> lina wrote: > >> On 6/04/2010 5:39 PM, lina wrote: > >>> Hi everyone, > >>> > >>> Here is the result of the mdrun which was performed on 16cpus. I am > not > >>> clear about it, was it due to using MPI reason? or some other > reasons. > >>> > >>> Writing final coordinates. > >>> > >>> Average load imbalance: 1500.0 % > >>> Part of the total run time spent waiting due to load imbalance: > 187.5 % > >>> Steps where the load balancing was limited by -rdd, -rcon and/or > -dds: > >>> X 0 % Y 0 % > >>> > >>> NOTE: 187.5 % performance was lost due to load imbalance > >>> in the domain decomposition. > >> You ran an inefficient but otherwise valid computation. Check out > the > >> manual section on domain decomposition to learn why it was > inefficient, > >> and whether you can do better. > >> > >> Mark > > > > I search the "decomposition" keyword on Gromacs manual, no match > found. > > Are you positive about that? Thanks any way, but can you make it more > > The title of section 3.17 is "Domain Decomposition" and discusses the > algorithm > and mdrun parameters relevant to controlling performance. > > -Justin > > Sorry, the acroread is really not sensitive in searching "domain" or > "decomposition" on version 3.3. I did the same search on version 3.2 and > I found it. I am not so familiar with this manual. Thanks again. > > lina
Since you performance roughly doubles when going from 8 to 16 cores, I think there is no significant load imbalance and there is a bug in the routine that calculates the total load imbalance. In my previous mail I asked which Gromacs version you are using. Could you please tell me this? Berk Hi, it's version 4.0.7. Sorry, mainly I will consider using the latest (better stable) version, so last time I forgot to answer you. I also run it on cluster before, it does not have such problems (by my careless mistakes, I overwrite it when I tried to compare the results from the multicores, and it's days ago and I barely could not remember exactly, I worried I might ignore the problems, so I re-run it again, and the results will wait for a while). Thanks for those suggestions they gave for me to read the manuals. The machine I used is single multicore machine with 64 bits kernel. Thanks and regards, lina
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