Benchmarks

Machine Specs

CPU = Dual x Quad Core Intel E5462 2.80 GHz
MPICH2.0 - 1.07
MKL 10.1.1.019
Ifort 10.1.018

GPU = Tesla C1060 /Tesla C2050 / GTX295
gfortran 4.1.2
nvcc v3.0
NVIDIA Driver Linux 64-195.36.20

Code Base = AMBER 11 Release

Precision Model = SPDP (GPU), Double Precision (CPU)

Benchmarks run with ECC turned OFF on C2050 card. If you see approximately 10% less performance than the numbers here then run the following (for each GPU) as root:

nvidia-smi -g 0 --ecc-config=0    (repeat with -g x for each GPU ID)

List of Benchmarks

Implicit Solvent (GB)

1. TRPCage = 304 atoms
2. Myoglobin = 2,492 atoms
3. Nucleosome = 25,095 atoms

Explicit Solvent (PME)

1. DHFR NVE = 23,558 atoms
2. DHFR NPT = 23,558 atoms
3. FactorIX NVE = 90,906 atoms
4. Cellulose NVE = 408,609 atoms

You can download a tar file containing the input files for all these benchmarks here (62.3 MB).

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Implicit Solvent GB Benchmarks

 

3) Nucleosome = 25095 atoms &cntrl   imin=0,irest=1,ntx=5,   nstlim=1000,dt=0.002,ntb=0,   ntf=2,ntc=2,tol=0.000001,   ntpr=100, ntwx=100, ntwr=50000,   cut=9999.0, rgbmax=15.0,   igb=1,ntt=0,nscm=0, /

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Explicit Solvent PME Benchmarks

 

2) DHFR NPT = 23,558 atoms Typical Production MD NPT &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=2, ntp=1, taup=10.0, ioutfm=1, /

 

3) FactorIX NVE = 90,906 atoms Typical Production MD NVE with GOOD energy conservation. &cntrl ntx=5, irest=1, ntc=2, ntf=2, tol=0.000001, nstlim=10000, ntpr=1000, ntwx=1000, ntwr=10000, dt=0.002, cut=8., ntt=0, ntb=1, ntp=0, ioutfm=1, / &ewald dsum_tol=0.000001,nfft1=128,nfft2=64,nfft3=64, /

 

4) Cellulose NVE = 408,609 atoms Typical Production MD NVE with GOOD energy conservation. &cntrl ntx=5, irest=1, ntc=2, ntf=2, tol=0.000001, nstlim=10000, ntpr=1000, ntwx=1000, ntwr=10000, dt=0.002, cut=8., ntt=0, ntb=1, ntp=0, ioutfm=1, / &ewald dsum_tol=0.000001, nfft1=256,nfft2=128,nfft3=128, /

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