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pmackenzpmackenz
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Adding the backend to the repository
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‎.gitignore

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images/.DS_Store
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.DS_Store
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Agave/utils/gmsh

‎Agave/LICENSE

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Date: 9-24-2018
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This LICENSE document pertains to the CWE back-end materials, comprising the files contained in the same folder or archive as this document and the files in all the subfolders contained therein.
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The 'gmsh' program, contained in the 'utils' folder is a copy of the freely available 'gmsh' program. It's license is accessible within the 'gmsh' program itself, and can be found at: http://gmsh.info/doc/LICENSE.txt
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All other programs and files in these materials are licensed under a BSD-style license as follows:
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Copyright (c) 2018 The University of Notre Dame
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Copyright (c) 2018 The Regents of the University of California
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Redistribution and use in source and binary forms, with or without modification,
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are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice, this
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list of conditions and the following disclaimer in the documentation and/or other
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materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its contributors may
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be used to endorse or promote products derived from this software without specific
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prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
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EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
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OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
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SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
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TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
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BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
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IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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SUCH DAMAGE.

‎Agave/apps/cwe-parallel/test/test.sh

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#!/bin/bash
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echo "Test not yet implemented. This script is a test placeholder."

‎Agave/apps/cwe-parallel/wrapper.sh

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# Copyright (c) 2018 The University of Notre Dame
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# Copyright (c) 2018 The Regents of the University of California
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#
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# Redistribution and use in source and binary forms, with or without modification,
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# are permitted provided that the following conditions are met:
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#
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# 1. Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# 2. Redistributions in binary form must reproduce the above copyright notice, this
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# list of conditions and the following disclaimer in the documentation and/or other
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# materials provided with the distribution.
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# 3. Neither the name of the copyright holder nor the names of its contributors may
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# be used to endorse or promote products derived from this software without specific
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# prior written permission.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
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# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
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# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
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# SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
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# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
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# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
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# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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# SUCH DAMAGE.
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# Contributors:
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# Written by Peter Sempolinski, for the Natural Hazard Modeling Laboratory, director: Ahsan Kareem, at Notre Dame
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set -x
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${AGAVE_JOB_CALLBACK_RUNNING}
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export STARTINGDIR=`pwd`
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export PYTHONDIR=$STARTINGDIR/python/CFDexec
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export PYTHONPATH=$PYTHONPATH:$STARTINGDIR/python
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unzip templates.zip
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export TEMPLATER_FOLDER=$STARTINGDIR/templates
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PARENTDIR="${directory}"
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TASKSTAGE="${stage}"
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export EXTRAFILE="${file_input}"
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function dump_logs {
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echo "Starting cwe cleanup"
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cd $STARTINGDIR
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mkdir logs
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mv .agave.log logs
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mv *.err logs/cwe-parallel.err
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mv *.out logs/cwe-parallel.out
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mv *.log logs
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if [ -f $EXTRAFILE ]
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then
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rm -rf $EXTRAFILE
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fi
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rm -rf $TEMPLATER_FOLDER
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echo "$1" > .exit
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exit $1
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}
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#Debug: output all inputs
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echo "dest is $PARENTDIR"
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echo "stage is $TASKSTAGE"
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cp -f ${directory}/.caseParams .varStore
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export DATA_FOLDER=`python $PYTHONDIR/Templater.py getdatafolder`
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Unable to retrive data folder path"
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dump_logs $STOP
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fi
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SCRIPT_FILE=`python $PYTHONDIR/Templater.py getscript $TASKSTAGE`
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Unable to retrive script name."
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dump_logs $STOP
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fi
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LAST_STAGE=`python $PYTHONDIR/Templater.py getlaststage $TASKSTAGE`
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Unable to retrive last stage name."
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dump_logs $STOP
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fi
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echo $LAST_STAGE
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if [ $LAST_STAGE != "None" ]
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then
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mv ${directory}/$LAST_STAGE/* .
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mv -f ${directory}/.caseParams .varStore
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rm -rf logs
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rm -f .exit
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fi
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rm -rf ${directory}
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if [ -d "stats" ]
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then
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python $PYTHONDIR/Templater.py paramset -s stats
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else
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python $PYTHONDIR/Templater.py paramset
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fi
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chmod 700 $SCRIPT_FILE
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$SCRIPT_FILE
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Error in job process"
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dump_logs $STOP
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fi
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if [ -d "stats" ]
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then
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python $PYTHONDIR/Templater.py paramset -s stats
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fi
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Error in job process"
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dump_logs $STOP
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fi
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echo "CWE task process complete."
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dump_logs 0
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‎Agave/apps/cwe-serial/test/test.sh

