<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"> <style type="text/css" style="display:none"></style> </head> <body dir="ltr" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;"> <p>Dear Hermann, Soman and all Gate users,<br> </p> <p><br> </p> <p>I am having the same problem as you Soman.<br> </p> <p><br> </p> <div>Compiling gjs.cc...</div> <div>Compiling GateMacfileParser.cc...</div> <div>./src/GateMacfileParser.cc: In constructor ‘GateMacfileParser::GateMacfileParser(G4String, G4int, G4int, G4String*)’:</div> <div>./src/GateMacfileParser.cc:41:26: error: ‘getpid’ was not declared in this scope</div> <div> srand(time(NULL)*getpid());</div> <div> ^</div> <div>make: *** [tmp/GateMacfileParser.o] Error 1</div> <div><br> <br> As you did I add the variables to my ~/.bashrc file:<br> </div> <div><br> </div> <div><br> </div> <div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr" class="" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif; font-size:16px"> <font size="2" class="" id="yui_3_16_0_1_1419081719114_4660"></font></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr" class="" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif; font-size:16px"> <div>export GC_DOT_GATE_DIR=/home/andre/workdir/</div> <div><br> </div> <div>export GC_GATE_EXE_DIR=/home/andre/programs/Gate/opt/simulation/gate.7.0-install/bin<br> </div> <div><br> I set these paths, because in other machine I have Gate v.6.1 installed with cluster tools that point <span style="font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">GC_DOT_GATE_DIR</span> to a work directory and <span style="font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">GC_GATE_EXE_DIR</span> where is present the Gate executable.<br> </div> <div><br> </div> <div>Does anyone know how to solve this problem?<br> </div> <div><br> </div> <div>Thank you.<br> </div> <div><br> </div> <div>Cheers,<br> </div> <div><br> </div> <div>André<br> </div> </div> <br> </div> <div id="Signature"> <div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0"> <div class="BodyFragment"> <div class="PlainText" style="font-family:Calibri,Arial,Helvetica,sans-serif"><font><br> <br> <font size="2" style="font-family:Calibri,Arial,Helvetica,sans-serif">--------------------------------</font><br> <font size="2" style="font-family:Calibri,Arial,Helvetica,sans-serif">MSc Student in Biomedical and Biophysics Engineering at Faculty of Sciences of the University of Lisbon</font><br> <br> <font color="black" size="3" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:small"><span dir="ltr" style="font-size:12pt; background-color:white"><font size="2"><span lang="en">Institute</span><span lang="en"> </span><span lang="en">of Biophysics and</span><span lang="en"> </span><span lang="en">Biomedical Engineering</span><span lang="en"><br> </span><span lang="en">Faculty</span><span lang="en"> </span><span lang="en">of Sciences, University</span><span lang="en"> </span><span lang="en">of Lisbon</span><br> Campo Grande<br> 1749-016 Lisbon<br> <br> </font></span></font><font size="2"><font style="font-family:Calibri,Arial,Helvetica,sans-serif">Room Office: 1.02</font><br> <font color="black" style="font-family:Calibri,Arial,Helvetica,sans-serif"><span dir="ltr" style="background-color:white">Extension: 20509 <br> Email: ammonteiro@fc.ul.pt</span></font></font></font></div> <div class="PlainText"><font size="2"><font color="black" style="font-family:Calibri,Arial,Helvetica,sans-serif"><span dir="ltr" style="background-color:white">LinkedIn Profile: </span></font><font color="#000000" style="text-decoration:none; line-height:21px; background-color:rgb(255,255,255)"><a tabindex="0" href="http://linkedin.com/in/andremmonteiro">http://linkedin.com/in/andremmonteiro</a></font><font color="black" style="font-family:Calibri,Arial,Helvetica,sans-serif"><span dir="ltr" style="background-color:white"><br> Website: <a tabindex="0" href="http://www.ibeb.fc.ul.pt/" target="_blank">http://www.ibeb.fc.ul.pt/</a></span></font></font><br> </div> </div> </div> </div> <div style="color:rgb(33,33,33)"> <hr tabindex="-1" style="display:inline-block; width:98%"> <div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> gate-users-bounces@lists.opengatecollaboration.org <gate-users-bounces@lists.opengatecollaboration.org> on behalf of S. Saghamanesh <s.saghamanesh@yahoo.com><br> <b>Sent:</b> Saturday, December 20, 2014 2:02 PM<br> <b>To:</b> Hermann Fuchs; gate-users@lists.opengatecollaboration.org<br> <b>Subject:</b> Re: [Gate-users] Problem with job splitter installation</font> <div> </div> </div> <div> <div style="color:#000; background-color:#fff; font-family:HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; font-size:16px"> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr"><span id="yui_3_16_0_1_1419081719114_3453"><font size="2" id="yui_3_16_0_1_1419081719114_3576">Dear Hermann,</font></span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr"><span><font size="2"><br> </font></span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr"><span id="yui_3_16_0_1_1419081719114_3452"><font size="2" id="yui_3_16_0_1_1419081719114_3572">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. </font></span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr"><span id="yui_3_16_0_1_1419081719114_10732"><font size="2" id="yui_3_16_0_1_1419081719114_10731">Based on the directions in Gate manual, I should add two environment variables in my ".bashrc" file as below, am I right?