[GRASS-user] GRASS BATCH JOB won't unset

Morrison, Bailey Danielle bdmorri2 at illinois.edu
Tue Jun 23 11:05:03 PDT 2015


I am fairly new to GRASS and I am having issues getting GRASS BATCH JOB to work properly. I need to run 40 r.sun calculations in less than 4 hours for my universities campus cluster that runs the linux version of grass. To do this I need to run 40  jobs that each perform the r.sun calculation since a single job alone could use most of the 4 hour time limit to calculate r.sun.

The basic idea of the project is that I have elevation data covering the entire extent of Alaska at about 14GB total.  R.sun is memory limited, so I have created windows for smaller regions of the elevation data that need to be run. I have created 40 shell files with the necessary commands/tools I need to alter the mapset region and use r.sun in only that region. An example of one of the files looks like this (all look similar except the bounding box extents change and the name of the output files:

(filename  = tile_1_1.sh)

g.region --overwrite --verbose n=56.5522222216437 s=50.996666666 e=-174.444444444375 w=-180
r.sun -p -m --overwrite --verbose elevation=mosaic_60m at PERMANENT aspect=aspect at bdmorri2 slope=slope at bdmorri2 beam=beam_tile_1_1 diff_rad=diffuse_tile_1_1 glob_rad=to$

To run these through the campus cluster externally, I created an additional 40 shell files that create a new mapset , sets the GRASS BATCH JOB as a variable and exports it, and starts grass up externally to run the file listed above and run the grass commands.


chmod u+x  /projects/oa/akpaleo/radiation/qsub_files/tile_1_1.sh
export GRASS_BATCH_JOB=/project/oa/akpaleo/radiation/qsub_files/tile_1_1.sh
grass70 -c  /projects/oa/akpaleo/gis/grass/alaska/tile_1_1

The big problem I am having with this step is that I always receive the error below, even though my shell files specifically use "unset GRASS_BATCH_JOB". I have also tried manually entering this in the terminal with no success. I am obviously doing something wrong to get this to work correctly.
ERROR: Job file '/project/oa/akpaleo/radiation/qsub_files/tile_1_1.sh' has been defined in the 'GRASS_BATCH_JOB' variable but not found. Exiting.
Use 'unset GRASS_BATCH_JOB' to disable batch job processing.

For now I am not submitting the job to the cluster using qsub, but rather testing it in an interactive job on the cluster and b just using the command sh command to test the files.

Thank you

Bailey Morrison
PhD student
University of Illinois at Urbana-Champaign
Program in Ecology, Evolution, and Conservation Biology
Global Environmental Analysis and Remote Sensing Lab (GEARS)
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