NERSCPowering Scientific Discovery Since 1974

NUG 2016

March 21-24, 2016

Wang Hall (LBNL Building 59) and Building 50 Auditorium
Lawrence Berkeley National Laboratory

Agenda Overview

Monday, March 21: Training and Hack-a-Thon

Parallel Track 1: Training


  New User Training   59-3101
9:00 am NERSC Overview Rebecca Hartman-Baker, NERSC User Engagement Group Lead 59-3101 
9:15  Accounts and Allocations Clayton Bagwell, Jr. 59-3101 
9:30 Connecting to NERSC Rebecca Hartman-Baker 59-3101 
10:00 Break    
10:30 User Computing Environment Ankit Bhagatwala 59-3101 
10:45 Submitting and Running Jobs Helen He 59-3101 
11:15 Filesystems Best Practices Steve Leak 59-3101 
12:00-1:30 Lunch    
  Data and Analytics and Visualization Training    
1:30  Data and Analytic Services Overview Prabhat, NERSC Data and Analytics Services Group Lead 59-3101
1.50 Introduction to ESNet Kathryn Mace 59-3101
2:00 Moving and Sharing Data Shreyas Cholia 59-3101
2:20 Databases Wahid Bhimji 59-3101
2:30 Storing Data in HDF5 Quincey Koziol 59-3101
2:50 Break    
3:00 Data Analytics Rollin Thomas 59-3101
3:20 Visualization Burlen Loring 59-3101
3:40 Shifter Lisa Gerhardt 59-3101
3:50 Workflows Debbie Bard 59-3101
4:10 End    

Remote connection info:

Join from PC, Mac, Linux, iOS or Android:

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Or Telephone:
Dial: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll)

Webinar ID: 156 671 133

International numbers available:

Or a H.323/SIP room system::
Dial: (US West) or (US East)
Webinar ID: 156 671 133

Parallel Track 2: Cray Led Hack-a-Thon

9:00-5:00 Advanced Training on Optimization with Tools Led by Cray Engineers Heidi Poxon, John Levesque, Luiz DeRose + Jack Deslippe, NERSC Application Performance Group Lead 59-4102
9:00-9:15 Welcome and Goals for the Day Heidi Poxon 59-4102
9:15-9:45 Update on Cori Jack Deslippe 59-4102
9:45-10:45 Using CCE and Cray Performance Tools Heidi, John, Luiz 59-4102
10:45-11:00 Break   59-4102
11:00-12:00 Using Reveal to add OpenMP and find Vectorization Opportunities Heidi, John, Luiz 59-4102
12:00-1:00 Lunch    
1:00-1:15 Where to find documentation Heidi, John, Luiz  59-4102
1:15-4:30 Hack-a-Thon! Profiling and tuning with Cray Software (hands on for those attending in person)    59-4102
4:30-4:45 Intel Xeon Phi (KNL) Roadmap Heidi, John, Luiz  59-4102
4:45-5:00 Adjourn    
Remote Connection info:

Join from PC, Mac, Linux, iOS or Android:

Or iPhone one-tap:  14086380968,899830179# or 16465588656,899830179#

Or Telephone:
    Dial: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll)
    Meeting ID: 899 830 179 
    International numbers available: 

Or a H.323/SIP room system:
    H.323: (US West) or (US East) 
    Meeting ID: 899 830 179

    SIP: [email protected]

Description of the training:

Full day training on optimizing your application for Cori Phase 2 including a significant hands-on time with your own applications. 

Attendees will learn about the Cray Performance Tools available for identifying performance bottlenecks and optimization opportunities within an HPC program. This session includes training on how to collect application performance information, tips on interpreting data in reports, and where to focus optimization efforts.  The training will include how to identify performance bottlenecks such as load imbalance. Attendees will also learn how to use Reveal to identify and parallelize performance critical loops within a program.

