From 6c0d1cc44f41a6edba3af72e3c45349ed29e9398 Mon Sep 17 00:00:00 2001
From: Max Liu <mjliu@mit.edu>
Date: Thu, 22 Mar 2018 14:09:19 -0400
Subject: [PATCH] New local testing workflow

---
 local/install_local.sh | 117 +++++++++++++++++++++++++++++++++++++++++
 local/run.sh           |  66 +++++++++++++++++++++++
 local/run_job.sh       | 100 +++++++++++++++++++++++++++++++++++
 local/submit.sl        |  39 ++++++++++++++
 local/submit_job.sl    |   8 +++
 local/thermo_val.sh    |  46 ++++++++++++++++
 6 files changed, 376 insertions(+)
 create mode 100644 local/install_local.sh
 create mode 100644 local/run.sh
 create mode 100644 local/run_job.sh
 create mode 100644 local/submit.sl
 create mode 100644 local/submit_job.sl
 create mode 100644 local/thermo_val.sh

diff --git a/local/install_local.sh b/local/install_local.sh
new file mode 100644
index 00000000..542dac54
--- /dev/null
+++ b/local/install_local.sh
@@ -0,0 +1,117 @@
+#!/bin/bash
+
+# Exit immediately on failure
+set -e
+
+###################
+# BENCHMARK SETUP #
+###################
+
+# Prepare temporary directory for benchmark RMG-Py and RMG-db
+benchmark=$DATA_DIR/code/benchmark/$(date +%Y-%m-%d:%H:%M:%S)
+rm -rf $benchmark
+mkdir -p $benchmark
+cd $benchmark
+
+# Prepare benchmark RMG-Py
+git clone -q https://github.com/ReactionMechanismGenerator/RMG-Py.git
+cd RMG-Py
+git checkout $RMGPY_BENCHMARK_BRANCH
+export benchmark_py_sha=$(git rev-parse HEAD)
+cd ..
+
+# Prepare benchmark RMG-database:
+git clone -q https://github.com/ReactionMechanismGenerator/RMG-database.git
+cd RMG-database
+git checkout $RMGDB_BENCHMARK_BRANCH
+export benchmark_db_sha=$(git rev-parse HEAD)
+
+# Rename benchmark code folder
+cd $DATA_DIR/code/benchmark
+
+export benchmark_tag=py${benchmark_py_sha:0:12}_db${benchmark_db_sha:0:12}
+
+if [ ! -d "${benchmark_tag}" ]; then
+    mv $benchmark $benchmark_tag
+else
+    rm -rf $benchmark
+fi
+
+export benchmark=$DATA_DIR/code/benchmark/$benchmark_tag
+
+# Prepare benchmark environment if requested
+if [ "$CLEAN_ENV" == true ]; then
+    cd $benchmark/RMG-Py
+    export benchmark_env="benchmark_env"
+    conda remove --name $benchmark_env --all -y 
+    conda env create -n $benchmark_env -f environment_${CURRENT_OS}.yml 
+else
+    export benchmark_env="rmg_env"
+fi
+
+# Compile benchmark RMG-Py:
+cd $benchmark/RMG-Py
+source activate $benchmark_env
+make
+source deactivate
+
+export RMG_BENCHMARK=$benchmark/RMG-Py
+export RMGDB_BENCHMARK=$benchmark/RMG-database
+
+#################
+# TESTING SETUP #
+#################
+
+# Prepare temporary directory for testing RMG-Py and RMG-db
+testing=$DATA_DIR/code/testing/$(date +%Y-%m-%d:%H:%M:%S)
+rm -rf $testing
+mkdir -p $testing
+cd $testing
+
+# Prepare testing RMG-Py:
+git clone -q https://github.com/ReactionMechanismGenerator/RMG-Py.git
+cd RMG-Py
+git checkout ${RMG_TESTING_BRANCH}
+export testing_py_sha=$(git rev-parse HEAD)
+cd ..
