[Gate-users] Gate on condor grid

[Simon Stute]

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
> 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>:
> > 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
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users