Hurricane Force Supercomputing: Petascale Simulations of Sandy

By Peter Johnsen, Mark Straka, Melvyn Shapiro, Alan Norton & Tom Galerneau

November 14, 2013

The devastation incurred by the landfall of Hurricane Sandy on the northeast coast of the United States just over one year ago exemplifies the need for further advances in accuracy and reliability in numerical weather prediction.  High resolution numerical weather simulations carried out on hundreds of thousands of processors on the largest supercomputers are providing these very insights.

The National Center for Atmospheric Research (NCAR) Weather Research and Forecasting (WRF) model has been employed on the largest yet storm prediction model using real data of over 4 billion points to simulate the landfall of Hurricane Sandy. Using an unprecedented 13,680 nodes (437,760 cores) of the Cray XE6 Blue Waters supercomputer at the National Center for Supercomputing Applications  at the University of Illinois, the team of Peter Johnsen from Cray, Inc., Mark Straka from NCSA, and Mel Shapiro, Alan Norton, and Tom Galarneau from NCAR achieved an unprecedented level of performance for any weather model.  The model used approximately 4 billion grid points at an extremely fine resolution of 500 meters.  Forecast data was written and analyzed by the NCAR team members using the NCAR VAPOR visualization suite.

The landfall of Hurricane Sandy along the New Jersey shoreline late on October 30th, 2012 produced a catastrophic storm surge extending from New Jersey to Rhode Island. The research highlighted here demonstrates the capability of the NCSA/Cray Blue Waters supercomputer to conduct a cloud-resolving WRF-ARW simulation of an intense cyclone over a relatively large domain at a very-fine spatial resolution.

The Blue Waters system is a Cray XE/XK hybrid machine composed of 362,240 AMD 6276 “Interlagos” processors and 4224 NVIDIA GK110 Kepler accelerators all connected by the Cray Gemini 3-D (24^3) torus interconnect. It provides sustained performance of 1 petaflop on a range of real-world science and engineering applications. Our motivation was to reduce time to solution as much as was under our control without major source code restructuring. The WRF version 3.3.1 source code was modified from the public distribution chiefly with concerns for reducing the I/O burden per MPI task and limiting the necessary information to a single MPI rank.

Topology Considerations Are Vital

Domain configuration and process layout using MPI rank ordering features of the Cray XE6 job scheduler (ALPS) form a cornerstone in efficiently using the XE6 3D torus interconnect and allowing WRF to scale this successfully.  We used the Cray grid_order utility to generate improved placement of the ranks for the primary communication pattern in the WRF solver, which is nearest neighbor halo exchanges. Reducing the number of neighbors communicating off-node is the primary goal. Using an alternate placement allows us to get 3 communication partners for most MPI ranks on the same node, instead of only 2, as would be with the default placement.  At very high scales, this strategy improves overall WRF performance by 18% or more.

We found the most effective way to run WRF on the AMD Bulldozer core-modules was to exploit WRF’s “hybrid” MPI/OpenMP structure, utilizing 2 OpenMP threads per MPI rank.  This puts 16 MPI ranks on each XE6 node.

The optimized placement we’ve employed also has the benefit of sending smaller east-west direction exchanges off-node and keeping as many larger north-south messages on-node as possible, resulting in 75% fewer bytes being sent over the network. We verified empirically the long-known tactic of decomposing WRF’s domain with many fewer MPI ranks in the X direction than the Y, as this leads to longer vectors on the inner compute loops.

Our simulations yielded an average Tflop count of 32.454 Tflops per second, per simulation time step. Parallel efficiency was still above 60% even on 13,680 XE6 nodes. Over 12 million off-node halo exchange messages totaling 280 GB were processed every WRF time step.

I/O Considerations at Scale

On the Blue Waters system, the Lustre file system was used for all file activity.

Two techniques were used to handle the large I/O requirements for the Sandy simulation –

  1. Parallel NetCDF (PnetCDF), jointly developed by Northwestern University and Argonne National Laboratory, was used where practical.  The MPICH library from Cray has a tuned MPI-IO implementation that aligns parallel I/O with the Lustre file system.  This format is required when post-processing tools are used.
  2. WRF has a multi-file option where each subdomain, or MPI rank, reads and writes unique files.  This was used for very large restart files and some of the pre-processing steps.  The Blue Waters Lustre file system was able to open and read 145,920 restart files in 18 seconds for a 4560 node case.

