[Gate-users] Gate on condor grid

[Albert Hirtl]

Hi Simon, Alexandre and Jon,

Thanks a lot for your help. Things are running now. For now I took the 
easy solution (getenv = True) since we have a homogeneous grid.

Cheers,
Albert

On 16/11/10 14:04, Simon Stute wrote:
> Hey,
>
> Much more simple :
>
> add the following line in your condor submit file : "getenv = True"
> this will import the current bash environment in which you are 
> working, when you will submit your job.
> but do not forget to source your environment before submitting the job.
>
> Of course, this probably does not work on heterogeneous grids if the 
> directory configuration is different, but usually paths are all the 
> same on every machine.
>
> Cheers,
> Simon
>
>
> On Tue, Nov 16, 2010 at 11:42 AM, Alexandre Dupas 
> <alexandre.dupas at gmail.com <mailto:alexandre.dupas at gmail.com>> wrote:
>
>     Dear Albert,
>
>     I doubt that sourcing the script before launching the script on the
>     grid can work. Condor tends to launch the job in a clean environment
>     without retaining previously defined variables. You have to create a
>     small script that source the gate environment script and then launch
>     your Gate process.
>
>     We are running Gate on a condor grid with about 40 heterogeneous nodes
>     (MacOS, Linux X86_64, and Linux i686). For each machine, we have a
>     small configuration script which is executed before launching Gate in
>     condor mode. Here is some code sample you can adapt to your particular
>     needs.
>
>     #
>     OPENGATE_PATH="/mnt/nfs/OpenGate/gate-i686" # path where the i686
>     flavor of the libraries are built
>
>     # set gate configuration variables
>     export GATEHOME="${OPENGATE_PATH}/gate-devel" # gate install directory
>     export G4VERSION="9.1"
>     export G4INSTALL="${OPENGATE_PATH}/geant_4.9.1.p02"
>     export ROOTSYS="${OPENGATE_PATH}/root_5.26"
>     export ROOTLIB="${ROOTSYS}/lib"
>     export ECAT7_HOME="${OPENGATE_PATH}/ecat_7"
>     export LMF_HOME="${OPENGATE_PATH}/lmf_3.0"
>
>     # set path variables
>     export PATH="${ROOTSYS}/bin:${GATEHOME}/bin/Linux-g++:${PATH}"
>     export LD_LIBRARY_PATH="${ROOTLIB}:${OPENGATE_PATH}/clhep_2.0.3.2/lib"
>
>     # Gate environment
>     . "${GATEHOME}/env_gate.sh" # source the environment
>     #
>
>     The gate process is launched by a job.sh script which source the
>     previously defined script and execute Gate with the correct macro.
>
>     #!/bin/sh
>     #
>     HOSTNAME=`hostname`
>     GATE_ENV=/mnt/nfs/hosts/$HOSTNAME/config-gate.sh
>
>     JOB_NUMBER=$1 # the first parameter to the script is the job number
>
>     GATE_SCRIPT="job-$JOB_NUMBER.mac"
>
>     # source the environment
>     . "$GATE_ENV"
>
>     # launch Gate with the correct job
>     Gate $GATE_SCRIPT
>     #
>
>     And here is the `submit' variable that makes condor launching my
>     job.sh script with the correct parameter (job number) :
>
>     Executable = /path/to/job.sh
>     Arguments = $(Process)
>
>     I hope this can help you solve your issue.
>
>     Best regards,
>     Alexandre
>
>     --
>     Alexandre Dupas
>     Postodoctoral Research Fellow
>     INSERM U698, Bichat Médecine Nucléaire
>
>     2010/11/16 Albert Hirtl <albert.hirtl at meduniwien.ac.at
>     <mailto:albert.hirtl at meduniwien.ac.at>>:
>     > Dear all,
>     >
>     > I am trying to get Gate running on a condor grid. When starting
>     a simulation
>     > (which ran perfectly in non-grid-mode) I get the following error
>     in the .err
>     > file:
>     >
>     > [G4-cerr] G4EMDataSet::FullFileName - G4LEDATA environment
>     variable not set
>     > [G4-cerr]
>     > [G4-cerr] *** G4Exception: Aborting execution ***
>     >
>     > Is it not enough to execute "source env_gate.sh" in the shell
>     before sending
>     > Gate to the grid? Do I have to set all variables that are set in the
>     > env_gate.sh globally in /etc/profile? Or am I on a completely
>     wrong track?
>     >
>     > Any help would be very much appreciated!
>     >
>     > Cheers,
>     > Albert
>     >
>     > --
>     > Medizinische Universität Wien - Allgemeines Krankenhaus Wien
>     > Universitätsklinik für Nuklearmedizin
>     > Währinger Gürtel 18-20
>     > 1090 Wien
>     > Austria
>     >
>     > Tel.: +43 (0) 1 / 40400 5545
>     >
>     > Web: http://www.meduniwien.ac.at/user/albert.hirtl
>     >
>     >
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>


-- 
Medizinische Universität Wien - Allgemeines Krankenhaus Wien
Universitätsklinik für Nuklearmedizin
Währinger Gürtel 18-20
1090 Wien
Austria

Tel.: +43 (0) 1 / 40400 5545

Web: http://www.meduniwien.ac.at/user/albert.hirtl

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