SuperMUC-NG Enables Innovative Science with ‘Best Scientific Visualization’

By Rob Farber

May 7, 2020

Ranked the 9th fastest supercomputer in the world as of the November 2019 Top500 list, SuperMUC-NG located at the Leibniz Supercomputing Centre (LRZ) is powering innovative and energy efficient science in Europe, and delivering ground-breaking visualization results. It is designed as a general-purpose system to support applications across all scientific domains – life sciences, meteorology, geophysics, and climatology, to name a few. Astrophysics has been a dominant user group on LRZ’s supercomputing systems. And most recently LRZ has made their supercomputing resources available for COVID-19 related research.

Built by Lenovo, the SuperMUC-NG system is powered by Intel Xeon Scalable processors and utilizes an Intel OmniPath fabric interconnect. Astrophysicist Hans-Thomas Janka (Scientist, Max-Plank-Institute for Astrophysics and lecturer at the Technical University of Munich) observes, “We are insatiable when it comes to data volumes and computing power.” He continues, “We get a lot of data from stars and explosions from the cosmos by measuring radiation, elementary particles or gravitational waves. But we can only really observe a few developments. Therefore, astrophysicists develop models for evaluation and calculate them with the help of mathematical and physical equations. This easily produces terabytes of data that we can only analyze or visualize with high performance computers.” [i]

Dubbed the “next geneneration” system as indicated by the “-NG” designation, the benefits of the new SuperMUC-NG system will be felt by many as LRZ supplies its high performance computing resources to German national and international research teams. LRZ is a member of the Gauss Centre for Supercomputing (GCS), which combines the three national centers, namely High Performance Computing Center Stuttgart (HLRS), Jülich Supercomputing Centre (JSC), and Leibniz Supercomputing Centre (LRZ), into Germany’s foremost supercomputing institution.[ii]

In a recent development, researchers can use the SuperMUC-NG and the infrastructure of the LRZ for COVID-19 research including the search for vaccines and therapeutics, analyzing and forecasting spread scenarios for contingency planning, as well as exploring the virus and its behavior. [iii]

Dr. Janka explains the extraordinary scientific impact of foundational turbulence calculations performed on the earlier SuperMUC clusters, “Previously, astrophysicists could only perform much smaller calculations and thus only calculate two-dimensional models. For us, SuperMUC was a gift. Even three-dimensional simulations became possible. That was a huge breakthrough for us.” [iv] His statement is based on simulated results that consumed more than 570 million core hours on the earlier clusters.

SuperMUC-NG allows even more detailed models

SuperMUC-NG significantly augments the abilities of researchers to advance the state-of-the-art in research. For example, a team of researchers led by Australian National University (ANU) Professor Christoph Federrath used the system to run the largest magneto-hydrodynamic (MHD) simulation of astrophysical turbulence ever performed. [v] In particular, the inclusion of magnetic fields made the computation twice as challenging. The details of this foundational simulation work are discussed in the 2016 article “The world’s largest turbulence simulations”.

Using Software Defined Visualization (SDVis), the performance benefits and capabilities of the SuperMUC-NG hardware made it possible for a team of experts collaborating with Luigi Iapichino and Salvatore Cielo at LRZ to visualize simulation results using static 3D grid resolutions as high as 100483. “This unprecedented resolution allows for a dynamic range of four orders of magnitude in length scale”. The resolution is extraordinary and the team was able to report that these extreme scale visualizations demonstrate an excellent quantitative characterization of the gas Mach number as a function of spatial scale (the so-called structure function) with theoretical models in both the supersonic and subsonic regimes. [vi]

This visualization work was selected as a finalist in the Supercomputing 2019 “Best Scientific Visualization” contest held in Denver, Colorado (Nov. 17-22). [vii] The LRZ YouTube video titled “Visualizing the world’s largest turbulence simulation” describes the work and illustrates the fine details and dynamics that can be seen in the LRZ simulations at this extreme resolution.

A collaborative effort

The team partnered with visualization experts at LRZ and Intel to create the scientific visualizations presented at SC19. [viii] Each snapshot required more than 23 terabytes of disk space, creating an enormous amount of data to visualize. Using the Intel OSPRay engine and VisIt, the team was able to take advantage of nearly all of SuperMUC-NG’s 6,336 nodes. [ix] The Intel OSPRay library is an open source, scalable, and portable ray tracing engine (e.g. OSPRay) that delivers interactive, high-fidelity visualizations using Intel Architecture CPUs and is part of the Intel oneAPI Rendering Toolkit.  The VisIt application is an open-source interactive parallel visualization and graphical analysis tool for viewing scientific data.

