A suggestion here: transiesta usually starts with a standard siesta run, if you’re not restarting from a .TSDE file for instance - this may explain the speedup you get.
arthur > On 29 Aug 2016, at 15:52, Yangchuan Li <liyangch...@utexas.edu> wrote: > > Hi Nick, > > Thank you for your answers. I appreciate it. > Recently, I do some other tests and I put it here. > > cores Transiesta Tbtrans > 32 8h 19m 41s 557ms 47m 46s 89ms > 48 6h 29m 41s 770ms 47m 37s 510ms > 64 4h 18m 26s 283ms 47m 32s 215ms > 96 4h 20m 11s 997ms 47m 28s 189ms > > The number of energy points is 43. I have two questions for the result. > 1. Why it takes longer time on 48 node if transiesta parallels across energy > points? > 2. Why it takes the same time for tbtrans if tbtrans parallels across energy > points? > > Another question is on the linear scalability for atom number. I have read > this article: The SIESTA method; developments and applicability > <http://iopscience.iop.org/article/10.1088/0953-8984/20/6/064208/meta;jsessionid=6E37FEDC0B8943CD097C536638603E54.c4.iopscience.cld.iop.org>. > It said siesta was coupled to several linear-scaling solvers. And also said > other method scaling as N^3. Does this means siesta scaling between linear > and N^3? What about transiesta and tbtrans? > > Thanks for your time. Really appreciate your help. > > Best, > Yangchuan > ME | UT Austin > > On Wed, Aug 24, 2016 at 3:58 PM, Nick Papior <nickpap...@gmail.com > <mailto:nickpap...@gmail.com>> wrote: > > > > On 24 Aug 2016 21:55, "Yangchuan Li" <liyangch...@utexas.edu > <mailto:liyangch...@utexas.edu>> wrote: > > > > Hi Nick, > > > > I really appreciate your answer. It makes my work more efficient. > > Recently I also do a siesta speed test. It's a geometry optimization > > running. I select k grid to be 1x1x4. And I run on 64, 128, 256 cores. > > There is no speed up as a result. > > So, is it right to make the following summary? > > 1. siesta is parallel across k points (points in .KP file which after > > symmetry analysis). > No, by default siesta is parallel over orbitals. Unless you specifically > request k parallelization. > However, there is a limit to the scalability (for any code), say if your > system have very few orbitals then parallelization to many cores will be > dominated by overhead. > > 2. transiesta is parallel across energy points, which is the sum of three > > variable (TS.ComplexContour.NumCircle, TS.ComplexContour.NumLine, > > TS.ComplexContour.NumPoles) > Yes. > > 3. tbtrans is parallel across k points, which is not related with kz. But > > the kxy point after symmetry analysis. > No, tbtrans is also parallel across energy points. > > 4. There is no need to use cores more than energy points. > For tbtrans and transiesta, this is currently true. > > > Is there anything wrong with my understanding? > > Thanks for your time. > > > > Best regards, > > Yangchuan Li > > Graduate research assistant > > ME | UT Austin > > > > On Fri, Aug 19, 2016 at 4:12 PM, Nick Papior <nickpap...@gmail.com > > <mailto:nickpap...@gmail.com>> wrote: > >> > >> Transiesta does not calculate the transmission, so the number of energy > >> points is irrelevant for this calculation. > >> > >> The number of points for transiesta is determined from the flags explained > >> in section 8.7.3 of siesta 4.0 manual. > >> See here: > >> https://launchpad.net/siesta/4.0/4.0/+download/siesta.pdf > >> <https://launchpad.net/siesta/4.0/4.0/+download/siesta.pdf> > >> > >> -- > >> > >> Kind regards Nick Papior > >> > >> > >> On 19 Aug 2016 22:16, "Yangchuan Li" <liyangch...@utexas.edu > >> <mailto:liyangch...@utexas.edu>> wrote: > >>> > >>> Hi Nick, > >>> > >>> Thank you for your answer. Yes, you are right. In the output of tbtrans > >>> the number of energy points is 43. > >>> But how can I know the number ahead? In electrode the k-points are > >>> 1x1x10, in system the k-pts are 1x1x100. And I select 121 points in > >>> transmission vs energy plot. How transiesta select the final points to be > >>> 43? > >>> Hope you can answer this so I can use resources efficiently. I appreciate > >>> your answer. Thanks. > >>> > >>> Yangchuan > >>> Graduate research assistant > >>> ME | UT Austin > >>> > >>> > >>> On Thu, Aug 18, 2016 at 12:00 AM, Nick Papior <nickpap...@gmail.com > >>> <mailto:nickpap...@gmail.com>> wrote: > >>>> > >>>> This is not surprising, transiesta is only parallelized across energy > >>>> points. This means you probably have between 33 and 64 energy points on > >>>> your contour. > >>>> > >>>> 2016-08-17 23:00 GMT+02:00 Yangchuan Li <liyangch...@utexas.edu > >>>> <mailto:liyangch...@utexas.edu>>: > >>>>> > >>>>> Dear siesta users, > >>>>> > >>>>> I did a speed up test of transiesta (version 4.0 stable) on a cluster. > >>>>> I run a job of 380 atoms with different number of cores. And here is > >>>>> the result. The running time doesn't include tbtrans running. > >>>>> cores Transiesta > >>>>> 32 8h 19m 41s 557ms > >>>>> 64 4h 18m 26s 283ms > >>>>> 96 4h 20m 11s 997ms > >>>>> 128 4h 18m 9s 189ms > >>>>> 256 4h 18m 37s 196ms > >>>>> 512 4h 19m 8s 984ms > >>>>> > >>>>> It seems strange because from 32 to 64 I got a perfect speed up, while > >>>>> increase the cores from 64 doesn't give me anything. > >>>>> So, why this happened and is there a way to speed up more? > >>>>> Any comments will be appreciated. Thanks. > >>>>> > >>>>> Yangchuan > >>>>> Graduate research assistant > >>>>> ME | UT Austin > >>>> > >>>> > >>>> > >>>> > >>>> -- > >>>> Kind regards Nick > >>> > >>> > > > > -- > Kind regards Nick >
