VTK_PATH=/project/nearsdc/software/vtk_all_platforms/linux64
JAVA=/disks/d0364/software/jdk1.8.0_51/jre/bin/java 
JAVA_LIB=/disks/d0364/software/jdk1.8.0_51/jre/lib/amd64
export LD_LIBRARY_PATH=$JAVA:JAVA/xawt:$VTK_PATH:$VTK_PATH/bin:$LD_LIBRARY_PATH

DIR_LIST_FILE=./inputFolders
TREE_OUTPUT_PATH=$PWD/tree
MAX_MB_PER_FILE=5
N_FILES=32	# max number of open output files

N_FILES_TO_PROCESS=-1	# use -1 for all

rm -rf ./tree
mkdir ./tree

CLASSPATH="$BIN_DIR:$LIB_DIR/mysql-connector-java-5.1.10-bin.jar:$LIB_DIR/spice-N0065.jar:$LIB_DIR/altwg-java-tools.jar:$LIB_DIR/jide-oss-3.6.9.jar:$SAAVTK_LIB_DIR/../target/classes:$SAAVTK_LIB_DIR/commons-io-2.0.jar:$SAAVTK_LIB_DIR/commons-math3-3.2.jar:$SAAVTK_LIB_DIR/guava-13.0.1.jar:$SAAVTK_LIB_DIR/Jama-1.0.2.jar:$SAAVTK_LIB_DIR/jcommon-1.0.16.jar:$SAAVTK_LIB_DIR/jfreechart-1.0.13.jar:$SAAVTK_LIB_DIR/jgoodies-common-1.1.1.jar:$SAAVTK_LIB_DIR/jgoodies-looks-2.4.0.jar:$SAAVTK_LIB_DIR/joda-time-1.6.jar:$SAAVTK_LIB_DIR/miglayout-3.7.1-swing.jar:$SAAVTK_LIB_DIR/nom-tam-fits-1.13.1m0.jar:$SAAVTK_LIB_DIR/quaqua-7.3.4-filechooser-only.jar:$SAAVTK_LIB_DIR/quaqua-7.3.4.jar:$SAAVTK_LIB_DIR/RelativeLayout-v1.0.jar:$SAAVTK_LIB_DIR/jogl/gluegen-rt.jar:$SAAVTK_LIB_DIR/jogl/jogl-all.jar:$SAAVTK_LIB_DIR/vtk6.3/vtk-6.3.jar:$SAAVTK_LIB_DIR/geotools/commons-pool-1.5.4.jar:$SAAVTK_LIB_DIR/geotools/core-0.26.jar:$SAAVTK_LIB_DIR/geotools/GeographicLib-Java-1.44.jar:$SAAVTK_LIB_DIR/geotools/jts-1.13.jar:$SAAVTK_LIB_DIR/geotools/jsr-275-1.0-beta-2.jar:$SAAVTK_LIB_DIR/geotools/jai_core-1.1.3.jar:$SAAVTK_LIB_DIR/geotools/gt-opengis-15.1.jar:$SAAVTK_LIB_DIR/geotools/gt-metadata-15.1.jar:$SAAVTK_LIB_DIR/geotools/jgridshift-1.0.jar:$SAAVTK_LIB_DIR/geotools/gt-referencing-15.1.jar:$SAAVTK_LIB_DIR/geotools/gt-api-15.1.jar:$SAAVTK_LIB_DIR/geotools/jdom-1.1.3.jar:$SAAVTK_LIB_DIR/geotools/gt-main-15.1.jar:$SAAVTK_LIB_DIR/geotools/jai_imageio-1.1.jar:$SAAVTK_LIB_DIR/geotools/imageio-ext-tiff-1.1.15.jar:$SAAVTK_LIB_DIR/geotools/imageio-ext-utilities-1.1.15.jar:$SAAVTK_LIB_DIR/geotools/imageio-ext-geocore-1.1.15.jar:$SAAVTK_LIB_DIR/geotools/imageio-ext-streams-1.1.15.jar:$SAAVTK_LIB_DIR/geotools/jt-zonalstats-1.4.0.jar:$SAAVTK_LIB_DIR/geotools/jt-utils-1.4.0.jar:$SAAVTK_LIB_DIR/geotools/jt-affine-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-algebra-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-bandmerge-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-bandselect-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-bandcombine-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-border-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-buffer-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-crop-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-iterators-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-lookup-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-mosaic-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-nullop-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-rescale-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-scale-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-stats-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-translate-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-utilities-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-warp-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-zonal-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-binarize-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-format-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-colorconvert-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-errordiffusion-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-orderdither-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-colorindexer-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-imagefunction-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-piecewise-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-classifier-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-rlookup-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/jt-vectorbin-1.0.9.jar:$SAAVTK_LIB_DIR/geotools/gt-coverage-15.1.jar:$SAAVTK_LIB_DIR/geotools/gt-cql-15.1.jar:$SAAVTK_LIB_DIR/geotools/gt-data-15.1.jar:$SAAVTK_LIB_DIR/geotools/hsqldb-2.3.0.jar:$SAAVTK_LIB_DIR/geotools/gt-epsg-hsql-15.1.jar:$SAAVTK_LIB_DIR/geotools/gt-render-15.1.jar:$SAAVTK_LIB_DIR/geotools/gt-shapefile-15.1.jar:$SAAVTK_LIB_DIR/geotools/jai_codec-1.1.3.jar:$SAAVTK_LIB_DIR/geotools/gt-swing-15.1.jar:$VTK_LIB_DIR/vtk.jar"
ENTRYPOINT=edu.jhuapl.sbmt.lidar.hyperoctree.mola.MolaFSHyperTreeGenerator
ARGS="inputDirectories ./tree 5 32 .75m45"

time $JAVA -Djava.awt.headless=true -Djava.library.path=$VTK_LIB_DIR -classpath $CLASSPATH $ENTRYPOINT $ARGS