Hi Marcos, Reading your suggestions for compiling SIESTA reminded me of a question I'd meant to ask at one point. In one of your messages about compiling SIESTA with ifort and MKL ( http://www.mail-archive.com/[email protected]/msg01702.html ) you include an example arch.make file that links to a non-mkl version of scalapack. Just out of curiosity, what is the advantage of using that instead of MKL's scalapack?
Have a nice evening, Mike On Sep 8, 2010, at 7:40 AM, Marcos Veríssimo Alves wrote: > 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 > > >
