Re: [gmx-users] why it is so slow in Blue gene?

On Tue, 24 Apr 2012 15:42:15 +0200 Albert wrote: > hello: > >I am running a 60,000 atom system with 128 core in a blue gene > cluster. and it is only 1ns/day here is the script I used for You don't give any information what exact system that is (L/P/Q?), if you run single or double pr

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

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] Announcement: Large biomolecule benchmark report

be because, to be honest, I have no overview what has been done in this area (besides the few benchmarks studies I have cited). Thanks again, Hannes. On Thu, 15 Mar 2012 22:02:21 +0100 David van der Spoel wrote: > On 2012-03-15 14:37, Hannes Loeffler wrote: > > Dear all, > > &g

[gmx-users] Announcement: Large biomolecule benchmark report

are open to any questions or comments related to our reports. Kind regards, Hannes Loeffler STFC Daresbury -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] crash with LINCS WARNING

On Mon, 2008-04-14 at 19:22 -0400, LeeHwan-kyu wrote: > Dear GMX-uers, > > I'm simulating alpha-hemolysin channel in DMPC bilayer and water > (using MARTINI protein FF), and my system keeps crashing with error > below (even with very low timestep). I suspect your problem is the MARTINI protein fo

Re: [gmx-users] Blue Gene/P

Ok, here just a few numbers. System: 52.000 atoms, coarse-grained, 500.000 steps BlueGene/P: 16(procs) x 4(threads) = 64 tasks (or whatever they are called) 8x4 7.25 h 16x4 11h 32x4 > 12 h (queue only allows <= 12 h) BlueGene/L: 16x2 10 h 64x2 > 12 h Note: the procs x thr