[Gate-users] cluser tool gjs (Hermann Fuchs)
Hermann Fuchs
hermann.fuchs at meduniwien.ac.at
Fri Jun 14 15:43:49 CEST 2013
Hi
The problem is that your cluster does not know the environmental
variables.
You have to find a way to set this variables on the machines(normally
not your own machine) your jobs is executing.
The procedure differs for each cluster system, but it is usually easy to
find.
Have you tried looking into the openmosix handbook?
Cheers,
Hermann
On Fri, 2013-06-14 at 16:16 +0800, 刘斌信件 wrote:
> 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
>
>
> > Send Gate-users mailing list submissions to
> > gate-users at lists.opengatecollaboration.org
> >
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> > or, via email, send a message with subject or body 'help' to
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> >
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> > 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...
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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
> >> *****************************************
> >
> > ------------------------------
> >
> > 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/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
> >> > *****************************************
> >> _______________________________________________
> >> 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 --------------
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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
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/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"
> > _________________________________
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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 9
> > *****************************************
> _______________________________________________
> 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
Währinger Gürtel 18-20
A-1090 Wien
Tel. + 43 / 1 / 40 400 7271
Mail. hermann.fuchs at meduniwien.ac.at
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