Yes, I should have caught this mail and posted a reply. I have posted a bug fix for this problem previously in the mailing list. See http://www.mail-archive.com/[email protected]/msg04365.html
There is also a guide to fix the problem. For the record I can see that in the newer versions > 3.1, the bugfix is implemented. Kind regards Nick PS. The problem is occuring as you are only allowed 1024 open file. Try ulimit -a and see your max, the easy fix is to increase "open files". However, I would recommend my code fix. 2012/5/7 Herbert Fruchtl <[email protected]> > Thanks. Restarting works, but is annoying. > > To answer my own question (in case somebody runs into the same problem): > > After a few more tests, the error is unrelated to the "Density Matrix > sparsity pattern" message, but turned out to be linked to too many open > files, and is somehow connected to NetCDF. It went away after compiling > without NetCDF. > > For the record: This is Siesta 3.1 on ifort 12.1 and Intel MPI 4.0.3. > > Herbert > > > On 05/05/12 08:26, kuilin lu wrote: > >> Dear Herbert, >> >> Which siesta version did you use in computing? Some versions have >> bugs(feature?) in reinitialize DM, see Docs/CHANGES, you could find >> some hints about this problem. Some version disabled "Extrapolating >> Density Matrix" by default such as siesta-trunk-367 version. >> >> I vaguely remember this problem could be solved just by restart >> computing, surely continuing, not restart from zero. If you still >> meet the problem, maybe you could considering tuning >> DM.AllowExtrapolation option, lower DM.MixingWeight should be more >> stable, but it will (generally) slower the convergence. >> >> This is just my experience, advanced user might have more >> appropriate opinion. >> >> Best Wishes, >> Kuilin >> >> On 5/5/12, Herbert Fruchtl<[email protected]> wrote: >> >>> Folks, >>> >>> I think I encountered this before... If an optimisation or dynamics >>> calculation >>> runs for 500 steps, it often (always?) fails with the following lines: >>> >>> ===================== >>> Folding of H and S is implicitly performed >>> New_DM. Step: 499 >>> Re-using DM from previous geometry... >>> Extrapolating Density Matrix... >>> Density Matrix sparsity pattern changed. >>> rank 24 in job 1 wardlaw63_48676 caused collective abort of all ranks >>> ===================== >>> >>> Is something reset or recalculated in the 500th step that breaks if the >>> geometry >>> has changed? Can I prevent that? >>> >>> Cheers, >>> >>> Herbert >>> -- >>> Herbert Fruchtl >>> Senior Scientific Computing Officer >>> School of Chemistry, School of Mathematics and Statistics >>> University of St Andrews >>> -- >>> The University of St Andrews is a charity registered in Scotland: >>> No SC013532 >>> >>> > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532 >
