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CSEweek - April 11, 2017

 
CSE Questions

Attention CSE Students:

For quick CSE educational responses via email, please make sure you use the CSE unit email address at cse@cse.illinois.edu.

 
Bioengineering Seminar

Systems Biology of Drug Combinations and Translational Precision Medicine

Joseph Lehar,  Head, Computational Biology at Verily Life Sciences LLC (formerly Google Life Sciences) in San Francisco

Tuesday, April 11, 2017 
2:00 pm
1000 Micro + Nanotechnology Lab

Seminar Flier

 
Students Earning CSE Certificates

CSE students who are graduating May 2017, please complete and submit the undergraduate or graduate certificate Approval Form and attach a copy of your DARS Report to receive your CSE certificate.  The certificates will be ready the second week of May, depending on your submission. 

  • Submit certificate form by: April 30, 2017
  • Attached your DARS report
  • Pick up Certificates starting May 10, 2017 in room at 2102A NCSA, 1205 W. Clark Street, Urbana.
  • If you cannot pick up your certificate, please email your forwarding address to CSE.

http://www.cse.illinois.edu/education/certificate-programs

 
CSE Spring 2017 Seminar Series

The CSE Seminar Series aims to bring together researchers from across campus who share a common interest in the use of computational techniques in all disciplines, and to engage students in both the development and application of numerical methods, data analysis, computer modeling, and related techniques. 

Thursdays
12:00 pm - 1:00 pm
1030 NCSA

LUNCH PROVIDED

Upcoming Spring 2017 CSE Seminar Series:
April 13 -  Dr. Minh Do - Electrical and Computer Engineering
April 20 -  Dr. Roy Dar - Bioengineering

 
The Hacker Within Student Group

The Hacker Within (THW) is an officially registered student organization with CSE affiliation. THW's goal is to encourage students to learn and share tenets of the scientific computing endeavor by arranging a venue for peer-driven teaching, discussions, and forums for sharing skills and best practices for scientific computation, events, and professional resources for putting them into practice.  The group meets bi-weekly with each meeting consisting of at least a discussion/tutorial on a scientific computing problem and a lightning research talk aimed to provide students an overview on a specific area of research.

12:00 pm - 1:00 pm
2100 NCSA
LUNCH PROVIDED at 11:30

2017 THW dates and topics:
Apr 19 — Managing Data with Databases
May 3 — Quantitative Plotting

For more information: The Hacker Within-IL | Github | Google Group

 
Algorithm Interest Group

The Algorithm Interest Group is hosting weekly meetings to facilitate inter-departmental dialogue EVERY TUESDAY at 2 pm in NCSA 2100 through the end of the semester.

Upcoming Speakers and Topics:
April 11, 2017:  Pratik Lahiri - Expectation Maximization
April 18, 2017:  TBD - TBD
April 25, 2017:  Alex Lindsay - Finite Element

Contact Paul Yang for details. 

 
CSE Training Workshops
Computational Science and Engineering is offering the following workshops to interested students and postdocs. Registration is encouraged, but not required. These workshops will be offered until May 3, 2017.
 
Python Workshops Tuesdays 1:00pm - 3:00 pm - L520 DCL
Fluent (CFD) Workshops Tuesdays 1:00pm - 3:00 pm - 1001 MEL
MATLAB Workshops Wednesdays 1:00pm - 3:00 pm - 1001 MEL

Please check go.illinois.edu/cse for more information.

 
RESEARCH SOFTWARE AND COMPUTING TRAINING LEAD

Computational Science and Engineering, National Center for Supercomputing Applications, and the Office of the Chief Information Officer

University of Illinois at Urbana-Champaign

The University of Illinois at Urbana-Champaign seek applicants for the position of Research Software and Computing Training Lead, which will serve as a member of the Computational Science and Engineering (CSE) program, the National Center for Supercomputing Applications (NCSA), and the campus Research IT Services (part of the Office of the Chief Information Officer).  The Research Software and Computing Training Lead will enable cutting-edge research involving the use and/or development of advanced digital software and hardware across all disciplines by coordinating, delivering, and administrating training programs for students and researchers at the University of Illinois and area institutions, including industry.  The person in this position will play a key role in the research life of the campus, identifying important computational and data science skills and technologies, demonstrating how they can be used to solve problems in computational science and engineering and other disciplines, and designing activities to increase them.  Please visit http://jobs.illinois.edu to view the complete position announcement and application instructions.  The closing date for this position is May 1, 2017. 