The following images illustrate some of the minute details in the LRZ turbulence data. Figure 1 shows the density of the turbulent gas, plus some velocity streamlines.  The data are explored in “slabs”, as the full box would contain too many small details.

Figure 1: Sample ray-tracing plus velocity streamlines rendering of the 10048^3 hydrodynamic simulation, using VisIt and OSPRay on SuperMUC-NG. The displayed data corresponds to a slab with a volume of 10% of the full data cube.  (Source: SC’19 proceedings)

Figure 2 reflects a first-time demonstration that the extreme resolution 11563 model can resolve the transition between the two sonic scales. The team reports, “This in turns lets scientists infer the width distribution of filamentary structures in star-forming regions and ultimately the critical density for the formation of stars.”[x]

Figure 2: Volume rendering of the gas density structures associated with the sonic scale (i.e. regions with the gas velocity transitions from supersonic to subsonic) in the MHD simulation with grid resolution of 11523

Not just limited to astrophysics, extreme-scale astrophysics turbulence simulations can also help shed light on the general nature of  turbulent flow problems, including those found in Earth-bound cases.

Capitalizing on a four-fold increase in performance

The LRZ team built and deployed a custom version of the VisIt software in order to fully utilize the high degree of parallelism (number of cores per node and large vector registers) provided by the SuperMUC-NG Intel Xeon Platinum 8174 processors. The team writes, “This version integrates the Intel OSPRay rendering engine, embodying the software defined visualization concept, optimized for CPU usage without the need of accelerators. OSPRay uses Intel Threading Building Blocks (Intel TBB) for parallel work sharing, and integrates additional features […] which are absent in the standard version of VisIt.”

LRZ reports the new Intel Xeon Scalable processors (SKX in the following graph) to deliver much improved scaling and performance compared to the SuperMUC Phase 2 Intel Xeon E5-2697 v3 processors (HSW).[xi] The improvement can be seen in the comparative scaling results reported by the LRZ visualization team when creating their visualizations included below. The introduction of OSPRay (yellow and red lines) brings a further 8x speedup with respect to older methods (blue line). (Note the log scale of the y-axis.)

Figure 3: Upper panel: VisIt-OSPRay node-level scaling behavior over MPI tasks (Intel TBB always at work). The yellow line shows the scaling for a SuperMUC-NG Intel Xeon Platinum node and, for comparison, for a SuperMUC Phase-2 Intel Xeon E5-2697 v3 node (red line). Moreover, for the best-scaling algorithm before OSPRay (kernel-based ray-casting, blue line), two scaling points are shown. Lower pane: VisIt-OSPRay strong scaling for tasks of the presented visualization, using one (yellow line) or four (red line) MPI tasks per node. The reported time to solution refers to a single snapshot of the tomography of the 10048^3 hydrodynamic simulation simulation, from 128 to 3076 nodes (i.e. one half of the whole SuperMUC-NG). Percentile confidence intervals after 20 measures are shown when significant. (Source: SC’19 proceedings)

Rob Farber is a global technology consultant and author with an extensive background in HPC, AI, and teaching. Rob can be reached at [email protected]

[i] https://www.lrz.de/presse/ereignisse/2019-12-04_Interview-Prof-Janka-_EN/

[ii] https://doku.lrz.de/display/PUBLIC/Books+with+results+on+LRZ+HPC+Systems

[iii] https://www.lrz.de/wir/newsletter/neu/

[iv] https://www.lrz.de/presse/ereignisse/2019-12-04_Interview-Prof-Janka-_EN/

[v] https://sciencenode.org/feature/How%20does%20a%20star%20form.php

[vi] https://sc19.supercomputing.org/proceedings/sci_viz/sci_viz_files/svs103s2-file1.pdf

[vii] Visualizing the world’s largest turbulence simulation

[viii] https://sciencenode.org/feature/How%20does%20a%20star%20form.php

[ix] ibid

[x] ibid

[xi] https://www.hpcwire.com/2018/09/26/germany-celebrates-launch-of-two-fastest-supercomputers/

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!

