[Gate-users] cluser tool gjs (Hermann Fuchs)

刘斌信件 golder_time at 163.com
Fri Jun 14 10:16:44 CEST 2013


Hi, 

   I added  all the enviroment  variables into the file of "env_gate.sh" ,the following  are the detailed content of "env_gate.sh":

 

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

export  LD_LIBRARY_PATH=$GATEHOME/tmp/Linux-g++/Gate:$ROOTSYS/lib:/usr/QT3-4/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: $ROOTSYS/cint/lib:/usr/local/Trolltech/Qt-4.7.3/lib:/usr/share/lintian/overrides:$LD_LIBRARY_PATH

export PATH=$PATH:$GATEHOME/tmp/Linux-g++/Gate:$ROOTSYS/bin:$GATEHOME/bin/Linux-g++:$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


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> 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
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>> 
>> 
>> 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
>> 
>> 
>> 
>> 
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> 
> ------------------------------
> 
> 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...
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>> > 
>> > ------------------------------
>> > 
>> > _______________________________________________
>> > 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
>> > *****************************************
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> 
> 
> -- 
> -------------
> 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
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> ------------------------------
> 
> 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
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> ------------------------------
> 
> 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"
> _________________________________
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