Hi everyone,
I'm having a problem with the memory usage of the IMP::Model::evaluate(bool) method.
I'm trying to optimize a set of particles as done for the alpha-globin domain (I'm doing some testing on a larger chromatin domain) using a large set of restraints (over 10^6 restraints). The memory usage is OK until all the restraints are generated (~2GB), and then increase to 100% of memory and swap (16GB + 16GB) when I first call m.evaluate(False) (to check the initial score) causing the script to stop. I understand that a large number of restraints are being evaluated, but I was wondering if this is an expected behavior (i.e. if there is a sort of limitation in the number of restraints that can be implemented per memory GB) or if there is a workaround, before trying to run the script on a (shared) machine with much more memory.
I'm using an old version of IMP (r7392) with the following optimizer: > # Set up optimizer > o = IMP.core.MonteCarlo() > o.set_return_best(True) > o.set_model(m) > fk = IMP.core.XYZ.get_xyz_keys() > mov = IMP.core.NormalMover(ps, fk, 0.25) > o.add_mover(mov) > lo = IMP.core.ConjugateGradients() > o.set_local_steps(lsteps) > o.set_local_optimizer(lo)
I've tried without the ConjugateGradients after reading this https://salilab.org/imp/bugs/show_bug.cgi?id=106, but I guess it does not depend on CG (I don't have ClosePairContainer in the current code).
Thanks and best regards, Davide
-- Davide Baù Structural Genomics Laboratory Bioinformatics & Genomics Department, Prince Felipe Research Center Avda. Autopista del Saler 16, 46012 Valencia, Spain Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 email: dbau@cipf.es web: http://bioinfo.cipf.es/dbau/
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