Hi Jonathan,<br><br>I have had a look in your last Gate-log's. It realy seams that you have an issue with the compilation and link of your Gate. This has nothing to do with your macro files.<br>Gate 3.1.x should compil with gcc 3.2.x. On my computer I have used gcc-4.1.2, x86_64, and on my cluster I've used gcc 3.x? (don't remember sub-version), x86.<br><br>You should have a look in the logs of your compilation about any errors.<br><br>Good luck,<br><br>Samuel Burg<br><br><br><b><i>kam kim <kimkam007@gmail.com></i></b> a écrit :<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> <div>Dear Samuel,</div> <div> </div> <div>I am thinking if there is something wrong with the linux version on the cluster---Red Hat 3.2.3-58. But which can only affect the compilation of GATE. I am really getting stucky. I'm checking with the adminstrator about whether the cluster has some librarys such as openGL. Do
you have any other suggestions? </div> <div>Thank you very much.</div> <div> </div> <div>Best regards,</div> <div>Jonathan</div> <div> </div> <div><br><br> </div> <div><span class="gmail_quote">On 10/26/07, <b class="gmail_sendername">kam kim</b> <<a href="mailto:kimkam007@gmail.com">kimkam007@gmail.com</a>> wrote:</span> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"> <div>Dear Samuel,</div> <div> </div> <div>I tried this mac and got the output of Gate in a log-file. Attached are the log-file and a file including environmental variables before I performed Gate.</div> <div> </div> <div>Thanks,</div> <div><span class="q" id="q_115de744707fa398_1"> <div>Jonathan</div> <div><br><br> </div> <div><span class="gmail_quote">On 10/26/07, <b class="gmail_sendername">Samuel BURG</b> <<a onclick="return top.js.OpenExtLink(window,event,this)"
href="mailto:samuel_burg@yahoo.fr" target="_blank">samuel_burg@yahoo.fr </a>> wrote:</span> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"><span>All right, <br><br>your macro files are good.<br><br>try this one ("an-other-benchmarkPET.mac "), and copy-past the output in a log-file, so we can try to figure out what's happening with your gate. <br><br>also show us the environment variables you set before to launch gate.<br><br></span> <div><span>best regards,<br><br>Samuel<br><br><b><i>kam kim <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:kimkam007@gmail.com" target="_blank">kimkam007@gmail.com </a>></i></b> a écrit :</span> </div> <blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;"> <div><span> <div>Dear Samuel,</div> <div> </div> <div>I used your benchmarkPET.mac file and got almost the same problem.
As you suggested, attached are a tar file including all mac files and a file named benchmarkPET.log including the output of Gate. I also attached a file including the environmental variable setup in the cluster, which is named cluster.env. I hope that these files will give you more information to help me figure out the problem. </div> <div> </div> <div>Thank you very much.<br><br>Best regards,</div> <div>Jonathan</div> <div> </div> <div> </div> <div><span class="gmail_quote">On 10/26/07, <b class="gmail_sendername">Samuel BURG</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:samuel_burg@yahoo.fr" target="_blank">samuel_burg@yahoo.fr </a>> wrote:</span> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Dear Jonathan,<br><br>I have test my benchmarkPET.mac, right out-of-the box from gate-v3.1.2, and it run exactly as it
should, so it seams that your benchmarkPET.mac file has been corrupted.<br><br>Check if the command :<br>"/run/initialize"<br>is call BEFORE the command :<br>"/control/execute digitizer.mac"<br>in your benchmarkPET.mac file.<br><br> For now, I don't see other explaination of your problem.<br><br>So,<br>1) can you send me all your *.mac file in a tar.gz file ?<br>2) try the benchmarkPET.mac file I've attached to this mail.<br>3) if there is error remaining copy-past all the output of Gate in a file and send it to us. <div><span><br><br>Regards,<br><br>Samuel<br><br><b><i>kam kim <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:kimkam007@gmail.com" target="_blank">kimkam007@gmail.com </a>></i></b> a écrit : <blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;"> <div>Dear Samuel;</div> <div> </div> <div>When I run Gate benchmarkPET.mac, I got errors as follows:</div> <div>***** COMMAND NOT
