[phenixbb] Phenix "hangs" on a Mac?

Nathaniel Echols nechols at lbl.gov
Mon Jul 22 14:22:14 PDT 2013

On Mon, Jul 22, 2013 at 2:13 PM, Joseph Noel <noel at salk.edu> wrote:
> Has anyone had a problem when using Phenix refine through the GUI on a Mac
> wherein the program after hitting Run locally starts but then hangs without
> proceeding? Seems to happen to me about one out of five times I run refine
> and always hangs when I experiment with ramachandran restraints for only a
> portion of the polypeptide chain. I've tried letting things alone for
> several hours and nothing happens. I can abort and then often resubmit and
> it then runs fine (except for rama restraints). I've found this happens with
> both nightly builds and stable releases. I am currently running the latest
> nightly build 1439.

I guess the moral here is "never use Ramachandran restraints", which
is good advice under nearly any circumstances, but this sounds like a
bug we need to address.  A few follow-up questions:

1) Can you please send me all inputs off-list?  The .eff file would be
helpful too - you can get to this from the job history tab by clicking
"Show details".

2) Open the console (in /Applications/Utilities) and look for
suspicious error messages.  In particular, I get occasional mysterious
crashes which output a mention of "malloc", and the phrase "set
breakpoint to debug".  (Totally unrelated to Ramachandran restraints,
as far as I know.)


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