Friday Nov 20, 2009

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

Significance of Results

A Sun Blade 6048 chassis with 48 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 32 Sun Blade X6275 server modules was 9.2x faster than the 512 processor configuration of the IBM BlueGene/L.

  • The cluster of 48 Sun Blade X6275 server modules exhibited excellent scalability for NAMD molecular dynamics simulation, up to 37.8x speedup for 48 blades relative to 1 blade.

  • For largest molecule considered, the cluster of 48 Sun Blade X6275 server modules achieved a throughput of 0.028 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. A smaller number implies better performance.

Cluster Name and Interconnect Throughput for 128 Cores
(seconds per step)
Throughput for 256 Cores
(seconds per step)
Throughput for 512 Cores
(seconds per step)
Sun Blade X6275 InfiniBand 0.014 0.0073 0.0048
Cambridge Xeon/3.0 InfiniPath 0.016 0.0088 0.0056
NCSA Xeon/2.33 InfiniBand 0.019 0.010 0.008
AMD Opteron/2.2 InfiniPath 0.025 0.015 0.008
IBM HPCx PWR4/1.7 Federation 0.039 0.021 0.013
SDSC IBM BlueGene/L MPI 0.108 0.061 0.044

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
48 768 0.0277 37.8 79% 0.0075 35.2 73% 0.0039 22.2 46%
36 576 0.0324 32.3 90% 0.0096 27.4 76% 0.0045 19.3 54%
32 512 0.0368 28.4 89% 0.0104 25.3 79% 0.0048 18.1 57%
24 384 0.0481 21.8 91% 0.0136 19.3 80% 0.0066 13.2 55%
16 256 0.0715 14.6 91% 0.0204 12.9 81% 0.0073 11.9 74%
12 192 0.0875 12.0 100% 0.0271 9.7 81% 0.0096 9.1 76%
8 128 0.1292 8.1 101% 0.0337 7.8 98% 0.0139 6.3 79%
4 64 0.2726 3.8 95% 0.0666 4.0 100% 0.0224 3.9 98%
1 16 1.0466 1.0 100% 0.2631 1.0 100% 0.0872 1.0 100%

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

(1) Satellite 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

    48 x Sun Blade X6275, each with
      2 x (2 x 2.93 GHz Intel QC Xeon X5570 (Nehalem) 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
    OpenMPI 1.3.2
    gcc 4.1.2 (1/15/2007), gfortran 4.1.2 (1/15/2007)

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 Satellite 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.

Key Points and Best Practices

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

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 3.33GHz. This feature was was enabled when generating the results reported here.

See Also

Disclosure Statement

NAMD, see http://www.ks.uiuc.edu/Research/namd/performance.html for more information, results as of 11/17/2009.

Tuesday Oct 13, 2009

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.

Tuesday Jun 30, 2009

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.

Tuesday Jun 23, 2009

New CPU2006 Records: 3x better integer throughput, 9x better fp throughput

Significance of Results

A Sun Constellation system, composed of 48 Sun Blade X6440 server modules in a Sun Blade 6048 chassis, running OpenSolaris 2008.11 and using the Sun Studio 12 Update 1 compiler delivered World Record SPEC CPU2006 rate results.

On the SPECint_rate_base2006 benchmark, Sun delivered 4.7 times more performance than the IBM power 595 (5GHz POWER6); this IBM system requires a slightly larger cabinet than the Sun Blade 6048 chassis (details below). 

On the SPECfp_rate_base2006 benchmark Sun delivered 3.9 times more performance than the largest IBM power 595 (5GHz POWER6); this IBM system requires a slightly larger cabinet than the Sun Blade 6048 chassis (details below).

  • The Sun Constellation System equipped with AMD Opteron QC 8384 2.7 GHz processors, running OpenSolaris 2008.11 and using the Sun Studio 12 update 1 compiler, delivered the World Record SPECint_rate_base2006 score of 8840.
  • This SPECint_rate_base2006 score beat the previous record holding score by over three times.
  • The Sun Constellation System equipped with AMD Opteron QC 8384 2.7 GHz processors, running OpenSolaris 2008.11 and using the Sun Studio 12 update 1 compiler, delivered the fastest x86 SPECfp_rate_base2006 score of 6500.
  • This SPECfp_rate_base2006 score beat the previous x86 record holding score by nine times.

