Significance of Results

A Sun Blade 6048 chassis with 12 Sun Blade X6275 server modules
ran benchmarks using the NAMD molecular dynamics applications
software.
NAMD is a parallel molecular dynamics code
designed for high-performance simulation of large biomolecular
systems. NAMD is driven by major trends in computing and structural
biology and received a 2002 Gordon Bell Award.

• The cluster of 12 Sun Blade X6275 server modules was 4.7x faster than
  256 processor configuration of the IBM BlueGene/L.
• The cluster of 12 Sun Blade X6275 server modules exhibited excellent
  scalability for NAMD molecular
  dynamics simulation, up to 10.4x speedup for 12 blades relative to 1 blade.
• For largest molecule considered, the cluster of 12 Sun Blade X6275
  server modules achieved a throughput
  of 0.094 seconds per simulation step.

Molecular dynamics simulation is important to biological and materials
science research. Molecular dynamics is used to determine the low energy
conformations or shapes of a molecule. These conformations are presumed to be
the biologically active conformations.

Performance Landscape

The NAMD
Performance Benchmarks web page plots the performance of NAMD when
the ApoA1 benchmark is executed on a variety of clusters. The
performance is expressed in terms of the time in seconds required to
execute one step of the molecular dynamics simulation, multiplied by
the number of "processors" on which NAMD executes in parallel. The
following table compares the performance of the Sun Blade X6275 cluster
to several of the clusters for which performance is reported on the web
page. In this table, the performance is expressed in terms of the time
in seconds required to execute one step of the molecular dynamics
simulation, however, not multiplied by the number of "processors". A smaller number implies better performance.

The following tables report results for NAMD molecular dynamics using a cluster
of Sun Blade X6275 server modules. The performance of the cluster is expressed
in terms of the time in seconds that is required to execute one step of
the molecular dynamics simulation. A smaller number implies better
performance.

spdup - speedup versus 1 blade result
effi’cy - speedup efficiency versus 1 blade result
Ave watts - the estimated average watt consumption during the run

(1) Synthetic Tobacco Mosaic Virus (STMV) molecule, 1,066,628 atoms,
12 Angstrom cutoff, Langevin dynamics, 500 time steps

(2) f1 ATPase molecule, 327,506 atoms,
11 Angstrom cutoff, particle mesh Ewald dynamics, 500 time steps

(3) ApoA1 molecule, 92,224 atoms,
12 Angstrom cutoff, particle mesh Ewald dynamics, 500 time steps

Results and Configuration Summary

Hardware Configuration

• Sun Blade[tm] 6048 Modular System with one shelf configured with
  • 12 x Sun Blade X6275, each 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

Software Configuration

• SUSE Linux Enterprise Server 10 SP2 kernel version 2.6.16.60-0.31_lustre.1.8.0.1-smp
• Scali MPI 5.6.6
• gcc 4.1.2 (1/15/2007), gfortran 4.1.2 (1/15/2007)

Key Points and Best Practices

• Scali MPI scales better and performs better than OpenMPI.

• Models with large numbers of atoms scale better than models with small numbers of atoms.

About the Sun Blade X6275

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 when generating the results reported here.

Benchmark Description

Molecular dynamics simulation is widely used in biological and materials
science research. NAMD
is a public-domain molecular dynamics software application for which a variety
of molecular input directories are available. Three of these directories
define:

• the Synthetic Tobacco Mosaic Virus (STMV) that comprises 1,066,628
  atoms

• the f1 ATPase enzyme that comprises 327,506 atoms
• the ApoA1 enzyme that comprises 92,224 atoms

Each input directory also specifies
the type of molecular dynamics simulation to be performed, for example,
Langevin dynamics with a 12 Angstrom cutoff for 500 time steps, or particle
mesh Ewald dynamics with an 11 Angstrom cutoff for 500 time steps.

See Also

• NAMD - Scalable Molecular Dynamics
• NAMD Performance
  Benchmarks

Disclosure Statement

NAMD, see http://www.ks.uiuc.edu/Research/namd/performance.html for more information, results as of 6/26/2009.

Source/Kaynak : http://blogs.sun.com/BestPerf/entry/sun_blade_6048_and_sun