University of Stuttgart Advances MegaMol Cross-Platform Visualization Framework

By Rob Johnson

April 16, 2018

The MegaMol team at the Visualization Research Center of the University of Stuttgart (VISUS) works each day to empower discoveries in fields like biochemistry, thermodynamics, medicine, and physics. Initially conceived by researcher Sebastian Grottel, the particle visualization framework MegaMol has been in development for over a decade with support from the Computer Graphics and Visualization Group of the TU Dresden and other colleagues. The framework enables imaging and exploration of the tiny-scale complexities of molecular dynamics in unprecedented three-dimensional detail. MegaMol supports rapid prototyping using powerful desktop systems utilizing both Microsoft Windows and Linux.

As science progresses, major research projects today must accommodate increasingly-challenging imaging workloads. With this evolution comes the need to render detailed visuals, often beyond those which a desktop system’s processing power can handle. Big data management and robust HPC systems present an additional opportunity for scientific breakthroughs. By furthering MegaMol’s existing GPU-centric framework with OSPRay’s ability to tap the speed and built-in capabilities of the latest Intel Xeon CPUs, increasingly-complex visualization middleware will drive science forward.

Jim Jeffers, senior director and senior principal engineer of SDVis engineering at Intel put this in context, “GPUs are very good rendering four to eight-gigabyte rasterized workloads and provide value for smaller data sets needing moderate fidelity on powerful workstations. However, many of today’s scientific endeavors using HPC, like molecular dynamics, fall into the Big Data category, requiring the handling of terabytes of information that require high fidelity rendering.” OSPRay addresses this need for grander scale.

More than meets the eye

In everyday life, many of us experience rendering technologies at work when watching films. Science fiction movies combine actual people with photorealistic computer rendered fantasy creatures using ray traced rendering that inherently models lighting. Biochemists require visualization to meet many different requirements when rendering objects on a molecular scale. Ray traced global lighting effects like ambient occlusion and shadowing can prove helpful when trying to understand the spatial structures in molecular dynamics simulations. However, in biochemistry “realistic” object rendering is not the priority for visualization efforts, but the ability to interact with the data is crucial. Especially in large-scale simulations, the sheer amount of detail which hundreds of millions of particles offer can overwhelm the human observer. Instead, scientists depend on visualization to make their datasets more comprehensible by offering greater clarity, simplicity, and abstraction. Doing that requires novel visualization metaphors and massive scalability from an HPC system and the software running on it.

Stuttgart’s recent efforts seek to leverage both MegaMol and OSPRay visualization frameworks to combine their prowess. MegaMol’s legacy design leverages a GPU (Graphical Processing Unit) for its interactive, cross-platform visualization framework. While innovative in many ways, MegaMol faces some limitations. The primary challenge resides in its reliance on GPUs. Years ago, when CPUs offered lesser compute performance, GPUs sped workloads by offloading challenging visualization tasks from constrained CPUs. However, today’s advanced CPUs are not bound by their predecessors’ limitations since they have built-in capability for ray-tracing algorithm parallelism. For this reason, OSPRay offers a complementary visualization framework for MegaMol.

Since OSPRay maximizes vectorization and ray-tracing capability ‘in-situ’ on the CPU, it can leverage the superior memory capacity, and advanced vector extensions (including Intel AVX-512) to accelerate workloads on Intel Xeon Scalable and Intel Xeon Phi processors. As a result, contemporary ray-tracing takes better advantage of many-node clusters making SDVis exascale-capable. Jeffers describes an additional benefit of Intel AVX integration on the CPU. “Visualization is not just about CPU clock rate. Intel AVX-512 is much more efficient because it enables parallel ‘multi-ray’ capability. Instead of evaluating rays one at a time, the vector processing can package multiple rays together for simultaneous processing. Through this ‘single instruction, multiple data’ capability, many efficiencies can be gained.”

MegaMol team colleague Tobias Rau has undertaken the challenging task of integrating their framework and OSPRay to reap the benefits of each’s inherent strength. OSPRay offers significant performance and scale improvements, while MegaMol remains highly effective at data integration, visual abstraction, interactive exploration, and analysis. Using MegaMol for UX, with OSPRay underlying it, the team maximizes both frameworks.

Beyond the latest hardware and rendering engines, other advancements in visualization provided by OSPRay’s use of the ever-improving Embree ray tracing kernel, available under the Apache 2.0 license, will help drive more detailed rendering.

Grand visions

In the future, the team behind MegaMol plans to forge ahead with additional optimization improvements, and other efforts to enhance the ray tracing framework. With support from Intel’s Parallel Computing Center, VISUS plans further integration of SDVis into MegaMol. The effort will enable additional scalability with more massive data sets. MegaMol’s 1.3 release to be posted on GitHub includes OSPRay support for volume and particle rendering. Additionally, OSPRay geometry for Solvent Excluded Surfaces will empower biochemists seeking a deeper understanding of proteins and other macromolecules.

