[gmx-users] Running GROMACS in cluster with SGE

[Mark Abraham]

Hi,

Your should ~always compile GROMACS for the hardware you'll run it on. The
distro versions are necessarily portable, and that means slow. I would also
not start new simulation work using a version of a simulation code that's
six years old, because that also means slow.

One would have to inspect your log files to analyse why your relative
performance was that way, but that effort is wasted compared with
installing newer, hardware-tuned code.

Mark

On Thu, 12 Jan 2017 11:58 Yasser Almeida Hernández <
yasser.almeida.hernandez at chemie.uni-hamburg.de> wrote:

> Hi all,
>
> I am trying to run a simulation on a cluster with SGE queue system with
> this script:
>
> *******
> #!/bin/bash
> #$ -cwd
> #$ -pe parallel 16 #number of cores
> #$ -q main.q  #name of the queue
> #$ -q main.q at xbes23.akbester.zz #one can choose particular node
> #$ -e stderr.log   # redirections for stdout,err
> #$ -o stdout.log
>
> export I_MPI_FABRICS=shm:ofa
>
> mpirun mdrun -v -deffnm sim1
>
> *******
>
> For some reason I get a very poor performance around 0.8 ns/day in a
> node with 16 cores, compared with a workstation with 8 cores, where I
> get 2 ns/day.
>
> I am running GROMACS 4.5.5 installed from the Ubuntu repository in each
> node. Could this be the reason for the poor performance?
> Should I compile GROMACS from source code on the cluster (cluster
> optimized)?
>
> Thanks in advance
>
> Yasser
>
> --
> Yasser Almeida Hernández
> PhD student
> Institute of Biochemistry and Molecular Biology
> Department of Chemistry
> University of Hamburg
> Martin-Luther-King-Platz 6
> 20146 Hamburg
> Germany
> +49 40 42838 2845
> yasser.almeida.hernandez at chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
> --
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