[gmx-developers] Re: gromacs-4.0.4

[David van der Spoel]

Bernhard Bandow wrote:
> Dear Prof. van der Spoel,
> 
> as I have reported some days before we observe a number of tests in
> gromacs-4.0.4 failing. Those of the complex category can all be fixed if
> the hints to change parameters for electrostatics or thermostats.
> Reducing the Compiler optimisation to -O0 does additionally fix problems
> with two of the pbd2gmx tests. For the kernel tests we observe the same
> pattern of failing tests that were also reported elsewhere:
> 
> Testing kernel020 . . . FAILED. Check files in kernel020
> Testing kernel120 . . . FAILED. Check files in kernel120
> Testing kernel121 . . . FAILED. Check files in kernel121
> Testing kernel122 . . . FAILED. Check files in kernel122
> Testing kernel123 . . . FAILED. Check files in kernel123
> Testing kernel124 . . . FAILED. Check files in kernel124
> Testing kernel220 . . . FAILED. Check files in kernel220
> Testing kernel221 . . . FAILED. Check files in kernel221
> Testing kernel222 . . . FAILED. Check files in kernel222
> Testing kernel223 . . . FAILED. Check files in kernel223
> Testing kernel224 . . . FAILED. Check files in kernel224
> Testing kernel320 . . . FAILED. Check files in kernel320
> Testing kernel321 . . . FAILED. Check files in kernel321
> Testing kernel322 . . . FAILED. Check files in kernel322
> Testing kernel323 . . . FAILED. Check files in kernel323
> Testing kernel324 . . . FAILED. Check files in kernel324
> 
> Changing parameters in these cases is not successful. The situation
> remains even if the program is linked against fftw3.1.2 libraries
> instead of the intel mkl.
> As a scientist it think it is very imnportant to have a tool which
> functionality can be tested well in order to obtain results which can be
> trusted. For my own problems this of course also depends on my abilities
> in writing proper input.
> My concern at the HLRN is to provide knowledge for the users of our
> computing center how to install and run the installed software.
> Please tell me if or how I can contribute to a solution e.g. by testing
> or writing to people of the gromacs team without addressing only one person.
> 

The best place is the gmx-developers list. You are also welcome to 
submit a bugzilla.

There were some rumors that the kernels fail in parallel, but not 
sequentially but I haven't tested.


> Best regards
> 
> Bernhard Bandow


-- 
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