On 24 Aug 2016 21:55, "Yangchuan Li" <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> 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 >> >> -- >> >> Kind regards Nick Papior >> >> >> On 19 Aug 2016 22:16, "Yangchuan Li" <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> 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>: >>>>> >>>>> 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