Performance Landscape

SPEC CPU2006 Performance Charts - bigger is better, selected results, please see www.spec.org for complete results.

SPECint_rate2006

System Processors Performance Results Notes (1)
Type GHz Chips Cores Peak Base
Sun Blade 6048 Opteron 8384 2.7 192 768
8840 New Record
SGI Altix 4700 Density System Itanium 9150M 1.66 128 256 3354 2893 Previous Best
SGI Altix 4700 Bandwidth System Itanium2 9040 1.6 128 256 2971 2715
Fujitsu/Sun SPARC Enterprise M9000 SPARC64 VII 2.52 64 256 2290 2090
IBM Power 595 POWER6 5.0 32 64 2160 1870 Best POWER6

(1) Results as of 23 June 2009 from www.spec.org.

SPECfp_rate2006

System Processors Performance Results Notes (2)
Type GHz Chips Cores Peak Base
SGI Altix 4700 Density System Itanium 9140M 1.66 512 1024
10580
Sun Blade 6048 Opteron 8384 2.7 192 768
6500 New x86 Record
SGI Altix 4700 Bandwidth System Itanium2 9040 1.6 128 256 3507 3419
IBM Power 595 POWER 6 5.0 64 32 2184 1681 Best POWER6
Fujitsu/Sun SPARC Enterprise M9000 SPARC64 VII 2.52 64 256 2005 1861
SGI Altix 4700 Bandwidth System Itanium 9150M 1.66 128 256 1947 1832
SGI Altix ICE 8200EX Intel X5570 2.93 8 32 742 723

(2) Results as of 23 June 2009 from www.spec.org.

(2) Results as of 23 June 2009 from www.spec.org.

Results and Configuration Summary

Hardware Configuration:
    1 x Sun Blade 6048
      48 x Sun Blade X6440, each with
        4 x 2.7 GHz QC AMD Opteron 8384 processors
        32 GB, (8 x 4GB)

Software Configuration:

    O/S: OpenSolaris 2008.11
    Compiler: Sun Studio 12 Update 1
    Other SW: MicroQuill SmartHeap Library 9.01 x64
    Benchmark: SPEC CPU2006 V1.1

Key Points and Best Practices

The Sun Blade 6048 chassis is able to contain a variety of server modules. In this case, the Sun Blade X6440 was used to provide this capacity solution. This single rack delivered results which have not been seen in this form factor.

To run this many jobs, the benchmark requires a reasonably good file server where the benchmark is run. The Sun Fire X4540 server was used to provide the disk space required being accessed by NFS by the blades.

Sun has shown 4.7x greater SPECint_rate_base2006 and 3.9x greater SPECfp_rate_base2006 in a slightly smaller cabinet. IBM specifications are at: http://www-03.ibm.com/systems/power/hardware/595/specs.html. One frame (slimline doors): 79.3"H x 30.5"W x 58.5"D weight: 3,376 lb. One frame (acoustic doors): 79.3"H x 30.5"W x 71.1"D weight: 3,422 lb. The Sun Blade 6048 specifications are at: http://www.sun.com/servers/blades/6048chassis/specs.xml One Sun Blade 6048: 81.6"H x 23.9"W x 40.3"D weight: 2,300 lb (fully configured). 

Disclosure Statement:

SPEC, SPECint, SPECfp reg tm of Standard Performance Evaluation Corporation. Results from www.spec.org as of 6/22/2009 and this report. Sun Blade 6048 chassis with Sun Blade X6440 server modules (48 nodes with 4 chips, 16 cores, 16 threads each, OpenSolaris 2008.11, Studio 12 update 1) - 8840 SPECint_rate_base2006, 6500 SPECfp_rate_base2006; IBM p595, 1870 SPECint_rate_base2006, 1681 SPECfp_rate_base2006.

See Also

About

BestPerf is the source of Oracle performance expertise. In this blog, Oracle's Strategic Applications Engineering group explores Oracle's performance results and shares best practices learned from working on Enterprise-wide Applications.

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