[gmx-users] short range nonbondeds = 0 in power4
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 18 14:38:14 CEST 2006
Atte Sillanpää wrote:
> On Fri, 15 Sep 2006, Atte Sillanpää wrote:
>>>>>> I've run into a mysterious problem. The versions 3.3. and 3.3.1
>>>>>> and execute, but the short range coulomb and LJ energies come out as
>>>>>> zero when using the mpi-version. Serial code works ok (mpi version
>>>>>> zero if run using just one cpu). No errors, no warnings.
> the problem seems solved. I removed the --enable-threads from the
> gromacs config options and now short range forces come out right.
> Simulations are stable and e.g. water rdfs are identical in power4 and
> amd opteron. It's a little bit nasty that compiler gets through the
> threads flag but then computes garbage.
> It has been said in the mailing list that threads don't work yet, but
> that's hard to find as the solution unless you know to look for it.
> To further check my binary I'd like to do some other tests. I tried
> looking for the benchmarks, but the link doesn't work (search for
> 'bench' at the gromacs site). Are they still available (and do they
> have some verified results to compare to?)
For now you can download them using good old ftp (user anonymous pass
We will fix the website.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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