Re: [gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

2012-03-28 Thread Hannes Loeffler
On Wed, 28 Mar 2012 17:31:47 +0200 Albert wrote: > I am using gromacs for membrane simulation (under CHARMM36 FF) which > contains around 80,000 atoms. I've submitted over 200 CPU in the > cluster for such system with 2 fs time step. And what really > astonished is that the efficiency for such

Re: [gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

2012-03-28 Thread Tsjerk Wassenaar
Hi Albert, You are doing neighboursearching every step! So every step all 200 CPUs need to know the how and what of all the other 199. Imagine the communication overhead. Furthermore, you have 400 atoms per CPU (neglecting the PME dedication). That will also make communication a bottle neck. Which

Re: [gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

2012-03-28 Thread Justin A. Lemkul
Albert wrote: Dear: I am using gromacs for membrane simulation (under CHARMM36 FF) which contains around 80,000 atoms. I've submitted over 200 CPU in the cluster for such system with 2 fs time step. And what really astonished is that the efficiency for such simulation is only 3ns/day.

[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

2012-03-28 Thread Albert
Dear: I am using gromacs for membrane simulation (under CHARMM36 FF) which contains around 80,000 atoms. I've submitted over 200 CPU in the cluster for such system with 2 fs time step. And what really astonished is that the efficiency for such simulation is only 3ns/day. I am wondering what