[gmx-users] Help: Gromacs Installation

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 22 10:41:46 CEST 2011

On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:
> Dear all,
> I would like to inform you that I have installed the gromacs4.0.7 
> package on the cluster (nodes of the cluster are 8 core Intel, OS: 
> RHEL4 Scientific Linux) with the following steps:
> yum install fftw3 fftw3-devel
> ./configure --prefix=/localuser/armen/gromacs --enable-mpi
> Also I have downloaded gmxbench-3.0 package and try to run d.villin to 
> test it.
> Unfortunately it wok fine until np is 1,2,3, if I use more than 3 
> procs I receive low CPU balancing and the process in hanging.
> Could you, please, help me to overcome the problem?

Probably you have only four physical cores (hyperthreading is not 
normally useful), or your MPI is configured to use only four cores, or 
these benchmarks are too small to scale usefully.

Choosing to do a new installation of a GROMACS version that is several 
years old is normally less productive than the latest version.


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