AMD EPYC and NAMD Powering the Future of HPC February, 2019

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AMD EPYC and NAMD Powering the Future of HPC February, 19 Exceptional Core Performance NAMD is a

design innovations that target the evolving needs of modern datacenters.

AMD s EPYC processor offers high core density with full access to all features.

Partner Ecosystem AMD s broad partner ecosystem and collaborative engineering provide tested and validated

NAMD NAMD, recipient of a Gordon Bell Award and a 1 Sidney Fernbach Award, is a parallel molecular

AMD EPYC: Nanoscale Molecular Dynamics Designed from the ground up for a new generation of solutions, AMD

Choose the number of cores and sockets that meet your needs without sacrificing key features like memory

Each EPYC processor can have from 8 to 3 cores with access to an exceptional amount of I/O and memory

memory per socket. EPYC s innovative architecture translates to tremendous performance at a low cost.

I/O intensive workloads can utilize the plentiful I/O bandwidth with the right number of cores avoiding

AMD EPYC processors bring a new balance to the datacenter.

capacity, ample memory bandwidth and massive I/O with the right ratios to help performance reach new

1 AMD EPYC and NAMD Powering the Future of HPC February, 19 Exceptional Core Performance NAMD is a compute-intensive workload that benefits from AMD EPYC s high core IPC (Instructions Per Clock) and high number of cores. Standards Based AMD is committed to industry standards, offering you a choice in x86 processors with design innovations that target the evolving needs of modern datacenters. High Density, Low Cost Compute requirements are increasing, datacenter space is not. AMD s EPYC processor offers high core density with full access to all features. Innovative architecture means outstanding performance at a low cost. Partner Ecosystem AMD s broad partner ecosystem and collaborative engineering provide tested and validated solutions that help lower your risk and total cost of ownership. NAMD NAMD, recipient of a Gordon Bell Award and a 1 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. AMD EPYC: Nanoscale Molecular Dynamics Designed from the ground up for a new generation of solutions, AMD EPYC processors implement a philosophy of choice without restriction. Choose the number of cores and sockets that meet your needs without sacrificing key features like memory and I/O. Each EPYC processor can have from 8 to 3 cores with access to an exceptional amount of I/O and memory regardless of the number of cores in use, including 18 PCIe lanes, and support for up to TB of high speed memory per socket. EPYC s innovative architecture translates to tremendous performance at a low cost. More importantly, the performance you re paying for is appropriate to the performance you need. I/O intensive workloads can utilize the plentiful I/O bandwidth with the right number of cores avoiding overpaying for unneeded power while compute-intensive workloads can make use of fully loaded core counts, dual sockets and plenty of memory. AMD EPYC processors help enable more performance, flexibility, and security PERFORMANCE. AMD EPYC processors bring a new balance to the datacenter. Utilizing an x86 architecture, the AMD EPYC processor, brings together high core counts, large memory capacity, ample memory bandwidth and massive I/O with the right ratios to help performance reach new heights. FLEXIBILITY. Match core count with application needs without compromising processor features. EPYC s balanced set of resources means more freedom to right-size the server configuration to the workload. SECURITY. AMD EPYC features the industry s first dedicated security processor embedded in an x86-architecture server processor. The processor manages secure boot, memory encryption, and secure virtualization on the processor itself. Encryption keys never leave the processor where they can be exposed to intruders. SCALABILITY. Scale-up or scale-out, AMD and its ecosystem partners offer high-performance network connectivity options for applications at massive scale. 18 Advanced Micro Devices, Inc.

your deployment. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 5, cores for the largest simulations.

2 AMD EPYC for Molecular Dynamics NAMD Core IPC is a critical factor in optimizing performance of NAMD. AMD EPYC server processors employing the revolutionary Zen microarchitecture helps ensure that you get the most out of your system, minimizing execution time and increasing overall utilization of your deployment. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 5, cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. The EPYC Advantage: AMD EPYC server processors offer 8 memory channels of DDR4-666 and up to TB of memory per processor, yielding exceptional memory bandwidth and capacity. Many High-Performance Compute (HPC) workloads require you to balance performance vs per-core license costs to manage your overall cost. AMD EPYC processors offer a consistent set of features across the product line, allowing users to optimize the number of cores required for their workloads without sacrificing features, memory channels, memory capacity, or I/O lanes. Whether you need 8, 16, 4, or 3 physical cores per socket, you will have access to 8 channels of memory per processor across all EPYC server processors. The EPYC Advantage: Performance - The AMD EPYC processor brings new balance to the datacenter. The highest core count yet in an AMD x86-architecture server processor, large memory capacity, memory bandwidth and I/O density are all brought together with the right ratios to help performance reach new heights. As workloads demand more processor cores, the communications between processor cores becomes critical to efficiently solving the complex problems faced by customers. As cluster sizes increase, the communication requirements between nodes rises quickly and can limit scaling at large node counts. 19 Advanced Micro Devices, Inc. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. NAMD Benchmarks The industry standard benchmarks for NAMD include STMV, ApoA1, and f1atpase. These benchmarks are well established NAMD workloads that allow users to compare performance of different hardware solutions to determine which solutions are best for their needs.

3 Performance Benchmarks and Testing NAMD benchmarks provide a basis of evaluating hardware performance. Standard models are provided that represent typical usage. The benchmarks used were STMV, APOA1, and f1atpase. NAMD testing was performed on a cluster of dualsocket systems. Tests were run using AMD EPYC 7351, AMD EPYC 7371, AMD EPYC 7451, and EPYC 761 processors. Both the EPYC 7351 processor and the EPYC 7371 processor have 16 cores. However, the EPYC 7371 processor runs at a higher frequency. The EPYC 7351 processor has a base frequency of.4 GHz and a boost frequency of.9 GHz. The EPYC 7371 processor runs at a base frequency of 3.1 GHz and a boost frequency of 3.6 GHz. Each EPYC 7451 processor has 4 cores with a base frequency of.3 GHz and a boost frequency of.9 GHz. Finally, the EPYC 761 processor has 3 cores and runs at a base frequency of. GHz and a boost frequency of.7 GHz. Each system has a total of 16 channels of dual-rank DDR4-666 memory, 8 channels per processor. Tested Hardware/Software configuration Compute Nodes CPUs x EPYC 7351 / x EPYC 7371 / x EPYC 7451 / x EPYC 761 Cores 16 cores, 3 threads per CPU (64 threads per system) / 16 cores, 3 threads per CPU (64 threads per system) / 4 cores, 48 threads per CPU (96 threads per system) / 3 cores, 64 threads per CPU (18 Memory NIC Storage: OS Storage: Data threads per system) 56GB (16x) Dual-Rank DDR4-666 Mellanox ConnectX-5 EDR 1Gb Infiniband x16 PCIe 1 x 56 GB NVMe 1 x 1 TB NVMe Software OS RHEL 7.5 ( el7.x86_64) Mellanox OFED Driver MLNX_OFED_LINUX (OFED ) MPI Version OpenMPI Application NAMD_.13b Switch BIOS Setting OS Settings Network Mellanox EDR 1Gb/s Managed Switch (MSB78-ESF) Configuration Options SMT=ON Boost=ON SMEE=Disabled Determinism Slider = Power SVM=Disabled Global C State Control=Enabled Governor=Performance, CC6 Disabled NAMD Compilation: NAMD version.13b was compiled from source on RHEL 7.5 using the gcc compiler and OpenMPI The default optimization flags were used. No further compile time optimizations were done. The FFTW and TCL libraries used are the precompiled versions from the NAMD website. The same binary was used for all benchmarks across all configurations. 19 Advanced Micro Devices, Inc. 3

4 NAMD Performance and Scaling: Single Node Performance Single node performance was compared between the 7351, 7371, 7451, and 761 processors. There were three different industry standard NAMD models used: STMV, ApoA1, and f1atpase. The STMV benchmark is one of the most common benchmarks used to compare NAMD performance across various platforms. STMV is useful for demonstrating scaling to thousands of processors. ApoA1 has been the standard NAMD cross-platform benchmark for years. Another commonly used NAMD benchmark is f1atpase. STMV: EPYC 7351 vs 7371 vs 7451 vs 761 Figure 1 details the performance of the benchmark on a single, two-socket system across 4 different AMD EPYC processors. The 7351 and 7371 processors have 16 cores per socket, however the clock speeds on the 7371 CPUs are higher. The 7451 CPU has 4 cores per socket. The 761 has 3 cores per socket. The performance increases with more cores and/or frequency as expected..8 NAMD STMV Performance EPYC 7351 vs 7371 vs 7451 vs ns/day (higher is better) Single socket node performance Figure 1 19 Advanced Micro Devices, Inc. 4

5 EPYC 7351 vs 7371 vs 7451 vs 761 ApoA1 Figure details the performance of the ApoA1 benchmark using the same configurations. Again, the 7351 and 7371 CPUs have 16 cores per socket however the clock speeds on the 7371 CPUs are higher. The 7451 CPU has 4 cores per socket. The 761 has 3 cores per socket. The performance increases with more cores and/or frequency as expected. 7 NAMD APOA1 Performance EPYC 7351 vs 7371 vs 7451 vs ns/day (higher is better) Single socket node performance Figure 19 Advanced Micro Devices, Inc. 5

