[Gate-users] Problem with job splitter installation

André Miguel Monteiro ammonteiro at fc.ul.pt
Wed Jan 21 16:53:25 CET 2015 

Hello Alex,

Thank you very much! 

I can compile now without errors, but it doesn't generate "libgjs.so" only "gjs.so" in the folder tmp, which I should expect according to: http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:How_to_use_Gate_on_a_Cluster

Here is the output of typing make:

Compiling gjs.cc...
Compiling GateMacfileParser.cc...
Compiling GateSplitManager.cc...
Compiling GateToPlatform.cc...
Linking...
Done

Regarding condor and the environment variables, my PATH is below in which I specify geant4 installation folder:

/home/andre/programs/Gate/opt/simulation/geant4.9.6.p03-install/bin:/home/andre/programs/Gate/opt/simulation/root_v5.34.24/bin:/home/andre/.rvm/gems/ruby-2.2.0/bin:/home/andre/.rvm/gems/ruby-2.2.0 at global/bin:/home/andre/.rvm/rubies/ruby-2.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/andre/.rvm/bin:/home/andre/.rvm/bin:/usr/local/cuda-6.5:/usr/local/cuda-6.5/bin:/home/andre/programs/Gate/opt/simulation/2.1.3.1-install/include:/home/andre/programs/Gate/opt/simulation/2.1.3.1-install/bin:/home/andre/programs/Gate/opt/simulation/gate.7.0-install/bin

What is missing here?

Cheers,
Andre

--------------------------------
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
LinkedIn Profile: http://linkedin.com/in/andremmonteiro
Website: http://www.ibeb.fc.ul.pt/

________________________________________
From: Alex Vergara Gil <alexvergaragil at gmail.com>
Sent: Wednesday, January 21, 2015 3:29 PM
To: André Miguel Monteiro
Cc: Hermann Fuchs; gate-users at lists.opengatecollaboration.org; S. Saghamanesh
Subject: Re: [Gate-users] Problem with job splitter installation

simply substitute the line
srand(time(NULL)*getpid());

by the line
srand(time(NULL)/**getpid()*/);

but there is an issue too with condor, that doesn't get environment
variables, so it doesn't know where geant4 installation is.

regards
alex

2015-01-21 8:29 GMT-05:00, André Miguel Monteiro <ammonteiro at fc.ul.pt>:
> 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
> 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
>
>
>
>
>
> _______________________________________________
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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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