On 1/27/2011 4:38 PM, Modeller Caretaker wrote: > On 01/27/2011 12:15 PM, Robert Healey wrote: >> I'm the systems administrator for a research lab using Modeller 9v3. > > While not the cause of the behavior you're seeing, 9v3 is really old. > Several bugs which in some cases affect the quality of output models > have been fixed over the past 3 years, and the latest version, 9v8, > should be entirely compatible with scripts written for 9v3. > >> I've installed the x86_64 RPM file on a pair of Xeon X5355 based systems >> and some Opteron 6136 based systems. The researchers are reporting >> getting radically different results between these two systems. > > This is completely normal and expected. Due to differences from machine > to machine, floating point results will differ. While these differences > are very very small (say 10^-8), during an optimization of a rugged > energy surface they can end up giving very different structures. > (Imagine the system is at a local maximum on the energy surface, like a > ball at the very top of a hill. The tiniest push will send it rolling > down the hill to a local minimum. The "push" might be +10^-8 on one > machine and -10^-8 on another, but the local minima could be angstroms > apart.) These differences could occur because different processors order > floating point instructions differently (e.g. a*b*c could be evaluated > as (a*b)*c or a*(b*c)) or move data from memory to processor registers > (which often have a different precision) at different times. > > Generally speaking, many models should be built for any modeling > problem, and something like the average of the best-scoring cluster > returned. Optimizations with the sorts of rugged energy surfaces common > in molecular modeling are very unlikely to find the global minimum if > only a single model is built. (Multiple models will also negate the > effects of differences between processors.) > > Ben Webb, Modeller Caretaker
Having the researchers run some more comparisons, I've found that the modeller9v3-absoft gives consistent results across both CPU platforms, unlike the default x86_64 RPM build which differed dramatically on AMD platforms.
They also tried them x86_64 RPM 9v8 and the results matched the 9v3 x86_64 RPM results on both platforms. We're switching to -absoft on all systems now for consistency, but it would be nice if that was available as a 64 bit build also.
Bob Healey Systems Administrator Biocomputation and Bioinformatics Constellation and Molecularium healer@rpi.edu (518) 276-4407