The University of Illinois conducts criminal background checks on all job candidates upon acceptance of a contingent offer.  Illinois is an EEO Employer/Vet/Disabled - www.inclusiveillinois.illinois.edu

 
Postdoc Position at ALCF in Computational Materials

Postdoc at Argonne National Laboratory - Metascalable Layered Materials Genome
 
Position Description

The mission of the Argonne Leadership Computing Facility (ALCF) is to accelerate major scientific discoveries and engineering breakthroughs for humanity by designing and providing world-leading computing facilities in partnership with the computational science community. We help researchers solve some of the world’s largest and most complex problems with our unique combination of supercomputing resources and expertise. We invite you to apply for a postdoctoral appointee position with the ALCF. 

We invite you to apply for a postdoctoral appointee position with the ALCF. You will research and develop massively parallel nonadiabatic quantum molecular dynamics (NAQMD) and reactive molecular dynamics (RMD) simulation programs. The specific project you will be working on is in the area of functional materials, which, as the name implies, have behaviors useful in science and industry. There is great interest today in engineering materials to have desired behaviors. One approach involves stacking atomically thin layers of different materials to achieve a complex molecular interplay throughout the stack. The resulting behavior of the stack cannot be explained by traditional theories and can only be predicted by directly simulating the layers as collections of molecules interacting with each other. Massive NAQMD and RMD simulations of functional layered materials will be validated by experiments on the same materials using a free-electron X-ray laser.
 
You will join the Computational Science group in ALCF; this is a highly collaborative environment involving science application teams, academia, industry as well as other national labs and agencies. The chosen applicant will have a rare chance to learn and exploit some of the world’s largest supercomputers, and use state-of-the-art techniques on current and upcoming supercomputing systems to help solve significant real-world problems.

Position Requirements

We expect you to have:
PhD + 0-3 years in computational sciences including physics, chemistry, material science and amp; engineering, or in a related field.
Comprehensive knowledge of numerical methods, parallel programming with pthreads, OpenMP, MPI.
Comprehensive experience in programming in one or more programming languages such as Fortran, C, C++, and Python.
Considerable knowledge of parallel algorithms, distributed memory architectures, and parallel performance evaluation/optimization of domain specific implementations.
Candidate should have the ability to create, maintain, and support high-quality software.
An ideal candidate would have published their scientific software in a public repository (e.g. GitHub).
Good communication skills both verbal and written.
Considerable independent judgment and critical thinking.
 
Desirable Knowledge and Skills:
Considerable knowledge of quantum chemistry and first principles molecular dynamics.
Coding experience in massively parallel NAQMD, RMD, molecular dynamics, or other particle methods.
Good experience and skills in interdisciplinary teams involving mathematicians, computer scientists, and discipline scientists.
Collaborative skills including the ability to work well with other laboratories and universities, supercomputer centers, and industry.
Good publication record, preferably including first-author publication(s).
Experience with scientific applications that scale to several thousand MPI processes on massively parallel platforms.
 
Those interested should apply at http://www.anl.gov/careers/apply-job/postdoctoral-applicants under requisition number 402078. Please describe/indicate in your cover letter, (1) your parallel programming experience, (2) desired start date, and (3) eligibility for working in the US, if known.

 
CSE Annual Meeting: 2017 Fellows Symposium

Wednesday, April 26, 2017
Room 1030 NCSA

In late spring each academic year, CSE hosts an Annual Fellows Symposium featuring keynote addresses by two distinguished invited speakers. In addition, each CSE Fellow gives a presentation on their research during the CSE Fellowship year.

REGISTER HERE

Keynote Speakers:
GREG VOTH
Haig P. Papazian Distinguished Service Professor - Department of Chemistry
The University of Chicago

SUSAN SINNOTT
Department Head and Professor of Materials Science and Engineering
Penn State University

CSE Fellows:
Antoine Blanchard (Aerospace Engineering), Dimitrios Fytanidis (Civil and Environmental Engineering), Rachel Mansbach (Physics), Shriyaa Mittal (Biophysics), Advitya Patyal (Theoretical and Applied Mathematics), Amirhossein Taghvaei (Mechanical Science and Engineering), Sixian You (Bioengineering), Xiao Zhang (Mechanical Science and Engineering).

 
Undergraduate Summer Research Opportunity

Accelerated Molecular Dynamics Simulation Using Deep Neural Networks
- Prof. Andrew Ferguson, Materials Science and Engineering

Molecular dynamics (MD) simulations are used to computationally model the conformational structure and motions of molecules including proteins, nucleic acids, and nanoscale materials. Simulations of proteins have been instrumental in improving our understanding of how these molecules fold and assemble, and in guiding the design and development of new drugs and therapeutics. Despite advances in simulation software and high-performance hardware, it remains a challenge to simulate large proteins for biologically relevant time scales. We have developed an approach to accelerate MD simulations by training deep neural networks with autoencoding topologies to discover the important collective dynamical motions governing protein folding dynamics, and to then use these artificial neural networks to accelerate MD simulations along these important directions. We have developed a prototype CPU implementation of this methodology that demonstrates its success. In this undergraduate research project, the student will work with the faculty member and graduate researcher to port the methodology into CUDA and integrate it into the state-of-the-art MD simulation package OpenMM to fully realize the power and acceleration of this approach by enabling it to run on high-performance GPU accelerators.

