[phenixbb] Out of Memory Errors

Heather Condurso condurso at bc.edu
Wed Apr 20 13:08:09 PDT 2011

Hello all,

I am currently running the Phenix GUI version 1.7-650 on an iMac with an 3.2Ghz Intel Core i3 processor, 8GB of memory operating under OS 10.6.  During many of my runs (mostly AutoMR runs but sometimes refine) I get out of memory errors.  I have my system booted in 64 bit mode and I watch the activity monitor and find that phenix doesn't use much more than 2GB of memory.  My search model is very large.  My unit cell contains 4 trimers (each monomer is 48kDa).  I hadn't encountered this issue until I began to increase my search model from one trimer to four.  Do you have any suggestions as to how I could avoid this error without minimizing my search model? Often my AutoMR runs get the out of memory error at the start of refinement, but just now the memory was exhausted during the fast rotation function.  During this run I used all default parameters with a max res of 4.0 and RMSD of 1.0.

Any advice you can give would be greatly appreciated!

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