Additionally, use of WRF’s auxiliary history output options to select only the output fields of greatest interest, thus reducing the volume of output considerably, was of great utility in our work.

graph_1

Scalability of Hurricane Sandy run.  Sustained performance in Tflops/second (y-axis, left) and parallel efficiency over base run on 8,192 cores (y-axis, right) are shown.

Forecast Analysis and Validation

The following figures show a comparison of the maximum radar reflectivity (a surrogate for precipitation) from the simulations at 3-km and 500-m horizontal resolution. In both simulations, a broad region of heavy precipitation is located on the west and southwest side of Sandy, and is organized in a region where warm moist northeasterly flow intersects a northwesterly surge of cold continental air (not shown).

graph_2

Comparison of (a) 3-km and (b) 500-m horizontal resolution ARW simulations of maximum radar reflectivity (shaded according to the color bar in dBZ) verifying at 1500 UTC 29 October 2012.

The 500-m simulation is superior to that at 3-km because it shows the fine-scale linear structure of the convective precipitation bands, consistent with the available observations (not shown). The next images show a zoomed-in view of maximum radar reflectivity and 300-m wind speed within the inner-core of Sandy at 1800 UTC 29 October 2012. This zoomed perspective allows for examination of the full detail of the simulation, noting that the resolution of the simulation (7000×7000 grid points) exceeds the resolution of standard computer monitors by a factor of seven. Here we note the utility of ultra-advanced computational capability to represent the full range of scales spanning the storm-scale circulations down to fine-scale turbulent motions and individual cloud and precipitation systems.

graph_3

500-m ARW simulation of (a) maximum radar reflectivity (shaded according to the color bar in dBZ) and (b) 300-m wind speed (shaded according to the color bar in m s−1) verifying at 1800 UTC 29 October 2012.

The model accuracy for predicting such key output fields as rainfall, pressures, wind speeds, and storm track was graphically validated against actual atmospheric measurements from the storm using NCAR’s VAPOR software suite. Given recent advances in accessing and displaying large volume geophysical datasets as exemplified by the VAPOR software, it is now possible to view the full temporal evolution of numerical simulations and predictions of atmospheric and other geophysical systems. Examples of the advanced visualizations of Hurricane Sandy with VAPOR can be found at:

https://www.vapor.ucar.edu/sites/default/files/movies/sandy_SC13_web_0.mp4

The results of this research will be presented at the Supercomputing conference this month in November.  See the conference agenda here:

http://sc13.supercomputing.org/schedule/event_detail.php?evid=pap255

Cutting Edge Forecasting

NOAA has initiated the ten-year Hurricane Forecast Improvement Project (HFIP), which is evaluating a variety of modeling approaches, exploring the feasibility of real-time fine-scale hurricane projections. Its enhanced Hurricane WRF model (HWRF) is already being run in real time at a somewhat smaller scale. In a collaborative effort involving NOAA’s Hurricane Research Division and Environmental Modeling Center, Cray , NCSA, and NCAR, this code is already being run on Blue Waters to conduct performance studies at scale with grid nesting never before possible. Results are already promising that coming years’ hurricane seasons will be able to incorporate much finer detailed real-time forecasts generated by these simulations. The team is also exploring high resolution simulations with the Office of Naval Research ONR using the COAMPS model.

Research Team:

Peter Johnsen is a performance engineer and meteorologist with Cray, Inc.  Peter’s expertise is optimizing environmental applications on HPC systems.

Mark Straka specializes in performance analysis of scientific applications on the Blue Waters system at the National Center for Supercomputing Applications.

