[Gate-users] Problem with job splitter installation

[André Miguel Monteiro]

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

Institute of Biophysics and Biomedical Engineering
Faculty of Sciences, University of Lisbon
Campo Grande
1749-016 Lisbon

Room Office: 1.02
Extension: 20509
Email: ammonteiro at fc.ul.pt
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________________________________
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





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--

-------------
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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