hi, On Wednesday 13 September 2006 13:10, Milan Melichercik wrote: > Dňa St 13. September 2006 12:42 Qiao Baofu napísal: > > Hi all, > > > > I have a question about parallazing gromacs: I run the same system on a > > cluster of my institute and my local computer, > > Cluster:* *dual processor boards AMD Opteron 270 (Dual-Core), 2.0 > > GHz Local computer: AMD X86-64 Cpu, double precision > > > > 1. The cluster (nodes=3:ppn=4) runs 87950 MD steps for one hour > > 2. The cluster (nodes=5:ppn=4) runs 42749 MD steps for one hour > > 3. The cluster (nodes=11:ppn=4) runs 5962 MD steps for one hour > > 3. My local computer runs 179090 MD steps For 1hour 51 mintues. > > > > It is verry strange that the more cpus I use, the slowest the gromacs > > runs.!!
Try something like multiple of 2 not something like 10 nodes, you need also a fast interconnection like infiniband to reach a good scaling with a higher node number, but always use 2 4 8 cpus/cores. Upcoming release of gromacs will have a better scaling with new algos. You can try the cvs version with seperate pme nodes and domain decomposing. Gromacs 3.3.1 scales well with infiniband up to 32 cores. > > > > Who knows what's wrong with my job? And for paralleled gromacs, how > > many cpus is prefered? > > As far as I know, the problem isn't your job but the interconnet between > nodes, cause MD (and many other paralel computations) are very sensitive to > the interconnect (network) bandwith and even more to the latencies - the > processes need to transfer large amount of data to the other nodes and > till the other nodes don't have them, they cannot compute. The other > problem can be related with the congestion of the network, so the switch > (or generally network) isn't able to transfer so large amount of data and > throw away some of them... > So (in the extreme case of the very slow net) you will have the fastest > system by using only one node (and all of available CPU cores on it). I > can't give you more specific answer cause I don't know your cluster. But > the best result, I think, you can have simply by try the job on 1, 2, 3, > etc. nodes... > > Milan Melichercik > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
