Hi, I added all the enviroment following are the detailed content of "env_gate.

sh": variables into the file of "env_gate.sh" ,the

export export export export export export export export export

G4WORKDIR=/home/liubin/simulation/gate6_2 G4ANALYSIS_USE_GENERAL=1 G4_USE_G4BESTUNIT_FOR_VERBOSE=1 GATEHOME=/home/liubin/simulation/gate6_2 G4INSTALL=/home/liubin/simulation/geant4_9_4_p03 G4VERSION=9.4 ROOTSYS=/home/liubin/simulation/root_5_32 ECAT7_HOME=/home/liubin/simulation/ecat7 LMF_HOME=/home/liubin/simulation/lmf_3_0

export LD_LIBRARY_PATH=$GATEHOME/tmp/Linux-g++/Gate:$ROOTSYS/lib:/usr/QT34/lib/:$ROOTSYS/lib/root:/home/liubin/simulation/CLHEP_2_1_0_1/lib: $GATEHOME/bin/Linux-g++: $GATEHOME/cluster_tools/jobsplitter/tmp/Linux-g++/gjs: $ROOTSYS/cint/lib:/usr/local/Trolltech/Qt4.7.3/lib:/usr/share/lintian/overrides:$LD_LIBRARY_PATH export PATH=$PATH:$GATEHOME/tmp/Linux-g++/Gate:$ROOTSYS/bin:$GATEHOME/bin/Linuxg++:$ROOTSYS/cint/bin:/usr/QT3-4/bin:/usr/local/Trolltech/Qt-4.7.3/bin export DYLD_LIBRARY_PATH=$ROOTSYS/lib:/home/liubin/simulation/CLHEP_2_1_0_1/lib: $DYLD_LIBRARY_PATH export G4ANALYSIS_USE_GENERAL=1 export G4_USE_G4BESTUNIT_FOR_VERBOSE=1 export GC_DOT_GATE_DIR=$GATEHOME The shared library libGate.so and libgjs.so are located in $GATEHOME/tmp/Linux-g++/Gate and $GATEHOME/cluster_tools/jobsplitter/tmp/Linux-g++/gjs respectively . The executable file of Gate and gjs are both placed in $GATEHOME/bin/Linux-g++, I set current directory as $GATEHOME/tmp/Linux-g++/Gate in terminal command window, then apply command sudo ./Gate or sudo ./gjs , Unfortunately, its output show error message again: ./gjs: error while loading shared libraries libGate.so or libgjs.so : cannot open shared object file: No such file or directory.. When I just type command Gate in terminal , Gate can work successfully.

How should I deal with that ? Thank you very much Yours, Bin

----- Original Message ----From: <gate-users-request <at> lists.opengatecollaboration.org> To: <gate-users <at> lists.opengatecollaboration.org> Sent: Friday, June 14, 2013 1:40 PM Subject: Gate-users Digest, Vol 85, Issue 9

> > > > >

Send Gate-users mailing list submissions to gate-users <at> lists.opengatecollaboration.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

> or, via email, send a message with subject or body 'help' to > gate-users-request <at> lists.opengatecollaboration.org > > You can reach the person managing the list at > gate-users-owner <at> lists.opengatecollaboration.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Gate-users digest..." > > > Today's Topics: > > 1. cluser tool gjs (????) > 2. Re: cluser tool gjs (Hermann Fuchs) > 3. Simulations terminate after NumberOfEvents = 4294967294 > (Matthew Belley) > 4. Re: Simulations terminate after NumberOfEvents = 4294967294 > (David Sarrut) > > > ---------------------------------------------------------------------> > Message: 1 > Date: Thu, 13 Jun 2013 21:59:28 +0800 > From: ???? <golder_time <at> 163.com> > To: <gate-users <at> lists.opengatecollaboration.org> > Subject: [Gate-users] cluser tool gjs > Message-ID: <E76A118BE01E4800A144691208240828 <at> b23499e2bb1f483> > Content-Type: text/plain; charset="UTF-8" > > hi David, > I try to use cluster tools "gjs", I utilize the commands " gjs -numberofsplits 5 -clusterplatform openmosix mac/total.mac , and got the output file of " total.submit ", but when I execut the it by "sudo ./total.submit" > the errors are coming , the folllowing are output: > /Gatedir/bin/Linux-g++/Gate : error while loading shared libraries: libGate.so: cannot open shared object file: No such file or directory? > > I found the libGate.so in the file directory "${GATEHOME}/tmp/$ {G4SYSTEM}/Gate" ,and I added the directory to the PATH or LD_LIBRARY_PATH , however the problem is still there , I don't know what cause this problem. > > Another prblem is the vv, I used Vv converting Ct.dcm data to .hdr or img data ,but the derived .hdr file cann't supported by Gate , it showed that the Gate didn't support voxel type of converted file " .hdr" . > > Can you give me a help . > Best wishes > yours > Bin.

> > > > > ----- Original Message ----> From: <gate-users-request <at> lists.opengatecollaboration.org> > To: <gate-users <at> lists.opengatecollaboration.org> > Sent: Saturday, June 08, 2013 6:00 PM > Subject: Gate-users Digest, Vol 85, Issue 6 > > >> Send Gate-users mailing list submissions to >> gate-users <at> lists.opengatecollaboration.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> or, via email, send a message with subject or body 'help' to gate-users-request <at> lists.opengatecollaboration.org You can reach the person managing the list at gate-users-owner <at> lists.opengatecollaboration.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Gate-users digest..." Today's Topics: 1. LMF segment fault (??) ---------------------------------------------------------------------Message: 1 Date: Fri, 7 Jun 2013 21:37:57 +0800 (GMT+08:00) From: ?? <chenze <at> impcas.ac.cn> To: gate-users <at> lists.opengatecollaboration.org Subject: [Gate-users] LMF segment fault Message-ID: <c4cd2a.a207.13f1edb9f4b.Coremail.chenze <at> impcas.ac.cn> Content-Type: text/plain; charset="gbk" Hi, I have occurred the the problem of LMF output, which is shown below. ************** LMF INIT ************** number of rsectors 1 rsector name =rsector *** Break *** segmentation violation I wonder how can I fix this problem, thank you for your reply. regards, chenze

-------------- next part -------------An HTML attachment was scrubbed... URL: <http://lists.opengatecollaboration.org/mailman/private/gate-

users/attachments/20130607/3d3dada2/attachment-0001.html> >> >> ----------------------------->> >> _______________________________________________ >> Gate-users mailing list >> Gate-users <at> lists.opengatecollaboration.org >> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users >> >> End of Gate-users Digest, Vol 85, Issue 6 >> ***************************************** > > -----------------------------> > Message: 2 > Date: Thu, 13 Jun 2013 16:43:52 +0200 > From: Hermann Fuchs <hermann.fuchs <at> meduniwien.ac.at> > To: gate-users <at> lists.opengatecollaboration.org > Subject: Re: [Gate-users] cluser tool gjs > Message-ID: > <1371134632.26595.0.camel <at> strahlen41.strahlen.meduniwien.ac.at> > Content-Type: text/plain; charset="utf-8" > > Hello > > This problem has nothing to do with gjs. > It seems your cluster does not know where to look for the library. Are > you sending along the environmental variables? > > Cheers, > Hermann > On Thu, 2013-06-13 at 21:59 +0800, ???? wrote: > >> hi David, >> I try to use cluster tools "gjs", I utilize the commands " gjs -numberofsplits 5 -clusterplatform openmosix mac/total.mac , and got the output file of " total.submit ", but when I execut the it by "sudo ./total.submit" >> the errors are coming , the folllowing are output: >> /Gatedir/bin/Linux-g++/Gate : error while loading shared libraries: libGate.so: cannot open shared object file: No such file or directory? >> >> I found the libGate.so in the file directory "${GATEHOME}/tmp/$ {G4SYSTEM}/Gate" ,and I added the directory to the PATH or LD_LIBRARY_PATH , however the problem is still there , I don't know what cause this problem. >> >> Another prblem is the vv, I used Vv converting Ct.dcm data to .hdr or img data ,but the derived .hdr file cann't supported by Gate , it showed that the Gate didn't support voxel type of converted file " .hdr" . >> >> Can you give me a help . >> Best wishes >> yours >> Bin. >> >> >> >>