Presentations will cover how to use CrayPat-lite, get optimization feedback from the Cray compiler (listings, Reveal), study performance data (imbalance, MPI rank reorder, etc.), look for OpenMP opportunities and use Reveal, look for vectorization opportunities, understand cache/memory access in preparation for KNL with CrayPat
During hands on time, users will use CCE (including generating loop mark, program library)


Tuesday, March 22 : Science and Technology

Video Streaming:

9:00 Welcome Kathy Yelick, Associate Lab Director for Computing Sciences Building 50 Auditorium
9:15 NERSC Now and Into the Future Richard Gerber, NERSC HPC Department Head Building 50 Auditorium
9:45 The Convergence of Big Data and High Performance Computing Katie Antypas, NERSC Deputy for Data Science Building 50 Auditorium
10:15  Break    
10:30  On the Road Toward Real-Time Virtual Prototyping of Particle Accelerators Jean-Luc Vay, Berkeley Lab Building 50 Auditorium
11:00 Picture Perfect - The Data Explosion in Microscopy Peter Denes, Berkeley Lab Building 50 Auditorium
11:30-12:15 Grab a lunch to go and return for next talk.    
12:15  Lunch Presentation: Supercomputers and Superintelligence  Horst Simon, Berkeley Lab Deputy Director  Building 50 Auditorium
1:30 NESAP: Preparing codes for Cori – Where we Are and What We've Learned So Far Jack Deslippe, NERSC Building 50 Auditorium
 2:00  2016 NERSC Science Achievement Awards    
 2:15  Understanding and Modeling of Climate Feedbacks from Permafrost   Carles Koven, Berkeley Lab  Building 50 Auditorium
 2:45  Imaging the Earth's Interior with Seismic Waves, Supercomputers, and PGAS (UPC++)  Scott French, UC Berkeley   Building 50 Auditorium
 3:15  Break    
3:30 Using NERSC to Understand Turbulence in Fusion Plasmas: Comparison with Experiment and Steps Toward a Predictive Model  Nathan Howard, MIT Building 50 Auditorium
 4:00  Casper: Process-based Asynchronous Progress Model for MPI One-Sided Communication  Min Si, University of Tokyo / Argonne National Laboratory (remote)  Building 50 Auditorium
 4:00-5:00  Tour of NERSC machine room and Wang Hall    59-4012
 7:00  NUG Executive Committee Dinner   NUGEX, speakers, out of town guests, NERSC staff  

Wednesday, March 23:  Scientific Application Readiness and Portability 

 Time Topic Speaker(s) Room
 9:00-11:00 Allinea Map tutorial and Hands On Allinea Reps  59-3101
 11:15-12:00 Advanced OpenMP and Applications in CESM Helen He  59-3101
 12:00-1:00 Lunch    
 1:00-1:45 HBM Tools and Applications in VASP  Zhengji Zhao  59-3101
 1:45-2:15 Vectorization Woo-Sun Yang  59-3101
 2:15-2:30 Break    

Roofline Model and Calculating Arithmetic Intensity

Doug Doerfler 59-3101

WARP Case Study

Ankit Bhagatwala 59-3101

Allinea Map Hands on and Follow-up

Allinea Reps 59-3101

 Remote Connection Info

Topic: NUG Wednesday Meeting
Time: Mar 23, 2016 9:00 AM (GMT-7:00) Pacific Time (US and Canada)

Join from PC, Mac, Linux, iOS or Android:

Or iPhone one-tap:  16465588656,336601536# or 14086380968,336601536#

Or Telephone:
    Dial: +1 646 558 8656 (US Toll) or +1 408 638 0968 (US Toll)
    Meeting ID: 336 601 536 
    International numbers available: 

Or a H.323/SIP room system:
    H.323: (US West) or (US East) 
    Meeting ID: 336 601 536

    SIP: [email protected]

Thursday, March 24: NERSC Status, Updates, and Future Plans (aka NUG Business Meeting)

Remote connection info below.

