[gmx-developers] Hands-on Tutorial - Brazil - 04/11 - For David

Erik Marklund erikm at xray.bmc.uu.se
Sun Nov 9 13:17:51 CET 2008

David van der Spoel skrev:
> Elton Carvalho wrote:
>> Hey there!
>> David, what's the probability that gcc4.1 causes Gromacs (or some
>> analysis tools) do 2+2=5 or something like that?
>> Would this be the reason for the non-reproduction of the results at
>> the tutorial sessions in São Carlos earlier this week, since those
>> machines had gcc4.1 running?
> Good point. I will try it on other machines first, but usually gcc 4 
> causes SEGVs. If it is broken on other machines as well we have a 
> problem, but probably localized in g_hbond.

Intresting. There WAS a memory issue in g_hbond that involved writing 
out of array bounds that cause SEGVs and outright erroneous results. The 
fix did go into the development branch before the release of 4.0 and 
also into the 3.3-patches as far as I know. Which version generated 
irreproducible results at the tutorial?

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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