IMS: Breakthroughs in Molecular Science

Institute for Molecular Science adopted new HPC system to support massively parallel operations and high-speed computations.

At a Glance:

  • Japan’s Institute for Molecular Science (IMS) provides a place for joint research and exchanges researchers through domestic and international relationships.

  • The Molecular Simulator’s two systems run on Intel® Xeon® Scalable processors and Intel® SSDs for massively parallel computations and deliver the speed necessary for more demanding serial operations.


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Executive Summary

The Institute for Molecular Science (IMS) significantly expanded its computing capabilities with a dual-purpose system designed to serve researchers that need high-performance parallel computing and memory-demanding serial processing. The new system was built on Intel® Xeon® Gold 6148 processors and Intel® Xeon® Gold 6154 processors with 800 GB Intel® SSD DC 3520 Series solid-state drives all interconnected by the Cornelis Networks1.


Japan’s Institute for Molecular Science (IMS) is a center for advanced research in the molecular sciences—both theoretical and experimental. IMS hosts four research departments: Theoretical and Computational Molecular Science, Photo- Molecular Science, Materials Molecular Science, and Life and Coordination- Complex Molecular Science. The organization provides a place of joint-research for the molecular science community, and it exchanges researchers through domestic and international relationships. IMS scientists also work collaboratively with a wide range of investigators across Japan and around the world, supporting breakthroughs in molecular science knowledge. IMS supercomputers have been used for important work in quantum chemistry calculations, band calculations, and molecular dynamics simulations. Recent work has appeared in scientific journals, including Nature (25 February 2016, vol. 530, pp. 465–468).

The biggest challenge for real breakthroughs comes from the huge number of trial-and-error calculations that researchers have to run on our supercomputers to reveal novel structures and behaviors."—Shinji Saito, director of Research Center for Computational Science (RCCS) at IMS

While molecular dynamics (MD) simulations are typically highly optimized for parallel computing, many quantum chemistry (QC) algorithms tend to run in serial fashion. In both types of computing, the large problems scientists need to study lead to long run times to gather the data they need to further their work. IMS provides enough CPU time for researchers to tackle such challenges, irrespective of the type of computing they need (serial or parallel).

“Our previous supercomputers were installed in 2011,” commented Saito. “They were running on six-year-old technologies. The numbers of cores and the speed of calculations were not enough for our users today.”


MD calculation can use thousands of cores at a time. More cores with a non-blocking interconnect allow researchers to run their jobs much faster, or run much larger jobs, compared to systems with fewer cores. But the serial processes of QC calculations require massive amounts of memory with the fastest CPU clock speeds to achieve results quickly.

Since IMS supports research in both types of computational domains, and since CPU core speeds typically are lower with more cores, we needed a solution that offered both configurations—a system with thousands of cores and one with fewer, faster cores and large memory."—Fumiyasu Mizutani, section chief of RCCS

IMS worked with NEC* to install two clusters with Supermicro* servers interconnected by Cornelis Networks. The new machine is called the High Performance Molecular Simulator. It placed 70 on the November 2017 Top500 list with 1.8 petaFLOPS LINPACK* and 3.1 petaFLOPS theoretical peak performance.2 It went into production at IMS on October 1, 2017.

The Molecular Simulator’s two systems run on Intel® Xeon® Gold 6148 processors with 20 cores for MD’s massively parallel computations, while the Intel® Xeon® Gold 6154 processors with 18 cores running at 3.0 to 3.7 GHz (Turbo) deliver the speed necessary for QC’s more demanding serial operations. To meet the requirements of different types of workloads, the 20-core nodes were configured in a full bi-sectional bandwidth (FBB) topology, while the faster nodes were 1:3 oversubscribed, considering they would not be communicating as much while running their memory-demanding jobs.

The Molecular Simulator also uses 800 GB Intel® SSD DC 3520 Series solid-state drives.


Since the Molecular Simulator went into production, it has run many benchmarks using quantum chemistry calculations, molecular dynamics simulation, memory transfer, and disk performance programs. Additionally, users have begun running their research on the new system. A benchmark of a modified Test397, which is the geometry optimization and frequency calculation, with Gaussian09 Rev.d01 on the new system is approximately 2.1 times faster than that on the old system.3 The new system, with 40,588 cores, provides 7.3X the computational capacity of IMS’ previous system.3

“While these Gaussian benchmark results of this memory intensive workload were calculated prior to applying any ‘Spectre’ and ‘Meltdown’ software mitigations and firmware updates,” Mizutani noted, “further testing of the code indicated no impact to performance after the security updates were applied.”

Now, approximately 1000 jobs using one to 1000 cores by 80 active users are running on the new system constantly and efficiently.

Solution Summary

IMS supports a wide range of molecular science research, including computational research, using its new High Performance Molecular Simulator. The new system provides high performance computing (HPC) for both massively parallel operations and high-speed, memory-demanding serial computations. It integrates 40,588 cores of both Intel® Xeon® Gold 6154 processors and Intel® Xeon® Gold 6148 processors interconnected by the Cornelis Networks. The system placed 70 in the November 2017 Top500 list.

Solution Configuration

  • 40,588 cores of Intel® Xeon® Gold 6148 processors and Intel® Xeon® Gold 6154 processors
  • Cornelis Networks fabric
  • Intel® SSD DC 3520 Series drives
  • 216,768 GB memory

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インテルは、Omni-Path 事業を独立系のインテルキャピタルのポートフォリオ企業である Cornelis Networks に分離しました。Cornelis Networks は、ハイパフォーマンス・コンピューティングと人工知能向けに先進的な専用の高性能ネットワーク製品を提供することで、既存および新規のお客様にサービスを提供し続けます。インテルは、Cornelis Networks が高性能ファブリック・ソリューションのエコシステムを拡大し、インテル® Xeon™ プロセッサー・ファミリー搭載の HPC と AI 向けのクラスターを構築するお客様へのオプションを提供していくと考えます。Omni-Path 製品の分離と移行に関する詳細については、 (英語) をご覧ください。


NEC LX クラスター、インテル® ジーオン® Gold 6148/6154 プロセッサー、インテル® Omni-Path アーキテクチャー (Intel® OPA) に 40,558 のコアを搭載、論理上の最大性能は 3.1 petaFLOPS。


Fujitsu PRIMERGY* CX250 および RX300、インテル® ジーオン® E5-2690/E5-2697v3 プロセッサー 2.9GHz/2.6Ghz、12,992 コアの InfiniBand FDR/QDR、 による論理性能は 437427 petaFLOPS。 パフォーマンス実績は、2018年8月6日に実施したテストに基づくものであり、公開されているすべてのセキュリティー・アップデートが適用されていない可能性があります。