[phenixbb] reduce hangs

Jeff Headd jjheadd at lbl.gov
Tue Dec 3 06:45:41 PST 2013

Hi Andreas,

We have seen in the past some cases that cause Reduce to go into an
infinite loop, which I thought had been corrected, but perhaps your model
has found a corner-case that I have not considered. NCS vs. no NCS is not
the direct problem, it likely has to do with a particular set of coordinate
positions that you are reaching during refinement which causes the hydrogen
position determination to end up in either an infinite loop, or just an
optimization that isn't tractable in a reasonable amount of time. Hydrogens
are added for both NQH flips and for clashscore calculation if your input
model does not have them.

Would you be willing to send me your files (off list) for debugging
purposes? If I can recreate the behavior here, I'll be able to figure out
exactly where Reduce is getting hung up.


On Tue, Dec 3, 2013 at 8:11 AM, Andreas Förster <docandreas at gmail.com>wrote:

> Dear all,
> I'm refining a structure with 11 molecules in the asymmetric unit.
> Recently I took out NCS (data are to 2.2A and differences between
> molecules of interest).  Refinement now stalls halfway through with two
> reduce jobs running at 100% CPU.  The current job has been sitting like
> this for four days.  The last entry in the log file are a few XYZ
> individual lines.
> Refinement includes XYZ, TLS, individual B, weight optimization.  I
> launched 8 cycles.  Phenix hangs after 4_bss.  I've observed this twice in
> a row.
> Any suggestions to overcome this, short of going back to using NCS?
> This is with Phenix dev-1538 on RHEL 6.3.
> Thanks.
> Andreas
> --
>                   Andreas Förster
>      Crystallization and Xray Facility Manager
>            Centre for Structural Biology
>               Imperial College London
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