[phenixbb] warning: do not upgrade Mac OS yet!

Nathaniel Echols nechols at lbl.gov
Fri Oct 25 16:21:25 PDT 2013

On Fri, Oct 25, 2013 at 11:45 AM, Petri Kursula <petri.kursula at oulu.fi>wrote:

>  What I saw were problems with phenix.refine (well-did not try anything
> else yet). The job seems to start normally (no error messages), but when
> you check the log file, nothing is happening (it remains empty or stops at
> initial steps). If you abort, close Phenix and restart it, the exactly same
> job runs just fine. I’m starting Phenix GUI from ‘Applications’, not
> command line.

Can you either a) try starting on the command line
and looking for console output, or b) open the Console app and see what is
printed out?  I suspect it will have an error message involving "malloc",
because that's what happens to be sometimes.  (Always with either
phenix.refine or phenix.maps.)  As far as I can tell this is some kind of
very low-level error in either Python or the compiler used to build Phenix
- as you note, it is not consistently reproducible either, and it doesn't
seem to be correlated with any specific model or data issues that I can see.

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