[GRASS-dev] Problem with R on cluster (HPC)

[Rainer M Krug]

Hi

I am trying to run a simulation on an HPC (high performance cluster).
To simulate, I have to start GRASS on each node and execute a script.
I wrote the script into .grass.bashrc in my home directory, which is
available on all nodes.

The .grass.bashrc is as follow:

rkrug at head001:~/sim> cat ./../.grass.bashrc

# R CMD BATCH ./spreadSim.BATCHCLUSTER.R
echo JuHu
pwd
echo JuHu 2
exit

The first line should startt R and execute the script
spreadSim.BATCHCLUSTER.R, but I just commented it out.

Everything is fine, when start grass on the commandline on the head of
the cluster - if I leave the 'exit' in, it exits immediately, if not I
see "JuHu" and the working directory and "JuHu 2". The strange thing
is that when I submit the script to the cluster to have it processed
by the nodes, it exits grass even when I comment the exit out or when
no .grass.bashrc is present.
Below an output from the cluster from one of the nodes:

######################################
Starting at Wed Oct 8 19:18:37 SAST 2008
SGE TASK ID:  1
---------------------
GRASS Version
Geographic Resources Analysis Support System (GRASS) is Copyright,
1999-2004 by the GRASS Development Team, and licensed under terms of
the GNU General Public License (GPL) version 2. This GRASS 6.3.0
release is coordinated and produced by the GRASS Development Team
headquartered at ITC-irst (Trento, Italy) with contributions from all
over the world. This program is distributed in the hope that it will
be useful, but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
---------------------
R Version
R version 2.7.1 (2008-06-23) Copyright (C) 2008 The R Foundation for
Statistical Computing ISBN 3-900051-07-0 R is free software and comes
with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under
the terms of the GNU General Public License version 2. For more
information about these matters see http://www.gnu.org/licenses/.
---------------------
Wed Oct 8 19:18:37 SAST 2008
Copying from
   /export/home/rkrug/sim/AlienSpread/
to Node Specific Directory
   /export/home/rkrug/sim/AlienSpread_1/
---------------------
Wed Oct 8 19:18:50 SAST 2008
grass dir /export/home/rkrug/sim/AlienSpread_1//grass/simulation
Starting simulation
Cleaning up temporary files.....
Starting GRASS ...
GRASS GUI should be text
ESC[HESC[2J          __________  ___   __________    _______________
         / ____/ __ \/   | / ___/ ___/   / ____/  _/ ___/
        / / __/ /_/ / /| | \__ \\_  \   / / __ / / \__ \
       / /_/ / _, _/ ___ |___/ /__/ /  / /_/ // / ___/ /
       \____/_/ |_/_/  |_/____/____/   \____/___//____/

Welcome to GRASS 6.3.0 (2008)
GRASS homepage:                          http://grass.osgeo.org/
This version running thru:               Bash Shell (/bin/bash)
Help is available with the command:      g.manual -i
See the licence terms with:              g.version -c
Start the GUI with:                      g.gui tcltk
When ready to quit enter:                exit

ESC[HESC[2JClosing monitors.....
Cleaning up temporary files.....
done



Goodbye from GRASS GIS

---------------------
Ending at Wed Oct 8 19:18:51 SAST 2008

######################################
I don't have any idea what is causing grass to close gracefully, as if
'exit' was executed and I am stuck. Any ideas on what might cause the
problem are welcome.

Thanks,

Rainer

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Faculty of Science
Natural Sciences Building
Private Bag X1
University of Stellenbosch
Matieland 7602
South Africa