[phenixbb] reduce hangs

Mark J van Raaij mjvanraaij at cnb.csic.es
Tue Dec 3 08:19:38 PST 2013

curiously, I observed the same thing yesterday in a refinement of a large a.u. (9 chains of just under 400 aa each), I only had 11 hours patience before cancelling the job.
In my case I am using MacOSX Snow Leopard and Phenix 1.8.4-1496, which was when I installed it recently the latest "stable" version.
I am rerunning it with more processors to see what happens and it has at least passed that same stage.
Also, the same job but without including secondary structure restraints finished correctly.

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616

On 3 Dec 2013, at 14:11, Andreas Förster 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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