Running AmberTools 1.4 and Amber 11 on Microsoft Windows

| General remarks | Installation on Windows using Cygwin |
| Installation of the native Windows version of PMEMD |
| PMEMD benchmarks | Return to Main Amber Page |

Benchmark plot provided by Microsoft Benchmark Labs.

PMEMD Benchmarks

The performance of the native Windows executable of PMEMD has been tested on the Windows HPC benchmarking cluster Rhiannon located at the Microsoft Enterprise Engineering Center. All benchmarks have been performed by Thorsten Wölfle, Andreas W. Götz and Ross C. Walker (WMD lab, SDSC). Machine Specs (Rhiannon) 64 IBM iDataPlex DX360 M2 compute nodes Intel Nehalem Xeon 5500 series (total 512 cores) 24GB DDR3 RAM per node Six 36-port QDR InfiniBand switches, 72 QDR InfiniBand Adapters Copper and optical cables for a fully connected non-blocking QDR IB fabric Windows HPC Server 2008 V2 SP1 IBndprov.dll Version 2.0.5.0 MSMPI.dll Version 2.1.1731.0 AMBER 11 PMEMD compiled with Intel Cluster Toolkit 3.2 List of benchmarks You can download the Amber11 Benchmark Suite used in this work here. This suite covers the range of sizes and parameters used in common, explicit-solvent MD simulations with PMEMD. Results for three benchmarks are reported below. 1) JAC NVT = 23,558 atoms 2) Factor IX NVT = 90,906 atoms 3) Cellulose NVT = 408,609 atoms You can download a Python script which can be used as a template to run the test suite on a Microsoft HPC cluster. Download it from here, copy it to the Amber11 Benchmark Suite directory and edit it as appropriate. Use this as follows: `CYGWIN> cp test_pmemd_win.py Amber11_Benchmark_Suite/PME CYGWIN> cd Amber11_Benchmark_Suite/PME CYGWIN> python test_pmemd_win.py` This will generate batch scripts for the submission of the benchmarks on up to 32 nodes using 8 cores per node and up to 64 nodes using 4 cores per node. Submit the jobs by executing the batch script now: `DOS> cd Amber11_Benchmark_Suite DOS> start.bat` ^
1) JAC (Joint Amber CHARMM) production benchmark for dihydrofolate reductase (DHFR), NVT This benchmark consists of 23,558 atoms including water. It has been updated from the original JAC benchmark to include more realistic simulation parameters that reflect production use. &cntrl ntx=5, irest=1, ntc=2, ntf=2, nstlim=10000, ntpr=1000, ntwx=1000, ntwr=10000, dt=0.002, cut=8., ntt=1, tautp=10.0, temp0=300.0, ntb=1, ntp=0, ioutfm=0, /

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2) Factor IX, NVT This benchmark simulates the blood coagulation factor IX. It consists of 90,906 atoms including water. &cntrl ntx=5, irest=1, ntc=2, ntf=2, nstlim=10000, ntpr=1000, ntwx=1000, ntwr=10000, dt=0.002, cut=8., ntt=1, tautp=10.0, temp0=300.0, ntb=1, ntp=0, ioutfm=0, /

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3) Cellulose, NVT This benchmark simulates a cellulose fiber. It consists of 408,609 atoms including water. &cntrl ntx=5, irest=1, ntc=2, ntf=2, nstlim=10000, ntpr=1000, ntwx=1000, ntwr=10000, dt=0.002, cut=8., ntt=1, tautp=10.0, temp0=300.0, ntb=1, ntp=0, ioutfm=0, /

last modification: 2010/06/01	^