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] ****************************************************************

On Nov 22, 2016, at 6:26 AM, Rajendra Sharma 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]