3 ms·
Alpineidyll already commented on QM calculations, but I can attest these machines are useless for molecular dynamics as well. In order to actually run in any ev
by mechagodzilla 4y ago
Alpineidyll already commented on QM calculations, but I can attest these machines are useless for molecular dynamics as well. In order to actually run in any even vaguely “efficient” regime (ie be faster than a single GPU on your exaflop machine), you need to scale the problem to the size that you can no longer approach interesting timescales for the dynamics involved. A 10 nanosecond simulation of a 100M particle system is useless. The problem almost immediately becomes latency bound when you use multiple chips. The first generation Anton machine from DE Shaw Research (which they built in 2008!) is still over an order or magnitude faster than any existing machine (in 2022!) that isn’t a newer Anton when it comes to MD.
If they wanted a GPU farm they could probably have built it for 1/10 the cost or less by throwing out the interconnect and infrastructure that makes it a “supercomputer”.
- alpineidyll3 4y agoWell put. Of course Anton's Force field isn't accurate enough to correctly predict conformational equilibria of proteins ;P although it does scale!
- mechagodzilla 4y agoThat’s just a general limitation of the fixed-charge Amber/charmm molecular mechanics force fields everyone uses for molecular dynamics (whether you’re running on an Anton, or running gromacs or namd on a cluster or GPU, they all use the same MMFFs).