<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Rajendra,</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Michael</div><div class=""><br class=""></div><br class=""><div apple-content-edited="true" class="">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Nov 22, 2016, at 6:26 AM, Rajendra Sharma <<a href="mailto:rajenbiotech@gmail.com" class="">rajenbiotech@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear all,</div><div class=""><br class=""></div><div class="">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. </div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class="">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?</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class="">Secondly, how can I restart the killed runs? </font></div><div class=""><br class=""></div><div class="">thanks in advance.</div><div class=""><br class=""></div><div class="">Raji</div><div style="font-size:12.8px" class=""><br class=""></div><div class=""><div class="gmail_signature"><div dir="ltr" class=""><font face="arial, helvetica, sans-serif" size="2" class=""><i class="">Rajendra Sharma<br class="">Research Scholar, PhD.<br class=""></i></font><div class=""><h3 style="padding-top:0px;padding-right:0px;padding-left:0px;margin:0px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap" class=""><em class=""><font face="arial, helvetica, sans-serif" size="2" style="font-weight:normal;background-color:rgb(243,243,243)" class=""><a href="http://www.cnb.csic.es/" target="_blank" class="">Centro Nacional de Biotecnología</a>,</font></em></h3><div class=""><font face="arial, helvetica, sans-serif" size="2" class=""><i class=""><u class=""><font color="#0000ff" class="">Universidad Autónoma de Madrid</font></u><font class="">,</font><font style="font-weight:normal;background-color:rgb(243,243,243)" class=""><br class=""></font></i></font></div><div class=""><em class=""><font face="arial, helvetica, sans-serif" size="2" class=""><h3 style="padding-top:0px;padding-right:0px;padding-left:0px;margin:0px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap" class=""><div style="color:rgb(34,34,34);font-weight:normal;white-space:normal" class=""><font face="arial, helvetica, sans-serif" size="2" class="">Madrid, Spain.<br class=""></font></div><div style="color:rgb(34,34,34);font-weight:normal;white-space:normal" class=""><font face="arial, helvetica, sans-serif" size="2" class="">Mobile No. +31-656688390</font></div></h3></font></em></div></div></div></div></div>
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