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#!/bin/bash
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echo "Test not yet implemented. This script is a test placeholder."

‎Agave/apps/cwe-serial/wrapper.sh

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# Copyright (c) 2018 The University of Notre Dame
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# Copyright (c) 2018 The Regents of the University of California
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#
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# Redistribution and use in source and binary forms, with or without modification,
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# are permitted provided that the following conditions are met:
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#
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# 1. Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# 2. Redistributions in binary form must reproduce the above copyright notice, this
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# list of conditions and the following disclaimer in the documentation and/or other
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# materials provided with the distribution.
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# 3. Neither the name of the copyright holder nor the names of its contributors may
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# be used to endorse or promote products derived from this software without specific
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# prior written permission.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
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# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
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# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
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# SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
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# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
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# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
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# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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# SUCH DAMAGE.
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# Contributors:
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# Written by Peter Sempolinski, for the Natural Hazard Modeling Laboratory, director: Ahsan Kareem, at Notre Dame
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set -x
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${AGAVE_JOB_CALLBACK_RUNNING}
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export STARTINGDIR=`pwd`
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export PYTHONDIR=$STARTINGDIR/python/CFDexec
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export PYTHONPATH=$PYTHONPATH:$STARTINGDIR/python
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unzip templates.zip
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export TEMPLATER_FOLDER=$STARTINGDIR/templates
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PARENTDIR="${directory}"
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TASKSTAGE="${stage}"
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export EXTRAFILE="${file_input}"
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function dump_logs {
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echo "Starting cwe cleanup"
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cd $STARTINGDIR
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mkdir logs
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mv .agave.log logs
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mv *.err logs/cwe-serial.err
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mv *.out logs/cwe-serial.out
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mv *.log logs
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if [ -f $EXTRAFILE ]
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then
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rm -rf $EXTRAFILE
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fi
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rm -rf $TEMPLATER_FOLDER
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echo "$1" > .exit
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exit $1
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}
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#Debug: output all inputs
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echo "dest is $PARENTDIR"
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echo "stage is $TASKSTAGE"
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cp -f ${directory}/.caseParams .varStore
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export DATA_FOLDER=`python $PYTHONDIR/Templater.py getdatafolder`
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Unable to retrive data folder path"
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dump_logs $STOP
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fi
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SCRIPT_FILE=`python $PYTHONDIR/Templater.py getscript $TASKSTAGE`
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Unable to retrive script name."
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dump_logs $STOP
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fi
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LAST_STAGE=`python $PYTHONDIR/Templater.py getlaststage $TASKSTAGE`
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Unable to retrive last stage name."
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dump_logs $STOP
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fi
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echo $LAST_STAGE
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if [ $LAST_STAGE != "None" ]
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then
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mv ${directory}/$LAST_STAGE/* .
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mv -f ${directory}/.caseParams .varStore
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rm -rf logs
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rm -f .exit
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fi
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rm -rf ${directory}
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if [ -d "stats" ]
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then
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python $PYTHONDIR/Templater.py paramset -s stats
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else
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python $PYTHONDIR/Templater.py paramset
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fi
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chmod 700 $SCRIPT_FILE
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$SCRIPT_FILE
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Error in cwe task process"
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dump_logs $STOP
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fi
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if [ -d "stats" ]
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then
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python $PYTHONDIR/Templater.py paramset -s stats
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fi
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STOP=$?
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if [ $STOP -ne 0 ]
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then
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echo "Error in cwe task process"
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dump_logs $STOP
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fi
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echo "CWE task process complete."
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dump_logs 0
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