</font></span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr"><span><font size="2"><br> </font></span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr" class="" style=""><font size="2" class="" id="yui_3_16_0_1_1419081719114_4660">export GC_DOT_GATE_DIR=/somedir/ >> (I set it to </font><span class="" id="yui_3_16_0_1_1419081719114_8642" style="font-size:small">/home/soman/Gate/gate_v7/cluster_tools/jobsplitter)</span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr"><font size="2"></font></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr" class="" style=""><font size="2" class="" id="yui_3_16_0_1_1419081719114_4037" style="">export GC_GATE_EXE_DIR=/somedir/bin/Linux-g++/ >> (</font><font size="2" class="" id="yui_3_16_0_1_1419081719114_4660" style="">I set it to </font><span class="" id="yui_3_16_0_1_1419081719114_8642" style="font-size:small">/home/soman/Gate/gate_v7/cluster_tools/jobsplitter)</span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr" class="" style=""><br> </div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr" class="" style=""><font size="2" class="" id="yui_3_16_0_1_1419081719114_5314" style="">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, </font><span class="" style="font-size:small">if any,</span><span class="" style="font-size:small"> on this.</span></div> <div id="yui_3_16_0_1_1419081719114_3390" dir="ltr" class="" style=""><font size="2" class="" id="yui_3_16_0_1_1419081719114_10730" style="">- Soman</font></div> <div class="qtdSeparateBR"><br> <br> </div> <div class="yahoo_quoted" style="display:block"> <div style="font-family:HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; font-size:16px"> <div style="font-family:HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; font-size:16px"> <div dir="ltr"><font size="2" face="Arial">On Tuesday, December 16, 2014 2:25 PM, Hermann Fuchs <hermann.fuchs@meduniwien.ac.at> wrote:<br> </font></div> <br> <br> <div class="y_msg_container"> <div id="yiv6214733651"> <div>Hi,<br clear="none"> <br clear="none"> at our place the following procedure worked on Scientific Linux 6 and Ubuntu 14.04 LTS.<br clear="none"> <br clear="none"> 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<br clear="none"> <br clear="none"> Cheers,<br clear="none"> Hermann<br clear="none"> <br clear="none"> On Wed, 2014-12-10 at 14:08 +0000, S. Saghamanesh wrote: <blockquote type="CITE">Hi, </blockquote> <blockquote type="CITE"> <div class="yiv6214733651yqt6400374327" id="yiv6214733651yqtfd22749"><br clear="none"> <br clear="none"> </div> </blockquote> <div class="yiv6214733651yqt6400374327" id="yiv6214733651yqtfd66471"> <blockquote type="CITE">I get this error when I try to make job splitter in its directory: </blockquote> <blockquote type="CITE"><br clear="none"> <br clear="none"> </blockquote> <blockquote type="CITE">Compiling GateMacfileParser.cc...<br clear="none"> ./src/GateMacfileParser.cc: In constructor ‘GateMacfileParser::GateMacfileParser(G4String, G4int, G4int, G4String*)’:<br clear="none"> ./src/GateMacfileParser.cc:41:26: error: ‘getpid’ was not declared in this scope<br clear="none"> make: *** [tmp/GateMacfileParser.o] Error 1<br clear="none"> <br clear="none"> </blockquote> <blockquote type="CITE"><br clear="none"> <br clear="none"> </blockquote> <blockquote type="CITE">What is it about? Does anybody know what's the procedure of installing job splitter? </blockquote> <blockquote type="CITE"><br clear="none"> <br clear="none"> </blockquote> <blockquote type="CITE">Thanks </blockquote> </div> <blockquote type="CITE"> <div class="yiv6214733651yqt6400374327" id="yiv6214733651yqtfd45353">- Soman</div> <br clear="none"> <br clear="none"> </blockquote> <blockquote type="CITE"><br clear="none"> <br clear="none"> </blockquote> <blockquote type="CITE"> <pre>_______________________________________________ Gate-users mailing list <a rel="nofollow" shape="rect" target="_blank" href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> <a rel="nofollow" shape="rect" target="_blank" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </pre> </blockquote> <br clear="none"> <table cellspacing="0" cellpadding="0" width="100%"> <tbody> <tr> <td colspan="1" rowspan="1">-- <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> <div class="yiv6214733651yqt6400374327" id="yiv6214733651yqtfd56695"></div> </td> </tr> </tbody> </table> <div class="yiv6214733651yqt6400374327" id="yiv6214733651yqtfd08167"></div> </div> </div> <br> _______________________________________________<br clear="none"> Gate-users mailing list<br clear="none"> <a shape="rect" href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br clear="none"> <a shape="rect" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br> <br> </div> </div> </div> </div> </div> </div> </div> </body> </html>