[gmx-users] problem with Threading during run

lina lina.lastname at gmail.com
Mon Oct 31 05:36:31 CET 2011

On Mon, Oct 31, 2011 at 9:28 AM, Sanku M <msanku65 at yahoo.com> wrote:
> Hi,
>  I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to
> make use of threading introduced in gromacs 4.5.x series, it does not work.
>  After issuing command like mdrun -v -s , I expected that for my 8-core
> processor which is not running any other jobs, the threading will show one
> job with 800 % cpu usage. But, it is showing 100 % cpu usage hence using
> only 1 of the 8 processors. I was wondering whether there is any command

mdrun -t number_of_processors

> line I need to use to ensure the gromacs understands that there is 8
> processors in a core and force make full use of the entire machine.
> I have tried the same thing in another different cluster where I found that
> threading works with showing 800 % cpu usage . But, for this cluster , the
> threading does not work.
and make sure during your compile process, enable --threads

> Any help will be appreciated.
> Sanku
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