<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN"> <HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8"> <META NAME="GENERATOR" CONTENT="GtkHTML/4.2.2"> </HEAD> <BODY> Hi, unfortunately I can not reproduce your problem. Could you be more specific? E.g. contents of your environmental variables (type printenv in a terminal and post the output). Generally GATE requires some environmental variables. It does not make a difference where these are set. You could put them in .bashrc, then they will be set automatically when you open a terminal. Alternatively, especially when using multiple geant4/Gate releases, you could create a script which sets the required varibles as soon as you source the script. Such a script may be called envGate.sh. You should create it yourself. The file should contain: source <PATHTOROOT>/bin/thisroot.sh source<PATHTOGEANT4>/bin/geant4.sh export PATH=$PATH:<PATHTOGATE>/bin export GC_GATE_EXE_DIR=<PATHTOGATE>/bin export GC_DOT_GATE_DIR=./ Please replace <PATHTOGATE>, <PATHTOGEANT4> and <PATHTOROOT> with the correct absolute file path to your installation directories. Cheers, Hermann On Wed, 2015-01-21 at 13:29 +0000, André Miguel Monteiro wrote: <BLOCKQUOTE TYPE=CITE> Dear Hermann, Soman and all Gate users, I am having the same problem as you Soman. </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Compiling gjs.cc... </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Compiling GateMacfileParser.cc... </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> ./src/GateMacfileParser.cc: In constructor ‘GateMacfileParser::GateMacfileParser(G4String, G4int, G4int, G4String*)’: </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> ./src/GateMacfileParser.cc:41:26: error: ‘getpid’ was not declared in this scope </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> srand(time(NULL)*getpid()); </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> ^ </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> make: *** [tmp/GateMacfileParser.o] Error 1 </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> As you did I add the variables to my ~/.bashrc file: </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> export GC_DOT_GATE_DIR=/home/andre/workdir/ </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> export GC_GATE_EXE_DIR=/home/andre/programs/Gate/opt/simulation/gate.7.0-install/bin </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> I set these paths, because in other machine I have Gate v.6.1 installed with cluster tools that point GC_DOT_GATE_DIR to a work directory and GC_GATE_EXE_DIR where is present the Gate executable. </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Does anyone know how to solve this problem? </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Thank you. </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Cheers, </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> André </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> -------------------------------- MSc Student in Biomedical and Biophysics Engineering at Faculty of Sciences of the University of Lisbon Instituteof Biophysics and Biomedical Engineering Faculty of Sciences, Universityof Lisbon Campo Grande 1749-016 Lisbon Room Office: 1.02 Extension: 20509 Email: ammonteiro@fc.ul.pt </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> LinkedIn Profile: <A HREF="http://linkedin.com/in/andremmonteiro">http://linkedin.com/in/andremmonteiro</A> Website: <A HREF="http://www.ibeb.fc.ul.pt/">http://www.ibeb.fc.ul.pt/</A> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> <HR ALIGN="center"> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> From: gate-users-bounces@lists.opengatecollaboration.org <gate-users-bounces@lists.opengatecollaboration.org> on behalf of S. Saghamanesh <s.saghamanesh@yahoo.com> Sent: Saturday, December 20, 2014 2:02 PM To: Hermann Fuchs; gate-users@lists.opengatecollaboration.org Subject: Re: [Gate-users] Problem with job splitter installation </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Dear Hermann, </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Thanks for your note. My problem is that my system can't find the "env_gate.sh". I even don't have a cmake file in the "job splitter" directory to compile. </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Based on the directions in Gate manual, I should add two environment variables in my ".bashrc" file as below, am I right? </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> export GC_DOT_GATE_DIR=/somedir/ >> (I set it to /home/soman/Gate/gate_v7/cluster_tools/jobsplitter) </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> export GC_GATE_EXE_DIR=/somedir/bin/Linux-g++/ >> (I set it to /home/soman/Gate/gate_v7/cluster_tools/jobsplitter) </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> However, when I go into above path in a terminal and write source env_gate.sh, my system can't find env_gate.sh. I don't know what's the problem. Thanks for any idea of yours and also ideas of other users, if any, on this. </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> - Soman </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> On Tuesday, December 16, 2014 2:25 PM, Hermann Fuchs <hermann.fuchs@meduniwien.ac.at> wrote: </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> Hi, at our place the following procedure worked on Scientific Linux 6 and Ubuntu 14.04 LTS. go to /opt/simulation/gate6_1/cluster_tools/jobsplitter <PRE> cd /opt/simulation/gate6_1/cluster_tools/jobsplitter </PRE> make sure Gate paths are set <PRE> source /opt/simulation/gate6_1/env_gate.sh </PRE> compile <PRE> make </PRE> Copy the library to the correct place <PRE> cp /opt/simulation/gate6_1/cluster_tools/jobsplitter/tmp/Linux-g++/gjs/libgjs.so /opt/simulation/gate6_1/cluster_tools/jobsplitter/bin/Linux-g++ </PRE> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/simulation/gate6_1/cluster_tools/jobsplitter/tmp/Linux-g++/gjs Cheers, Hermann On Wed, 2014-12-10 at 14:08 +0000, S. Saghamanesh wrote: <BLOCKQUOTE TYPE=CITE> Hi, </BLOCKQUOTE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> <BLOCKQUOTE TYPE=CITE> I get this error when I try to make job splitter in its directory: Compiling GateMacfileParser.cc... ./src/GateMacfileParser.cc: In constructor ‘GateMacfileParser::GateMacfileParser(G4String, G4int, G4int, G4String*)’: ./src/GateMacfileParser.cc:41:26: error: ‘getpid’ was not declared in this scope make: *** [tmp/GateMacfileParser.o] Error 1 What is it about? Does anybody know what's the procedure of installing job splitter? Thanks </BLOCKQUOTE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> <BLOCKQUOTE TYPE=CITE> - Soman </BLOCKQUOTE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> <BLOCKQUOTE TYPE=CITE> <PRE> _______________________________________________ Gate-users mailing list <A HREF="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</A> <A HREF="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</A> </PRE> </BLOCKQUOTE> <TABLE CELLSPACING="0" CELLPADDING="0" WIDTH="100%"> <TR> <TD> -- <PRE> ------------- DI Hermann Fuchs Christian Doppler Laboratory for Medical Radiation Research for Radiation Oncology Department of Radiation Oncology Medical University Vienna Währinger Gürtel 18-20 A-1090 Wien Tel. + 43 / 1 / 40 400 72710 Mail. hermann.fuchs@meduniwien.ac.at </PRE> </TD> </TR> </TABLE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> </BLOCKQUOTE> <BLOCKQUOTE TYPE=CITE> _______________________________________________ Gate-users mailing list <A HREF="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</A> <A HREF="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</A> </BLOCKQUOTE> <TABLE CELLSPACING="0" CELLPADDING="0" WIDTH="100%"> <TR> <TD> -- <PRE> ------------- DI Hermann Fuchs Christian Doppler Laboratory for Medical Radiation Research for Radiation Oncology Department of Radiation Oncology Medical University Vienna Währinger Gürtel 18-20 A-1090 Wien Tel. + 43 / 1 / 40 400 72710 Mail. hermann.fuchs@meduniwien.ac.at </PRE> </TD> </TR> </TABLE> </BODY> </HTML>