[gmx-users] link gromacs i7

XAvier Periole x.periole at rug.nl
Wed Apr 7 10:10:26 CEST 2010

We have been using gromacs-4.0.7 on I7 with up to 8 CPUs. The
scaling is pretty good.
Note that upgrading to openmpi-1.4.1 was necessary to be able
to scale to up to 8 CPUs, if not the jobs where hanging ...
Since you have it already, I do not see where the problem can
come from. Are you sure you are using openmpi-1.4.1?

On Apr 7, 2010, at 12:50 AM, Mark Abraham wrote:

> 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
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