[gmx-users] scaling of replica exchange
losasso at sissa.it
Wed Feb 23 08:59:45 CET 2011
Sorry Luca, my mistake in writing. I used actually 2048.
On Wed, 23 Feb 2011, Luca wrote:
> Hi Valeria,
>> Dear all,
>> I am making some tests to start using replica exchange molecular dynamics
>> on my system in water. The setup is ok (i.e. one replica alone runs
>> correctly), but I am not able to parallelize the REMD. Details follow:
>> - the test is on 8 temperatures, so 8 replicas
>> - Gromacs version 4.5.3
>> - One replica alone, in 30 minutes with 256 processors, makes 52500 steps.
>> 8 replicas with 256x8 = 2048 processors, make 300 (!!) steps each = 2400
>> in total (I arrived to these numbers just to see some update of the log
>> file: since I am running on a big cluster, I can not use more than half an
>> hour for tests with less than 512 processors)
>> - I am using mpirun with options -np 256 -s md_.tpr -multi 8 -replex 1000
> I think that with this option you are using 256/8=32 cpu for each replica.
> If you want use 256 for each replica you cna try set up -np option
> equal to 256x8 = 2048.
>> Do you have any idea?
>> Thanks in advance
More information about the gromacs.org_gmx-users