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
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle