Namd gpu architecture pdf

This soc contains 2 cpu cores, outlined in orange boxes. Namd, recipient of a 2002 gordon bell award and a 2012 sidney fernbach award, is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. Process technology underlying polaris architecture is the choice of process technology, which determines what is physically possible. This is a tutorial on the usage of gpuaccelerated namd for molecular dynamics simulations. Volta gpu architecture almost 2x faster than previous gen pascal. Gpu architecture cuda models the gpu architecture as a multicore system. Amd epyc processors innovative architecture translates to tremendous performance. The architecture and evolution of cpugpu systems for. G80 based geforce 8800 introduced several k ey innovations in the gpu architecture. The twentyfold acceleration provided by the gpu decreases the runtime for the nonbonded force evaluations such that it can be overlapped with bonded forces and pme longrange force calculations on the cpu.

This tutorial will demonstrate how to use features in namd and vmd to. Gcn powered radeon gpus were built purposefully with an architecture that excels at pushing pixels at an incredibly fast rate while providing phenomenal. The data shows that for a small molecular system such as apoa1, efficiency drops off at after 8 nodes 828 224 cores. Manycore gpu computing current victories and coming battles wenmei hwu. These and other cpubound operations must be ported to the gpu before further acceleration of the entire namd application can be realized. Graphics core next gcn architecture is designed to fuel the most modern pc gaming experiences, excel at content design and creation, as well as break new boundaries in compute performance. Outlined in the blue dashed box, is intel iris graphics 6100. Any documentation updates will appear in the nightly build users guide online or 5. The infiniband cpu benchmarks were performed with namd 2. The group at uiuc working on namd were early pioneers of using gpus for compute acceleration and namd has very good performance acceleration using nvidia cuda. Introduction to gpu architecture ofer rosenberg, pmts sw, opencl dev. Active or dynamic power consumption increases linearly with. Gpu pipelining new data from the cpu are being transferred to the gpu while previous commands are queued for launch and others are executing.

This white paper describes the system architecture and performance characterization of the poweredge c4. Pdf scalable molecular dynamics with namd on the summit. Molecular dynamics programs can achieve very good performance on modern gpu accelerated workstations giving job performance that was only achievable using cpu compute clusters only a few years ago. We make it simple to test your codes on the latest highperformance systems you are free to use your own applications on our cluster and we also provide a variety of preinstalled applications with builtin gpu support. Hpcxxl 2019 summer meeting spectrum scalegpfs user group 92319 the storage layer in the nvidia dgx superpod jacci cenci, technical marketing engineer, nvidia systems engineering. Zen is the codename for a computer processor microarchitecture from amd, and was first used with their ryzen series of cpus in february 2017. Namd molecular dynamics performance on nvidia gtx 1080. Performance and power analysis of highdensity multigpgpu architectures.

Weve got new broadwell xeon and corei7 cpus thrown into the mix too. One processor is transforming vertices of triangle 4 while another rasterizing triangle 3, another is shading pixels of. Gpu acceleration of molecular modeling applications. The compute architecture of intel processor graphics gen8 v1. Developed with parallelization in mind, namd can scale to hundreds of processors and is often used to simulate large systems millions of atoms. A gpu implementation for improved granular simulations with. Gpu hardware assigns patchpairs to multiprocessors dynamically.

Opencl zone the aim of this webinar to provide a general background to modern gpu architectures to place the amd gpu designs in context. The fifth edition of hennessy and pattersons computer architecture a quantitative approach has an entire chapter on gpu architectures. Namd released gpu features and future plans 100,000 users namd 2. Benchmarking namd on a gpuaccelerated hpc cluster with. Powered by nvidia volta, the latest gpu architecture, tesla v100 offers the performance of up to 100 cpus in a single gpuenabling data. History of the gpu 3dfx voodoo graphics card implements texture mapping, zbuffering, and rasterization, but no vertex processing gpus implement the full graphics pipeline in fixedfunction hardware nvidia geforce 256, ati radeon 7500. The performance benefit namds gpu acceleration feature is most clearly.

Improving namd performance on multigpu platforms parallel. Namd uses the popular molecular graphics program vmd for. Is every gpu instruction preceded by a cpu instruction or is it seamless. To improve efficiency, namd includes a scripting engine, which enables the automation of many tasks. If someone succeeds in doing such, please send us your submit script to add to this page. The original intent when designing gpus was to use them exclusively for graphics rendering. Gpu accelerated molecular dynamics simulation, visualization. Building a programmable gpu the future of high throughput computing is programmable stream processing so build the architecture around the unified scalar stream processing cores geforce 8800 gtx g80 was the first gpu architecture built with this new paradigm. Amd epyc 7371 processors accelerating hpc innovation. The new nvidia geforce gtx 1080 and gtx 1070 gpus are out and ive received a lot of questions about namd performance. Petascale molecular dynamics with namd james phillips beckman institute, university of illinois.