UT Dallas Grows HPC Storage Footprint for Animation and Game Development

October 28, 2020

Computer-generated animation and video game development are extraordinarily computationally intensive fields, with studios often requiring large server farms with hundreds of terabytes – or even petabytes – of storag Read more…

By Staff report

Frame by Frame, Supercomputing Reveals the Forms of the Coronavirus

October 27, 2020

From the start of the pandemic, supercomputing research has been targeting one particular protein of the coronavirus: the notorious “S” or “spike” protein, which allows the virus to pry its way into human cells a Read more…

By Oliver Peckham

AMD Reports Record Revenue and $35B Deal to Buy Xilinx

October 27, 2020

AMD this morning reported record quarterly revenue of $2.8 billion and a finalized deal to buy FPGA-maker Xilinx for $35 billion in an all-stock transaction. The acquisition helps AMD keep pace during a time of consolida Read more…

By John Russell

Nvidia-Arm Deal a Boon for RISC-V?

October 26, 2020

The $40 billion blockbuster acquisition deal that will bring chip maker Arm into the Nvidia corporate family could provide a boost for the competing RISC-V architecture. As regulators in the U.S., China and the Europe Read more…

By George Leopold

OpenHPC Progress Report – v2.0, More Recipes, Cloud and Arm Support, Says Schulz

October 26, 2020

Launched in late 2015 and transitioned to a Linux Foundation Project in 2016, OpenHPC has marched quietly but steadily forward. Its goal “to provide a reference collection of open-source HPC software components and bes Read more…

By John Russell

AWS Solution Channel

Rapid Chip Design in the Cloud

Time-to-market and engineering efficiency are the most critical and expensive metrics for a chip design company. With this in mind, the team at Annapurna Labs selected Altair AcceleratorRead more…

Intel® HPC + AI Pavilion

Berlin Institute of Health: Putting HPC to Work for the World

Researchers from the Center for Digital Health at the Berlin Institute of Health (BIH) are using science to understand the pathophysiology of COVID-19, which can help to inform the development of targeted treatments. Read more…

NASA Uses Supercomputing to Measure Carbon in the World’s Trees

October 22, 2020

Trees constitute one of the world’s most important carbon sinks, pulling enormous amounts of carbon dioxide from the atmosphere and storing the carbon in their trunks and the surrounding soil. Measuring this carbon sto Read more…

By Oliver Peckham

AMD Reports Record Revenue and $35B Deal to Buy Xilinx

October 27, 2020

AMD this morning reported record quarterly revenue of $2.8 billion and a finalized deal to buy FPGA-maker Xilinx for $35 billion in an all-stock transaction. Th Read more…

By John Russell

OpenHPC Progress Report – v2.0, More Recipes, Cloud and Arm Support, Says Schulz

October 26, 2020

Launched in late 2015 and transitioned to a Linux Foundation Project in 2016, OpenHPC has marched quietly but steadily forward. Its goal “to provide a referen Read more…

By John Russell

Nvidia Dominates (Again) Latest MLPerf Inference Results

October 22, 2020

The two-year-old AI benchmarking group MLPerf.org released its second set of inferencing results yesterday and again, as in the most recent MLPerf training resu Read more…

By John Russell

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

HPE to Build Australia’s Most Powerful Supercomputer for Pawsey

October 20, 2020

The Pawsey Supercomputing Centre in Perth, Western Australia, has had a busy year. Pawsey typically spends much of its time looking to the stars, working with a Read more…

By Oliver Peckham

DDN-Tintri Showcases Technology Integration with Two New Products

October 20, 2020

DDN, a long-time leader in HPC storage, announced two new products today and provided more detail around its strategy for integrating DDN HPC technologies with Read more…

By John Russell

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Aurora’s Troubles Move Frontier into Pole Exascale Position

October 1, 2020

Intel’s 7nm node delay has raised questions about the status of the Aurora supercomputer that was scheduled to be stood up at Argonne National Laboratory next year. Aurora was in the running to be the United States’ first exascale supercomputer although it was on a contemporaneous timeline with... Read more…

By Tiffany Trader

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Leading Solution Providers

Contributors

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Oracle Cloud Infrastructure Powers Fugaku’s Storage, Scores IO500 Win

August 28, 2020

In June, RIKEN shook the supercomputing world with its Arm-based, Fujitsu-built juggernaut: Fugaku. The system, which weighs in at 415.5 Linpack petaflops, topp Read more…

By Oliver Peckham

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

DOD Orders Two AI-Focused Supercomputers from Liqid

August 24, 2020

The U.S. Department of Defense is making a big investment in data analytics and AI computing with the procurement of two HPC systems that will provide the High Read more…

By Tiffany Trader

Oracle Cloud Deepens HPC Embrace with Launch of A100 Instances, Plans for Arm, More 

September 22, 2020

Oracle Cloud Infrastructure (OCI) continued its steady ramp-up of HPC capabilities today with a flurry of announcements. Topping the list is general availabilit 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