[gmx-users] problem with Threading during run

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 31 02:38:28 CET 2011

On 31/10/2011 12:28 PM, Sanku M 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 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.

These metrics are unreliable unless you have documentation stating what 
800% vs 100% means, and that you have 8 physical cores - virtual cores 
are not useful for GROMACS, because they derive their benefit from 
overlapping downtime on one process (e.g. accessing memory) with compute 
time on another and GROMACS does not have significant downtime.

If you have compiled with threading, then the top of the .log file 
reports how many threads GROMACS has automatically determined to use. 
You should then look at performance of runs over several minutes to 
determine what speed-up is occurring.

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