On 4/6/10 11:43 AM, Harianto Tjong wrote: > I am playing IMP with a large numbers of particles, e.g. > 10^5 and fail > to optimize due to memoryError even though I still have enough VMEM and MEM.
It is possible that this isn't memory being exhausted, but rather a bug in the system somewhere (maybe because you have 0 restraints - what happens if you add a single distance restraint, for example?). 10^5 particles isn't that huge, and shouldn't exhaust system memory on a typical modern system. You should check your shell limits though ('limit' or 'ulimit') to make sure the process isn't being restricted to a smaller amount of memory. Can you open a bug in our bug tracker at https://salilab.org/imp/bugs/ and attach your input files so we can reproduce the problem here? It should be fixed, of course.
> I suppose I have to increase the memory usage limit during compilation. > How is the proper way to do it?
No, IMP is limited only by system memory. There shouldn't be any hard-coded compile-time limits.
Ben