics
who is also affiliated to the Coastal Ocean Dynamics Group. Congratulations to Dr. Bailey and Colette! https://lnkd.in/
bFGwNDS.
CSRC Associated faculty Dr. Ilenia Battiato is starting a new job on January 1, 2017 as Assistant Professor in the Energy
Resources Engineering Department at Stanford University, Stanford CA. Congratulations Ilenia!
Antoni Luque, Mathematics and CSRC, published a new paper which reports on the use of a mesoscale computational model
to understand the molecular mechanism regulating the structural state of chromatin in the eukaryotic cell. Luque, A. Ozer, G.
and Tamar Schlick, “Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin,”
Biophys. J. 2016 Jun 7;110(11):2309-19.
CSRC Associate Director Dr. Satchi Venkataraman received a $199,800 grant from the company N&R Engineering
Management and Services Corporation to support his project on: “Uncertainty Quantification ofTest Derived Model Parameters
for Life Prediction of Composite Bolted Joints in an ICME Framework.” Congratulations Satchi!
Board member Dr. Gary Fogel opened the CSRC Industry Lecture Series on December 5th with a talk on “A Survey of
Applications and Future Directions of Computational Intelligence.” The lecture was held in the Gold Auditorium at the
Bioscience Center at 3PM. Dr. Fogel currently serves on the IEEE CIS Administrative Committee as well as the Finance
Chair for the IEEE World Congress on Computational Intelligence to be held in Rio de Janiero, Brazil in 2018.
This year, the CSRC has expanded its role at SC through
its participation in the annual Student Cluster Competition
(see http://www.studentclustercompetition.us/). The Student
Cluster Competition (SCC) was developed in 2007 to immerse
undergraduate and high school students in high performance
computing. Student teams design and build small clusters,
with hardware and software vendor partners, learn designated
scientific applications, apply optimization techniques for their
chosen architectures, and compete
in a non-stop, 48-hour challenge,
at the SC conference, to complete
a real-world scientific workload,
while impressing conference
attendees and interview judges
with their HPC knowledge. The
CSRC team, led by Dr. Mary
Thomas (CS), consists of six
(6) undergraduate students,
from CS and Engineering, and
several faculty mentors including
Drs. Jose Castillo and James
Otto (CSRC), Dr. Chris Paolini
(Engineering), Drs. Robert
Edwards and Steve Price (CS),
and Dr. Peter Blomgren (Math). They have conducted research
experiments to examine how well the Open HPC software stack
performs on a cluster based on the Intel Kenney Pass chipset.
It is about learning the designated scientific applications and to
apply optimization techniques for their chosen architectures.
The team is sponsored by a grant from the Intel Corporation,
who have loaned SDSU a 320 core Kennedy pass server, and
paid for all team travel expenses. For more information, see
the CSRC SCC project web page at: http://www.csrc.sdsdu.
edu/SC/SC16/SCC.
. . .
For questions or more information about how we can help you
or your students participate or represent your program, please
contact Dr. Mary Thomas (mthomas@sciences.sdsu.edu)
or Dr. Jose Castillo (jcastillo@mail.sdsu.edu).
N E W S W O R T H Y. . .
P r e s e n t a t i o n s a t S C 1 6
CSRC’s Research Associate Dr. Mariangel Garcia gave her talk about her research on: “CCOM/DART A Data Assimilation
System for a 3D High-Resolution Non-hydrostatic Coastal Ocean Model” at the National Center for Atmospheric Research
(NCAR) booth at the SC2016 in Salt Lake City. She presented her talk on November 15th, 2016. The authors of the paper are:
Mariangel Garcia, Tim Hoar, Barbara Bailey, Mary Thomas and Jose Castillo.
CSRC graduate Ron Caplan presented new research from his company: Predictive Science, Inc. The poster title was: “Advancing
Parabolic Pperators in Thermodynamic MHD Models: Explicit Super Time-Stepping Versus Implicit Schemes with Krylov
Solvers.” His poster was presented on November 15th, 2016.