FOUND </gate/digitizer/Singles/insert adder> *****<br>and</div> <div>***** COMMAND NOT FOUND </gate/output/ascii/setOutFileHitsFlag 0> *****<br> </div> <div>Then I looked at GATE-USER talk. I noticed that you answered a similiar question to MJ. But in my case, the linking gate was successfully done and root version is 5.14. Could you please help me out? Thanks in advance. </div> <div> </div> <div>Best regards,</div> <div>Jonathan</div> <div> </div> <div><br> </div> <div><span class="gmail_quote">On 10/18/07, <b class="gmail_sendername">Samuel BURG</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:samuel_burg@yahoo.fr" target="_blank">samuel_burg@yahoo.fr </a>> wrote:</span> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Dear Kam Kim,<br><br>I sugjest you to upgrade to version 3.1.2, as last month in a mail from one of the main
developer we can read this: <br><br><<<<<br><pre><tt>Dear<br> Gaters,<br><br>To perform correctly the <span style="font-weight: bold; color: rgb(0, 0, 255);">compressed voxel</span> capabilities and the gamma <br>backtoback emission with the last Gate version (<br><br>3.1.2), you must use<br><br> the <br>patch which is provided<br>with this e-mail;<br>Sorry for these<br> inconveniences.<br><br>All the best<br><br>Sebastien</tt></pre><<<<<<br><br>in fact this patch has already been apply on the Gate v3.1.2 available from the download area.<br><br>Second point is that g++/gcc version can matter in compilation error, but I'm not sure it will solve your specific problem. <br><br>Hope this will help,<br><br>best regards, <div><span><br><br>Samuel<br><br><b><i>kam kim <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:kimkam007@gmail.com" target="_blank">kimkam007@gmail.com</a>> </i></b>a écrit : <blockquote
style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;">Dear Samuel;<br><br>Thank you for your email. <br><br>In my local linux system, I installed CLHEP1.9.2.2, root5.14, geant4.8.0.p01 and gate_v3.1.1. It seems that this comibination works well, and then I decided to install them into a linux cluster. One possibility could be that linux-gcc or linux-g++ in the cluster is different from that in my local linux system. I don't know whether this would cause any problem. <br><br>Best regards,<br>Jonathan<br><br> <div><span class="gmail_quote">On 10/17/07, <b class="gmail_sendername">Samuel BURG</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:samuel_burg@yahoo.fr" target="_blank">samuel_burg@yahoo.fr </a>> wrote:</span> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Well, <br><br>it seems you have a problem with the version of
Geant4.<br><br>you should restart the install with the good versions : <br><br>Gate 3.1.1 + Geant4 8.1p2 + Root 5.12 + clhep <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://1.9.2.3/" target="_blank">1.9.2.3</a><br>or<br>Gate 3.1.2 + Geant4 9.0 + Root 5.14 + clhep <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://1.9.3.1/" target="_blank"> 1.9.3.1</a> / <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://2.0.3.1/" target="_blank">2.0.3.1</a><br><br>don't mix the versions.<br><br>Regards,<br><br>Samuel<br><b><i>kam kim <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:kimkam007@gmail.com" target="_blank"> kimkam007@gmail.com </a>></i></b> a écrit : <blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;"> <div><span> <table width="100%"> <tbody> <tr> <td dir="ltr"> <div><font face="Times New Roman,Times,serif"><span> <div></div>