+
+# Prepare testing RMG-database
+git clone -q https://github.com/ReactionMechanismGenerator/RMG-database.git
+cd RMG-database
+git checkout ${RMGDB_TESTING_BRANCH}
+export testing_db_sha=$(git rev-parse HEAD)
+
+# Rename testing code folder
+cd $DATA_DIR/code/testing
+
+export testing_tag=py${testing_py_sha:0:12}_db${testing_db_sha:0:12}
+
+if [ ! -d "${testing_tag}" ]; then
+    mv $testing $testing_tag
+else
+    rm -rf $testing
+fi
+export testing=$DATA_DIR/code/testing/$testing_tag
+
+# Prepare testing environment if requested
+if [ "$SEPARATE_ENV" == true]; then
+    cd $testing/RMG-Py
+    export testing_env="testing_env"
+    conda remove --name $testing_env --all -y 
+    conda env create -n $testing_env -f environment_${CURRENT_OS}.yml
+else
+    export testing_env=$benchmark_env
+fi
+
+# Compile RMG-Py:
+cd $testing/RMG-Py
+source activate $testing_env
+make
+source deactivate
+
+export RMG_TESTING=$testing/RMG-Py
+export RMGDB_TESTING=$testing/RMG-database
+
+# Go to RMG-tests folder:
+cd $DATA_DIR
+
diff --git a/local/run.sh b/local/run.sh
new file mode 100644
index 00000000..b6ded6b1
--- /dev/null
+++ b/local/run.sh
@@ -0,0 +1,66 @@
+#!/bin/bash
+
+# Set RMG-tests base directory
+export BASE_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )/.." && pwd )"
+echo "Local tests base dir: "$BASE_DIR
+
+# Set data directory
+export DATA_DIR=$BASE_DIR/data_dir
+
+# Figure out OS
+if [[ $MACHTYPE == *"apple"* ]]; then
+    export CURRENT_OS="mac"
+elif [[ $MACHTYPE == *"linux"* ]]; then
+    export CURRENT_OS="linux"
+else
+    echo "$MACHTYPE not supported. Exiting..."
+    exit 0
+fi
+echo "Current OS: "$CURRENT_OS
+
+# Print input settings
+echo "Benchmark Branches:"
+echo "    RMG-Py:       "$RMGPY_BENCHMARK_BRANCH
+echo "    RMG-database: "$RMGDB_BENCHMARK_BRANCH
+echo "Testing Branches:"
+echo "    RMG-Py:       "$RMGPY_TESTING_BRANCH
+echo "    RMG-database: "$RMGDB_TESTING_BRANCH
+echo "Testing Jobs:     "$JOBS
+echo "Data Directory:   "$DATA_DIR
+
+. $BASE_DIR/color_define.sh
+. $BASE_DIR/local/install_local.sh
+. $BASE_DIR/version_summary.sh
+
+echo "INSTALLATION COMPLETE"
+
+cd $BASE_DIR/local
+
+# Run RMG test jobs
+if [ $JOBS == "all" ]; then
+    for i in eg1 eg3 eg5 eg6 eg7 NC solvent_hexane MCH
+    do
+        if [ $PARALLEL == "true" ]; then
+            export SBATCH_JOB_NAME=run_$i
+            sbatch $BASE_DIR/local/submit_job.sl $i no
+        else
+            . $BASE_DIR/local/run_job.sh $i no
+        fi
+    done
+else
+    if [ $PARALLEL == "true" ]; then
+        export SBATCH_JOB_NAME=run_$i
+        sbatch $BASE_DIR/local/submit_job.sl $JOBS no
+    else
+        . $BASE_DIR/local/run_job.sh $JOBS no
+    fi
+fi
+
+# Run thermo validation jobs
+if [ $THERMOVAL == "true" ]; then
+    for i in hc_cyclics hco_cyclics rmg_internal_cyclics
+    do
+        . $BASE_DIR/local/thermo_val.sh $i
+    done
+fi
+
diff --git a/local/run_job.sh b/local/run_job.sh
new file mode 100644
index 00000000..7acb1f67
--- /dev/null
+++ b/local/run_job.sh
@@ -0,0 +1,100 @@
+#!/bin/bash
+
+job=$1
+scoop_test=$2
+
+set -e
+
+if [ -z ${RMG_BENCHMARK+x} ]; then 
+    echo "RMG variable is unset. Exiting..."
