<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Michael,<div class=""><br class=""></div><div class="">I came across this problem, I am also running GATE in docker containers via HTCondor.</div><div class="">I didn’t know about the --login argument.</div><div class=""><br class=""></div><div class="">Try this in your this-job.sh (change the paths with yours):</div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><span class="">#!/bin/sh</span><span class=""><br class=""></span><span class=""># set up environment variables<br class=""></span><span class="">source /geant4/geant4.10.02.p02-install/bin/geant4.sh<br class=""></span><span class="">export PATH=\$PATH:/gate/gate_v7.2-install/bin</span><span class=""><br class=""></span><div class=""><span class=""># start</span></div><div class=""><span class="">cd `dirname $0`</span></div><div class=""><span class="">Gate this_macro.mac > run.log</span></div></blockquote><div class=""><span class=""><br class="">Cheers,</span></div><div class=""><span class=""> Maxime Chauvin<br class=""><br class=""><blockquote type="cite" class="">On 9 Oct 2018, at 22:22, Miller, Michael <<a href="mailto:Michael.a.Miller@philips.com" class="">Michael.a.Miller@philips.com</a>> wrote:<br class=""><br class="">Dear gate-users,<br class=""> <br class="">I’ve been running Gate in the docker container and now want to use HT condor to schedule jobs. When I run the gate container in scripts or manually, I mount a local drive for the gate output:<br class=""> <br class=""> docker run -it --mount type=bind,source=/scratch-for-this-job,target=/scratch \<br class="">opengatecollaboration/gate /scratch/this-job.sh<br class=""> <br class="">I start gate with the script /scratch-for-this-job/this-job.sh:<br class=""> #!/usr/bin/bash --login<br class=""> cd `dirname $0`<br class="">Gate this_macro.mac<br class=""> <br class="">The “--login" is needed to ensure that the shell in the container finds Gate. I’ve tried moving this to HT condor with this submit file:<br class="">universe = docker<br class="">docker_image = opengatecollaboration/gate<br class="">executable = /scratch-for-this-job‑/this-job.sh<br class="">output = docker-gate.out.$(ClusterID)-$(ProcID)<br class="">error = docker-gate.err.$(ClusterID)-$(ProcID)<br class="">log = docker-gate.log.$(ClusterID)-$(ProcID)<br class="">queue<br class=""> <br class="">This fails with a “Gate: command not found” error. I think this is because the script is not starting as a login shell, even with the “--login" option. <br class=""> <br class="">Can anyone provide an example of how they’ve used the docker universe with the opengatecollaboration/gate? Or have people been using the vanilla universe and managing directories separately from condor?<br class=""> <br class="">Thanks, Mike<br class=""><br class="">The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.<br class="">_______________________________________________<br class="">Gate-users mailing list<br class=""><a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">Gate-users@lists.opengatecollaboration.org</a><br class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users<br class=""></blockquote><br class=""></span></div></body></html>