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
