Re: [IMP-dev] Particle removal and deactivation

[Daniel Russel <drussel@salilab.org>]

Ben Webb wrote:
> Daniel Russel wrote:
> > I can't find the imp-commit email for some reason. Anyway, there was 
> > a recent patch (581) changing a
> > model::remove_particle to deactivating the particle. This change is 
> > wrong as the particles are currently reference counted in C++ and 
> > removing the particle from the model should do the right thing 
> > assuming there are no python references hanging around. If it does 
> > not, it is a bug in kernel code which should be fixed.
> The testcase tried to use a Python reference to a particle which had 
> already been deleted. This clearly won't work, which is why I fixed it 
> in the patch. Running that testcase through valgrind clearly showed 
> access to freed memory, as I wrote in the svn log. By all means, 
> submit a patch which fixes the bug if you like. But the reference 
> counting clearly does not work with Python right now, and I don't have 
> time to fix this the "right" way.
No. The nbl should have been keeping the particle alive until the 
evaluate call (and the evaluate call will have memory issues if the 
memory is no longer valid since it needs to check if the particle is 
active or not). So there are probably deeper bugs.