>> >> >> >> >> >> >> >> >> >> >> >>

----- Original Message ----From: <gate-users-request <at> lists.opengatecollaboration.org> To: <gate-users <at> lists.opengatecollaboration.org> Sent: Saturday, June 08, 2013 6:00 PM Subject: Gate-users Digest, Vol 85, Issue 6 > > > > > Send Gate-users mailing list submissions to gate-users <at> lists.opengatecollaboration.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

>> > or, via email, send a message with subject or body 'help' to >> > gate-users-request <at> lists.opengatecollaboration.org >> > >> > You can reach the person managing the list at >> > gate-users-owner <at> lists.opengatecollaboration.org >> > >> > When replying, please edit your Subject line so it is more specific >> > than "Re: Contents of Gate-users digest..." >> > >> > >> > Today's Topics: >> > >> > 1. LMF segment fault (??) >> > >> > >> > --------------------------------------------------------------------->> > >> > Message: 1 >> > Date: Fri, 7 Jun 2013 21:37:57 +0800 (GMT+08:00) >> > From: ?? <chenze <at> impcas.ac.cn> >> > To: gate-users <at> lists.opengatecollaboration.org >> > Subject: [Gate-users] LMF segment fault >> > Message-ID: <c4cd2a.a207.13f1edb9f4b.Coremail.chenze <at> impcas.ac.cn> >> > Content-Type: text/plain; charset="gbk" >> > >> > >> > Hi, >> > I have occurred the the problem of LMF output, which is shown below. >> > ************** >> > LMF INIT >> > ************** >> > number of rsectors 1 >> > rsector name =rsector >> > >> > *** Break *** segmentation violation >> > I wonder how can I fix this problem, thank you for your reply. >> > regards, >> > chenze >> > >> > >> > >> > >> > -------------- next part ------------->> > An HTML attachment was scrubbed... >> > URL: <http://lists.opengatecollaboration.org/mailman/private/gateusers/attachments/20130607/3d3dada2/attachment-0001.html> >> > >> > ----------------------------->> >

>> >> >> >> >> >> >> >> >> >> >>

> > > >

_______________________________________________ Gate-users mailing list Gate-users <at> lists.opengatecollaboration.org http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

> > End of Gate-users Digest, Vol 85, Issue 6 > ***************************************** _______________________________________________ Gate-users mailing list Gate-users <at> lists.opengatecollaboration.org http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

>> > > > -> ------------> DI Hermann Fuchs > Christian Doppler Laboratory for Medical Radiation Research for Radiation Oncology > Department of Radiation Oncology > Medical University Vienna > W?hringer G?rtel 18-20 > A-1090 Wien > > Tel. + 43 / 1 / 40 400 7271 > Mail. hermann.fuchs <at> meduniwien.ac.at > -------------- next part -------------> An HTML attachment was scrubbed... > URL: <http://lists.opengatecollaboration.org/mailman/private/gateusers/attachments/20130613/d042fac2/attachment-0001.html> > > -----------------------------> > Message: 3 > Date: Thu, 13 Jun 2013 14:41:24 -0400 > From: Matthew Belley <mdb52 <at> duke.edu> > To: gate-users <at> lists.opengatecollaboration.org > Subject: [Gate-users] Simulations terminate after NumberOfEvents = > 4294967294 > Message-ID: > <CAPPx498qO_UZHvd2pexadgW+2QBqUy0emGQWoERM4rYaR6iLYg <at> mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gate Users, > > I am running simulations with a very high number of particles to obtain > good statistics. I am storing dose output using Actors. The simulations > terminate early with an error, before running the total number of particles > I have specified. I noticed that in my StatsOutput.txt file, that the > "NumberOfEvents" value is always equal to 4294967294 when the program > terminates. > > Considering that 2^32 = 4294967296 is very close to the value of 4294967294 > -- it seems like I have exceed the storage capacity of the data type that > stores event data? > > Is there a fix for this issue to allow me to run a simulation with more > events? > > Best regards,

