<div dir="ltr"><div><div><div><div><div><div>Hi Amy,<br><br></div><div>Hopefully, Sebastiens suggestion will help you, but if not, you can try the followings:<br></div><div><br></div>Gergely Patay and me sent some source code patches in June to the mailing list, they could help.<br></div>The only drawback is that you have to compile GATE from source.<br><br>Most of my fixes are related to memory leaks, but actually most of them are ITK related, and I do not see any alfa/beta source specific modification. Anyway, you can try these patches, it will not harm. If you do so, please let us (the mailing list) know the result (helped or did not). <br><br></div>Applying the patches is actually quite easy:<br><br>First you have to download the patch files (see below), and uncompress them with gunzip.<br><br></div><div>After that you have to do everything exactly like the GATE install manual says, except this part:<br></div><div><br>- when you get a copy from the source:<br></div><div>git clone <a href="http://git.opengatecollaboration.org/git/opengate-public.git">http://git.opengatecollaboration.org/git/opengate-public.git</a><br></div><div><br>- then you have to enter to the GATE source directory:<br>cd opengate-public<br></div></div><div><br>- and you have to apply the patches:<br></div>git apply cppfix_dvolgyes.patch geant4-geometry.patch interfile.patch<br></div><br>(the actual filenames can contain path-parts, like ../patches/cppfix_dvolgyes.patch, it depends on your actual directory layout.)<br><br><div><div><div>After that you should follow the manual. (cmake, compile, install, etc.)<br><br></div><div>As a last hope without actually debugging the code, you can try different geant/root/gate/clhep versions, <br></div><div>maybe it comes from a recently introduced or recently fixed bug. Of course, this takes a lot of time, and there is no guarantee for the success.<br><br></div><div>(The original e-mail what contained the patches is quoted below my signature.)<br></div><div><br></div><div>Good luck!<br><br></div><div>Cheers,<br></div><div> David<br></div><div><br>On Wed, Jun 18, 2014 at 10:54 AM, Patay Gergely <<a href="mailto:patay.gergely@mediso.hu">patay.gergely@mediso.hu</a>> wrote:<br>> Dear Gaters,<br>><br>> here are a few patches against the upstream (ie. master branch) Gate source<br>> code. Since I am not a member of the collaboration, I cannot directly commit<br>> them into the git repository.<br>><br>> The first patch was written by Dávid Völgyes (formerly at Mediso and at<br>> COMPET). These are C++ bugfixes (unchecked ranges, memory corruptions).<br>> [1]<br>> <a href="https://dl.dropboxusercontent.com/u/43097994/gate7/cppfix_dvolgyes.patch.gz">https://dl.dropboxusercontent.com/u/43097994/gate7/cppfix_dvolgyes.patch.gz</a><br>><br>> The second patch contains Gate wrappers to all the missing Geant4 solid<br>> objects from<br>> <a href="http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04.html">http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04.html</a><br>> .<br>> With this patch the following extra shapes will be available: cut tube,<br>> elliptical cone, generic trapezoid, hyperbolic tube, parallelepiped,<br>> paraboloid tube, tetrahedron, torus, twisted box, twisted trapezoid, generic<br>> twisted trapezoid and twisted tube segment.<br>> [2]<br>> <a href="https://dl.dropboxusercontent.com/u/43097994/gate7/geant4-geometry.patch.gz">https://dl.dropboxusercontent.com/u/43097994/gate7/geant4-geometry.patch.gz</a><br>><br>> The third patch is a heavy modification of the Interfile reader. Besides<br>> some code cleaning and refactoring, it solves the following issues:<br>> - if the key 'name of data file' is present in the header file then it won't<br>> guess the name<br>> - the 'number of bytes per pixel' key (1,2,4,8...) is implemented<br>> - the 'data offset in bytes' key is implemented<br>> - the 'number format' key now accepts 'signed integer', 'unsigned integer',<br>> 'short float', 'long float' and (for convenience) 'float', as seen in the<br>> Interfile 3.3 standard.<br>> The interfile reader thus accepts signed or unsigned 8, 16, 32 or 64 bit<br>> integer as well as 32 (float) or 64 bit (double) floating point data from<br>> little or big endian binary file.<br>> [3] <a href="https://dl.dropboxusercontent.com/u/43097994/gate7/interfile.patch.gz">https://dl.dropboxusercontent.com/u/43097994/gate7/interfile.patch.gz</a><br>><br>> cheers,<br>> Gergely<br>><br>> ---<br>> Gergely Patay<br>> physicist<br>> Mediso Medical Imaging Systems Ltd.<br>> Hungary<br><br><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 16, 2014 at 11:40 AM, JAN Sebastien <span dir="ltr"><<a href="mailto:sebastien.jan@cea.fr" target="_blank">sebastien.jan@cea.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div link="blue" vlink="purple" lang="FR"> <div> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">Hi Amy,<u></u><u></u></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">As explained by Marc, this is a memory leak…probably du to the fact that the energy of optical photons which are generated is out of the range defined in the xml files (material & surface). Try to correct that point and fell free to tell us if the problem is solved.<u></u><u></u></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">Cheers<u></u><u></u></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US">Sebastien<u></u><u></u></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p> <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" lang="EN-US">De :</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" lang="EN-US"> </span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a> [mailto:<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>] <b>De la part de</b> Marc Chamberland<br> <b>Envoyé :</b> lundi 15 septembre 2014 16:06<br> <b>À :</b> Amy Meldrum<br> <b>Cc :</b> Gate Users<br> <b>Objet :</b> Re: [Gate-users] Jobs killed "memory exceeded"?<u></u><u></u></span></p> </div> </div><div><div class="h5"> <p class="MsoNormal"><u></u> <u></u></p> <p class="MsoNormal">Hi Amy, <u></u><u></u></p> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Perhaps there is a memory leak? If there is, it's gonna be very annoying for you to troubleshoot if you have no C++ experience.<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">I'd suggest you look at using Valgrind to detect memory leaks. You can find Valgrind here: <a href="http://valgrind.org" target="_blank">http://valgrind.org</a><u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">The Quick Start page should help you run it. Feel free to post the output to the mailing list or send it to me and I'll have a quick look.<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Good luck!<u></u><u></u></p> </div> <div> <p class="MsoNormal">Marc <u></u><u></u></p> <div> <div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">__________________________<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Marc Chamberland, MSc<u></u><u></u></p> </div> <p class="MsoNormal">PhD candidate<br> Department of Physics<br> Carleton University<br> Ottawa (ON)<u></u><u></u></p> </div> </div> <p class="MsoNormal"><u></u> <u></u></p> <div> <div> <p class="MsoNormal">On Sep 14, 2014, at 8:55, Amy Meldrum <<a href="mailto:ameldru@g.clemson.edu" target="_blank">ameldru@g.clemson.edu</a>> wrote:<u></u><u></u></p> </div> <p class="MsoNormal"><br> <br> <u></u><u></u></p> <div> <p class="MsoNormal">Gate users, <u></u><u></u></p> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">I have been running simulations using optical photons that run to completion when I am using a beta source. However, when I change the source to an alpha source, suddenly all of my simulations only run for a few minutes before being killed. It seems like the memory usage skyrockets beyond some limit and get killed. <u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Why would changing only the source do this? Is there something I can do to stop this from happening? The simulation runs fine for a few particles, but I am not sure why it would behave like this.<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Please help. Thank you,<u></u><u></u></p> </div> <div> <p class="MsoNormal"><u></u> <u></u></p> </div> <div> <p class="MsoNormal">Amy<u></u><u></u></p> </div> </div> <p class="MsoNormal">_______________________________________________<br> Gate-users mailing list<br> <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><u></u><u></u></p> </div> <p class="MsoNormal"><u></u> <u></u></p> </div> </div></div></div> </div> <br>_______________________________________________<br> Gate-users mailing list<br> <a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br></blockquote></div><br></div></div>