[phenixbb] ensemble refinement crash.

R.M. Garavito garavito at msu.edu
Tue Nov 22 06:24:00 PST 2016


Any errors reported from the crashes?  You might check your memory usage.  I had crashes with ensemble refinement using phenix-1.10 (and later versions) during the ensemble reducer stage.  While the memory usage is quite stable during the MD phase, during the ensemble reducer stage, memory usage increases quite a bit, sometime by 2X.  It will get up to 12-16 GB active memory (not including swap space) with a 2x360 residue asymmetric unit.  If you are using the computer for something else with higher priority, it may cause problems.  I just bought more memory (24-32 GB) and that solved the problem.



R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513   
Michigan State University      
East Lansing, MI 48824-1319
Office:  (517) 355-9724     Lab:  (517) 353-9125
FAX:  (517) 353-9334        Email:  garavito at msu.edu

> On Nov 22, 2016, at 6:26 AM, Rajendra Sharma <rajenbiotech at gmail.com> wrote:
> Dear all,
> I am running  ensemble refinement using phenix-1.10. The calculations are running good until the Ensemble reducer where the jobs get killed  in some cases automatically without giving output pdb. I am using default setting to run the jobs. 
> pdb_stored_per_block is 50 totaling 500 towards the end. Is the crash happening because of memory? Will reducing the number of pdb per block help?
> Secondly, how can I restart the killed runs? 
> thanks in advance.
> Raji
> Rajendra Sharma
> Research Scholar, PhD.
> Centro Nacional de Biotecnología <http://www.cnb.csic.es/>,
> Universidad Autónoma de Madrid,
> Madrid, Spain.
> Mobile No. +31-656688390
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