Hi All, I was looking at a blog post from greg:
https://rdkit.blogspot.com/2019/07/a-couple-of-substructure-search-topics.html about fingerprint screenout. The part that got me confused was the timings in his blog post because run times in my case where a lot slower. Gregs numbers: [07:21:19] INFO: mols from smiles [07:21:27] INFO: Results1: 7.77 seconds, 50000 mols [07:21:27] INFO: queries from smiles [07:21:27] INFO: Results2: 0.16 seconds [07:21:27] INFO: generating pattern fingerprints for mols [07:21:43] INFO: Results3: 16.11 seconds [07:21:43] INFO: generating pattern fingerprints for queries [07:21:43] INFO: Results4: 0.34 seconds [07:21:43] INFO: testing frags queries [07:22:03] INFO: Results5: 19.90 seconds. 6753 tested (0.0003 of total), 3989 found, 0.59 accuracy. 0 errors. [07:22:03] INFO: testing leads queries [07:22:23] INFO: Results6: 19.77 seconds. 1586 tested (0.0001 of total), 1067 found, 0.67 accuracy. 0 errors. [07:22:23] INFO: testing pieces queries [07:23:19] INFO: Results7: 55.37 seconds. 3333202 tested (0.0810 of total), 1925628 found, 0.58 accuracy. 0 errors. | 2019.09.1dev1 | 7.8 | 0.2 | 16.1 | 0.3 | 19.9 | 19.8 | 55.4 | Machine 1: Virtual machine, Windows Server 2012 R2 with an intel xeon (4 virtual cores) Since the test is single-threaded it makes a bit of sense that it isn't fast here but it's not just a bit slower, but a lot slower, depending on test almost 3xtimes slower [09:03:19] INFO: mols from smiles [09:03:38] INFO: Results1: 19.44 seconds, 50000 mols [09:03:38] INFO: queries from smiles [09:03:38] INFO: Results2: 0.36 seconds [09:03:38] INFO: generating pattern fingerprints for mols [09:04:54] INFO: Results3: 75.99 seconds [09:04:54] INFO: generating pattern fingerprints for queries [09:04:56] INFO: Results4: 1.55 seconds [09:04:56] INFO: testing frags queries [09:05:34] INFO: Results5: 37.59 seconds. 6753 tested (0.0003 of total), 3989 f ound, 0.59 accuracy. 0 errors. [09:05:34] INFO: testing leads queries [09:06:11] INFO: Results6: 37.34 seconds. 1586 tested (0.0001 of total), 1067 f ound, 0.67 accuracy. 0 errors. [09:06:11] INFO: testing pieces queries [09:08:39] INFO: Results7: 147.79 seconds. 3333202 tested (0.0810 of total), 19 25628 found, 0.58 accuracy. 0 errors. | 2019.03.3 | 19.4 | 0.4 | 76.0 | 1.5 | 37.6 | 37.3 | 147.8 | I thought maybe another issue with windows being slow so I tested on a linux VM on my laptop Machine 2: Virtual machine, Lubuntu 16.04 on a laptop i7-8850H 6-core [09:23:31] INFO: mols from smiles [09:23:54] INFO: Results1: 23.71 seconds, 50000 mols [09:23:54] INFO: queries from smiles [09:23:55] INFO: Results2: 0.48 seconds [09:23:55] INFO: generating pattern fingerprints for mols [09:24:53] INFO: Results3: 58.31 seconds [09:24:53] INFO: generating pattern fingerprints for queries [09:24:54] INFO: Results4: 1.19 seconds [09:24:54] INFO: testing frags queries [09:25:41] INFO: Results5: 46.22 seconds. 6753 tested (0.0003 of total), 3989 found, 0.59 accuracy. 0 errors. [09:25:41] INFO: testing leads queries [09:26:26] INFO: Results6: 45.84 seconds. 1586 tested (0.0001 of total), 1067 found, 0.67 accuracy. 0 errors. [09:26:26] INFO: testing pieces queries [09:28:33] INFO: Results7: 126.78 seconds. 3333202 tested (0.0810 of total), 1925628 found, 0.58 accuracy. 0 errors. | 2019.03.3 | 23.7 | 0.5 | 58.3 | 1.2 | 46.2 | 45.8 | 126.8 | Pretty weird sometimes even slower sometimes faster than the windows VM but still a lot slower than Gregs numbers (I repeated with rdkit 2019.09.2 and got comparable results) So I also tested on above laptop directly: Machine 3: physical install, windows 10 on a laptop i7-8850H 6-core (same machine as 2) [09:51:43] INFO: mols from smiles [09:51:54] INFO: Results1: 10.59 seconds, 50000 mols [09:51:54] INFO: queries from smiles [09:51:54] INFO: Results2: 0.20 seconds [09:51:54] INFO: generating pattern fingerprints for mols [09:52:24] INFO: Results3: 29.50 seconds [09:52:24] INFO: generating pattern fingerprints for queries [09:52:24] INFO: Results4: 0.61 seconds [09:52:24] INFO: testing frags queries [09:52:44] INFO: Results5: 19.71 seconds. 6753 tested (0.0003 of total), 3989 found, 0.59 accuracy. 0 errors. [09:52:44] INFO: testing leads queries [09:53:04] INFO: Results6: 19.48 seconds. 1586 tested (0.0001 of total), 1067 found, 0.67 accuracy. 0 errors. [09:53:04] INFO: testing pieces queries [09:54:05] INFO: Results7: 61.94 seconds. 3333202 tested (0.0810 of total), 1925628 found, 0.58 accuracy. 0 errors. | 2019.09.1 | 10.6 | 0.2 | 29.5 | 0.6 | 19.7 | 19.5 | 61.9 | This is much closer to Gregs results, except for the fingerprinting which takes almost double the time. Also notice how the fingerprinting on the linux VM is much faster also compared to other results than on the windows VM? Conclusions: 1. Form what I see, it seems that the pattern fingerprinter runs a lot slower on windows. Is this known issue? 2. In virtual machines the rdkits performance simply tanks, is much worse. A certain penalty is to be expected but not this much. Or what am I missing? Machine 1 runs on central infrastructure so I would assume virtualization is configured correctly. For the local VM, vt-x is enabled. Yet it is much slower compared to the physical machine (plus that AFAIK rdkit runs faster in linux vs windows) Especially the virtual machine aspect is kind of troubling because I would assume many real-world applications are deployed as VM and hence might suffer from this too? I don't have a well defined question but more interested in other users experience especially regarding the virtualization. Best Regards, Thomas
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
