[gmx-users] linux kernel 2.4 vs 2.6

[David L. Bostick]

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?

Thanks,
David