[phenixbb] Out of Memory Errors

Nathaniel Echols nechols at lbl.gov
Wed Apr 20 13:51:00 PDT 2011

On Wed, Apr 20, 2011 at 1:08 PM, Heather Condurso <condurso at bc.edu> wrote:
> 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.

If you downloaded the binary installer, it is compiled as 32-bit
objects, which means it will never be able to use more than 2GB of
memory.  The source installer will compile as 64-bit, but we didn't
distribute that for 1.7 because I hadn't yet figured out how to turn
my Mac into a build system.  That problem was solved a few weeks ago,
so the latest nightly builds all have 64-bit binary installers
available for Mac.  These use a newer version of wxPython that is
noticeably buggier, but the most catastrophic problems with the GUI
are now fixed, and it seems to run well for most things.

However, another user just notified me this morning that AutoMR will
not run from the GUI in the nightly builds - we are sorting this
problem out now, but for the immediate future you will need to compile
1.7 from source.  (Or wait until tomorrow, when I hope we will have a
working installer with the bug fix.)


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