<div>Dear All,</div> <div>When I tried to install gate_v3.1.1 in a linux cluster, I got an error as follows:</div> <div>src/GateCompressedVoxelOutput.cc:97: no method 'G4Material::GetMaterialTable' <br>src/GateCompressedVoxelOutPut.cc:130: no method 'G4Material::GetMaterialTable'<br>src/GateCompressedVoxelOutput.cc:131: invalid use of undefined type 'struct G4Material' </div> <div>make: *** Error 1</div> <div>I should point out that I successfully installed root-5.14, CLHEP1.9.2.2 and geant4.8.0.p01 in the cluster. </div> <div>Any suggestion would be appreciated.<br><br>Best regards, <br>Jonathan</div></span></font></div> <div></div></td></tr></tbody></table></span></div>_______________________________________________<br>Gate-users mailing list<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:Gate-users@lists.healthgrid.org" target="_blank"> Gate-users@lists.healthgrid.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)"
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<div><span>PATH=/usr/local/mpich-1.2.5..12-intel/bin:/usr/local/gm-1.6.5/bin:/usr/local/clustersuite-20040816/silver/bin:/usr/local/clustersuite-20040816/moab/bin:/usr/local/pbs-2.3.12-14/bin:/usr/local/intel-8.0-20040412/bin:/usr/local/pgi-5.1.3/linux86/5.1/bin:/usr/local/modules-env-3.1.6-6/bin:/usr/kerberos/bin:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:/home/zhibin/geant4/bin/Linux-g++:.:/home/zhibin/geant4/bin/Linux-g++:/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:/home/zhibin/geant4/bin/Linux-g++:.:/home/zhibin/geant4/bin/Linux-g++:/home/zhibin/.GATE/gate_v3.1.2::/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:/home/zhibin/geant4/bin/Linux-g++::/home/zhibin/geant4/bin/Linux-g++
<br>LANG=en_US.UTF-8<br>PBS_O_HOME=/home/zhibin<br>PBS_O_LANG=en_US.UTF-8<br>PBS_O_LOGNAME=zhibin<br>PBS_O_PATH=/usr/local/mpich-1.2.5..12-intel/bin:/usr/local/gm-1.6.5/bin:/usr/local/clustersuite-20040816/ silver/bin:/usr/local/clustersuite-20040816/moab/bin:/usr/local/pbs- 2.3.12-14/bin:/usr/local/intel-8.0-20040412/bin:/usr/local/pgi-5.1.3/linux86/5.1/bin:/usr/local/modules-env-3.1.6-6/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/home/zhibin/.GATE/ROOT5.14/bin:.:/home/zhibin/.GATE/autoconf/bin:.:/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:.:/home/zhibin/geant4/bin/Linux-g++:/home/zhibin/.GATE/ROOT5.14/bin:/home/zhibin/.GATE/autoconf/bin:/home/zhibin/geant4/bin/Linux-g++::/home/zhibin/geant4/bin/Linux-g++ <br>PBS_O_MAIL=/var/mail/zhibin<br>PBS_O_SHELL=/bin/tcsh<br>PBS_O_HOST=<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://wiglaf.phys.cwru.edu/"
target="_blank">wiglaf.phys.cwru.edu</a><br>PBS_O_WORKDIR=/home/zhibin <br>PBS_O_QUEUE=batch<br>HOME=/home/zhibin<br>LOGNAME=zhibin<br>PBS_JOBNAME=STDIN<br>PBS_JOBID=<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://8002.heorot.phys.cwru.edu/" target="_blank">8002.heorot.phys.cwru.edu </a><br>PBS_QUEUE=parallel<br>SHELL=/bin/tcsh<br>USER=zhibin<br>PBS_JOBCOOKIE=90E2C29AC84EF94099C3CF9CFCD851FB<br>PBS_NODENUM=0<br>PBS_TASKNUM=1<br>PBS_MOMPORT=15003<br>PBS_NODEFILE=/var/spool/pbs/aux/ <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://8002.heorot.phys.cwru.edu/" target="_blank"> 8002.heorot.phys.cwru.edu</a><br>PBS_ENVIRONMENT=PBS_INTERACTIVE<br>TERM=xterm<br>HOSTTYPE=i386-linux<br>VENDOR=intel<br>OSTYPE=linux<br>MACHTYPE=i386<br>SHLVL=1<br>PWD=/home/zhibin/.GATE/gate_v3.1.2/TEST-GATE<br>GROUP=rwb
<br>HOST=node22<br>LS_COLORS=no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.bz=00;31:*.tz=00;31:*.rpm=00;31:*.cpio=00;31:*.jpg=00;35:*.gif=00;35:*.bmp=00;35:*.xbm=00;35:*.xpm=00;35:*.png=00;35:*.tif=00;35: <br>G_BROKEN_FILENAMES=1<br>SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass<br>SUPPORTED=en_US.UTF-8:en_US:en<br>LESSOPEN=|/usr/bin/lesspipe.sh %s<br>LANGVAR=en_US.UTF-8<br>MANPATH=/usr/local/mpich-1.2.5..12-intel/man:/usr/local/clustersuite-20040816/moab/man:/usr/local/clustersuite-20040816/silver/man:/usr/local/pbs-2.3.12-14/man:/usr/local/intel-8.0-20040412/man:/usr/local/pgi-5.1.3/linux86/5.1/man:/usr/local/modules-env-3.1.6-6/man:
<br>MODULESHOME=/usr/local/modules-env-3.1.6-6<br>MODULE_VERSION=3.1.6<br>MODULE_VERSION_STACK=3.1.6<br>MODULEPATH=/usr/local/modules-env-3.1.6-6/version:/usr/local/modules-env-3.1.6-6/modulefiles:/usr/local/share/modulefiles:/usr/share/modulefiles: <br>LOADEDMODULES=modules:pgi:intel-compilers:pbs:clustersuite:gm:mpi:mkl<br>_MODULESBEGINENV_=/home/zhibin/.modulesbeginenv<br>_LMFILES_=/usr/local/modules-env-3.1.6-6/modulefiles/modules:/usr/local/share/modulefiles/pgi:/usr/local/share/modulefiles/intel-compilers:/usr/local/share/modulefiles/pbs:/usr/local/share/modulefiles/clustersuite:/usr/local/share/modulefiles/gm:/usr/local/share/modulefiles/mpi:/usr/local/share/modulefiles/mkl <br>LD_LIBRARY_PATH=/home/zhibin/.GATE/ROOT5.14/lib/root:/home/zhibin/.GATE/CLHEP2.0.3.1/lib<br>PGI=/usr/local/pgi-5.1.3<br>LM_LICENSE_FILE=28518@foyer2.osc.edu:/usr/local/pgi-5.1.3/license.dat<br>IA64ROOT=/usr/local/intel-
8.0-20040412/<br>GCCROOT=/usr<br>PBS_HOME=/var/spool/pbs<br>PBS_INSTALL=/usr/local/pbs-2.3.12-14<br>SILVERHOMEDIR=/var/spool/moab<br>MOABHOMEDIR=/var/spool/moab<br>MPI_FFLAGS=-I/usr/local/mpich-1.2.5..12-intel/include<br> MPI_F90FLAGS=-I/usr/local/mpich-1.2.5..12-intel/include<br>MPI_CXXFLAGS=-I/usr/local/mpich-1.2.5..12-intel/include<br>MPI_CFLAGS=-I/usr/local/mpich-1.2.5..12-intel/include<br>MPI_LIBS="-L/usr/local/mpich-1.2.5..12-intel/lib -lmpich -L/usr/local/gm/lib -lgm "<br>MKL=-L/usr/local/mkl-7.0.17/mkl70/lib/32 -lmkl -lmkl_lapack32 -lmkl_lapack64 -lguide<br>MKL_HOME=/usr/local/mkl-7.0.17<br>OMP_NUM_THREADS=1<br>MKL_STATIC=-L/usr/local/mkl-7.0.17 /mkl70/lib/32 -lmkl_lapack -lmkl_ia32 -lguide<br>PVM_RSH=/usr/bin/rsh<br>PVM_ROOT=/usr/share/pvm3<br>QTDIR=/usr/lib/qt-3.1<br>TMPDIR=/tmp/pbstmp.8002.heorot.phys.cwru.edu<br>ENVIRONMENT=BATCH<br>HOSTNAME=node22<br>GATEHOME=/home/zhibin/.GATE/gate_v3.1.2 <br>ROOTSYS=/home/zhibin/.GATE/ROOT5.14<br>XMFLAGS=
-I/usr/X11R6/include <br>XMLIBS= -lXm -lXpm <br>XAWFLAGS=<br>XAWLIBS=<br>G4WORKDIR=/home/zhibin/geant4<br>G4VERSION=9.0<br>G4SYSTEM=Linux-g++<br>G4INSTALL=/home/zhibin/.GATE/geant4.9.0/src/geant4 <br>G4INCLUDE=/home/zhibin/.GATE/geant4.9.0/include/geant4<br>G4LIB=/home/zhibin/.GATE/geant4.9.0/lib/geant4<br>G4LEVELGAMMADATA=/home/zhibin/.GATE/geant4.9.0-data/PhotonEvaporation2.0<br>G4RADIOACTIVEDATA=/home/zhibin/.GATE/geant4.9.0-data/RadioactiveDecay3.2 <br>G4LEDATA=/home/zhibin/.GATE/geant4.9.0-data/G4EMLOW4.3<br>G4NEUTRONHPDATA=/home/zhibin/.GATE/geant4.9.0-data/G4NDL0.2<br>CLHEP_BASE_DIR=/home/zhibin/.GATE/CLHEP2.0.3.1<br>CLHEP_INCLUDE_DIR=/home/zhibin/.GATE/CLHEP2.0.3.1/include <br>CLHEP_LIB_DIR=/home/zhibin/.GATE/CLHEP2.0.3.1/lib<br>CLHEP_LIB=CLHEP<br>G4VIS_BUILD_DAWN_DRIVER=1<br>G4VIS_BUILD_OPENGLX_DRIVER=1<br>G4VIS_BUILD_OPENGLXM_DRIVER=1<br>G4VIS_BUILD_RAYTRACERX_DRIVER=1<br>G4VIS_BUILD_VRML_DRIVER=1
<br>G4VIS_USE_DAWN=1<br>G4VIS_USE_OPENGLX=1<br>G4VIS_USE_OPENGLXM=1<br>G4VIS_USE_RAYTRACERX=1<br>G4VIS_USE_VRML=1< br>G4LIB_BUILD_STATIC=1<br>G4LIB_USE_GRANULAR=1<br>G4UI_USE_TCSH=1<br></span></div></blockquote><span> <br> <div> </div><hr size="1"> Ne gardez plus qu'une seule adresse mail ! <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.trueswitch.com/yahoo-fr/" target="_blank">Copiez vos mails</a> vers Yahoo! Mail <div></div> <div></div><div></div></span><br>_______________________________________________<br>Gate-users mailing list<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:Gate-users@lists.healthgrid.org" target="_blank"> Gate-users@lists.healthgrid.org </a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://lists.healthgrid.org/mailman/listinfo/gate-users" target="_blank">http://lists.healthgrid.org/mailman/listinfo/gate-users </a><br><br><br
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