[gmx-users] cluster types supported

Erik Lindahl lindahl at stanford.edu
Mon Aug 18 10:09:00 CEST 2003

Hi Mike,

Single-cpu Gromacs runs work great on any system. As for openmosix, 
there is nothing we can do to support it - it is they who don't support 
MPI :-)

However, since parallel molecular dynamics involve a lot of 
communication and is quite sensitive to load balancing you would get 
really bad performance on an openmosix-style cluster. OpenMosix relies 
on moving processes around, and that would be very bad idea when we 
need to communicate with the other processors 10-100 times per second - 
you would always have one CPU falling behind, and then everybody else 
has to wait for that one. In theory I guess it would work well on an 
unloaded cluster (less than one job per cpu), but last time I checked 
mosix didn't support sockets (used for MPI communication).

Big shared memory machines are great with MPI, but quite costly, so 
most people use linux clusters (with or without fast myrinet or scali 



On Sunday, August 17, 2003, at 10:22 PM, Mike Grommet wrote:

> I have learned from this group that Gromacs cannot utilize an openmosix
> cluster...
> Can gromacs utilize an openssi cluster, a single system image cluster?
> This seems like it might be a FAQ but I had no luck finding 
> information on
> the site, or in the mailing list...
> Thanks for your help...
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