Sun Blade 6048 and Sun Blade X6275 NAMD Molecular Dynamics Benchmark beats IBM BlueGene/L

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 was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. 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 6.2x 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 NAMD version 2.6 when executed on the Sun Blade X6275 cluster to the performance of NAMD as reported for several of the clusters 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.
Cluster Name and Interconnect Throughput for 128 Cores
(seconds per step)
Throughput for 192 Cores
(seconds per step)
Throughput for 256 Cores
(seconds per step)
Sun Blade X6275 InfiniBand 0.013 0.010
Cambridge Xeon/3.0 InfiniPath 0.016
0.0088
NCSA Xeon/2.33 InfiniBand 0.019
0.010
AMD Opteron/2.2 InfiniPath 0.025
0.015
IBM HPCx PWR4/1.7 Federation 0.039
0.021
SDSC IBM BlueGene/L MPI 0.108
0.062

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.

Blades Cores STMV molecule (1) f1 ATPase molecule (2) ApoA1 molecule (3)
Thruput
(secs/ step)
spdup effi'cy Thruput
(secs/ step)
spdup effi'cy Thruput
(secs/ step)
spdup effi'cy
12 192 0.0941 10.6 88% 0.0270 9.1 76% 0.0102 8.1 68%
8 128 0.1322 7.5 94% 0.0317 7.7 97% 0.0131 6.3 79%
4 64 0.2656 3.7 94% 0.0610 4.0 101% 0.0204 4.1 102%
1 16 0.9952 1.0 100% 0.2454 1.0 100% 0.0829 1.0 100%

spdup - speedup versus 1 blade result
effi'cy - speedup efficiency versus 1 blade result

(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

  • 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

Disclosure Statement

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

Admittedly, 12 blades in one shelf means 192 cores, but still, why stop at 192 cores and not 256 to cover the rest of the competitive configurations? Or 512 for that matter, which appears to be where the chart on the referenced NAMD page stops. Seems like a missed opportunity.

Also, there is a definition of "Ave watts" as "the estimated average watt consumption during the run" to go along with spdup and effi'cy, but the table with which it is associated does not seem to be displaying any watts.

Posted by rick jones on June 30, 2009 at 02:24 PM PDT #

Rick, this is a great result on 192 cores. Speaking of "missed opportunity", where are IBM Power6 or HP or Dell results?

Posted by Russell Brown on July 01, 2009 at 04:42 AM PDT #

I didn't mean to imply anything one way or the other about the greatness of the 192 core result, it just looked, well, odd - full overlap with the listed competitive results at 128 cores, then a 192 cores with just the Sun result, and then everyone else with a 256 core result but no Sun 256 core result. Following the provided link to the NAMD pages showed that all but one seemed to take their results out to 512 cores, so it looked a bit strange is all.

As for the present whereabouts of IBM Power6 or HP or Dell results, I've no clue. Most if not all of the non-Sun results in that NAMD site graph certainly look very old although it is difficult to tell since there are no explicit dates given that I could find. I don't know if that simply means people aren't sending results to the NAMD folks or if it means the benchmark was in stasis until this result or what.

Posted by rick jones on July 01, 2009 at 11:52 AM PDT #

Question.
Are your posted results obtained with Namd 2.6 or with the recently released (March) Namd 2.7b1?
Thanks,
Roberto

Posted by Roberto Gomperts on July 09, 2009 at 02:39 AM PDT #

Roberto, this result was obtained using NAMD version 2.6.

Posted by Russ Brown on July 09, 2009 at 03:49 AM PDT #

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