David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 1 21:48:01 CEST 2008
Roland Schulz wrote:
> On Fri, Aug 1, 2008 at 4:47 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> chris.neale at utoronto.ca <mailto:chris.neale at utoronto.ca> wrote:
> Roll back to gcc 3.x.
> There is information available that says something like "don't
> use gcc 4.x, it is broken", but I stand by my previous comments
> that it is unfortunate that it is up to the end user to search
> the gromacs archives to find this out, not withstanding that it
> is a gcc-based problem.
> In my opinion, you're fortunate to have found this out and there
> are probably *lots* of people running gcc 4.x installations of
> gromacs right now.
> We discussed including the test set with the distribution, which
> would simplify the procedure, but decided against it, because the
> distribution would become a lot bigger.
> Maybe we should reconsider this?
> I think we also need some larger tests with few hundred thousands up to
> a few million atoms. Because I had several issues in the last weeks that
> mdrun binaries with different compilers were all working fine with
> smaller systems but gave total different results (became unstable) with
> some compiler (I had problems with: gcc 4.2.0 with barcelona patches,
> pgi, IBM xlc, it worked with gcc 4.2.4 and pathscale). Without common
> tests for these larger systems it is hard to report these problems.
From a software point of view this is just coincidence. Often it turns
out that if you hit such a problem, be it due to the software or due to
the compiler, that you can reduce the size of the still reproduce it.
But more tests and more diverse tests would be good. We don't have any
coarse grained tests, and very few non-water tests. However, you don't
want to run hundreds of tests for each installation, so the problem
Maybe we should endorse a few specific compilers (and versions), and
bail out on others, unless you force configure to use those? In that
case you presumably know what you're doing and can run the test set.
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
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