+    exit 0
+fi
+
+export ORIGIN_PYTHONPATH=$PYTHONPATH
+echo "Running Job: $1"
+
+#############
+# BENCHMARK #
+#############
+
+# Make folder for models generated by the benchmark version of RMG-Py/RMG-database:
+export benchmark_tests=$DATA_DIR/tests/benchmark/$benchmark_tag
+mkdir -p $benchmark_tests/rmg_jobs/$job
+rm -rf $benchmark_tests/rmg_jobs/$job/*
+cp $BASE_DIR/examples/rmg/$job/input.py $benchmark_tests/rmg_jobs/$job/input.py
+
+source activate ${benchmark_env}
+
+echo "Benchmark Version of RMG: "$RMG_BENCHMARK
+export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH 
+
+python $RMG_BENCHMARK/rmg.py $benchmark_tests/rmg_jobs/$job/input.py > /dev/null
+
+source deactivate
+export PYTHONPATH=$ORIGIN_PYTHONPATH
+
+###########
+# TESTING #
+###########
+
+# Make folder for models generated by the test version of RMG-Py and RMG-database:
+export testing_tests=$DATA_DIR/tests/testing/$testing_tag
+mkdir -p $testing_tests/rmg_jobs/$job
+rm -rf $testing_tests/rmg_jobs/$job/*
+cp $BASE_DIR/examples/rmg/$job/input.py $testing_tests/rmg_jobs/$job/input.py
+
+source activate ${testing_env}
+
+echo "Test Version of RMG: "$RMG_TESTING
+export PYTHONPATH=$RMG_TESTING:$ORIGIN_PYTHONPATH 
+
+python $RMG_TESTING/rmg.py $testing_tests/rmg_jobs/$job/input.py > /dev/null
+
+export PYTHONPATH=$ORIGIN_PYTHONPATH
+source deactivate
+
+###########
+# COMPARE #
+###########
+
+export check_tests=$DATA_DIR/tests/check/$testing_tag
+mkdir -p $check_tests/rmg_jobs/$job
+rm -rf $check_tests/rmg_jobs/$job/*
+cd $check_tests/rmg_jobs/$job
+
+source activate ${benchmark_env}
+export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH 
+
+bash $BASE_DIR/check.sh $job $benchmark_tests/rmg_jobs/$job $testing_tests/rmg_jobs/$job
+
+export PYTHONPATH=$ORIGIN_PYTHONPATH
+source deactivate
+
+if [ $scoop_test == "yes" ]; then
+    # Make folder for models generated by the test version of RMG-Py and RMG-database, with scoop enabled:
+    mkdir -p $testing_tests/rmg_jobs/$job/scoop
+    rm -rf $testing_tests/rmg_jobs/$job/scoop/*
+    cp $BASE_DIR/examples/rmg/$job/input.py $testing_tests/rmg_jobs/$job/scoop/input.py
+    echo "Version of RMG running with SCOOP: $RMG"
+    source activate ${testing_env}
+    export PYTHONPATH=$RMG_TESTING:$ORIGIN_PYTHONPATH
+
+    python -m scoop -n 1 $RMG_TESTING/rmg.py $testing_tests/rmg_jobs/$job/scoop/input.py > /dev/null
+
+    export PYTHONPATH=$ORIGIN_PYTHONPATH
+    source deactivate
+
+    # compare both generated models
+    mkdir -p $check_tests/rmg_jobs/$job/scoop
+    cd $check_tests/rmg_jobs/$job/scoop
+    source activate ${benchmark_env}
+    export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH 
+
+    bash $BASE_DIR/check.sh $job $benchmark_tests/rmg_jobs/$job $testing_tests/rmg_jobs/$job/scoop
+
+    export PYTHONPATH=$ORIGIN_PYTHONPATH
+    source deactivate
+fi
+
+echo "$job: TEST JOB COMPLETE"
+
diff --git a/local/submit.sl b/local/submit.sl