Qualified applicants for this undergraduate research position will possess a strong background in C++, parallel CPU (MPI, OpenMP) and GPU (CUDA, OpenACC) programming. Some experience in software engineering and data analysis for machine learning models is also desirable. This is an ~8-week paid research position for Summer 2017. Interested applicants should contact Prof Andrew Ferguson.

 
CSE Certificate Option and Transcriptable Enrollment

CSE offers interdisciplinary undergraduate and graduate specializations which are designed to provide students with a solid foundation in problem-solving using computation as a major tool for modeling complicated problems in science and engineering.

Graduate Concentration—transcriptable option available to both Ph.D. and M.S. students
Undergraduate Minor—transcriptable option available to students in the Colleges of Engineering and LAS
Undergraduate Certificate Option—available to undergraduate students enrolled in participating departments

For more information: https://cse.illinois.edu/education-programs

New Students:
Madeleine Biagioli – Chemical & Biomolecular Engineering
Haohang Huang – Civil Engineering
Linjian Ma – Mechanical Engineering
Yao Xiao – MechSE

 
Funding Opportunities

CSE works hand-in-hand with our affiliates to assist you in staying up-to-date with the latest funding opportunities. All the funding opportunities are listed on the CSE website, please view our comprehensive list: http://cse.illinois.edu/research/funding-opportunity-announcements. Our staff is available to support team formation and proposal development. CSE is in the process of creating teams around the solicitations. If you are interested in joining or would like more information about funding opportunities, please send us an email at cse@cse.illinois.edu.

Miscellaneous Funding Opportunities

DoE - Creating Innovative and Reliable Circuits Using Inventive Topologies and Semi Conductors (CIRCUITS)
DoE - CIRCUITS - SBIR
DoE - Creating Innovative and Reliable Circuits Using Inventive Topologies and Semi Conductors (CIRCUITS) DoD - Diverse Collegiate Research and Development Collaboration Program
DoE - Advanced Manufacturing Projects for Emerging Research Exploration
DoE - Innovative Pathways
DoE - Request for Information (RFI): Hydrogen and Fuel Cell Manufacturing: Identifying Specific Components for Manufacturing Standardization
DoE - SENSOR
DoE - SENSOR SBIR/STTR
DoD - Armament Technology Broad Agency Announcement
DoD - Expanded Multidisciplinary Analysis and Design Optimization (MADO) for Effectiveness Based Design Technologies (EXPEDITE) Program
DoD - Fiscal Year (FY) 2018 Department of Defense Multidisciplinary Research Program of the University Research Initiative (MURI)
DoD - Fiscal Year 2018 Defense University Research Instrumentation Program (DURIP)
DoD - 2017 Broad Agency Announcement: Engineer Research and Development Center
DoD - RadioBio
DoD - Distributed and Collaborative Intelligent Systems and Technology (DCIST) Collaborative Research Alliance (CRA)
DoD: Defense University Research Instrumentation Program (DURIP)
DoD: Late-stage Software Customization and Complexity Reduction S&T for Legacy Naval Systems
DoD: NRL Wide Broad Agency Announcement
DoD - Distributed and Collaborative Intelligent Systems and Technology (DCIST) Collaborative Research Alliance (CRA)
DoD - Internet of Battlefield Things (IoBT) Collaborative Research Alliance (CRA)
HHS - Lab to Marketplace: Tools for Brain and Behavioral Research (R43/R44)
HHS - Research Education Program Grants for CryoEM Curriculum Development (R25)
HHS - Academic-Industrial Partnerships to Translate and Validate in vivo Cancer Imaging Systems (R01)
HHS - Academic-Industrial Partnerships to Translate and Validate in vivo Cancer Imaging Systems (R01)
HHS - Rehabilitation Engineering Research Centers (RERCs) Program: RERC on Rehabilitation Strategies, Techniques, and Interventions
HHS - Enhancing Science, Technology, EnginEering, and Math Educational Diversity (ESTEEMED) Research Education Experiences (R25)
NASA - ROSES 2016: New Frontiers Data Analysis Program
NASA - ROSES 2017: Research Opportunities in Space and Earth Science
NASA: ROSES 2017: Astrophysics Data Analysis Program
NSF - Biological and Environmental Interactions of Nanoscale Materials
NSF - Ideas Lab: Practical Fully-Connected Quantum Computer Challenge (PFCQC)
NSF - Dear Colleague Letter: Encouraging Submission of Industry/University Cooperative Research Centers (IUCRC) Proposals in Areas Related to the Internet of Things
NSF - Dear Colleague Letter: Growing Convergence Research at NSF
NSF - Dear Colleague Letter: Research on Integrated Photonics Utilizing AIM Photonics Capabilities
NSF - Dear Colleague Letter: Simulated and Synthetic Data for Infrastructure Modeling (SSDIM)
NSF - Ideas Lab: Practical Fully-Connected Quantum Computer Challenge (PFCQC)
NSF - Petrology and Geochemistry (CH)
NSF - Tomorrow's Internet Project Office (TIPOFF) Building on the Success of the Global Environment for Network Innovations
NSF - Big Data Regional Innovation Hubs: Establishing Spokes to Advance Big Data Applications
NSF - Communications, Circuits, and Sensing-Systems  (CCSS)
NSF - Electronics, Photonics and Magnetic Devices  (EPMD)
NSF - Energy, Power, Control, and Networks  (EPCN)
NSF - Catalysis
NSF - Algorithms for Modern Power Systems (AMPS)
NSF - Centers of Research Excellence in Science and Technology (CREST) and HBCU Research Infrastructure for Science and Engineering (RISE)
NSF - Critical Techniques, Technologies and Methodologies for Advancing Foundations and Applications of Big Data Sciences and Engineering
NSF - EPSCoR Research Infrastructure Improvement Program: Track-2 Focused EPSCoR Collaborations (RII Track-2 FEC)
NSF - Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science (NSF INCLUDES)
NSF - Smart and Connected Communities (S&CC)
NSF - Cybersecurity Innovation for Cyberinfrastructure (CICI)
NSF - Dear Colleague Letter: Request for Input on Federal Datasets with Potential to Advance Data Science
NSF - Geotechnical Engineering and Materials
NSF - Mind, Machine and Motor Nexus
NSF - Tomorrow's Internet Project Office
NSF - ADVANCE: Increasing the Participation and Advancement of Women in Academic Science and Engineering Careers (ADVANCE)
NSF - Building Community and Capacity in Data Intensive Research in Education  (BCC-EHR)
NSF - Geotechnical Engineering and Materials
NSF - Innovation Corps (I-Corps TM) - National Innovation Network Nodes Program (I-Corps Nodes)
NSF - Innovation Corps Teams Program (I-Corps Teams)
NSF - Robert Noyce Teacher Scholarship Program
NSF - Transdisciplinary Research in Principles of Data Science Phase I (TRIPODS)
NSF - Biophotonics
NSF - Cellular and Biochemical Engineering
NSF - Disability and Rehabilitation Engineering
NSF - Engineering of Biomedical Systems
NSF - Environmental Engineering
NSF - Fluid Dynamics
NSF - Nano-Biosensing
NSF - Particulate and Multiphase Processes
NSF - Process Systems, Reaction Engineering and Molecular Thermodynamics
NSF - STEM + Computing Partnerships (STEM+C)
NSF - Thermal Transport Processes
NSF - Dear Colleague Letter: Encouraging Submission of Industry/University Cooperative Research Centers (IUCRC) Proposals in the Area of Cybersecurity

