[gmx-users] Different Results with Different Platforms

[Mark Abraham]

Hi,

This sounds totally normal. Individual MD trajectories are only
reproducible if you take great pains to make them so, and that is typically
not a relevant objective (and definitely not implemented for GROMACS on
GPUs). If you're trying to do an ergodic sampling, then that's the thing
you want to reproduce. But if a single trajectory hasn't done such
sampling, wanting to reproduce it doesn't address the real issue that that
trajectory was an observation of low significance. You could e.g. run again
on your old cluster with a different set of initial velocities, and I
expect you will observe divergence. You see to have gotten "lucky" to miss
that on the first time you repeated the work. See also
http://www.gromacs.org/Documentation/Terminology/Reproducibility

Mark

On Tue, Oct 4, 2016 at 2:08 PM Kelechi Okoroafor <kvokoroa at g.syr.edu> wrote:

> Hello, All.
>
> I had previously run the same coarse-grained MD simulations using the
> Martini force field with PME electrostatics on TACC's Stampede GPU cluster
> and my school's CPU cluster and gotten the same results.
>
> I recently built two desktop computers and the results from both my
> computers match each other but are completely different from the results
> from TACC's Stampede and my school's cluster.
>
> I have checked through and I have listed the differences between the
> architecture of the different platforms I have run the simulations on
> below.
>
> Please has anyone else experienced this?
> Does anyone know what may be the issue with my build of Gromacs?
>
> Stampede TACC:
>
>    - Gromacs Version  = 5.0.6
>    - FFT library  = Intel MKL
>    - SIMD instruction set = AVX_256
>    - CPU = Intel(R) Xeon(R) CPU E5-2680 0
>    -
>
>    GPU   = NVIDIA Tesla K20m
>
>    -
>
>    CUDA driver  = 7.0
>
>    -
>
>    CUDA runtime = 7.0
>
>
>
>
> School's CPU Cluster:
>
>    - Gromacs Version  = 5.1.2
>    -  FFT library  = fftw-3.3.4-sse2
>    - SIMD instruction set = SSE4.1
>    - CPU  = Intel(R) Xeon(R) CPU E5-2699 v3
>
>
>
> My Computer 1
>
>    - Gromacs Version = 5.1.2
>    - FFT library  = fftw-3.3.4-sse2-avx
>    - SIMD instruction set = AVX2_256
>    - CPU = Intel(R) Core(TM) i7-6800K
>    - GPU = NVIDIA GeForce GTX 1080
>    - CUDA driver = 8.0
>    - CUDA runtime = 8.0
>
>
> My Computer 2
>
>    - Gromacs Version = 5.1.2
>    - FFT library  = fftw-3.3.4-sse2-avx
>    - SIMD instruction set = AVX2_256
>    - CPU = Intel(R) Core(TM) i5-6600K
>    - GPU = NVIDIA GeForce GTX 1070
>    - CUDA driver = 8.0
>    - CUDA runtime = 8.0
>
>
> Best wishes,
> Kae
> --
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