Adun

adundevel: This build service is a real stickler about not allowing code that generates certain (meaningless) compiler warnings - annoying

adundevel: Moment of truth - may have got working Adun rpms

adundevel: Trying out openSuse Build Service (#OBS)- first impression is that its not as slick as #SuseStudio

adundevel: Just discovered that the method I had been using to analyse threading performance has a name - Amdahl's law

The user manual has been extend with an entry describing linking – this is the ability to initialise the state (i.e.  coordinates/velocities) of molecules in a simulation with their state from a checkpoint in another simulation. For example if you were a simulating a protein you could initialise it with a configuration generated from a [...]

adundevel: You can now link velocities from one simulation to another, enabling a restart mechanims (of sorts)

adundevel: method swizzling - the ability to switch the implementations of two methods at runtime - turns out to be very handy. #Objc rules.

The current CVS of Adun now automatically threads nonbonded and Generalized Born calculations to multiple cores if they are available. The attached graph shows the speed-up for Gas phase and GB simulations of a 6500 atom protein. Since the threading ... [More] only applies to certain calculations you don’t get a linearly scaling speed-up. Instead the expected speed [...] [Less]

Its been a long time since we made an official release even though there have been over a lot of changes (over 1500 commits) since then. This is because most Adun users are working directly from the current CVS (and also because it requires a lot of effort to ensure a working installation package). We’re [...]

The quickstart guide has been updated to reflect the current cvs version of Adun and links added to relevant sections of the user manual. A further update in the works will replace the “toy” examples it contains with more relevant information.