> Matthew Belley > -------------- next part -------------> An HTML attachment was scrubbed... > URL: <http://lists.opengatecollaboration.org/mailman/private/gateusers/attachments/20130613/84ef6bb1/attachment-0001.html> > > -----------------------------> > Message: 4 > Date: Fri, 14 Jun 2013 07:51:32 +0200 > From: David Sarrut <David.Sarrut <at> creatis.insa-lyon.fr> > To: Matthew Belley <mdb52 <at> duke.edu> > Cc: gate-users <gate-users <at> lists.opengatecollaboration.org> > Subject: Re: [Gate-users] Simulations terminate after NumberOfEvents = > 4294967294 > Message-ID: > <CAKTJC4AkV6Ya=uzC+jomoSFuuQ_vWHhPMrLaGY=gh8vk17jDcA <at> mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Matthew, > > you're right 4294967294 is (almost) the max value for "unsigned long". I > did a quick check : in "GateSimulationStatisticActor" the number of events > is stored as a "long int" (not unsigned), so the max value should be > 2147483647 (2^31), it can be changed to "unsigned long long int" (uulong to > get to 2^64). There are probably other places in the code that can lead to > crash with this overflow. > > As a quick workaround, I suggest, that you split you simulation in smaller > bunches (around 10^9 max). > > You can try to seek in the code for such variables that store events or > track number and check if the used types could be changed to something like > "ullong". > > We will also try to do it, but our todo list is full for the next coming > weeks. Albertine => could you please add this issue to the bug tracker ? > > FYI : the read-only access to the current git repository of Gate (that > contains the current development version with some corrected bugs, and > still non-validated features) will be available soon, but it's a bit > delayed for technical reasons. > > Sincerely, > David > > > > On Thu, Jun 13, 2013 at 8:41 PM, Matthew Belley <mdb52 <at> duke.edu> wrote: > >> Dear Gate Users, >> >> I am running simulations with a very high number of particles to obtain >> good statistics. I am storing dose output using Actors. The simulations >> terminate early with an error, before running the total number of particles >> I have specified. I noticed that in my StatsOutput.txt file, that the >> "NumberOfEvents" value is always equal to 4294967294 when the program >> terminates. >> >> Considering that 2^32 = 4294967296 is very close to the value of4294967294 -it seems like I have exceed the storage capacity of the data

>> >> >> >> >> >> >> >> >> >> >> >>

type that stores event data? Is there a fix for this issue to allow me to run a simulation with more events? Best regards, Matthew Belley _______________________________________________ Gate-users mailing list Gate-users <at> lists.opengatecollaboration.org http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

>> > > > > -> David Sarrut, Phd > Charg? de recherche CNRS > CREATIS, UMR CNRS 5220, Inserm U 1044 > Centre de lutte contre le cancer L?on B?rard > 28 rue La?nnec, 69373 Lyon cedex 08 > Tel : 04 78 78 51 51 / 06 74 72 05 42 > http://www.creatis.insa-lyon.fr/~dsarrut > _________________________________ > "2 + 2 = 5, for extremely large values of 2" > _________________________________ > -------------- next part -------------> An HTML attachment was scrubbed... > URL: <http://lists.opengatecollaboration.org/mailman/private/gateusers/attachments/20130614/cd39fa5c/attachment.html> > > -----------------------------> > _______________________________________________ > Gate-users mailing list > Gate-users <at> lists.opengatecollaboration.org > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users > > End of Gate-users Digest, Vol 85, Issue 9 > ***************************************** _______________________________________________ Gate-users mailing list Gate-users <at> lists.opengatecollaboration.org http://lists.opengatecollaboration.org/mailman/listinfo/gate-users