> > Dear all, > > I have 2 Intel Xeon clusters: > > (1) CPU is 2.8 Ghz with linux kernel 2.4.21 (gcc version 3.2.3) > (2) CPU is 2.4 Ghz with linux kernel 2.6.13 (gcc version 4.0.2) > > I run a ~50000 atom system for 500 ps with PME on 8 processors > (LAM-MPI) with either machine. With machine (1) the job completes in > 12h44:48. On the other hand, for machine (2) the job does not complete > within 24 hours. > > I am accustomed to such jobs completing in the time demonstrated by > machine > (1) with the older kernel. > > Apparently the only major difference is the kernel. Has anyone else > experienced anything like this? Is it possible that fftw works > differently > under these two systems? Would it be worth it to try intel based ffts?
How about comparing runs that don't use PME, and thus don't use fftw? I can't really see the kernel version having any impact... you could compare the output from ./configure to see if anything else significant is different. The most likely problem is not using the same number of processors, but you say you've done that! :-) You could also check whether there is a horrible MPI latency problem with machine (2) Mark _______________________________________________ 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
