Dear Marcos, Thank you very much!
I will follow your advice on the compilation. PS: Yes, I am using the intel mkl, compiling with ifort. Thank you again! Best wishes! Yours sincerely, leila 发件人: Marcos Veríssimo Alves [mailto:[email protected]] 发送时间: 2010年9月8日 19:40 收件人: [email protected] 主题: Re: 答复: [SIESTA-L] how to accerlarate MD calculations? 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
