MOLECULAR DYNAMICS,

NUMERICAL ANALYTICS,

PHYSICS,

WEATHER AND CLIMATE FORECASTING AND MORE

SkyScale’s high performance computing appliances can add tremendous compute power  for many research applications providing up to 16 Tesla P100GPU engines per platform for the World’s Fastest Cloud compute capability.

Molecular Dynamics (MD) is a field of research in which a computer simulates the physical movements of atoms and molecules. Molecular Dynamics relies heavily on computational power. The details of the simulation have to be chosen carefully so that the calculation can finish within a reasonable time period while still producing useful results. In order for the conclusions to be statistically valid, the simulated time span should match the kinetics of the natural process. For example, you can’t draw conclusions about how humans walk by looking at only one step. For many applications of Molecular Dynamics, several CPU-days or even CPU-years are needed to process the

simulations. Programs that run algorithms in a parallel manner allow the computations to be distributed among CPUs, allowing for more complicated, time consuming simulations.

However, a system with multiple CPUs running parallel algorithms is not the most powerful way to compute molecular dynamics simulations. GPUs are much faster at processing parallel tasks and thus would be a better option for a molecular dynamics system. SkyScale GPU platforms accommodate up to 16 high end P100 GPUs. With this much compute power, simulations can be much longer without taking unreasonable amounts of time; in fact, this much power might allow for simulations that previously would not have been possible.

Here are some molecular dynamics applications that can be sped up by using GPUs:

  • ACEMD

  • AMBER

  • CHARMM

  • DESMOND

  • DL-POLY

  • Folding@Home

  • GPUGrid.net

  • GROMACS

  • HOOMD-Blue

  • LAMMPS

  • NAMD

  • OpenMM

AMBER-

KEY FEATURES OF THE TESLA P100 FOR MOLECULAR DYNAMICS

  • Servers with P100 replace up to 40 CPU servers for applications such as HOOMD-Blue, LAMMPS, AMBER, GROMACS, and NAMD

  • 100% of the top MD applications are GPU-accelerated

  • Key math libraries like FFT and BLAS

  • Up to 11 TFLOPS per second of single precision performance per GPU

  • Up to 732 GB per second of memory bandwidth per GPU

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1LAMMPS

Numerical Analysis

Numerical analysis is the study of algorithms that use numerical approximation for the problems of mathematical analysis. Exact answers are often impossible to find in math; thus, numerical analysis does not pursue exact answers. Rather, numerical analysis seeks approximate answers that do not cause too many errors. Numerical analysis applies to many different fields including engineering and the physical sciences, such as astronomy, medicine and biology. More recently, it has also applied to life sciences and even the arts. Before computers, numerical analysis was done by hand; now, computers are used to calculate instead. There are many widely used numerical computing applications such as MATLAB, ArrayFire, Mathematica Wolfram, and NMath Premium that can benefit from the additional compute power GPUs can provide. The more GPUs used, the faster the algorithms in numerical analysis can be computed.

Weather and Climate Forecasting

Weather and climate forecasting can be used to create short term weather forecasts, or long-term climate forecasts. This has been helpful for interpreting and predicting climate change. In regional models, improvement has been made when tracking tropical cyclones and predicting air quality. All weather and climate forecasting models are made up of huge amounts of data. Computing the vast amount of data and executing the intricate calculations required for modern weather and climate forecasting necessitates the use of some of the most powerful supercomputers in the world.

Here are some climate applications that can be sped up by using GPUs:

  • ASUCA

  • CAM – SE

  • COSMO

  • GEOS-5

  • HOMME

  • NEMO

  • NIM

  • WRF

From fusion energy to high energy particles, physics simulations span a wide range of applications in the HPC data center. Many of the top physics applications are GPU-accelerated, enabling insights previously not possible.

1QUADA

KEY FEATURES OF THE TESLA P100 FOR PHYSICS

  • Servers with P100 replace up to 50 CPU servers for applications such as GTC-P, QUDA, MILC and Chroma

  • Most of the top physics applications are GPU-accelerated

  • Up to 5.3 TFLOPS of double precision floating point performance

  • Up to 16 GB of memory capacity with up to 732 GB/s memory bandwidth

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Only lease what you need when you need it. Save the capital investment and don’t worry about having idle time when you are between projects.  Save the cost of maintaining and staffing your own data center.

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With exclusive access to as many as 16 NVIDIA P100s in a single node you are running your applications on the world’s absolute highest performing multi-GPU platform in the world. Couple that with state-of-the-art high speed low latency NVMe storage and your project time just got a lot shorter.