CP2K Life Sciences, Ab-initio Dynamics - Sun Blade 6048 Chassis with Sun Blade X6275 - Scalability and Throughput with Quad Data Rate InfiniBand

Significance of Results

Clusters of Sun Blade X6275 and X6270 server modules were used to run benchmarks using the CP2K ab-initio dynamics applications software.

  • For the X6270 cluster with Dual Data Rate (DDR) InfiniBand the rate of increase of scalability slows dramatically at 16 nodes, whereas for the X6275 cluster with QDR InfiniBand the scalability continues to 72 nodes.
  • For 64 nodes, the speed of the Sun Blade X6275 cluster with QDR InfiniBand was 2.7X that of a Sun Blade X6270 cluster with DDR InfiniBand.

Ab-initio dynamics simulation is important to materials science research.  Dynamics simulation is used to determine the trajectories of atoms or molecules over time.

Performance Landscape

The CP2K Bulk Water Benchmarks web page plots the performance of CP2K ab-initio dynamics benchmarks that have from 32 to 512 water molecules for a cluster that comprises two 2.66GHz Xeon E5430 quad core CPUs per node and that uses Dual Data Rate InfiniBand.

The following table reports the execution time for the 512 water molecule benchmark when executed on the Sun Blade X6275 cluster having Quad Data Rate InfiniBand and on the Sun Blade X6270 cluster having Dual Data Rate InfiniBand. Each node of either Sun Blade cluster comprises two 2.93GHz Intel Xeon X5570 quad core CPUs. In the following table, the performance is expressed in terms of the "wall clock" time in seconds required to execute ten steps of the ab-initio dynamics simulation for 512 water molecules. A smaller number implies better performance.

Number
of Nodes
X6275 QDR InfiniBand
(seconds for 10 steps)
X6270 DDR InfiniBand
(seconds for 10 steps)
96
1184.36
72 564.16
64 598.41 1591.35
32 706.82 1436.49
24 950.02 1752.20
16 1227.73 2119.50
12 1440.16 1739.26
8 1876.95 2120.73
4 3408.39 3705.44

Results and Configuration Summary

Hardware Configuration:

    Sun Blade[tm] 6048 Modular System with 3 shelves, each shelf with
      12 x Sun Blade X6275, each blade with
        2 x (2 x 2.93 GHz Intel QC Xeon X5570 processors)
        2 x (24 GB memory)
        Hyper-Threading (HT) off, Turbo Mode on
    QDR InfiniBand
    96 x Sun Blade X6270, each blade with
      2 x 2.93 GHz Intel QC Xeon X5570 processors)
      1 x (24 GB memory)
      Hyper-Threading (HT) off, Turbo Mode off
    DDR InfiniBand
Software Configuration:
    SUSE Linux Enterprise Server 10 SP2 kernel version 2.6.16.60-0.31_lustre.1.8.0.1-smp
    OpenMPI 1.3.2
    Sun Studio 12 f90 compiler, ScaLAPACK, BLACS and Performance Libraries
    FFTW (Fastest Fourier Transform in the West) 3.2.1

Benchmark Description

CP2K is a parallel ab-initio dynamics code that is designed to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

Ab-initio dynamics simulation is widely used in materials science research. CP2K is a public-domain ab-initio dynamics software application.

Key Points and Best Practices

  • QDR InfiniBand scales better than DDR InfiniBand.
  • The Intel QC X5570 processors include a turbo boost feature coupled with a speed-step option in the CPU section of the Advanced BIOS settings. Under specific circumstances, this can provide cpu overclocking which increases the processor frequency from 2.93GHz to 3.2GHz. This feature was was enabled for the X6275 and disabled for the X6270 when generating the results reported here.

See Also

Disclosure Statement

CP2K, see http://cp2k.berlios.de/ for more information, results as of 10/13/2009.
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