[phenixbb] Phenix crashes during refinement of a large structure

Nathaniel Echols nechols at lbl.gov
Fri May 18 14:18:38 PDT 2012

On Fri, May 18, 2012 at 2:12 PM, Gino Cingolani
<Gino.Cingolani at jefferson.edu> wrote:
> PHENIX keeps crashing while refining a large structure (>18,000 residues/asym unit).
> Can anybody make sense of the following error message (see below)?
> ...
>  File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 1015, in _execute_child
>    self.pid = os.fork()

It's a memory error - the stage at which it crashes is running
phenix.clashscore (which has been used internally by phenix.refine
since version 1.7.2).  Unfortunately there's no way around this other
than installing more memory and/or upgrading to a 64-bit OS.  What is
the output of boost_adaptbx.show_platform_info?


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