[gmx-users] Scaling GROMACS

[Mark Abraham]

Hi,

Once you've compiled GROMACS for this machine (will run at least twice as
fast), your setup is likely optimal. The options and what to do with them
are all in the 5.1 gromacs user guide online.

Mark

On Fri, 23 Jun 2017 16:10 Sergio Manzetti <sergio.manzetti at fjordforsk.no>
wrote:

> Hi, I have the following system:
>
> Running on 1 node with total 24 cores, 24 logical cores
> Hardware detected:
> CPU info:
> Vendor: AuthenticAMD
> Brand: AMD Opteron(tm) Processor 6344
> SIMD instructions most likely to fit this hardware: AVX_128_FMA
> SIMD instructions selected at GROMACS compile time: SSE2
>
> Compiled SIMD instructions: SSE2, GROMACS could use AVX_128_FMA on this
> machine, which is better
>
> Reading file topol.tpr, VERSION 5.1.2 (single precision)
> Using 12 MPI threads
> Using 1 OpenMP thread per tMPI thread
>
>
> When running 4 separate jobs, does gcom -1 or other options in mdrun help
> in subdividing the tasks?
>
>
> Sergio
>
> Sergio Manzetti
>
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