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New local testing workflow
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‎local/install_local.sh‎

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#!/bin/bash
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# Exit immediately on failure
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set -e
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###################
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# BENCHMARK SETUP #
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###################
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# Prepare temporary directory for benchmark RMG-Py and RMG-db
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benchmark=$DATA_DIR/code/benchmark/$(date +%Y-%m-%d:%H:%M:%S)
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rm -rf $benchmark
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mkdir -p $benchmark
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cd $benchmark
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# Prepare benchmark RMG-Py
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git clone -q https://github.com/ReactionMechanismGenerator/RMG-Py.git
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cd RMG-Py
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git checkout $RMGPY_BENCHMARK_BRANCH
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export benchmark_py_sha=$(git rev-parse HEAD)
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cd ..
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# Prepare benchmark RMG-database:
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git clone -q https://github.com/ReactionMechanismGenerator/RMG-database.git
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cd RMG-database
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git checkout $RMGDB_BENCHMARK_BRANCH
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export benchmark_db_sha=$(git rev-parse HEAD)
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# Rename benchmark code folder
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cd $DATA_DIR/code/benchmark
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export benchmark_tag=py${benchmark_py_sha:0:12}_db${benchmark_db_sha:0:12}
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if [ ! -d "${benchmark_tag}" ]; then
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mv $benchmark $benchmark_tag
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else
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rm -rf $benchmark
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fi
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export benchmark=$DATA_DIR/code/benchmark/$benchmark_tag
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# Prepare benchmark environment if requested
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if [ "$CLEAN_ENV" == true ]; then
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cd $benchmark/RMG-Py
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export benchmark_env="benchmark_env"
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conda remove --name $benchmark_env --all -y
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conda env create -n $benchmark_env -f environment_${CURRENT_OS}.yml
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else
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export benchmark_env="rmg_env"
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fi
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# Compile benchmark RMG-Py:
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cd $benchmark/RMG-Py
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source activate $benchmark_env
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make
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source deactivate
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export RMG_BENCHMARK=$benchmark/RMG-Py
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export RMGDB_BENCHMARK=$benchmark/RMG-database
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#################
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# TESTING SETUP #
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#################
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# Prepare temporary directory for testing RMG-Py and RMG-db
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testing=$DATA_DIR/code/testing/$(date +%Y-%m-%d:%H:%M:%S)
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rm -rf $testing
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mkdir -p $testing
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cd $testing
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# Prepare testing RMG-Py:
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git clone -q https://github.com/ReactionMechanismGenerator/RMG-Py.git
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cd RMG-Py
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git checkout ${RMGPY_TESTING_BRANCH}
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export testing_py_sha=$(git rev-parse HEAD)
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cd ..
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# Prepare testing RMG-database
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git clone -q https://github.com/ReactionMechanismGenerator/RMG-database.git
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cd RMG-database
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git checkout ${RMGDB_TESTING_BRANCH}
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export testing_db_sha=$(git rev-parse HEAD)
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# Rename testing code folder
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cd $DATA_DIR/code/testing
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export testing_tag=py${testing_py_sha:0:12}_db${testing_db_sha:0:12}
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if [ ! -d "${testing_tag}" ]; then
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mv $testing $testing_tag
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else
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rm -rf $testing
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fi
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export testing=$DATA_DIR/code/testing/$testing_tag
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# Prepare testing environment if requested
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if [ "$SEPARATE_ENV" == true]; then
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cd $testing/RMG-Py
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export testing_env="testing_env"
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conda remove --name $testing_env --all -y
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conda env create -n $testing_env -f environment_${CURRENT_OS}.yml
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else
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export testing_env=$benchmark_env
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fi
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# Compile RMG-Py:
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cd $testing/RMG-Py
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source activate $testing_env
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make
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source deactivate
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export RMG_TESTING=$testing/RMG-Py
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export RMGDB_TESTING=$testing/RMG-database
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# Go to RMG-tests folder:
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cd $DATA_DIR
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‎local/run.sh‎

