Merge pull request #67 from Noam-Elisha/master

CI pipeline to test PBE

.github/workflows/main.yml

@@ -0,0 +1,29 @@
+name: Run PBE tests
+
+on: push
+  # workflow_dispatch:
+  # schedule:
+  #   - cron: "0 5 * * *"
+
+jobs:
+  setup_and_test:
+    name: Setup and run tests
+    runs-on: ubuntu-latest
+    environment: PBE
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Bootstrap
+        run: |
+            chmod +x bootstrap.sh
+            sh ./bootstrap.sh
+      - name: Build SimCenter Applications
+        run: |
+            chmod +x build_backend_apps.sh
+            sh ./build_backend_apps.sh
+      - name: Run Examples
+        run: |
+            chmod +x run_examples.sh
+            sh ./run_examples.sh

bootstrap.sh

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+#!/bin/bash
+
+# Set Timezone (needed for python install)
+sudo ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+# Updates the package lists for upgrades and new package installations
+apt-get update
+apt-get install sudo -y
+apt-get install wget -y
+sudo apt install -y software-properties-common cmake git
+
+# Installs the  python 3.9 package. The '-y' flag automatically answers yes to prompts.
+sudo add-apt-repository ppa:deadsnakes/ppa -y
+sudo apt update 
+sudo apt install python3.9 python3.9-dev python3.9-venv python3.9-distutils -y
+
+# Install pip
+wget https://bootstrap.pypa.io/get-pip.py
+python3.9 get-pip.py
+
+# Upgrades pip (Python package installer) to the latest version
+sudo python3.9 -m pip install -U pip
+
+# Installs the Conan package manager
+python3.9 -m pip install conan==1.60.1
+python3.9 -m pip install nheri-simcenter
+
+python3.9 --version
+
+sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.9.20
+sudo update-alternatives --install /usr/bin/python python3 /usr/bin/python3.9.20
+sudo update-alternatives --config python
+
+which python3
+
+which conan
+
+wget https://github.com/snl-dakota/dakota/releases/download/v6.15.0/dakota-6.15.0-public-src-cli.tar.gz
+sudo apt-get install -y cmake libboost-dev libboost-all-dev libopenmpi-dev openmpi-bin xorg-dev libmotif-dev libblas-dev liblapack-dev g++
+tar zxBf dakota-6.15.0-public-src-cli.tar.gz 
+mv dakota-6.15.0-public-src-cli dakota-6.15.0 
+cd dakota-6.15.0 
+mkdir build; cd build 
+cmake .. 
+make -j 16
+cd ../.. 
+export PATH=$PWD/dakota-6.15.0/build/src:$PATH
+alias python3=python3.9
+
+sudo apt-get install -y cmake liblapack-dev libomp-dev libssl-dev apt-transport-https ca-certificates wget         
+wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | sudo tee /etc/apt/trusted.gpg.d/kitware.gpg >/dev/null 
+sudo apt-add-repository -y "deb https://apt.kitware.com/ubuntu/ $(lsb_release -cs) main" 
+sudo apt-get update 
+sudo apt-get install -y cmake gfortran gcc g++ 
+git clone -b v3.7.0 --single-branch https://github.com/OpenSees/OpenSees.git
+cd OpenSees 
+mkdir build; cd build 
+conan install .. --build missing 
+cmake .. 
+cmake --build . --config Release 
+cmake --install . 
+sudo mv ./lib/* /usr/local/lib 
+cd ../..
+
+export PATH=$PATH:/usr/local/OpenSees/bin:/usr/local/Dakota/bin
+sudo sh ~/.profile

build_backend_apps.sh

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+#!/bin/bash
+
+git clone --depth 1 https://github.com/NHERI-SimCenter/SimCenterBackendApplications.git
+
+cp ./SimCenterBackendApplications/modules/performUQ/SimCenterUQ/nataf_gsa/CMakeLists.txt.UBUNTU ./SimCenterBackendApplications/modules/performUQ/SimCenterUQ/nataf_gsa/CMakeLists.txt
+
+rm -fr ~/.conan
+
+sudo apt-get install -y liblapack-dev libomp-dev libssl-dev apt-transport-https ca-certificates \
+
+sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+
+sudo apt-get update
+
+sudo apt-get install -y gcc-11 g++-11 gfortran-11
+
+export CC=gcc-11
+
+export CXX=g++-11
+
+export FC=gfortran-11
+
+cd SimCenterBackendApplications
+
+mkdir build
+
+cd build
+
+conan install .. --build missing
+
+cmake ..
+
+cmake --build . --config Release
+
+cmake --install .
+
+cd ../..

