tag:blogger.com,1999:blog-7844526396210378482.post8282380498383950472..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: QM Speed Test: NWChemNoel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger15125tag:blogger.com,1999:blog-7844526396210378482.post-91611866130414796882018-09-10T07:13:09.004+01:002018-09-10T07:13:09.004+01:00Hello to all learned people here.
I know I am joi...Hello to all learned people here. <br />I know I am joining too late. Just came across this blog of @Noel Sir. I specifically work with FIREFLY and I have done few tests on single point and hessian calculations. <br />I found that for single point, single core works most efficiently, while for hessian, multiple cores perform better (not substantial performance boost though). In general single core seems the best bet, considering the RAM and even for large molecules then. <br />I haven't yet tested any GPU based calculations though. Any reviews on that would be great.Dr. Siddheshwar Choprahttps://www.blogger.com/profile/18088847296796639226noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-79572009287396405712014-01-21T15:14:08.855+00:002014-01-21T15:14:08.855+00:00Sure - it's on the list.Sure - it's on the list.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-24010477204385130572014-01-21T15:07:15.406+00:002014-01-21T15:07:15.406+00:00Why not try Firefly? I would love to see speed tes...Why not try Firefly? I would love to see speed tests of Firefly vs. other free software, as its authors claim it is one of the fastest codes available.MPKhttps://www.blogger.com/profile/01846010848634411754noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-64464561374596222542014-01-07T11:59:42.762+00:002014-01-07T11:59:42.762+00:00Great. Just to note that I'm not merging the f...Great. Just to note that I'm not merging the forks. We are basically using the repos as independents records of people's calculations.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-82206697700368708882014-01-06T22:55:25.636+00:002014-01-06T22:55:25.636+00:00I also ran the inputs through several programs. No...I also ran the inputs through several programs. Noel, should we send you pull requerst? :)Karolhttps://www.blogger.com/profile/17032498937126368914noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-26175577436065218702014-01-02T20:34:26.481+00:002014-01-02T20:34:26.481+00:00@Noel: I got my hands on GAMESS(US), MOLPRO, Turbo...@Noel: I got my hands on GAMESS(US), MOLPRO, Turbomole and some other proprietary package, as well as NWChem for reference, via a login at a compute facility. Will report back.Michael Banckhttps://www.blogger.com/profile/10019023009908861248noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-59027494541683831042014-01-02T19:48:50.293+00:002014-01-02T19:48:50.293+00:00@everyone: I love the peer reviewing of the QM. Se...@everyone: I love the peer reviewing of the QM. Seriously. Open Notebook Science or what! :-)<br /><br />@Henry: The scope of this benchmark is deliberately constrained to make the barrier to entry fairly easy (small molecule, small basis, etc.). If successful, we can start looking at scaling and other effects that you mention.<br /><br />However, I am specifically targeting serial calculations, because I feel that speed for serial calculations has been forgetten in the rush to massively scale QM for supercomputers (see my initial post).<br /><br />@Michael: I hope to try as many as possible of the comp chem packages listed on the <a href="http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software" rel="nofollow">Wikipedia page</a>.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-38364640545826593582014-01-02T19:34:11.856+00:002014-01-02T19:34:11.856+00:00At least Dalton does. From the manual:
B3LYPg
Hy...At least Dalton does. From the manual:<br /><br />B3LYPg <br />Hybrid functional with VWN3 form used for correlation. This is the form used by<br />the Gaussian quantum chemistry program. Keyword B3LYPGauss is a synonym for B3LYPg. This functional can be explicitly set up by the<br /><br />Combine HF=0.2 Slater=0.8 Becke=0.72 LYP=0.81 VWN3=0.19<br /><br />option in the .DFT section, cf. the manual.Janus J. Eriksenhttps://www.blogger.com/profile/02165062009721597719noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-77084230573567240722014-01-02T18:47:07.854+00:002014-01-02T18:47:07.854+00:00@Eric Berquist: the DALTON/ORCA results you have p...@Eric Berquist: the DALTON/ORCA results you have posted are using VWN5 for the LYP correlation functional, not VWN3.<br /><br />VWN5 is generally considered more correct, however, the B3LYP functional in Gaussian uses VWN3 so most other codes use that as well by default.<br /><br />Note the rather large energy difference between the DALTON/ORCA results and Q-Chem. Not sure whether those packages allow for an explicit tuning of the VWN variant. <br /><br />(Erkale and NWChem both use VWN3 by default)Michael Banckhttps://www.blogger.com/profile/10019023009908861248noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-20069624521006479072014-01-02T17:14:04.423+00:002014-01-02T17:14:04.423+00:00Noel, if you are going for non-free/proprietary pa...Noel, if you are going for non-free/proprietary packages, I suggest to also compare GAMESS (probably the US version, as the UK version is really only accessible to UK residents I think), which appears to be rather popular overall.Michael Banckhttps://www.blogger.com/profile/10019023009908861248noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-20644409260221169802014-01-02T10:36:11.591+00:002014-01-02T10:36:11.591+00:00@Eric Berquist. Could you try to repeat the calcs ...@Eric Berquist. Could you try to repeat the calcs with LSDalton also, in case you've build that as well?Janus J. Eriksenhttps://www.blogger.com/profile/02165062009721597719noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-81588809863654735612014-01-02T10:22:31.596+00:002014-01-02T10:22:31.596+00:00Another benchmark follow up might be to see how an...Another benchmark follow up might be to see how any code scales in parallel mode. Some scale linearly with the number of processors up to at least 16 processors, but it is desirable for this to extend up to say 64 processors, which are becoming more common.<br /><br />Another crucial aspect is how the benchmark scales with available memory. Obviously, the more memory the better (and some configurations now have access to 96 Gbytes), but how does the code cope on lower memory systems? Anonymoushttps://www.blogger.com/profile/11270810017308924145noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-66539957292540279322014-01-02T10:16:07.141+00:002014-01-02T10:16:07.141+00:00A useful further benchmark might be a calculation ...A useful further benchmark might be a calculation that involves 2nd derivatives (frequencies). These are tough to compute quickly and to do so is essential for transition states and intrinsic reaction coordinates.<br /><br />My gut feeling is that there will be a vast difference in this (depending on the Hamiltonian) some codes only have finite difference 2nd derivatives available (which take an age, and scale horribly as the molecule gets larger). <br /><br />It would be important when running a benchmark to include a reasonably large molecule (~100 atoms?), since an important aspect of the benchmark is how it scales with molecule size. And 2nd derivatives can potentially scale very badly.<br /><br />I can guess that two codes will beat all the others, but they are both commercial (and one is not allowed to publish benchmarks for one of these codes). But in a sense, for this type of calculation, you pays for what you gets.Anonymoushttps://www.blogger.com/profile/11270810017308924145noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-36838438208335931782014-01-02T09:11:38.955+00:002014-01-02T09:11:38.955+00:00Thanks for the details. I'll try to get licens...Thanks for the details. I'll try to get licenses for all of these.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-1529508997768911352014-01-01T21:56:38.936+00:002014-01-01T21:56:38.936+00:00Both ORCA and Dalton are free for academic usage. ...Both ORCA and Dalton are free for academic usage. ORCA requires accepting a license, but only binaries are distributed, with no access to the source. Dalton requires a signed (!) license agreement, but is only distributed as source.Eric Berquisthttps://www.blogger.com/profile/17852754538099611748noreply@blogger.com