[gmx-users] Platform-specific differences in grompp's .tpr output

David spoel at xray.bmc.uu.se
Thu Feb 26 22:01:02 CET 2004

On Thu, 2004-02-26 at 20:18, Danny Ngo wrote:
> Hi,
> This concerns the water simulation from the tutorial and GROMACS 3.2 with 
> FFTW 2.1.5.
> I've been running the simulation on three different platforms:
> Red Hat Linux 7.1 on i686 (i686-pc-linux-gnu)
> IRIX64 (mips-sgi-irix6.5)
> OSF1 (alphaev68-dec-osf5.1)
> The issue is that grompp produces a slightly different .tpr file on each 
> of these platforms.  Consequently, the mdrun results (ie. water.trr, 
> water_out.gro) from each .tpr file are also slightly different.  Is this 
> to be expected from varying platforms?
> I ran the same simulation using GROMACS 3.1.4 before, and the odd thing is 
> that grompp produced the same .tpr file on IRIX64 and OSF1 (I compared 
> their md5 sums).  The one produced on Linux was different, however.  Was 
> this just coincidence??
> Any comments/suggestions are appreciated.  Thanks.

this probably has to do with random number generation. If you turn off
velocity generation they should be identical. We've even seen
differences between P4 and P4-Celeron chips.

> Please let me know if you want to see the .tpr files and results.
> Danny
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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