Computational Chemistry Benchmarks - Nvidia

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Molecular Dynamics (MD) Applications Application Features Supported GPU Perf Release Status Notes/<strong>Benchmarks</strong> AMBER PMEMD Explicit Solvent & GB Implicit Solvent > 100 ns/day JAC NVE on 2X K20s Released Multi-GPU, multi-node AMBER 12, GPU Revision Support 12.2 http://ambermd.org/gpus/benchmarks. htm#<strong>Benchmarks</strong> CHARMM Implicit (5x), Explicit (2x) Solvent via OpenMM 2x C2070 equals 32-35x X5667 CPUs Released Single & multi-GPU in single node Release C37b1; http://www.charmm.org/news/c37b1.html#po stjump DL_POLY Two-body Forces, Link-cell Pairs, Ewald SPME forces, Shake VV 4x Release V 4.03 Multi-GPU, multi-node Source only, Results Published http://www.stfc.ac.uk/CSE/randd/ccg/softwa re/DL_POLY/25526.aspx GROMACS Implicit (5x), Explicit (2x) 165 ns/Day DHFR on 4X C2075s Released Multi-GPU, multi-node Release 4.6; 1 st Multi-GPU support LAMMPS Lennard-Jones, Gay-Berne, Tersoff & many more potentials 3.5-18x on Titan Released. Multi-GPU, multi-node http://lammps.sandia.gov/bench.html#desktop and http://lammps.sandia.gov/bench.html#titan NAMD Full electrostatics with PME and most simulation features 4.0 ns/days F1-ATPase on 1x K20X Released 100M atom capable Multi-GPU, multi-node NAMD 2.9 GPU Perf compared against Multi-core x86 CPU socket. GPU Perf benchmarked on GPU supported features and may be a kernel to kernel perf comparison
New/Additional MD Applications Ramping Application Features Supported GPU Perf Release Status Notes Abalone Simulations (on 1060 GPU) 4-29X (on 1060 GPU) Released, Version 1.8.51 Single GPU Agile Molecule, Inc. Ascalaph Computation of non-valent interactions 4-29X (on 1060 GPU) Released, Version 1.1.4 Single GPU Agile Molecule, Inc. ACEMD Written for use only on GPUs 150 ns/day DHFR on 1x K20 Released Single and multi-GPUs Production bio-molecular dynamics (MD) software specially optimized to run on GPUs Folding@Home Powerful distributed computing molecular dynamics system; implicit solvent and folding Depends upon number of GPUs Released; GPUs and CPUs http://folding.stanford.edu GPUs get 4X the points of CPUs GPUGrid.net High-performance all-atom biomolecular simulations; explicit solvent and binding Depends upon number of GPUs Released; NVIDIA GPUs only http://www.gpugrid.net/ HALMD Simple fluids and binary mixtures (pair potentials, highprecision NVE and NVT, dynamic correlations) Up to 66x on 2090 vs. 1 CPU core Released, Version 0.2.0 Single GPU http://halmd.org/benchmarks.html#supercool ed-binary-mixture-kob-andersen HOOMD-Blue Written for use only on GPUs Kepler 2X faster than Fermi Released, Version 0.11.2 Single and multi-GPU on 1 node http://codeblue.umich.edu/hoomd-blue/ Multi-GPU w/ MPI in March 2013 OpenMM Implicit and explicit solvent, custom forces Implicit: 127-213 ns/day Explicit: 18- 55 ns/day DHFR Released Version 4.1.1 Multi-GPU Library and application for molecular dynamics on high-performance GPU Perf compared against Multi-core x86 CPU socket. GPU Perf benchmarked on GPU supported features and may be a kernel to kernel perf comparison
Page 1 and 2: update Updated: February 4, 2013
Page 3 and 4: New/Additional MD Applications Ramp
Page 5 and 6: Quantum Chemistry Applications Appl
Page 7 and 8: Quantum Chemistry Applications Appl
Page 9: Bioinformatics Applications Applica
Page 14 and 15: Built from Ground Up for GPUs Compu
Page 16 and 17: Nanoseconds / Day Kepler - Our Fast
Page 18 and 19: Speedup Compared to CPU Only K20 Ac
Page 20 and 21: Nanoseconds / Day K10 Strong Scalin
Page 22 and 23: Nanoseconds / Day K10 Extreme Perfo
Page 24 and 25: Replace 8 Nodes with 1 K20 GPU 90.0
Page 26 and 27: Nanoseconds / Day 1 CPU 2 GPUs 2 CP
Page 28 and 29: Recommended GPU Node Configuration
Page 30 and 31: NAMD 2.9
Page 32 and 33: Speedup Compared to CPU Only Accele
Page 34 and 35: Nanoseconds / Day Outstanding Stron
Page 36 and 37: Energy Expended (kJ) K20 - Greener:
Page 38 and 39: Recommended GPU Node Configuration
Page 40 and 41: LAMMPS, Jan. 2013 or later
Page 42 and 43: Speedup Relative to CPU Alone K20X,
Page 44 and 45: Loop Time (seconds) Excellent Stron
Page 46 and 47: Energy Expended (kJ) 140 Faster, Gr
Page 48 and 49: Time (s) Time (s) Time (s) Time (s)
Page 50 and 51: Early Titan XK6/XK7 Benchmarks 18 1
Page 52 and 53: GROMACS 4.6 Final, Pre-Beta and 4.6
Page 54 and 55: Nanoseconds / Day Great Scaling in
Page 56 and 57: Replace 3 Nodes with 2 GPUs 9 8 7 6
Page 58 and 59: The Power of Kepler 140 RNase Solva
Page 60 and 61: K20X, the Fastest Yet Nanoseconds /
Page 62 and 63:
CHARMM Release C37b1
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More Bang for your Buck Scaled Perf
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www.acellera.com 470 ns/day on 1 GP
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Quantum Chemistry Applications Appl
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Quantum Chemistry Applications Appl
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BigDFT
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Performance Relative to CPU Only Ke
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Energy Expended (kJ) Kepler, keepin
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Gaussian Key quantum chemistry code
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GAMESS Partnership Overview Mark Go
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Upcoming GAMESS Q4 2012 Release Mul
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GPAW
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NWChem
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Quantum Espresso/PWscf
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Scaled to CPU Only Extreme Performa
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Elapsed Time (minutes) Replace 72 C
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Power Consumption [kW/h] NVIDIA GPU
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Time (s) QE/PWscf - More Powerful S
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Time (Seconds) TeraChem Supercomput
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Seconds Seconds Kepler’s Even Bet
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FastROCS OpenEye Japan Hideyuki Sat
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Shape Overlays per Second Riding Mo
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Benefits of GPU Accelerated Computi
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Computational Chemistry Benchmarks - Nvidia

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