80 lines
1.8 KiB
Plaintext
80 lines
1.8 KiB
Plaintext
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#!/bin/bash
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#PBS -A GEO106
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#PBS -N Juanes
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#PBS -j oe
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#PBS -l walltime=02:00:00,nodes=1
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##PBS -l walltime=01:00:00,nodes=18
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##PBS -l gres=widow2%widow3
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##PBS -q killable
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##PBS -q debug
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#cd /tmp/work/$USER
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date
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cd $PBS_O_WORKDIR
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LBPM_WIA_INSTALL_DIR=/ccs/proj/geo106/eos/LBPM-WIA
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source $MODULESHOME/init/bash
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module swap PrgEnv-intel PrgEnv-gnu
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module load cray-hdf5-parallel
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module load cray-netcdf-hdf5parallel
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module load python_anaconda
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export LD_LIBRARY_PATH=${CRAY_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}
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## This is the code used to extract the tifs to subdirectories
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for i in `seq -w 0 804`; do
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file="ConcatenatedStacks0"$i".tif"; cp $file SubSet1;
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done
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for i in `seq -w 805 1609`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet2;
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done
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for i in `seq -w 1610 2414`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet3;
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done
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for i in `seq -w 2415 3219`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet4;
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done
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for i in `seq -w 3220 4024`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet5;
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done
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for i in `seq -w 4025 4829`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet6;
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done
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for i in `seq -w 4830 5634`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet7;
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done
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for i in `seq -w 5635 6439`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet8;
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done
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for i in `seq -w 6440 7244`; do
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file="ConcatenatedStacks"$i".tif"; cp $file SubSet9;
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done
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# This is the code used to convert tif to raw 8-bit binary
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LIST=$(ls | grep SubSet)
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for dir in $LIST; do
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echo "Processing $dir"
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cd $dir
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python $LBPM_WIA_INSTALL_DIR/example/Tiff/TiffPreprocessor.py
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cd ..
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done
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# aprun -n 64 $LBPM_WIA_INSTALL_DIR/bin/lbpm_segmented_decomp 0 2
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# aprun -n 64 $LBPM_WIA_INSTALL_DIR/bin/lbpm_segmented_pp
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exit;
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