Hi Mark, Many thanks for your fast response!
What's the network hardware? Can other machine load influence your network performance? The supercomputer system is based on the Cray Gemini interconnect technology. I suppose this is a fast network hardware... Are the systems in the NVT ensemble? Use diff to check the .mdp files differ only how you think they do. The systems are in NPT ensemble. I saw some discussions on the mailing list that NPT ensemble is superior to NVT ensemble for REMD. And the .mdp files differ only in the temperature. What are the values of nstlist and nstcalcenergy? Previously, nstlist=5, nstcalcenergy=1 Thank you for pointing this out. I checked the manual again that this option affects the performance in parallel simulations because calculating energies requires global communication between all processes. So I have set this option to -1 this time. This should be one reason for the low parallel efficiency. And after I changed nstcalcenergy=-1, I found there was a 3% improvement on the efficiency compared with those when nstcalcenergy=1. Take a look at the execution time breakdown at the end of the .log files, and do so for more than one replica. With the current implementation, every simulation has to synchronize and communicate every handful of steps, which means that large scale parallelism won't work efficiently unless you have fast network hardware that is dedicated to your job. This effect shows up in the "Rest" row of the time breakdown. With Infiniband, I'd expect you should only be losing about 10% of the run time total. The 30-fold loss you have upon going from 24->42 replicas keeping 4 CPUs/replica suggests some other contribution, however. I checked the time breakdown in the log files for short REMD simulations. For the REMD simulaiton with 168 cores for 42 replicas, as you see below, the “Rest” makes up as surprisingly high as 96.6% of the time for one of the replicas. This parameter is almost the same level for the other replicas. For the REMD simulation with 96 cores for 24 replicas, the “Rest” takes up about 24%. I was also aware of your post: http://www.mail-archive.com/gmx-users@gromacs.org/msg37507.html As you suggested such big loss should be ascribed to other factors. Do you think it is the network hardware to blame or there are other reasons please? Any suggestion would be greatly appreciated Computing: Nodes Number G-Cycles Seconds % ----------------------------------------------------------------------- Domain decomp. 4 442 2.604 1.2 0.0 DD comm. load 4 6 0.001 0.0 0.0 Comm. coord. 4 2201 1.145 0.5 0.0 Neighbor search 4 442 14.964 7.1 0.2 Force 4 2201 175.303 83.5 2.0 Wait + Comm. F 4 2201 1.245 0.6 0.0 PME mesh 4 2201 30.314 14.4 0.3 Write traj. 4 11 17.346 8.3 0.2 Update 4 2201 2.004 1.0 0.0 Constraints 4 2201 26.593 12.7 0.3 Comm. energies 4 442 28.722 13.7 0.3 Rest 4 8426.029 4012.4 96.6 ----------------------------------------------------------------------- Total 4 8726.270 4155.4 100.0 Qiong On 7/02/2011 9:52 PM, Qiong Zhang wrote: Dear all gmx-users, I have recently been testing the REMD simulations. I was running simulations on a supercomputer system based on the AMD Opteron 12-core (2.1 GHz) processors. The Gromacs 4.5.3 version was used. I have a system of 5172 atoms, of which 138 atoms belong to solute and the other are water molecules. An exponential distribution of temperatures was generated ranging from 276 to 515 K in total of 42 replicas or from 298 to 420 K in total of 24 replicas, ensuring that the exchange ratio between all adjacent replicas is about 0.25. The replica exchange was carried out every 0.5ps. The integrate step size was 2fs. For the above system, when REMD is simulated over 24 replicas, the simulation speed is reasonably fast. However, when REMD is simulated over 42 replicas, the simulation speed is awfully slow.Please see the following table for the speed. ---------------------------------------------------------------------------- Replica number CPU number speed 24 96 58015steps/15minutes 42 42 865steps/15minutes 42 84 1175steps/15minutes 42 168 1875steps/15minutes 42 336 2855steps/15minutes The command line for the mdrun is: aprun -n (CPU number here) mdrun_d -s md.tpr -multi (replica number here) -replex 250 My questions are : 1) why the REMD for the 42 replicas is so slow for the same system? 2) On what aspects can I improve the operating efficiency please? What's the network hardware? Can other machine load influence your network performance? Are the systems in the NVT ensemble? Use diff to check the .mdp files differ only how you think they do. What are the values of nstlist and nstcalcenergy? Take a look at the execution time breakdown at the end of the .log files, and do so for more than one replica. With the current implementation, every simulation has to synchronize and communicate every handful of steps, which means that large scale parallelism won't work efficiently unless you have fast network hardware that is dedicated to your job. This effect shows up in the "Rest" row of the time breakdown. With Infiniband, I'd expect you should only be losing about 10% of the run time total. The 30-fold loss you have upon going from 24->42 replicas keeping 4 CPUs/replica suggests some other contribution, however. Mark
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