6 EPYC 7351 vs 7371 vs 7451 vs 761 f1atpase Finally, figure 3 details the performance of the f1atpase benchmark using the same configurations. The 7351 and 7371 CPUs have 16 cores per socket however the clock speeds on the 7371 CPUs are higher. The 7451 CPU has 4 cores per socket. The 761 has 3 cores per socket. The performance increases with more cores and/or frequency as expected..5 NAMD f1atpase Performance EPYC 7351 vs 7371 vs 7451 vs 761 ns/day (higher is better) Single socket node performance Figure 3 19 Advanced Micro Devices, Inc. 6

7 NAMD Performance and Scaling: Multi Node Scaling Each of the 3 benchmarks, STMV, ApoA1, and f1atpase, were then scaled out to multiple nodes and hundreds of cores to see how well the workload scales. EPYC 7351 Multi Node Scaling STMV Figure 4 details the performance of the STMV model when running across multiple systems, showing how the performance of the benchmark improves through 16 nodes, 51 cores, 14 threads. Each node has 3 physical cores with SMT (simultaneous multi-threading) enabled for 64 logical threads. Each node runs 64 MPI ranks with each rank bound to one thread. The data shows exceptional scaling for this workload. 16 NAMD STMV EPYC 7351 Scaling 14 1 Scaling Factor Number of Threads Figure 4 19 Advanced Micro Devices, Inc. 7

8 EPYC 7451 Multi Node Scaling STMV Figure 5 details the performance of the benchmark when adding additional nodes, showing how the performance of the benchmark improves through 8 nodes, 384 cores, 768 threads. Each node has 48 cores with SMT enabled for 96 logical threads. Each node runs 96 MPI ranks with each rank bound to one thread. The data shows exceptional scaling for this model as well. 8 NAMD STMV EPYC 7451 Scaling 7 6 Scaling Factor Number of Threads Figure 5 19 Advanced Micro Devices, Inc. 8

9 EPYC 7351 Multi Node Scaling f1atpase Figure 6 & 7 show the performance of the f1atpase model when adding additional systems. Each 7351 system has 3 cores with SMT enabled for 64 logical threads, running 1 MPI rank each. The 7451 systems have 48 physical cores with SMT enabled for a total of 96 logical threads, each running 1 MPI rank. Scaling remains very good, even though this model is smaller than SMTV NAMD f1atpase EPYC 7351 Scaling Scaling Factor Number of Threads Figure 6 NAMD f1atpase EPYC 7451 Scaling Scaling Factor Number of Threads Figure 7 19 Advanced Micro Devices, Inc. 9

Results were as expected with higher core frequencies and more cores resulting in better overall performance. NAMD scales very well across all benchmarks to a large number of cores.

10 Summary NAMD benchmarks were conducted on single, two-socket systems, running AMD EPYC 7351, 7371, 7451, and 761 processors. Scaling testing was run on the SMTV and f1atpase models on both the 7351 and 7451 processors. Results were as expected with higher core frequencies and more cores resulting in better overall performance. NAMD scales very well across all benchmarks to a large number of cores. Conclusion AMD empowers the development of fast, accurate molecular dynamics simulations running on costeffective clustered systems. For more information about AMD s EPYC line of processors visit: For more information about NAMD visit: Authors This paper is authored by Anre Kashyap in collaboration with Marc Baker and Kevin Mayo. Scale-out testing on the EPYC cluster shows impressive results on these benchmarks. Pure performance was highest with the 3-core EPYC 761. Per-core performance was highest with the 16-core EPYC Whether you need the dominating system level performance and density of the EPYC 761 or the equally dominating percore performance of the EPYC 7371, all products offer exceptional core IPC, and both provide your organization a significant benefit. Customers can pick the most optimal part based on their unique requirements. DISCLAIMER The information contained herein is for informational purposes only and is subject to change without notice. While every precaution has been taken in the preparation of this document, it may contain technical inaccuracies, omissions and typographical errors, and AMD is under no obligation to update or otherwise correct this information. Advanced Micro Devices, Inc. makes no representations or warranties with respect to the accuracy or completeness of the contents of this document, and assumes no liability of any kind, including the implied warranties of noninfringement, merchantability or fitness for particular purposes, with respect to the operation or use of AMD hardware, software or other products described herein. No license, including implied or arising by estoppel, to any intellectual property rights is granted by this document. Terms and limitations applicable to the purchase or use of AMD s products are as set forth in a signed agreement between the parties or in AMD's Standard Terms and Conditions of Sale. GD Advanced Micro Devices, Inc. All rights reserved. AMD, the AMD Arrow logo, EPYC, and combinations thereof are trademarks of Advanced Micro Devices, Inc. Other product names used in this publication are for identification purposes only and may be trademarks of their respective companies. 19 Advanced Micro Devices, Inc. 1

Memory Population Guidelines for AMD EPYC Processors

Memory Population Guidelines for AMD EPYC Processors Publication # 56301 Revision: 0.70 Issue Date: July 2018 Advanced Micro Devices 2018 Advanced Micro Devices, Inc. All rights reserved. The information