[gmx-users] .log file documentaion

[David]

On Fri, 2005-06-10 at 14:49 -0500, Nathan Moore wrote:
> I'd like to understand the output of the mdrun_d .log file more fully.  Is
> full description of the output (when running mdrun w/ -v) available
> online?  I can't seem to find discussion of this file in the paper manual.
> 
> Specifically, in an 8 processor parallel job (working on benchmark dpcc,
> 121856 atoms), does the following matrix provide a summary of the division
> of labor (I note that 8*15232=121856)?
> 
> Nodeid   index  homenr  cgload  workload
>      0       0   15232    7552      7552
>      1   15232   15232   15104     15104
>      2   30464   15232   22656     22656
>      3   45696   15232   30208     30208
>      4   60928   15232   37760     37760
>      5   76160   15232   45312     45312
>      6   91392   15232   52864     52864
>      7  106624   15232   60416     60416
> 
> I'm guessing that the 3rd column (homenr) specifies the number of atoms
> initially assigned to each processor - is that correct?  A reference
> giving general summary of the .log output would be wonderful.
Your guess is correct. Don't expect any documentation for this stuff. If
something we could add some output in specific places (read: extremely
obscure output). But since you geussed what it means, it doesn't seem to
be a big problem...

If you put this system on 512 nodes you will have an integer number
(238) atoms per processor! Have you tried scaling the dppc benchmark?
> 
> regards,
> 
> Nathan Moore
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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