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#!/bin/bash
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# Set RMG-tests base directory
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export BASE_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )/.." && pwd )"
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echo "Local tests base dir: "$BASE_DIR
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# Set data directory
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export DATA_DIR=$BASE_DIR/data_dir
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# Figure out OS
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if [[ $MACHTYPE == *"apple"* ]]; then
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export CURRENT_OS="mac"
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elif [[ $MACHTYPE == *"linux"* ]]; then
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export CURRENT_OS="linux"
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else
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echo "$MACHTYPE not supported. Exiting..."
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exit 0
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fi
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echo "Current OS: "$CURRENT_OS
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# Print input settings
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echo "Benchmark Branches:"
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echo " RMG-Py: "$RMGPY_BENCHMARK_BRANCH
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echo " RMG-database: "$RMGDB_BENCHMARK_BRANCH
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echo "Testing Branches:"
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echo " RMG-Py: "$RMGPY_TESTING_BRANCH
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echo " RMG-database: "$RMGDB_TESTING_BRANCH
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echo "Testing Jobs: "$JOBS
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echo "Data Directory: "$DATA_DIR
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. $BASE_DIR/color_define.sh
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. $BASE_DIR/local/install_local.sh
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. $BASE_DIR/version_summary.sh
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echo "INSTALLATION COMPLETE"
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cd $BASE_DIR/local
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# Run RMG test jobs
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if [ $JOBS == "all" ]; then
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for i in eg1 eg3 eg5 eg6 eg7 NC solvent_hexane MCH
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do
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if [ $PARALLEL == "true" ]; then
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export SBATCH_JOB_NAME=run_$i
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sbatch $BASE_DIR/local/submit_job.sl $i no
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else
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. $BASE_DIR/local/run_job.sh $i no
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fi
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done
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else
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if [ $PARALLEL == "true" ]; then
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export SBATCH_JOB_NAME=run_$i
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sbatch $BASE_DIR/local/submit_job.sl $JOBS no
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else
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. $BASE_DIR/local/run_job.sh $JOBS no
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fi
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fi
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# Run thermo validation jobs
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if [ $THERMOVAL == "true" ]; then
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for i in hc_cyclics hco_cyclics rmg_internal_cyclics
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do
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. $BASE_DIR/local/thermo_val.sh $i
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done
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fi
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‎local/run_job.sh‎

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#!/bin/bash
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job=$1
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scoop_test=$2
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set -e
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if [ -z ${RMG_BENCHMARK+x} ]; then
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echo "RMG variable is unset. Exiting..."
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exit 0
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fi
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export ORIGIN_PYTHONPATH=$PYTHONPATH
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echo "Running Job: $1"
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#############
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# BENCHMARK #
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#############
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# Make folder for models generated by the benchmark version of RMG-Py/RMG-database:
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export benchmark_tests=$DATA_DIR/tests/benchmark/$benchmark_tag
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mkdir -p $benchmark_tests/rmg_jobs/$job
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rm -rf $benchmark_tests/rmg_jobs/$job/*
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cp $BASE_DIR/examples/rmg/$job/input.py $benchmark_tests/rmg_jobs/$job/input.py
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source activate ${benchmark_env}
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echo "Benchmark Version of RMG: "$RMG_BENCHMARK
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export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH
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python $RMG_BENCHMARK/rmg.py $benchmark_tests/rmg_jobs/$job/input.py > /dev/null
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source deactivate
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export PYTHONPATH=$ORIGIN_PYTHONPATH
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###########
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# TESTING #
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###########
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# Make folder for models generated by the test version of RMG-Py and RMG-database:
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export testing_tests=$DATA_DIR/tests/testing/$testing_tag
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mkdir -p $testing_tests/rmg_jobs/$job
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rm -rf $testing_tests/rmg_jobs/$job/*
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cp $BASE_DIR/examples/rmg/$job/input.py $testing_tests/rmg_jobs/$job/input.py
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source activate ${testing_env}
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echo "Test Version of RMG: "$RMG_TESTING
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export PYTHONPATH=$RMG_TESTING:$ORIGIN_PYTHONPATH
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python $RMG_TESTING/rmg.py $testing_tests/rmg_jobs/$job/input.py > /dev/null
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export PYTHONPATH=$ORIGIN_PYTHONPATH
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source deactivate
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###########
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# COMPARE #
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###########
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export check_tests=$DATA_DIR/tests/check/$testing_tag
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mkdir -p $check_tests/rmg_jobs/$job
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rm -rf $check_tests/rmg_jobs/$job/*
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cd $check_tests/rmg_jobs/$job
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source activate ${benchmark_env}
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export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH
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bash $BASE_DIR/check.sh $job $benchmark_tests/rmg_jobs/$job $testing_tests/rmg_jobs/$job
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export PYTHONPATH=$ORIGIN_PYTHONPATH
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source deactivate
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if [ $scoop_test == "yes" ]; then
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# Make folder for models generated by the test version of RMG-Py and RMG-database, with scoop enabled:
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mkdir -p $testing_tests/rmg_jobs/$job/scoop
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rm -rf $testing_tests/rmg_jobs/$job/scoop/*
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cp $BASE_DIR/examples/rmg/$job/input.py $testing_tests/rmg_jobs/$job/scoop/input.py
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echo "Version of RMG running with SCOOP: $RMG"
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source activate ${testing_env}
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export PYTHONPATH=$RMG_TESTING:$ORIGIN_PYTHONPATH
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python -m scoop -n 1 $RMG_TESTING/rmg.py $testing_tests/rmg_jobs/$job/scoop/input.py > /dev/null
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export PYTHONPATH=$ORIGIN_PYTHONPATH
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source deactivate
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# compare both generated models
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mkdir -p $check_tests/rmg_jobs/$job/scoop
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cd $check_tests/rmg_jobs/$job/scoop
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source activate ${benchmark_env}
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export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH
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bash $BASE_DIR/check.sh $job $benchmark_tests/rmg_jobs/$job $testing_tests/rmg_jobs/$job/scoop
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export PYTHONPATH=$ORIGIN_PYTHONPATH
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source deactivate
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fi
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echo "$job: TEST JOB COMPLETE"
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‎local/submit.sl‎

