[gmx-users] linux kernel 2.4 vs 2.6

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 19 04:24:45 CEST 2006

David L. Bostick wrote:
> Dear all,
> I have done some testing on the two different Xeon clusters.  For clarity


> Clearly machine (2) does not scale at all when using PME. I suspected it
> was due to fftw3, and compiled using intel mkl, but it doesn't appear to behave
> differently. Right now I am at a loss for an explanation, and would
> appreciate some help.

OK, it seems you've got a real problem - you've demonstrated correct 
non-PME parallel scaling behaviour, so the problem seems not to be with 
your command lines, parallel gromacs install, MPI install, MPI config, 
or networking hardware.

>>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)

It's still worth checking the gromacs ./configure output for meaningful 

You could try looking for parallel FFTW benchmarks to see if the problem 
can be isolated there. Perhaps their source distribution includes a test 
suite, or Google might be your friend here.


More information about the gromacs.org_gmx-users mailing list