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!

Russian and American Scientists Achieve 50% Increase in Data Transmission Speed

September 20, 2018

As high-performance computing becomes increasingly data-intensive and the demand for shorter turnaround times grows, data transfer speed becomes an ever more important bottleneck. Now, in an article published in IEEE Tra Read more…

By Oliver Peckham

IBM to Brand Rescale’s HPC-in-Cloud Platform

September 20, 2018

HPC (or big compute)-in-the-cloud platform provider Rescale has formalized the work it’s been doing in partnership with public cloud vendors by announcing its Powered by Rescale program – with IBM as its first named Read more…

By Doug Black

Democratization of HPC Part 1: Simulation Sheds Light on Building Dispute

September 20, 2018

This is the first of three articles demonstrating the growing acceptance of High Performance Computing especially in new user communities and application areas. Major reasons for this trend are the ongoing improvements i Read more…

By Wolfgang Gentzsch

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

Clouds Over the Ocean – a Healthcare Perspective

Advances in precision medicine, genomics, and imaging; the widespread adoption of electronic health records; and the proliferation of medical Internet of Things (IoT) and mobile devices are resulting in an explosion of structured and unstructured healthcare-related data. Read more…

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Gordon Bell Prize used Summit in their work. That’s impres Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and developm Read more…

By John Russell

Nvidia Accelerates AI Inference in the Datacenter with T4 GPU

September 14, 2018

Nvidia is upping its game for AI inference in the datacenter with a new platform consisting of an inference accelerator chip--the new Turing-based Tesla T4 GPU- Read more…

By George Leopold

DeepSense Combines HPC and AI to Bolster Canada’s Ocean Economy

September 13, 2018

We often hear scientists say that we know less than 10 percent of the life of the oceans. This week, IBM and a group of Canadian industry and government partner Read more…

By Tiffany Trader

Rigetti (and Others) Pursuit of Quantum Advantage

September 11, 2018

Remember ‘quantum supremacy’, the much-touted but little-loved idea that the age of quantum computing would be signaled when quantum computers could tackle Read more…

By John Russell

How FPGAs Accelerate Financial Services Workloads

September 11, 2018

While FSI companies are unlikely, for competitive reasons, to disclose their FPGA strategies, James Reinders offers insights into the case for FPGAs as accelerators for FSI by discussing performance, power, size, latency, jitter and inline processing. Read more…

By James Reinders

Update from Gregory Kurtzer on Singularity’s Push into FS and the Enterprise

September 11, 2018

Container technology is hardly new but it has undergone rapid evolution in the HPC space in recent years to accommodate traditional science workloads and HPC systems requirements. While Docker containers continue to dominate in the enterprise, other variants are becoming important and one alternative with distinctly HPC roots – Singularity – is making an enterprise push targeting advanced scale workload inclusive of HPC. Read more…

By John Russell

At HPC on Wall Street: AI-as-a-Service Accelerates AI Journeys

September 10, 2018

AIaaS – artificial intelligence-as-a-service – is the technology discipline that eases enterprise entry into the mysteries of the AI journey while lowering Read more…

By Doug Black

TACC Wins Next NSF-funded Major Supercomputer

July 30, 2018

The Texas Advanced Computing Center (TACC) has won the next NSF-funded big supercomputer beating out rivals including the National Center for Supercomputing Ap Read more…

By John Russell

IBM at Hot Chips: What’s Next for Power

August 23, 2018

With processor, memory and networking technologies all racing to fill in for an ailing Moore’s law, the era of the heterogeneous datacenter is well underway, Read more…

By Tiffany Trader

Requiem for a Phi: Knights Landing Discontinued

July 25, 2018

On Monday, Intel made public its end of life strategy for the Knights Landing "KNL" Phi product set. The announcement makes official what has already been wide Read more…

By Tiffany Trader

CERN Project Sees Orders-of-Magnitude Speedup with AI Approach

August 14, 2018

An award-winning effort at CERN has demonstrated potential to significantly change how the physics based modeling and simulation communities view machine learni Read more…

By Rob Farber

ORNL Summit Supercomputer Is Officially Here

June 8, 2018

Oak Ridge National Laboratory (ORNL) together with IBM and Nvidia celebrated the official unveiling of the Department of Energy (DOE) Summit supercomputer toda Read more…

By Tiffany Trader

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

By John Russell

AMD’s EPYC Road to Redemption in Six Slides

June 21, 2018

A year ago AMD returned to the server market with its EPYC processor line. The earth didn’t tremble but folks took notice. People remember the Opteron fondly Read more…

By John Russell

Sandia to Take Delivery of World’s Largest Arm System

June 18, 2018

While the enterprise remains circumspect on prospects for Arm servers in the datacenter, the leadership HPC community is taking a bolder, brighter view of the x86 server CPU alternative. Amongst current and planned Arm HPC installations – i.e., the innovative Mont-Blanc project, led by Bull/Atos, the 'Isambard’ Cray XC50 going into the University of Bristol, and commitments from both Japan and France among others -- HPE is announcing that it will be supply the United States National Nuclear Security Administration (NNSA) with a 2.3 petaflops peak Arm-based system, named Astra. Read more…

By Tiffany Trader

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17


AMD @ SC17


ASRock Rack @ SC17

ASRock Rack



DDN Storage @ SC17

DDN Storage

Huawei @ SC17


IBM @ SC17


IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17


Lenovo @ SC17


Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17


Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17


Tyan @ SC17


Univa @ SC17


MLPerf – Will New Machine Learning Benchmark Help Propel AI Forward?

May 2, 2018

Let the AI benchmarking wars begin. Today, a diverse group from academia and industry – Google, Baidu, Intel, AMD, Harvard, and Stanford among them – releas Read more…

By John Russell

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and developm Read more…

By John Russell

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

Intel Pledges First Commercial Nervana Product ‘Spring Crest’ in 2019

May 24, 2018

At its AI developer conference in San Francisco yesterday, Intel embraced a holistic approach to AI and showed off a broad AI portfolio that includes Xeon processors, Movidius technologies, FPGAs and Intel’s Nervana Neural Network Processors (NNPs), based on the technology it acquired in 2016. Read more…

By Tiffany Trader

Intel Announces Cooper Lake, Advances AI Strategy

August 9, 2018

Intel's chief datacenter exec Navin Shenoy kicked off the company's Data-Centric Innovation Summit Wednesday, the day-long program devoted to Intel's datacenter Read more…

By Tiffany Trader

TACC’s ‘Frontera’ Supercomputer Expands Horizon for Extreme-Scale Science

August 29, 2018

The National Science Foundation and the Texas Advanced Computing Center announced today that a new system, called Frontera, will overtake Stampede 2 as the fast Read more…

By Tiffany Trader

GPUs Power Five of World’s Top Seven Supercomputers

June 25, 2018

The top 10 echelon of the newly minted Top500 list boasts three powerful new systems with one common engine: the Nvidia Volta V100 general-purpose graphics proc Read more…

By Tiffany Trader

The Machine Learning Hype Cycle and HPC

June 14, 2018

Like many other HPC professionals I’m following the hype cycle around machine learning/deep learning with interest. I subscribe to the view that we’re probably approaching the ‘peak of inflated expectation’ but not quite yet starting the descent into the ‘trough of disillusionment. This still raises the probability that... Read more…

By Dairsie Latimer

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