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#!/bin/bash
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#SBATCH -p debug
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#SBATCH -J RMG-test
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#SBATCH -n 1
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#SBATCH --nodelist=node03
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#SBATCH --output=main_log.out
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# Usage: sbatch submit.sl
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# Specify testing branches here
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RMGPY_TESTING_BRANCH="test_branch"
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RMGDB_TESTING_BRANCH="master"
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# Specify benchmark branches here
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# These should generally be left as master
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RMGPY_BENCHMARK_BRANCH="master"
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RMGDB_BENCHMARK_BRANCH="master"
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# Specify jobs to run
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# Current jobs available: eg1, eg3, eg5, eg6, eg7, NC, solvent_hexane, MCH, methane
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JOBS="all"
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# Specify whether to run thermo validation
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THERMOVAL=true
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# Specify whether or not to recreate the Anaconda environment
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# This is generally not necessary, and can be left as false
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CLEAN_ENV=false
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# Specify whether or not the testing and benchmark jobs should use separate environments
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# This is generally not necessary, and can be left as false
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SEPARATE_ENV=false
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# Specify whether to run jobs in parallel or serial
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PARALLEL=true
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# Start the job
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. ./run.sh
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‎local/submit_job.sl‎

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#!/bin/bash
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#SBATCH -p debug
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#SBATCH -n 1
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JOB=$1
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SCOOP=$2
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. $BASE_DIR/local/run_job.sh $JOB $SCOOP

‎local/thermo_val.sh‎

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#!/bin/bash
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job=$1
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export ORIGIN_PYTHONPATH=$PYTHONPATH
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#############
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# BENCHMARK #
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#############
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# Make folder for models generated by the benchmark version of RMG-Py/RMG-database:
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export benchmark_tests=$DATA_DIR/tests/benchmark/$benchmark_tag
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mkdir -p $benchmark_tests/thermo_val_jobs/$job
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cp $BASE_DIR/examples/thermo_val/$job/dataset.txt $benchmark_tests/thermo_val_jobs/$job/dataset.txt
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echo "Benchmark Version of RMG: "$RMG_BENCHMARK
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echo "Running thermo validation on benchmark version..."
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source activate ${benchmark_env}
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export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH
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python $BASE_DIR/thermo_val/evaluate.py -d $benchmark_tests/thermo_val_jobs/$job/dataset.txt -pb $RMGPY_BENCHMARK_BRANCH -dbb $RMGDB_BENCHMARK_BRANCH -psha ${benchmark_py_sha} -dbsha ${benchmark_db_sha}
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source deactivate
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export PYTHONPATH=$ORIGIN_PYTHONPATH
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###########
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# TESTING #
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###########
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# Make folder for models generated by the test version of RMG-Py and RMG-database:
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export testing_tests=$DATA_DIR/tests/testing/$testing_tag
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mkdir -p $testing_tests/thermo_val_jobs/$job
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cp $BASE_DIR/examples/thermo_val/$job/dataset.txt $testing_tests/thermo_val_jobs/$job/dataset.txt
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echo "Testing Version of RMG: "$RMG_TESTING
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echo "Running thermo validation on testing version..."
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source activate ${testing_env}
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export PYTHONPATH=$RMG_TESTING:$ORIGIN_PYTHONPATH
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python $BASE_DIR/thermo_val/evaluate.py -d $testing_tests/thermo_val_jobs/$job/dataset.txt -pb $RMGPY_TESTING_BRANCH -dbb $RMGDB_TESTING_BRANCH -psha ${testing_py_sha} -dbsha ${testing_db_sha}
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source deactivate
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export PYTHONPATH=$ORIGIN_PYTHONPATH

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