Re: [gmx-users] Scaling/performance on Gromacs 4

Apologies for reviving such an old thread. For clarifications, interlagos and bulldozer both have a modular architecture, as mentioned earlier. Each bulldozer module has 2 integer cores and one floating point unit shared between the two cores. So, although you have 64 cores (counting integer

Re: [gmx-users] Scaling/performance on Gromacs 4

Hi Sara, The bad performance you are seeing is most probably caused by the combination of the new AMD Interlagos CPUs, compiler, operating system and it is very likely the the old Gromacs version also contributes. In practice these new CPUs don't perform as well as expected, but that is partly

[gmx-users] Scaling/performance on Gromacs 4

Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD steps: 1500 Electrostatics treatment: PME Gromacs version:

Re: [gmx-users] Scaling/performance on Gromacs 4

Hi Sara, my guess is that 1500 steps are not at all sufficient for a benchmark on 64 cores. The dynamic load balancing will need more time to adapt the domain sizes for optimal balance. It is also important that you reset the timers when the load is balanced (to get clean performance numbers);

Re: [gmx-users] Scaling/performance on Gromacs 4

is to switch to gromacs 4.5 and run using thread-level parallelisation, bypassing MPI entirely. From: Sara Campos srrcam...@gmail.com To: gmx-users@gromacs.org Sent: Monday, 20 February 2012, 17:12 Subject: [gmx-users] Scaling/performance on Gromacs 4 Dear

Re: [gmx-users] Scaling/performance on Gromacs 4

, 17:12 *Subject:* [gmx-users] Scaling/performance on Gromacs 4 Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD