<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div> <!--StartFragment--><div>Hi Abderrahim,<br></div><div><br data-mce-bogus="1"></div><div>Below there are some tips regarding a similar question. I hope it works for you.<br data-mce-bogus="1"></div><div><br data-mce-bogus="1"></div><div>Best,<br data-mce-bogus="1"></div><div>Consuelo.<br data-mce-bogus="1"></div><div><br data-mce-bogus="1"></div><div><br data-mce-bogus="1"></div><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>De: </b>"Consuelo Guardiola" <guardiola@imnc.in2p3.fr><br><b>À: </b>"meryem fiak" <fiakmeryem.13@gmail.com><br><b>Envoyé: </b>Dimanche 24 Mars 2019 12:23:33<br><b>Objet: </b>Re: [Gate-users] GATE ON CLUSTER<br></div><br><div data-marker="__QUOTED_TEXT__"><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;" data-mce-style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;"><div>Hi Meryem,<br></div><br><div>You are welcome.</div><br><div>The last part is the execution of Gate of ALL the jobs that are inside .Gate/folder. It is: when you, first, export <span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-">GC_DOT_GATE_DIR</span></span></span></span>= /home/m.fiak/mywork and right after make ¨gjs -c openmosix -n 100 main.mac" (assuming that you are splitting100 jobs, for example, of a main job called "main.mac"), it will create a folder of split jobs inside .Gate/main/ path automatically, i.e. main1.mac, main2.mac, main3.mac...to main100.mac. Therefore, the script <br></div><br><div>#!/bin/bash<br>Gate <b>.Gate/main/main$</b>(($SLURM_PROCID+1)).mac</div><br><div>runs Gate of ALL the main1.mac, main2.mac....to main100.mac of the 100 split jobs above. <br></div><br><div>Try it and let me know if it works,<br></div><div>Best<br></div><div>Consuelo<br></div><br><hr id="zwchr"><div><b>De: </b>"meryem fiak" <fiakmeryem.13@gmail.com><br><b>À: </b>"Consuelo Guardiola" <guardiola@imnc.in2p3.fr><br><b>Envoyé: </b>Samedi 23 Mars 2019 17:42:12<br><b>Objet: </b>Re: [Gate-users] GATE ON CLUSTER<br></div><br><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Hi Consuelo,</div><div>Thank you so much for your reply and reactivity. <span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-">I understood that <span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-">I have to export GC_DOT_GATE_DIR. to my working directory <span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-">as indicated in the GATE users guide, but I didn't completely understand the last part : <br></span></span></span></span></span></span></div><div><div>------------------------------------------------------------------<br></div><div>#!/bin/bash<br>Gate <b>.Gate/main/main$</b>(($SLURM_PROCID+1)).mac<br>-------------------------------------------------------------------<br></div><br><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"></span></span></span></span></span></span></div><div><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"><br></span></span></span></span></span></span></div><div><span class="gmail-tlid-translation gmail-translation"><span title="" class="gmail-"></span></span>Here is my working directory: /home/m.fiak/mywork.<br></div><div>Here is my script <b>Job.sl</b> that I use for running GATE in sequential mode.</div><div>===================================================================<br></div><div>#!/bin/bash<br>#SBATCH -J GATE-Jobs <br>#SBATCH -o %x-%j.out<br>#SBATCH -e %x-%j.err<br>#SBATCH --partition=mediumq<br><br>ml xerces-c/gcc/64<br>ml qt/gcc/64<br>ml geant4/gcc/64/4.10.04.p02<br>ml root/gcc/64/6.14.02<br>ml gate/gcc/64/8.1.p01<br><br><br><br>mkdir -p $PWD/$SLURM_JOB_ID <br>cp $PWD/*.mac $PWD/*.db $PWD/$SLURM_JOB_ID<br>cd $PWD/$SLURM_JOB_ID<br>Gate main.mac</div><div>=====================================================</div><br><div>Best Regards.<br></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le ven. 22 mars 2019 à 11:34, Consuelo Guardiola <<a href="mailto:guardiola@imnc.in2p3.fr" target="_blank" data-mce-href="mailto:guardiola@imnc.in2p3.fr">guardiola@imnc.in2p3.fr</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left: 1px solid #cccccc; padding-left: 1ex;" data-mce-style="margin: 0px 0px 0px 0.8ex; border-left: 1px solid #cccccc; padding-left: 1ex;"><div><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt; color: #000000;" data-mce-style="font-family: arial,helvetica,sans-serif; font-size: 12pt; color: #000000;"><div>Hi Meriem,<br></div><br><div>I'm using a HPC platform with SLURM, which is not a problem for GATE submission jobs since it is just an utility for batch processing. A job (i.e. one of the files in which you split your main macro file) is the execution unit for SLURM. To ensure the proper scheduling of jobs, you have to fit together nodes and cores that can be used at the same time in a group (number of total jobs).</div><br><div>That said, you may split your macro as usual with the gjs splitter tool (***Note: before it, you must export GC_DOT_GATE_DIR= "where_you_want_to_store_the_data"). Then, you can launch your jobs using "sbatch" command as follows:</div><br><div>> sbatch "job_script"<br></div><br><div>where your "job_script" can be something like this (e.g. 480 jobs):<br></div><div>-----------------------------------------------------------------<br></div><div>#!/bin/bash<br>#SBATCH --ntasks 480<br>#SBATCH --qos=prace<br>#SBATCH --time=24:00:00<br>#SBATCH --job-name=O<br>#SBATCH --output=c_%j.out<br>#SBATCH --error=c_%j.err<br><br>srun ./Beam.sh<br>-----------------------------------------------------------------</div><div><br>in turn, "Beam.sh" file is:<br></div><br><div>------------------------------------------------------------------<br></div><div>#!/bin/bash<br>Gate .Gate/main/main$(($SLURM_PROCID+1)).mac<br>-------------------------------------------------------------------<br></div><br><div>which executes Gate for all your jobs that are into .Gate/ folder (pointed at ***)<br></div><br><br><div>I hope it works! <br></div><br><div>Best,<br></div><div>Consuelo<br></div><br><br><br><br><br><br><hr id="gmail-m_5688335968571731103zwchr"><div><b>De: </b>"Grevillot Loic" <<a href="mailto:loic.grevillot@medaustron.at" target="_blank" data-mce-href="mailto:loic.grevillot@medaustron.at">loic.grevillot@medaustron.at</a>><br><b>À: </b>"meryem fiak" <<a href="mailto:fiakmeryem.13@gmail.com" target="_blank" data-mce-href="mailto:fiakmeryem.13@gmail.com">fiakmeryem.13@gmail.com</a>><br><b>Cc: </b>"gate-users" <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank" data-mce-href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br><b>Envoyé: </b>Vendredi 22 Mars 2019 10:56:41<br><b>Objet: </b>Re: [Gate-users] GATE ON CLUSTER<br></div><br><div><div class="gmail-m_5688335968571731103WordSection1"><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" lang="EN-US">Dear Meriem,</span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" lang="EN-US"> </span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" lang="EN-US">please always use the GATE mailing-list. For cluster business, I am sure you will find much more experienced users than I am…</span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" lang="EN-US"> </span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" lang="EN-US">Best,</span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" lang="EN-US">Loïc</span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif; color: #1f497d;" lang="EN-US"> </span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><b><span style="font-size: 11pt; font-family: 'Calibri',sans-serif;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif;" lang="EN-US">From:</span></b><span style="font-size: 11pt; font-family: 'Calibri',sans-serif;" data-mce-style="font-size: 11pt; font-family: 'Calibri',sans-serif;" lang="EN-US"> meryem fiak [mailto:<a href="mailto:fiakmeryem.13@gmail.com" target="_blank" data-mce-href="mailto:fiakmeryem.13@gmail.com">fiakmeryem.13@gmail.com</a>] <br> <b>Sent:</b> Freitag, 22. März 2019 00:02<br> <b>To:</b> Grevillot Loic <<a href="mailto:loic.grevillot@medaustron.at" target="_blank" data-mce-href="mailto:loic.grevillot@medaustron.at">loic.grevillot@medaustron.at</a>><br> <b>Subject:</b> GATE ON CLUSTER</span></p><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"> </p><div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;">Hello,</p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;">I'm a phd student in medical physics and I have a question regarding "Running GATE on a cluster".