 9:00 Welcome  Sudip Dosanjh
 9:05 News from DOE HQ  Dave Goodwin 59-4102
 9:10 User Survey Results  Richard Gerber 59-4102
 9:40 Operational Review Results  Katie Antypas  59-4102
10:10 NERSC 9  Nick Wright 59-4102
10:40 - 11:00 Break    
11:00 Cori Phase 2 plans and status  Katie Antypas 59-4102
11:30 NERSC allocation for 2016 and beyond  Richard Gerber and Clayton Bagwell Jr 59-4102
12:00 Support for data-intensive science  Prabhat 59-4102
12:30 - 1:30 Lunch    
  1:30 Cori and Edison updates (System, User)  Doug Jacobsen, Helen He, Zhengji Zhao 59-4102
  2:10 Burst Buffer news   Debbie Bard 59-4102
  2:30  Storage systems updates  Damian Hazen 59-4102
  2:50  NESAP and application readiness  Jack Deslippe 59-4102
  3:20 - 3:30  break   59-4102

Topics proposed by NUGEX
      - Batch queues issues and feeback
      - Use of scavenger QOS

 4:30 - 5:00

Optional tour of CRT machine room

Elizabeth Bautista

Departing from 

Remote Connection info: 

Join from PC, Mac, Linux, iOS or Android:

Or iPhone one-tap: 16465588656,5104865180# or 14086380968,5104865180#

Or Telephone:
Dial: +1 646 558 8656 (US Toll) or +1 408 638 0968 (US Toll)
Meeting ID: 510 486 5180
International numbers available:

Or a H.323/SIP room system:
H.323: (US West) or (US East)
Meeting ID: 510 486 5180
SIP: [email protected]


Lawrence Berkeley National Laboratory
Wang Hall
1 Cyclotron Road, Bldg. 59
Berkeley, CA 94720
Tel: 510.486.4000

Lawrence Berkeley National Laboratory is a multidisciplinary national laboratory located in Berkeley, California on a hillside directly above the campus of the University of California at Berkeley. The site consists of 76 buildings located on 183 acres, which overlook both the campus and the San Francisco Bay. »More Visitor Information.

Site Access

All non-LBNL participants must register to obtain a visitor bus pass or parking pass in advance.  We recommend carpooling, shuttle and taxi.

Please fill out the following form to request site access:

Check-in with Security and picture ID is required.  LBNL Security requires the names, citizenship and country of birth of all visitors.  If you have questions, please contact Norma Early.

The Blackberry Canyon entrance is closest to Wang Hall. The shuttle buses stop at the 65 building or main shuttle bus stop (across the street from Wang Hall).

»LBNL Printable Map

»LBNL Interactive Map


Parking at LBNL is limited due to a number of construction projects. We recommend car pooling, LBNL shuttle, or taxi. If you drive, a parking space may be reserved.  For those visitors who plan to drive to LBNL, we will reserve general parking near Wang Hall.

Shuttle Information

There is an LBNL shuttle bus from various locations around the City of Berkeley, including near the Downtown Berkeley BART station.  If you plan to take the LBNL shuttle, you are required to have an LBNL Visitor Bus Pass  (requires advance notice) and picture ID to show the bus driver. 

Bay Area Rapid Transit Train (BART)

The Downtown Berkeley BART station is two short blocks from the LBNL shuttle line on the corner of Addison and Shuttuck.  The LBNL Blue Shuttle Bus will take you to the Blackberry Canyon entrance and the CRT Building.  The CRT building is across the street from LBNL's main bus stop. »BART Web site


It is recommended lodging reservations be booked early.

Downtown Berkeley Inn
2001 Bancroft Way
Berkeley, CA 94720

Hotel Durant
2600 Durant St., Berkeley, CA 94705
Tel: 510.845.8981

Hotel Shattuck
2086 Allston Way, Berkeley, CA 94704
Tel: 510.845.7300
(One short block from the Downtown Berkeley BART station and LBNL shuttle stop)

LBNL Guest House
1 Cyclotron Road
Berkeley, CA 94720
Rate: $124

Courtyard Oakland Airport 
350 Hegenberger Road, Oakland, CA 94710
Tel: 510.568.7600

Additional Lodging.


 Registration is free, but we need you to register for planning purposes and to assure your spot. See the Registration link in the menu at the left of this page.

Remote Participants

Remote participation will be available. See schedule above for each day.

Meeting Logistics

Norma Early
[email protected]
Tel: 510.486.5893