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:
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: " target="_blank">dbau@cipf.es web: http://bioinfo.cipf.es/dbau/ *** http://www.saveaswwf.com *** |