GPU Benchmarks for RIDE Rapid Isoster Discovery Engine

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Andrew Orry

May 11, 2020, 11:29:26 PM5/11/20
to MolSoft ICM Knowledge Base
Q. Are there any GPU benchmarks for RIDE Rapid Isoster Discovery Engine
RIDE is a fast 3D molecular similarity search method based on Atomic Property Fields, developed at MolSoft. RIDE searches databases of compound conformers for molecules that are isosteric to the query, i.e. have similar 3D configurations and distributions of atomic properties. GPU-based implementation is capable of searching ~0.5mln conformers/second on a single GPU card and perform 3D virtual screens of millions of compounds with the level of interactivity comparable to 2D searches. VLS benchmarking on DUDe indicates that RIDE searches produce enrichments on par with much slower standard flexible APF VLS.

MolSoft has tested RIDE on two GPUs:

  • Tesla P100 (12Gb RAM) (3 years old model)   ~$4K
  • GeForce RTX 2080 (8Gb RAM) (last year model)   ~$700

Surprisingly, the RIDE performance on RTX  was even better ~10%-15% than on the more expensive Tesla. It can be explained because we don't use double precision arithmetic in RIDE superposition, so P100 doesn't give you any advantage and the RTX newer model has higher GPU clock rate.

The algorithm performance linearly depends on the size of your template (number of bonds). 0.5 million conformers/sec performance refers the ligand with ~22 bonds. The GPU RAM required for that ligand size is ~200Mb. For multiple templates everything (speed/RAM requirements) is also scaled linearly.

The other important requirement for the fast RIDE performance is that conformer DB should be located on SDD drive, otherwise the bottleneck will be just reading data from the disk.

In Summary

  • For good RIDE performance you don't need expensive professional GPU (like Tesla).  Good recent GeForce card will perform even better.
  • So, any modern gamer PC will actually work.
  • For example we've bought this box some time ago (under $2000) and it works pretty well on RIDE

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