Scalable molecular dynamics with namd on the summit system 1. Io intensive workloads can utilize the plentiful io bandwidth with the right number of cores avoiding overpaying for unneeded power. Amd navi rdna architecture a gpu designed purely for pc. Important gpu architecture trends cpucpu fusion architectures. Nvidia tesla v100 gpu accelerator the most advanced data center gpu ever built. More importantly, the performance youre paying for is. Gpu accelerated molecular dynamics simulation, visualization, and analysis pdf, 443k required tutorial files. Trends in computing architecture cmsc828e ramani duraiswami. Vmd visualization, system preparation and analysis. Extreme gpu computing with the dell poweredge c4 a dell technical white paper. I assume they do, but i have been wondering if it is proprietary or if there is some sort of open standard.

Namd performance and acceleration compared to cpuonly 11 figure 11. A cpu perspective 29 gpu core gpu core gpu gpu architecture opencl early cpu languages were light abstractions of physical hardware e. Scaling in a heterogeneous environment with gpus gpu architecture, concepts, and strategies openacc openacc handson lab cuda programming 1 cuda handson lab cuda programming 2 gpu optimization and scaling with profiling and debugging open handson lab. Do graphic cards have instruction sets of their own. Namds use of gpus as coprocessors, a historical perspective. Molecular dynamics performance on gpu workstations namd. Gpu clusters for highperformance computing volodymyr v. Bringing stateoftheart gpuaccelerated molecular modeling tools to the research community. History and evolution of gpu architecture a paper survey chris mcclanahan georgia tech college of computing chris. Gpu computing gpu is a massively parallel processor nvidia g80. Over 14,000 citations of namd one program available on all platforms. Molecular dynamics recipes for genome research iris uniroma1. Algorithms and protocols such as led, smd, and tmd are implemented. The new hardware refresh gives a nice step up in performance.

Pdf performance and power analysis of highdensity multi. How gpu shader cores work, by kayvon fatahalian, stanford university. Epycs innovative architecture translates to tremendous performance at a low cost. With these needs in mind, the radeon technologies group set out to build a new architecture known as vega. Architectural evolution of nvidia gpus for highperformance computing. Meanwhile, the throughput of nearly all types of highperformance processors has been increasingly gated by power consumption. The gpuenabled namd is also mpi aware, so we should be able to run on multiple nodes. With other types of architecture with other gpu designs to. Demystifying gpu microarchitecture through microbenchmarking henry wong, miselmyrto papadopoulou, maryam sadooghialvandi, and andreas moshovos department of electrical and computer engineering, university of toronto. Owing to architectural features resulting from their graphics lineage, gpus are well suited to arithmeticintensive computational workloads that are highly dataparallel. Namd makes use of both gpu and cpu, therefore we recommend to have a relatively modern cpu to achieve the best namd application performance. The navi 10 gpu was the first rdna graphics processor to implement the new amd architecture, and its complete specs are being brought to bear on the new radeon rx 5700 xt card. Applications that run on the cuda architecture can take advantage of an. Namd is a parallel md software developed using the.

Namd power consumption and relative power consumption compared to cpuonly. In this sense, developers of gpuaccelerated molecular modeling applications have benefited from the techniques and experiences gained on the other accelerator platforms. Three major ideas that make gpu processing cores run fast 2. The following features have been released in namd 2. Pdf namd is a parallel molecular dynamics application that has been used to make. Running namd cuda gpu acceleration compiling namd memory usage. Any bug fixes will appear in the nightly build version on the download site. Hpc lsdyna hpc namd hpc openfoam hpc simulia abaqus hpc vasp hpc wrf. This is a venerable reference for most computer architecture topics. Nvidia v100 performance characteristics on ibm ac922. Pdf architectural evolution of nvidia gpus for high. This is my final project for my computer architecture class at community college.

Evolution of the nvidia gpu architecture jason lowden advanced computer architecture november 7, 2012. The challenge posed by todays multigpu architectures. The cuda architecture is a revolutionary parallel computing architecture that delivers the performance of nvidias worldrenowned graphics processor technology to general purpose gpu computing. More importantly, the performance youre paying for can be matched to the appropriate to the performance you need.