[gmx-users] mpi performance issues

[istvan at kolossvary.hu]

Hi, 

I see there are a lot of threads on the mailing list on Gromacs mpi scaling. 
I also tried to do this "out of the box" and got similar, horrible scaling 
as others. I read through the archive and got some clues, although it seems 
that scaling is extremely (molecular)system sensitive and I shouldn't expect 
much with PME. However, looking at the 20-50% CPU usage on dual processor 
nodes (3.06 GHz Xeons w/ 100Mbit Ethernet and Redhat 9.0) I was wondering if 
the payload, which is the size of the packets sent between nodes is too 
small. I believe Erik has mentioned this once on the list. Apparently the 
payload size is 1000 bytes (plus 40 bytes TCP/IP overhead) on our system. It 
would be much more efficient having larger payload, say 1400 bytes. My 
question is whether this is something that can be set in Gromacs, or is this 
an OS parameter. In either case, how can I change this? 

Many thanks, 

  Istvan Kolossvary