Hi Ben,
Thanks for the respond.
What you see 0 restrant is because I did 'm.show()' before adding restraint. With the attached code running on my desktop (8 GB memory with ulimit: unlimited):
------
Setting up score state for container ListSingletonContainer 0
total bead: 100619
Setting up score state for container ListSingletonContainer 3
Setting up score state for container ClosePairContainer
Setting up score state for container MovedSingletonContainer
Model(Model, kernel 1.0)201230 particles
2 restraints
4 score states

  Restraint SingletonsRestraint 0 has weight 1
  Restraint PairsRestraint 1 has weight 1
Traceback (most recent call last):
  File "memtest.py", line 102, in <module>
    o.optimize(1000)
  File "/home/htjong/bin/imp-1.0/build/lib/IMP/core/__init__.py", line 665, in optimize
    def optimize(self, *args): return _IMP_core.ConjugateGradients_optimize(self, *args)
MemoryError: std::bad_alloc
------------
When I did 'top' on shell, the mem never went more than 15% before it crashed. Is there any IMP liner that can print out memory consumed during run?
I'm not sure what whether it's a bug, but when I reduce the number of particle it's fine.
One bug I found: set_name("blabla") of IMP.display.XYZRsGeometry doesn't print 'blabla'.

Harianto.

On Thu, Apr 8, 2010 at 12:32 PM, Ben Webb <ben@salilab.org> wrote:
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
--
ben@salilab.org                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
       - Sir Arthur Conan Doyle
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