[gmx-users] link gromacs i7

[Mark Abraham]

On 7/04/2010 5:32 AM, Maurício Menegatti Rigo wrote:
>
> We are using an i7 920 processor to run Gromacs-4.0.7 with
> openmpi-1.4.1. The simulations run well using 4 threads (using "mpirun
> -np 4 mdrun...") but the performance is worse when we use 6 or 8
> threads.

Sure. You have four physical cores. If you're trying to get more across 
a network, unless it is Infiniband you will take a big performance hit. 
Intel's hyperthreading may work (it did 5 years ago on different 
technology), but only if it is turned on, the MPI processes are all on 
the same piece of processor, and you compile with MPI and use mpirun -np 
x for x=1-8.

Even then, 8 virtual cores might over-saturate cache bandwidth, or 
something. You'll need to provide a lot more information for more help 
there.

> Looking for some way to improve our performance we found out
> this forum and then started to try use threads without openmpi. We
> compiled gromacs again and used the command line as described here
> ("mdrun -nt 8..."), but the following error appears:
>
> ------
> Program mdrun, VERSION 4.0.7
> Source code file: mdrun.c, line: 410
>
> Fatal error:
> GROMACS compiled without threads support - can only use one thread
> ------
>
> But in gromacs-4.0.7 threads are not supposed to be ON by default?

No post to this list has implied that threads work, because they will 
not before GROMACS 4.1. The fact that the installation guides on the 
website don't suggest using threads would also have guided you here.

Mark