Additional Funding Opportunities can be found on the CSE Website.

 
2017 LCI Workshops

For the first time, LCI is offering trainings for HPC administrators at two different levels:  Introductory AND Intermediate!

Introductory Workshop
http://www.linuxclustersinstitute.org/workshops/may2017/

May 22-26, 2017
University of Wyoming (in collaboration with University Corporation for Atmospheric Research)
Laramie, WY
If you are a Linux system administrator new to HPC, this is the workshop for you! Learn more!  Register today!

Intermediate Workshop
http://www.linuxclustersinstitute.org/workshops/aug2017/

August 14-18, 2017
Georgia Institute of Technology
Atlanta, GA
If you have some experience as an HPC system administrator and want to expand your skills, this is the workshop for you! Learn more!
Register today!

 
Sandia National Laboratories Technical Intern Program

Center for Cyber Defenders (CCD)
The Center for Cyber Defenders (CCD) program is focused on developing the next generation of
experts in the field of computer security from the software stack down to embedded hardware. Our
program fosters students’ abilities to address the serious and unique challenges existing in the
realm of cyber security research, and encourages the exploration of original ideas necessary to
keep pace with the rapid changes in information technology and the increasing sophistication of
cyber threats. Students will gain experience in some of the following: operating systems analysis,
virtualization technologies including software defined networking, distributed systems, storage,
and algorithm analysis and development, advanced modeling and emulation, machine learning, reverse
engineering, network programming, cryptography research and analysis, and much more. Projects range
from working on small research and development (R&D) efforts to large, multidisciplinary team
collaborations.

Summer, Year-­‐round and Co-­‐op Internships
High school, undergraduate and graduate students:
•     Computer Science
•     Computer Engineering
•     Cybersecurity

For more info: http://www.sandia.gov/careers/students_postdocs/internships/institutes/cyber_defenders.html

 
 
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