Hi Michael, I am sorry I took so long to answer your mail, but I was at the Psi-K conference in Berlin.
I have not managed to compile siesta successfully using -ipo, only -ip. Please note that I have written "If you manage to do it successfully, do -ipo" :) exactly because I never managed to do it. I have, though, compiled simpler codes like those of Wien2K using ipo. Marcos 2010/9/10 Michael R. C. Williams <[email protected]> > Dear Marcos, > > Do you have an example of an arch.make file using Intel compilers (any > version) and -ipo? I haven't had much luck getting that to work, even with > older versions of ifort. Specifically, if I add -ipo to FCFLAGS for ifort > 10.0.x or 10.1.x, configure crashes with the following error: > > checking whether ifort accepts -D... no > checking whether ifort accepts -I... no > checking whether ifort fulfils requested features... no > checking preprocessing mode we may therefore use... indirect > checking how to run the C preprocessor... icc -E > checking how to preprocess Fortran files... fpp > checking how to redirect fpp output... > conftest.f > checking whether fpp needs the -P option... unknown > configure: error: fpp cannot produce code that ifort compiles > > Without -ipo among the other optimization settings, configure decides that > ifort can do direct preprocessing. If I try to use -ipo with the latest > ifort 11.1, configure also recognizes that ifort can do direct > preprocessing, although make ends up failing to build the executable. > > Many thanks, > > 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 >> >> >> > >