Melvyn Shapiro, Alan Norton, and Thomas Galarneau are research meteorologists with the National Center for Atmospheric Research and are studying many weather phenomena, including Hurricane Sandy’s unique nature.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Better Scientific Software: Turn Your Passion into Cash

September 13, 2019

Do you know your way around scientific software and programming? You think you can contribute to the community by making scientific software better? If so, then the Better Scientific Software (BSSW) organization wants yo Read more…

By Dan Olds

Google’s ML Compiler Initiative Advances

September 12, 2019

Machine learning models running on everything from cloud platforms to mobile phones are posing new challenges for developers faced with growing tool complexity. Google’s TensorFlow team unveiled an open-source machine Read more…

By George Leopold

HPC Perspectives with Dr. Seid Koric

September 12, 2019

Brendan McGinty, director of Industry for the National Center for Supercomputing Applications (NCSA), University of Illinois at Urbana-Champaign, kicks off the first in a series of pieces profiling leaders in high performance computing (HPC), writing for the... Read more…

By Brendan McGinty

AWS Solution Channel

A Guide to Discovering the Best AWS Instances and Configurations for Your HPC Workload

The flexibility and heterogeneity of HPC cloud services provide a welcome contrast to the constraints of on-premises HPC. Every HPC configuration is potentially accessible to any given workload in a well-resourced cloud HPC deployment, with vast scalability to spin up as much compute as that workload demands in any given moment. Read more…

HPE Extreme Performance Solutions

Intel FPGAs: More Than Just an Accelerator Card

FPGA (Field Programmable Gate Array) acceleration cards are not new, as they’ve been commercially available since 1984. Typically, the emphasis around FPGAs has centered on the fact that they’re programmable accelerators, and that they can truly offer workload specific hardware acceleration solutions without requiring custom silicon. Read more…

IBM Accelerated Insights

Building a Solid IA for Your AI

The journey to high performance precision medicine starts with designing and deploying a solid Information Architecture that addresses the spectrum of challenges from data and applications that need to be managed and orchestrated together to empower workloads from analytics to AI. Read more…

IDAS: ‘Automagic’ HPC With Training Wheels

September 12, 2019

High-performance computing (HPC) for research is notorious for having steep barriers to entry. For this reason, high-tech disciplines were early adopters, have used the most cycles and typically drove hardware and softwa Read more…

By Elizabeth Leake

IDAS: ‘Automagic’ HPC With Training Wheels

September 12, 2019

High-performance computing (HPC) for research is notorious for having steep barriers to entry. For this reason, high-tech disciplines were early adopters, have Read more…

By Elizabeth Leake

Univa Brings Cloud Automation to Slurm Users with Navops Launch 2.0

September 11, 2019

Univa, the company behind Grid Engine, announced today its HPC cloud-automation platform NavOps Launch will support the popular open-source workload scheduler Slurm. With the release of NavOps Launch 2.0, “Slurm users will have access to the same cloud automation capabilities... Read more…

By Tiffany Trader

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

Eyes on the Prize: TACC’s Frontera Quickly Ramps up Science Agenda

September 9, 2019

Announced a year ago and officially launched a week ago, the Texas Advanced Computing Center’s Frontera – now the fastest academic supercomputer (~25 petefl Read more…

By John Russell

Quantum Roundup: IBM Goes to School, Delft Tackles Networking, Rigetti Updates

September 5, 2019

IBM today announced a new open source quantum ‘textbook’, a series of quantum education videos, and plans to expand its nascent quantum hackathon program. L Read more…

By John Russell

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

Fastest Academic Supercomputer Enters Full Production at TACC, Just in Time for Hurricane Season

September 3, 2019

Frontera, the NSF supercomputer installed at the Texas Advanced Computing Center (TACC) in June, passed its formal acceptance last week and is now officially la Read more…

By Tiffany Trader

MIT Prepares for Satori…and a New 2 Petaflops Computer Too

August 27, 2019

Sometime this fall, MIT will fire up Satori – an $11.6 million compute cluster donated by IBM and coinciding with the opening of the MIT Stephen A. Schwarzma Read more…

By John Russell

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

Qualcomm Invests in RISC-V Startup SiFive

June 7, 2019

Investors are zeroing in on the open standard RISC-V instruction set architecture and the processor intellectual property being developed by a batch of high-flying chip startups. Last fall, Esperanto Technologies announced a $58 million funding round. Read more…

By George Leopold

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This