Leila, The reason I wanted to see an output was because I suspect that the slowness of your calculations could be linked to your compilation, actually. One thing I have noticed is that you use the -g flag for the compilation, which produces debugging info. This is only good in case you will debug the code in case of an error; otherwise it is worth having one version compiled with -g and one without; use the version without -g for production and, if you get an error which you don't know what subroutine caused it, THEN use the one with -g to determine it. The lack of -g could, by itself, speed your calculation up.
Next: optimizations. Use the flags -pad and -opt-prefetch. In my own compilations they make quite a difference. If you manage to do it successfully, do -ipo, which also speeds your code up significantly - up to 30% in some cases! Finally, it is not clear from your output: since you compile with ifort, are you using the intel mkl? If not, do compile with these libraries immediately - Siesta's blas and lapack are not optimized, and the mkl also speed your code up enormously. Good luck, Marcos 2010/9/7 leila <[email protected]> > Dear Marcos, > > Thank you very much for your reply! > > I used to do first-principles calculations on bcc Fe with SIESTA. The PP > and basis set are almost the same with Fu et al. (C.C. Fu, E. Willaime, > and P. Ordejón, Phys. Rev. Lett. 92 (2004) p.175503.), and also > thoughtfully tested in my work (L. Zhang, Journal of Physics: Condensed > Matter 22 (2010) p.375401.) I used these PP and basis for the MD test > calculations. Please see the input and output in the attached files. > > Because I am new to MD, I will be really grateful if you can point me > some difference in DFT and MD calculations with SIESTA, for example, the > basis, K points, or any other aspects. > > Thank you in advance! > > Yours sincerely, > > Leila > > > > > > *发件人:* Marcos Veríssimo Alves [mailto:[email protected]] > *发送时间:* 2010年9月7日 17:27 > *收件人:* [email protected] > *主题:* Re: [SIESTA-L] how to accerlarate MD calculations? > > > > Leila, > > There could be many reasons for your md calculation taking so long to > complete. With two atoms and 5x5x5 grid, reasons could range from your using > an executable created with an inefficient compiler and/or without optimized > libraries, to a wrong geometric setup, bad calculation settings, heavy > basis set (f.e. very long) and many others that do not come to my mind > right now. If any of these is the reason, you should correct for them before > resorting to more incomplete basis sets, which will compromise the quality > of your calculation. Please provide some details on what you are > calculating, and an input and output, to check for possible problems. > > Marcos > > El 7 de sep de 2010, 10:25 a.m., "leila" <[email protected]> escribió: > > Hi, everyone! > > > > I did an ab-initio molecular dynamics calculations (MD) by SIESTA with a > unit cell containing 2 atoms, using 5 × 5 × 5 k-point grid. The basis and > PP are the same as those for the first-principles calculations. > > I set 100 MD steps with 1.0 fs as the time length. However, the simple test > took more than 3 hours by serial processing. > > This test almost demonstrates the impossibility for ~100 atoms > calculations. > > > > I wonder if there are any methods, for example using SZ, less K-points, > or larger smearing to make ab initio MD calculations feasible. > > > > Any advice is welcome! Thanks in advance! > > > > Yours sincerely, > > > > Leila > > > >
