RIKEN, Japan’s largest comprehensive research institution, recently expanded the capacity and capabilities of its HOKUSAI supercomputer, a key resource managed by the institution’s Advanced Center for Computing and Communications (ACCC). RIKEN is known for its high-quality research in a wide range of scientific disciplines, including health, brain, and life sciences, accelerator science, physical sciences, and computational science, among others.
“In 2015, with ongoing advances in research and technology,” commented Hiroo Kenzaki of the ACCC, “we needed to support more large-scale and medium-scale computation-intensive workloads across the sciences in which our researchers work.” These fields of computational science include quantum chromodynamics (QCD), condensed matter physics, quantum chemistry, biophysics, genomics, and more. RIKEN scientists run a wide range of commercially available software from ISVs, open source software, and their own, internally developed codes. “We introduced HOKUSAI, our next-generation cluster for general-purpose computing,” added Kenzaki.
GreatWave + BigWaterfall = Hokusai
HOKUSAI was built in two stages. In 2015, the first stage called GreatWave—designed for highly parallelized calculations—was put into production. It includes a 1.0 petaflops massively parallel general-purpose system built on the Fujitsu PRIMEHPC FX100 platform based on the SPARC64 processor. Thus, it has compatibility with Japan’s K computer. This first stage also provides two workload-specialized application computing systems, one with two 60-core large-memory nodes using Intel Xeon E7 v2 processors and the other with 30 nodes housing four Nvidia GPUs and two 12-core Intel Xeon E5 v3 processors per node.
Early in 2017, BigWaterfall, a second and larger general-purpose cluster, was acquired; it was placed into production on October 11, 2017. “BigWaterfall accommodates a growing demand for higher performance supercomputing for computational research,” stated Kenzaki. BigWaterfall extends HOKUSAI’s capacity for workloads built on software optimized for Intel processors. BigWaterfall is built on Fujitsu PRIMERGY CX2550 M4 servers, based on the Intel Xeon Gold 6148 (Skylake) processor. With 840 dual-socket nodes, the system contains 1,680 CPUs (33,600 cores) with 78.7 TB of memory. It provides 2.5 petaflops theoretical performance—2.6X more performance than the old system—and placed at 82 on the November 2017 Top500 list.
Skylake—Processor of Choice
In 2016, prior to building BigWaterfall, RIKEN ran a proof of concept (PoC) using a few nodes built on Intel Xeon Phi processors. “With Intel Advanced Vector Extensions 512 (Intel AVX512) and six-channel memory, the Intel Xeon Phi processors offered high performance for computation-intensive codes, but it did not perform well on I/O-intensive workloads,” stated Kenzaki. That led the ACCC to look at the Intel Xeon Scalable Processor. “Skylake has Intel AVX512 and six-channel memory, plus it features high operating frequency,” said Kenzaki. “The combination delivered very high parallel floating-point performance and computational throughput on the tests we ran, which will benefit the types of workloads RIKEN researchers run.” Additionally, RIKEN ACCC can leverage many IA programming tools and software, including the Intel Parallel Studio XE Cluster Edition, to help developers optimize their codes.
Both GreatWave and BigWaterfall are interconnected with common storage systems—both general storage and hierarchical storage resources—based on the Fujitsu Exabyte File System (FEFS), and they utilize common login and control nodes. RIKEN chose the InfiniBand Enhanced Data Rate (EDR, 100 Gbps) fabric for the new clusters.
2.6X the Performance of Previous Cluster
“Our biggest challenge was to ensure uninterrupted service on GreatWave as we brought BigWaterfall into production. Since they had common components, special care was taken to minimize the impact on users and avoid problems. We needed to maintain accessibility for users and sustain running jobs, while BigWaterfall was built, tested, and released,” commented Kenzaki.
During the build out phase of BigWaterfall, benchmarks were conducted for various performance measurements, including LINPACK, HimenoBMT, Gaussian, and network performance. “The computation power and the memory bandwidth are particularly important to us in order to maintain a balanced system that delivers optimal application performance,” he added.
With BigWaterfall, Riken is able to run many types of workloads—memory-intensive, IO intensive, and compute-intensive—because of Intel AVX512, high-bandwidth memory, and high operating frequency. Overall, the new system delivers 2.6X more performance and twice the memory capacity for bio-informatics, genomics, and engineering workloads, enabling RIKEN to accelerate their engineering research and projects.
More information about HOKUSAI can be found at http://accc.riken.jp/en/tag/hokusai/.
Ken Strandberg is a technical story teller. He writes articles, white papers, seminars, web-based training, video and animation scripts, and technical marketing and interactive collateral for emerging technology companies, Fortune 100 enterprises, and multi-national corporations. Mr. Strandberg’s technology areas include Software, HPC, Industrial Technologies, Design Automation, Networking, Medical Technologies, Semiconductor, and Telecom. He can be reached at [email protected].