[gmx-users] GNU compilers

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 30 20:23:30 CET 2007

giordano mancini wrote:
> Greetings to all,
> I have just downloaded gromacs-3.3.2 and read the notice on the website 
> regarding the 4.1.x series of GNU compilers. Since I'm running Linux 
> (Slackware 12) on my pentium IV and the default compile is gcc-4.1.2 I
> previously installed gcc-3.4.6 and compiled first fftw-3.1.2 and second 
> gromacs-3.3.2 with it. The I've run the tests in gmxtest-3.3.2.tgz with 
> command
> $> ./gmxtest.pl all
> obtaining the following failures:
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in acetonitrilRF
> FAILED. Check files in dec+water
> 2 out of 14 complex tests FAILED
probably harmless, see wiki.

> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
> Finally to test more things I have also performed the simulation of the 
> gromacs tutorial by John Kerrigan about the spider toxin peptide and all 
> seems ok at a first look.
> Since fftw compiled with gcc4 were already on my pc I've tried (just for 
> a test) also with it and the results of the test suite were exactly the 
> same. Also the run with the spider toxin seems k although I must still 
> check out differences.
> Meanwhile I have searched the mailing list but I was not able to 
> understand wath is wrongwtih gcc4.
> Can you help me (repetita iuvant...)

There are some instances where correct code gives wrong results 
(predominantly in analysis tools). Some of these issues have been wored 
around. This is necertheless troublesome because it is difficult to know 
when to trust the compiler and when not.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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