[Gate-users] Problem with job splitter installation
Hermann Fuchs
hermann.fuchs at meduniwien.ac.at
Wed Feb 11 08:46:29 CET 2015
Hi,
unfortunately I can not reproduce your problem.
Could you be more specific?
E.g. contents of your environmental variables (type printenv in a
terminal and post the output).
Generally GATE requires some environmental variables. It does not make a
difference where these are set.
You could put them in .bashrc, then they will be set automatically when
you open a terminal.
Alternatively, especially when using multiple geant4/Gate releases, you
could create a script which sets the required varibles as soon as you
source the script.
Such a script may be called envGate.sh.
You should create it yourself.
The file should contain:
source <PATHTOROOT>/bin/thisroot.sh
source<PATHTOGEANT4>/bin/geant4.sh
export PATH=$PATH:<PATHTOGATE>/bin
export GC_GATE_EXE_DIR=<PATHTOGATE>/bin
export GC_DOT_GATE_DIR=./
Please replace <PATHTOGATE>, <PATHTOGEANT4> and <PATHTOROOT> with the
correct absolute file path to your installation directories.
Cheers,
Hermann
On Wed, 2015-01-21 at 13:29 +0000, André Miguel Monteiro wrote:
> Dear Hermann, Soman and all Gate users,
>
>
>
> I am having the same problem as you Soman.
>
>
>
>
> Compiling gjs.cc...
> Compiling GateMacfileParser.cc...
> ./src/GateMacfileParser.cc: In constructor
> ‘GateMacfileParser::GateMacfileParser(G4String, G4int, G4int,
> G4String*)’:
> ./src/GateMacfileParser.cc:41:26: error: ‘getpid’ was not declared in
> this scope
> srand(time(NULL)*getpid());
> ^
> make: *** [tmp/GateMacfileParser.o] Error 1
>
>
> As you did I add the variables to my ~/.bashrc file:
>
>
>
>
>
>
> export GC_DOT_GATE_DIR=/home/andre/workdir/
>
>
> export
> GC_GATE_EXE_DIR=/home/andre/programs/Gate/opt/simulation/gate.7.0-install/bin
>
>
> I set these paths, because in other machine I have Gate v.6.1
> installed with cluster tools that point GC_DOT_GATE_DIR to a work
> directory and GC_GATE_EXE_DIR where is present the Gate executable.
>
>
>
> Does anyone know how to solve this problem?
>
>
>
> Thank you.
>
>
>
> Cheers,
>
>
>
> André
>
>
>
>
>
>
> --------------------------------
> MSc Student in Biomedical and Biophysics Engineering at Faculty of
> Sciences of the University of Lisbon
>
> Instituteof Biophysics and Biomedical Engineering
> Faculty of Sciences, Universityof Lisbon
> Campo Grande
> 1749-016 Lisbon
>
> Room Office: 1.02
> Extension: 20509
> Email: ammonteiro at fc.ul.pt
> LinkedIn Profile: http://linkedin.com/in/andremmonteiro
> Website: http://www.ibeb.fc.ul.pt/
>
>
> ______________________________________________________________________
>
> From: gate-users-bounces at lists.opengatecollaboration.org
> <gate-users-bounces at lists.opengatecollaboration.org> on behalf of S.
> Saghamanesh <s.saghamanesh at yahoo.com>
> Sent: Saturday, December 20, 2014 2:02 PM
> To: Hermann Fuchs; gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] Problem with job splitter installation
>
>
> Dear Hermann,
>
>
> 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.
> Based on the directions in Gate manual, I should add two environment
> variables in my ".bashrc" file as below, am I right?
>
>
> export GC_DOT_GATE_DIR=/somedir/ >> (I set it
> to /home/soman/Gate/gate_v7/cluster_tools/jobsplitter)
>
> export GC_GATE_EXE_DIR=/somedir/bin/Linux-g++/ >> (I set it
> to /home/soman/Gate/gate_v7/cluster_tools/jobsplitter)
>
>
> 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, if any, on this.
> - Soman
>
>
>
> On Tuesday, December 16, 2014 2:25 PM, Hermann Fuchs
> <hermann.fuchs at meduniwien.ac.at> wrote:
>
>
>
>
>
> Hi,
>
> at our place the following procedure worked on Scientific Linux 6 and
> Ubuntu 14.04 LTS.
>
> go to /opt/simulation/gate6_1/cluster_tools/jobsplitter
>
> cd /opt/simulation/gate6_1/cluster_tools/jobsplitter
>
> make sure Gate paths are set
>
> source /opt/simulation/gate6_1/env_gate.sh
>
> compile
>
> make
>
> Copy the library to the correct place
>
> cp /opt/simulation/gate6_1/cluster_tools/jobsplitter/tmp/Linux-g++/gjs/libgjs.so /opt/simulation/gate6_1/cluster_tools/jobsplitter/bin/Linux-g++
>
> export LD_LIBRARY_PATH=
> $LD_LIBRARY_PATH:/opt/simulation/gate6_1/cluster_tools/jobsplitter/tmp/Linux-g++/gjs
>
> Cheers,
> Hermann
>
> On Wed, 2014-12-10 at 14:08 +0000, S. Saghamanesh wrote:
>
> > Hi,
> >
> >
> >
> >
> > I get this error when I try to make job splitter in its directory:
> >
> >
> > Compiling GateMacfileParser.cc...
> > ./src/GateMacfileParser.cc: In constructor
> > ‘GateMacfileParser::GateMacfileParser(G4String, G4int, G4int,
> > G4String*)’:
> > ./src/GateMacfileParser.cc:41:26: error: ‘getpid’ was not declared
> > in this scope
> > make: *** [tmp/GateMacfileParser.o] Error 1
> >
> >
> >
> > What is it about? Does anybody know what's the procedure of
> > installing job splitter?
> >
> >
> > Thanks
> > - Soman
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > 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 72710
> Mail. hermann.fuchs at meduniwien.ac.at
>
>
>
>
>
> _______________________________________________
> 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 72710
Mail. hermann.fuchs at meduniwien.ac.at
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