</p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;">I'm working on MC simulation of linacs in radiotherapy via GATE/GEANT4 platforme and i'm hoping to use the gjs Gate jobsplitter on a cluster (parallel mode), but the cluster uses <b>Slurm</b> which <span class="gmail-m_5688335968571731103gmail-m-5363044377995467041gmail-m7212328658302863106gmail-m-3840770012175089402gmail-"> does not belong to the 4 clusterplatform listed by GATE ( HT Condor, openPBS, openmosix and Xgrid).</span></p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"> </p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;">I would like to know how can I split my Gate macros into several jobs using slurm (job scheduler).</p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span class="gmail-m_5688335968571731103gmail-">I already posted the problem in Gate-users list forum but I haven't received any response.</span></p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;">Thank you so much for your help.</p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"> </p></div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><b><span style="font-size: 10.5pt; font-family: 'Arial',sans-serif;" data-mce-style="font-size: 10.5pt; font-family: 'Arial',sans-serif;" lang="EN-GB">Kind regards.</span></b></p><div><div id="gmail-m_5688335968571731103gmail-:2y3"><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><img id="gmail-m_5688335968571731103_x0000_i1025" src="https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif"></p></div></div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><br clear="all"> <br> --</p><div><div><div><div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><b><span style="font-size: 9.5pt;" data-mce-style="font-size: 9.5pt;">Ms</span></b><span style="font-size: 9.5pt;" data-mce-style="font-size: 9.5pt;">.<b><i><span style="color: #38761d;" data-mce-style="color: #38761d;">FIAK Meriem</span></i></b></span></p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 9.5pt;" data-mce-style="font-size: 9.5pt;">-------------------------------------------------------------------</span></p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><b><span style="font-size: 9.5pt;" data-mce-style="font-size: 9.5pt;">Job Title: <i><span style="color: #38761d;" data-mce-style="color: #38761d;">Phd Student</span></i><span style="color: #38761d;" data-mce-style="color: #38761d;"> </span></span></b><span style="font-size: 9.5pt;" data-mce-style="font-size: 9.5pt;"></span></p></div><div><p class="MsoNormal" style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 9.5pt;" data-mce-style="font-size: 9.5pt;">--------------------------------------------------------------------</span></p></div></div></div></div></div></div></div></div></div></div></blockquote></div></div></div></div><!--EndFragment--> </div><div><br></div><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>De: </b>"Abderrahim Abderrahim" <abderrahimphy@gmail.com><br><b>À: </b>gate-users@lists.opengatecollaboration.org<br><b>Envoyé: </b>Jeudi 2 Mai 2019 19:13:14<br><b>Objet: </b>[Gate-users] GATE in CLUSTER<br></div><br><div data-marker="__QUOTED_TEXT__"><div dir="ltr"><div dir="ltr"><b>Hello every body ;</b><div><b>First' I'm PhD student in medical physics.</b></div><div><b>I have an problem , How to running GATE in cluster with <i><span data-mce-style="color: #ff0000;" style="color: #ff0000;" color="#ff0000">SLURM</span></i><span style="font-style:italic"> </span>? please can you help me everyone !!</b></div><div><b>My E-Mail: <a href="mailto:abderrahimphy@gmail.com" target="_blank">abderrahimphy@gmail.com</a></b><br data-mce-bogus="1"></div><div><b>Best regards<br></b></div><div><b>Thank you !!</b></div><div><b><br></b></div><br><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><b>Abderrahim </b><br><div><b><i> </i></b></div></div></div></div></div></div>
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