new file mode 100644
index 00000000..c0e28356
--- /dev/null
+++ b/local/submit.sl
@@ -0,0 +1,39 @@
+#!/bin/bash
+#SBATCH -p debug
+#SBATCH -J RMG-test
+#SBATCH -n 1
+#SBATCH --nodelist=node03
+#SBATCH --output=main_log.out
+
+# Usage: sbatch submit.sl
+
+# Specify testing branches here
+RMGPY_TESTING_BRANCH="test_branch"
+RMGDB_TESTING_BRANCH="master"
+
+# Specify benchmark branches here
+# These should generally be left as master
+RMGPY_BENCHMARK_BRANCH="master"
+RMGDB_BENCHMARK_BRANCH="master"
+
+# Specify jobs to run
+# Current jobs available: eg1, eg3, eg5, eg6, eg7, NC, solvent_hexane, MCH, methane
+JOBS="all"
+
+# Specify whether to run thermo validation
+THERMOVAL=true
+
+# Specify whether or not to recreate the Anaconda environment
+# This is generally not necessary, and can be left as false
+CLEAN_ENV=false
+
+# Specify whether or not the testing and benchmark jobs should use separate environments
+# This is generally not necessary, and can be left as false
+SEPARATE_ENV=false
+
+# Specify whether to run jobs in parallel or serial
+PARALLEL=true
+
+# Start the job
+. ./run.sh
+
diff --git a/local/submit_job.sl b/local/submit_job.sl
new file mode 100644
index 00000000..3a27c4e3
--- /dev/null
+++ b/local/submit_job.sl
@@ -0,0 +1,8 @@
+#!/bin/bash
+#SBATCH -p debug
+#SBATCH -n 1
+
+JOB=$1
+SCOOP=$2
+
+. $BASE_DIR/local/run_job.sh $JOB $SCOOP
diff --git a/local/thermo_val.sh b/local/thermo_val.sh
new file mode 100644
index 00000000..50aebc3a
--- /dev/null
+++ b/local/thermo_val.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+job=$1
+
+export ORIGIN_PYTHONPATH=$PYTHONPATH
+
+#############
+# BENCHMARK #
+#############
+
+# Make folder for models generated by the benchmark version of RMG-Py/RMG-database:
+export benchmark_tests=$DATA_DIR/tests/benchmark/$benchmark_tag
+mkdir -p $benchmark_tests/thermo_val_jobs/$job
+
+cp $BASE_DIR/examples/thermo_val/$job/dataset.txt $benchmark_tests/thermo_val_jobs/$job/dataset.txt
+
+echo "Benchmark Version of RMG: "$RMG_BENCHMARK
+echo "Running thermo validation on benchmark version..."
+
+source activate ${benchmark_env}
+export PYTHONPATH=$RMG_BENCHMARK:$ORIGIN_PYTHONPATH
+
+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 ${benchmark_db_sha}
+
+source deactivate
+export PYTHONPATH=$ORIGIN_PYTHONPATH
+
+###########
+# TESTING #
+###########
+
+# Make folder for models generated by the test version of RMG-Py and RMG-database:
+export testing_tests=$DATA_DIR/tests/testing/$testing_tag
+mkdir -p $testing_tests/thermo_val_jobs/$job
+
+cp $BASE_DIR/examples/thermo_val/$job/dataset.txt $testing_tests/thermo_val_jobs/$job/dataset.txt
+
+echo "Testing Version of RMG: "$RMG_TESTING
+echo "Running thermo validation on testing version..."
+
+source activate ${testing_env}
+export PYTHONPATH=$RMG_TESTING:$ORIGIN_PYTHONPATH 
+
+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 ${testing_db_sha}
+
+source deactivate
+export PYTHONPATH=$ORIGIN_PYTHONPATH