[gmx-users] Re: GPU version of Gromacs

Hi Grita, Yes it is. You need to re-compile a GPU version of Gromacs from source codes. You also need to use Verlet cutoff-scheme. That is, place a new line like cutoff-scheme = Verlet in your mdp file. Finally, run the GPU version of mdrun, adding a parameter -gpu_id 0if you have

[gmx-users] RE: average pressure of a system

Hi Dallas and Justin, Thanks for the reply. Yes, I did plot pressure changes over time by g_energy and I have been aware of the note at http://www.gromacs.org/Documentation/Terminology/Pressure I am concerned about the average pressure is because our experiment shows that our target

[gmx-users] RE: average pressure of a system

True, but thermostats allow temperatures to oscillate on the order of a few K, and that doesn't happen on the macroscopic level either. Hence the small disconnect between a system that has thousands of atoms and one that has millions or trillions. Pressure fluctuations decrease on the order

[gmx-users] RE: average pressure of a system

Justin Lemkul wrote On 9/11/13 12:12 AM, Dwey Kauffman wrote: True, but thermostats allow temperatures to oscillate on the order of a few K, and that doesn't happen on the macroscopic level either. Hence the small disconnect between a system that has thousands of atoms and one that has

[gmx-users] RE: average pressure of a system

I carried out independent NPT processes with different tau_p values = 1.5, 1.0 and 0.5 ## tau_p 1.5 Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.62859

[gmx-users] Re: Hardware for best gromacs performance?

Hi Timo, Can you provide a benchmark with 1 Xeon E5-2680 with 1 Nvidia k20x GPGPU on the same test of 29420 atoms ? Are these two GPU cards (within the same node) connected by a SLI (Scalable Link Interface) ? Thanks, Dwey -- View this message in context:

[gmx-users] Re: Gromacs-4.6 on two Titans GPUs

Hi Szilard, Thanks for your suggestions. I am indeed aware of this page. In a 8-core AMD with 1GPU, I am very happy about its performance. See below. My intention is to obtain a even better one because we have multiple nodes. ### 8 core AMD with 1 GPU, Force evaluation time GPU/CPU: 4.006

[gmx-users] Re: Hardware for best gromacs performance?

Hi Szilard, Thanks. From Timo's benchmark, 1 node142 ns/day 2 nodes FDR14 218 ns/day 4 nodes FDR14 257 ns/day 8 nodes FDR14 326 ns/day It looks like a infiniband network is required in order to scale up when running a task across nodes. Is it correct ? Dwey -- View

Re: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)

Hi Szilard, Thank you very much for your suggestions. Actually, I was jumping to conclusions too early, as you mentioned AMD cluster, I assumed you must have 12-16-core Opteron CPUs. If you have an 8-core (desktop?) AMD CPU, than you may not need to run more than one rank per GPU. Yes, we do

Re: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)

Hi Mark and Szilard Thanks for your both suggestions. They are very helpful. Neither run had a PP-PME work distribution suitable for the hardware it was running on (and fixing that for each run requires opposite changes). Adding a GPU and hoping to see scaling requires that there be