Rajendra,

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.

Cheers,

Michael


****************************************************************

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:  [email protected]

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On Nov 22, 2016, at 6:26 AM, Rajendra Sharma <[email protected]> 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,

Universidad Autónoma de Madrid,

Madrid, Spain.
Mobile No. +31-656688390

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