[gmx-developers] GROMACS 4.0.1 still broken on Bluegene

David van der Spoel spoel at xray.bmc.uu.se
Sun Nov 9 19:41:14 CET 2008

Axel Kohlmeyer wrote:
> On Sun, 9 Nov 2008, Erik Lindahl wrote:
> hi,
> just a generic comment about the XLF and GCC-4.x compilers.
> i haven't compiled gmx recently, so i don't know whether
> this applies or not, but a _lot_ of MD and related codes seem 
> to get miscompiled these days by both compiler families, due to 
> in complete conformance to ANSI-C aliasing issues.
> i saw these popping up in the weirdest places recently while
> compiling a lot of software on a new RHEL 5.1(plus patches)
> machine. so for general distribution it may be worth considering
> adding -fno-strict-aliasing to CFLAGS for safety. for XLF there
> is a similar flag (-qansi=none?). for the codes that i was testing
> this made all the difference, particularly when using lookup
> tables etc. ;)
I just followed your advice and neither on my Mac nor on a Centos Linux 
5.0 box did I get any warnings. Doubtlessly compilers are getting 
better, but they have come from a very low starting quality. We 
regularly check compilation in this manner, usually without finding 
anything beyond the obvious. A new development is that the GNU C library 
has become more picky with memory management. Due to this some problems 
in very old code have surfaced (although the code was correct according 
to the book...). We try to follow the developments, and are grateful for 
tips like this.

David van der Spoel, Ph.D., Professor of Biology
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

More information about the gromacs.org_gmx-developers mailing list