pbe_input_cleaner.py

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+import sys
+
+if __name__ == "__main__":
+    path = sys.argv[1]
+    text = None
+    with open(path, "r") as f:
+        text = f.read()
+
+    text = text.replace("{Current_Dir}", "templatedir")
+
+    with open(path, "w") as f:
+        f.write(text)

run_examples.sh

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+#!/bin/bash
+
+
+export PATH=$PATH:/usr/local/OpenSees/bin:/usr/local/Dakota/bin
+echo In folder $PWD
+
+# Clone the examples
+git clone --branch master https://github.com/NHERI-SimCenter/PBE.git
+
+# make sure all packages are installed
+python3 -m pip install --upgrade pip
+python3 -m pip install nheri-simcenter --upgrade
+python3 -m pip install GPy==1.13.2
+
+# Read JSON from file
+json_file="$PWD/PBE/Examples/Examples.json"
+
+# Install jq
+sudo apt-get install -y jq
+rm -rf cache
+mkdir cache
+# Iterate over array elements
+jq -c '.Examples[]' "$json_file" | while read -r example; do
+
+  name=$(echo "$example" | jq -r '.name')
+  description=$(echo "$example" | jq -r '.description')
+  inputfile=$(echo "$example" | jq -r '.inputFile')
+
+  inputfile="$PWD/PBE/Examples/$inputfile"
+  srcDir="$(dirname $inputfile)"
+  examplenumber="$(dirname $srcDir)"
+  examplenumber="$(basename $examplenumber)"
+
+  echo "==========================================="
+  echo "Example Number: $examplenumber"
+  echo "Example Name: $name"
+  echo "Example Description: $description"
+  echo "Input File: $inputfile"
+  echo "srcDir: $srcDir"
+  echo "---------------------------"
+  # Change {Current_Dir} in input to templatedir
+  python3 pbe_input_cleaner.py $inputfile
+
+  # Add JSON Arguments to input
+  echo "Adding json params to input file..."
+  echo $(cat $inputfile | jq '. + { "runDir": "'"$PWD/tmp.SimCenter"'" }') > $inputfile
+  echo $(cat $inputfile | jq '. + { "localAppDir": "'"$PWD/SimCenterBackendApplications"'" }') > $inputfile
+  echo $(cat $inputfile | jq '. + { "remoteAppDir": "'"$PWD/SimCenterBackendApplications"'" }') > $inputfile
+  echo $(cat $inputfile | jq '. + { "runType": "runningLocal" }') > $inputfile
+
+  echo "copying files"
+  rm -rf tmp.SimCenter
+  mkdir tmp.SimCenter
+  mkdir tmp.SimCenter/templatedir
+  cp -a $srcDir/. $PWD/tmp.SimCenter/templatedir/
+
+
+
+  #echo "Input file contents:"
+  #python3 -m json.tool $inputfile
+
+  #echo "Template dir contents"
+  #ls $PWD/tmp.SimCenter/templatedir
+
+
+  # Run the example in the backend
+  echo "Running python:"
+  echo "==============="
+  python3 $PWD/SimCenterBackendApplications/applications/Workflow/sWHALE.py "runningLocal" $inputfile $PWD/SimCenterBackendApplications/applications/Workflow/WorkflowApplications.json
+  mkdir "cache/tmp.SimCenter.$examplenumber/"
+  cp -r tmp.SimCenter/. "cache/tmp.SimCenter.$examplenumber/"
+done
+
+# Check with archives have a dakotaTab.out file
+echo ""
+echo ""
+echo "======================================"
+for dir in $PWD/cache/*; do
+  if [ -f "$dir/dakotaTab.out" ]; then
+    echo "$dir: PASS"
+    # Do something if the file exists
+  else
+    echo "$dir: FAIL"
+    # Do something else if the file does not exist
+  fi
+done