Sorry Luca, my mistake in writing. I used actually 2048.
Valeria
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.
Luca
Do you have any idea?
Thanks in advance
Valeria
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
