Dear Nick, I compiled siesta-4.1-b4 with -O1 and used unbuffer as recommended.
It is running with 7 processor since yesterday (almost 24h now) but I can not see any information in the output file (I imaging that the file will be updated at the end). Hopping everything goes well. []'s, Camps On Tue, Apr 16, 2019 at 5:01 PM Nick Papior <[email protected]> wrote: > Could you: > > 0) Send the FORCE_STRESS file? > 1) Use siesta-4.1 b4 (you are using b3) > 2) Add MinSCFIterations 3 to the options > 3) I would probably try and relax the system a bit first in a > non-polarized calculation (but this is unrelated to the failure) > > Also, you are compiling with Intel -O3 which I typically won't advice. > Intel compilers are extremely aggressive which may lead to small numerical > problems. I would stick with -O2 and compile atom.F with -O1. > > It seems the output was truncated since the failing call is *after* the > atoms has been moved. I.e. try this: > $> unbuffer mpirun -np ... siesta RUN.fdf > RUN.out > or equivalent, then send the output again. > > Den man. 15. apr. 2019 kl. 22.02 skrev I. Camps <[email protected]>: > >> Hi Nick, >> >> Here it is. >> >> []'s, >> >> Camps >> >> >> On Sun, Apr 14, 2019 at 5:02 PM Nick Papior <[email protected]> wrote: >> >>> Could you please do a tar.gz or zip file? rar is horrible ;) >>> >>> Den lør. 13. apr. 2019 kl. 22.01 skrev I. Camps <[email protected]>: >>> >>>> Hello Nick, >>>> >>>> Here are the files. >>>> >>>> []'s, >>>> >>>> Camps >>>> >>>> >>>> On Fri, Apr 12, 2019 at 5:02 PM Nick Papior <[email protected]> >>>> wrote: >>>> >>>>> Could you attach the output, fdf and psf files? >>>>> >>>>> Den tor. 11. apr. 2019 kl. 22.01 skrev I. Camps <[email protected]>: >>>>> >>>>>> Hello, >>>>>> >>>>>> My system is a nanotube with 123 atoms (B, N, Ni). I am running a >>>>>> geometry optimization and the calculations are stopped (after 10 CG >>>>>> steps) >>>>>> with the following message: >>>>>> >>>>>> "*Sparse pattern is oversubscribed with nodes, please reduce number >>>>>> of nodes*" >>>>>> >>>>>> The calculation are running using 7 and 3 cores (in the same node). >>>>>> In both cases, the error message is the same. >>>>>> >>>>>> System: OpenSUSE 64bits, Intel and siesta-4.1--736 >>>>>> >>>>>> >>>>>> I appreciate any help. >>>>>> >>>>>> []'s, >>>>>> >>>>>> Camps >>>>>> >>>>> >>>>> >>>>> -- >>>>> Kind regards Nick >>>>> >>>> >>> >>> -- >>> Kind regards Nick >>> >> > > -- > Kind regards Nick >