With these and more improvements on the way, VISUS plans to enable visualization of experiments like a simulation of human muscle fibers. Interfacing MegaMol and simulations, plus the ability to internet-stream resulting observations, will facilitate research not possible just a few years ago. By advancing and integrating visualization frameworks, efforts among the MegaMol team and many others around the world will undoubtedly make a substantial impact in life sciences.

About the Author

Rob Johnson spent much of his professional career consulting for a Fortune 25 technology company. Currently, Rob owns Fine Tuning, LLC, a strategic marketing and communications consulting company based in Portland, Oregon. As a technology, audio, and gadget enthusiast his entire life, Rob also writes for TONEAudio Magazine, reviewing high-end home audio equipment.

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!

InfiniBand Still Tops in Supercomputing

July 19, 2018

In the competitive global HPC landscape, system and processor vendors, nations and end user sites certainly get a lot of attention--deservedly so--but more than ever, the network plays a crucial role. While fast, perform Read more…

By Tiffany Trader

HPC for Life: Genomics, Brain Research, and Beyond

July 19, 2018

During the past few decades, the life sciences have witnessed one landmark discovery after another with the aid of HPC, paving the way toward a new era of personalized treatments based on an individual’s genetic makeup Read more…

By Warren Froelich

WCRP’s New Strategic Plan for Climate Research Highlights the Importance of HPC

July 19, 2018

As climate modeling increasingly leverages exascale computing and researchers warn of an impending computing gap in climate research, the World Climate Research Programme (WCRP) is developing its new Strategic Plan – and high-performance computing is slated to play a critical role. Read more…

By Oliver Peckham

HPE Extreme Performance Solutions

Introducing the First Integrated System Management Software for HPC Clusters from HPE

How do you manage your complex, growing cluster environments? Answer that big challenge with the new HPC cluster management solution: HPE Performance Cluster Manager. Read more…

IBM Accelerated Insights

Are Your Software Licenses Impeding Your Productivity?

In my previous article, Improving chip yield rates with cognitive manufacturing, I highlighted the costs associated with semiconductor manufacturing, and how cognitive methods can yield benefits in both design and manufacture.  Read more…

U.S. Exascale Computing Project Releases Software Technology Progress Report

July 19, 2018

As is often noted the race to exascale computing isn’t just about hardware. This week the U.S. Exascale Computing Project (ECP) released its latest Software Technology (ST) Capability Assessment Report detailing progress so far. Read more…

By John Russell

InfiniBand Still Tops in Supercomputing

July 19, 2018

In the competitive global HPC landscape, system and processor vendors, nations and end user sites certainly get a lot of attention--deservedly so--but more than Read more…

By Tiffany Trader

HPC for Life: Genomics, Brain Research, and Beyond

July 19, 2018

During the past few decades, the life sciences have witnessed one landmark discovery after another with the aid of HPC, paving the way toward a new era of perso Read more…

By Warren Froelich

D-Wave Breaks New Ground in Quantum Simulation

July 16, 2018

Last Friday D-Wave scientists and colleagues published work in Science which they say represents the first fulfillment of Richard Feynman’s 1982 notion that Read more…

By John Russell

AI Thought Leaders on Capitol Hill

July 14, 2018

On Thursday, July 12, the House Committee on Science, Space, and Technology heard from four academic and industry leaders – representatives from Berkeley Lab, Argonne Lab, GE Global Research and Carnegie Mellon University – on the opportunities springing from the intersection of machine learning and advanced-scale computing. Read more…

By Tiffany Trader

HPC Serves as a ‘Rosetta Stone’ for the Information Age

July 12, 2018

In an age defined and transformed by its data, several large-scale scientific instruments around the globe might be viewed as a ‘mother lode’ of precious data. With names seemingly created for a ‘techno-speak’ glossary, these interferometers, cyclotrons, sequencers, solenoids, satellite altimeters, and cryo-electron microscopes are churning out data in previously unthinkable and seemingly incomprehensible quantities -- billions, trillions and quadrillions of bits and bytes of electro-magnetic code. Read more…

By Warren Froelich

Tsinghua Powers Through ISC18 Field

July 10, 2018

Tsinghua University topped all other competitors at the ISC18 Student Cluster Competition with an overall score of 88.43 out of 100. This gives Tsinghua their s Read more…

By Dan Olds

HPE, EPFL Launch Blue Brain 5 Supercomputer

July 10, 2018

HPE and the Ecole Polytechnique Federale de Lausannne (EPFL) Blue Brain Project yesterday introduced Blue Brain 5, a new supercomputer built by HPE, which displ Read more…

By John Russell

Pumping New Life into HPC Clusters, the Case for Liquid Cooling

July 10, 2018

High Performance Computing (HPC) faces some daunting challenges in the coming years as traditional, industry-standard systems push the boundaries of data center Read more…

By Scott Tease

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

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