[gmx-users] linux kernel 2.4 vs 2.6

Mark Abraham mark.abraham at anu.edu.au
Sun Jul 16 08:19:36 CEST 2006

> 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)


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