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 ms/2.578 ms = 1.554 For optimal performance this ratio should be close to 1! NOTE: The GPU has >20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. Core t (s) Wall t (s) (%) Time: 216205.510 27036.812 799.7 7h30:36 (ns/day) (hour/ns) Performance: 31.956 0.751 ### 8 core AMD with 2 GPUs Core t (s) Wall t (s) (%) Time: 178961.450 22398.880 799.0 6h13:18 (ns/day) (hour/ns) Performance: 38.573 0.622 Finished mdrun on node 0 Sat Jul 13 09:24:39 2013 >However, in your case I suspect that the >bottleneck is multi-threaded scaling on the AMD CPUs and you should >probably decrease the number of threads per MPI rank and share GPUs >between 2-4 ranks. OK but can you give a example of mdrun command ? given a 8 core AMD with 2 GPUs. I will try to run it again. >Regarding scaling across nodes, you can't expect much from gigabit >ethernet - especially not from the cheaper cards/switches, in my >experience even reaction field runs don't scale across nodes with 10G >ethernet if you have more than 4-6 ranks per node trying to >communicate (let alone with PME). However, on infiniband clusters we >have seen scaling to 100 atoms/core (at peak). >From your comments, it sounds like a cluster of AMD cpus is difficult to scale across nodes in our current setup. Let's assume we install Infiniband (20 or 40GB/s) in the same system of 16 nodes of 8 core AMD with 1 GPU only. Considering the same AMD system, what is a good way to obtain better performance when we run a task across nodes ? in other words, what dose mudrun_mpi look like ? Thanks, Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-6-on-two-Titans-GPUs-tp5012186p5012279.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists