Merge pull request #51 from plasmapotential/main

Merging main into runaway electrons

.github/workflows/ci.yml

@@ -2,26 +2,43 @@ name: CI
 
 on:
   push:
-    branches: [ plasma3D ]
+    branches: [ main ]
   pull_request:
-    branches: [ plasma3D ]
+    branches: [ main ]
 
 jobs:
-  test:
+  check-final-image:
     runs-on: ubuntu-latest
+    steps:
+    - name: Check if final Docker image exists on Docker Hub
+      id: check-final-image
+      run: |
+        if docker pull plasmapotential/heat:v4.1; then
+          echo "Image exists on Docker Hub."
+        else
+          echo "::error ::Final HEAT Docker image v4.1 does not exist."
+          exit 1 
+        fi
 
+  test:
+    needs: check-final-image
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
 
     - name: Pull Docker image
-      run: docker pull plasmapotential/heat:v4.0
+      run: docker pull plasmapotential/heat:v4.1
 
     - name: Run simple CI configuration test 
-      run: docker run -v ${{ github.workspace }}:/root/source/HEAT plasmapotential/heat:v4.0 python3 /root/source/HEAT/tests/integrationTests/ciTest.py
+      run: docker run -v ${{ github.workspace }}:/root/source/HEAT plasmapotential/heat:v4.1 python3 /root/source/HEAT/tests/integrationTests/ciTest.py
 
     - name: NSTX-U Optical HEAT Calculation
-      run: docker run -v ${{ github.workspace }}:/root/source/HEAT plasmapotential/heat:v4.0 /root/source/HEAT/source/runTerminalModeTestOptical
+      run: docker run -v ${{ github.workspace }}:/root/source/HEAT plasmapotential/heat:v4.1 /root/source/HEAT/source/runTerminalModeTestOptical
+
+    - name: NSTX-U Optical Elmer FEM HEAT Calculation
+      run: docker run -v ${{ github.workspace }}:/root/source/HEAT plasmapotential/heat:v4.1 /root/source/HEAT/source/runTerminalModeTestOpticalElmer
 
+
 #    - name: NSTX-U Gyro-orbit HEAT Calculation
 #      run: docker run -v ${{ github.workspace }}:/root/source/HEAT plasmapotential/heat:v4.0 /root/source/HEAT/source/runTerminalModeTestGyro
 #

docker/Dockerfile

@@ -1,49 +1,53 @@
 #Dockerfile
 #Engineer: T Looby
-#Date: 01/27/2022
+#Date: 03/20/2024
 #Description:  Dockerfile for building HEAT docker image
 #
-#this script should only be run on dev machine
-#script is not run directly, but is used when buildDocker bash
-#script is run.  buildDocker script calls this file using syntax
-#similar to this:
-# docker build -t plasmapotential/heat -f ./Dockerfile ./github/source
-
+# This dockerfile is broken into two stages.  The first stage
+# clones all the source code repos and builds everything from
+# source inside of a container.  This is time consuming, so
+# it is made into its own stage called HEATbuilder.  HEATbuilder
+# will also be saved on dockerhub from now on, with a version 
+# tag.  Users can pull HEATbuilder to save time.
+#
+# The second stage is the final HEAT container.  It only contains
+# the packages required to run HEAT, and none of the files used
+# to build everything from source.  
+#
+# A user can build both stages like this (command also works to only
+#   build final stage if HEATbuilder is already complete):
+#   docker build -t plasmapotential/heat .
+#
+# note:  cross platform build (for apple silicon)
+#   docker buildx build --platform linux/amd64,linux/arm64 -t plasmapotential/heat -f ./Dockerfile . --push
+#
+# User can also only build the first stage (HEATbuilder) like this:
+#   docker build --target HEATbuilder -t plasmapotential/heatbuilder .
+#
+# after creating an image, tag it using a command like this
+#   docker tag plasmapotential/heat:latest plasmapotential/heat:<tag>
+#
+# upload to dockerhub via a command like this
+#   docker push plasmapotential/heat:<tag>
+#
+# launch bash terminal in container interatively
+#   docker-compose run HEAT /bin/bash
+#
+#======================================================================
+#1st build stage.  build all necessary packages from source
+#======================================================================
 # start from base
-FROM ubuntu:22.04
+FROM ubuntu:22.04 AS HEATbuilder
+SHELL ["/bin/bash", "-c"] 
 
 LABEL maintainer="[email protected]"
 
 # environment variables
+ENV SHELL /bin/bash
 ENV runMode docker
-ENV AppDir /root
-ENV APPDIR /root
 ENV DEBIAN_FRONTEND noninteractive
 ENV PYTHONPATH /usr/lib/freecad-python3/lib
 
-#set up paths for libs
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/qt5
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/netgen
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/mafot/lib
-#ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/paraview/lib #comment to prevent qt5 conflicts
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/openfoam/lib
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/openfoam/platforms/linux64GccDPInt32Opt/lib
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/openfoam/platforms/linux64GccDPInt32Opt/lib/sys-openmpi
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/swak4foam/lib
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/openfoam/platforms/linux64GccDPInt32Opt/lib/dummy
-#ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/open3d/lib:/root/opt/open3d/lib/python_package
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/m3dc1/lib
-
-#set up paths for bins
-ENV PATH $PATH:/root/opt/mafot/bin
-ENV PATH $PATH:/root/opt/paraview/bin
-ENV PATH $PATH:/root/opt/openfoam/bin
-ENV PATH $PATH:/root/opt/openfoam/platforms/linux64GccDPInt32Opt/bin
-ENV PATH $PATH:/root/opt/swak4foam/bin
-#ENV PATH $PATH:/root/opt/open3d/bin
-ENV PATH $PATH:/root/opt/m3dc1/bin
-
-#===system-wide deps for HEAT
 #update layer
 RUN apt-get -yqq update
 
@@ -54,6 +58,97 @@ RUN apt-get -yqq install python3 && \
     apt-get -yqq install python3-distutils
 #RUN apt-get -yqq install mdsplus-python
 
+#utility tools/libs layers
+#RUN apt-get -yqq libnglib-6.2 
+RUN apt-get -yqq install coreutils libcurl4 libunwind-dev nano git gfortran iputils-ping iproute2 htop
+
+#3D plasmas layer
+RUN apt-get -yqq install libopenmpi-dev libhdf5-openmpi-dev libnetcdf-dev libnetcdff-dev libblas-dev liblapack-dev
+
+#linking layer
+RUN ln -s /usr/lib/x86_64-linux-gnu/libunwind.so /usr/lib/x86_64-linux-gnu/libunwind.so.1
+
+#clone EFIT
+#RUN git clone https://github.com/ORNL-Fusion/EFIT.git /root/source/EFIT
+
+#clone HEAT
+RUN git clone https://github.com/plasmapotential/HEAT.git /root/source/HEAT
+
+#change to root (home) dir
+WORKDIR /root
+
+#clone and build M3DC1 fusion-io libs
+RUN git clone https://github.com/nferraro/fusion-io.git /root/source/M3DC1/fusion-io
+COPY buildM3DC1 /root/source/M3DC1/fusion-io/buildM3DC1
+COPY make.inc.ubuntu_x86 /root/source/M3DC1/fusion-io/install/make.inc.ubuntu_x86
+RUN mkdir -p /root/source/M3DC1/build && /root/source/M3DC1/fusion-io/buildM3DC1
+
+#clone and build MAFOT
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+#note branch here can be changed if PR goes thru
+RUN git clone -b HEATv4.1 --single-branch https://github.com/ORNL-Fusion/MAFOT.git /root/source/MAFOT
+COPY buildMAFOT /root/source/MAFOT/buildMAFOT
+RUN mkdir -p /root/source/MAFOT/build/bin && \
+    mkdir -p /root/source/MAFOT/build/lib && \
+    /root/source/MAFOT/buildMAFOT
+
+#clone openfoam, third party libs
+#OpenFOAM version defined by user
+ARG OFversion=2306
+RUN apt-get -yqq update && \
+    apt-get install -yqq python-is-python3 flex bison wget mercurial libscotch-dev libptscotch-dev && \
+    wget -P /root/source/openfoam/ https://dl.openfoam.com/source/v${OFversion}/ThirdParty-v${OFversion}.tgz && \
+    wget -P /root/source/openfoam/ https://dl.openfoam.com/source/v${OFversion}/OpenFOAM-v${OFversion}.tgz && \
+    tar -xzf /root/source/openfoam/ThirdParty-v${OFversion}.tgz -C /root/source/openfoam/ && \
+    tar -xzf /root/source/openfoam/OpenFOAM-v${OFversion}.tgz -C /root/source/openfoam/ && \
+    mkdir -p /root/source/openfoam/swak4Foam
+
+#build openfoam
+ENV WM_THIRD_PARTY_DIR /root/source/openfoam/ThirdParty-v${OFversion}
+WORKDIR /root/source/openfoam/OpenFOAM-v${OFversion}
+RUN mkdir -p /root/source/openfoam/OpenFOAM-v${OFversion}/applications/solvers/custom && \
+    cp -au /root/source/HEAT/source/heatFoam /root/source/openfoam/OpenFOAM-v${OFversion}/applications/solvers/custom/heatFoam && \
+    source /root/source/openfoam/OpenFOAM-v${OFversion}/etc/bashrc && \
+    ./Allwmake -j -s -q -l && \
+    cd /root/source/openfoam/OpenFOAM-v${OFversion}/applications/solvers/custom/heatFoam && \
+    wmake
+
+#clone and build swak4foam
+WORKDIR /root/source/openfoam/
+RUN source /root/source/openfoam/OpenFOAM-v${OFversion}/etc/bashrc && \
+    hg clone http://hg.code.sf.net/p/openfoam-extend/swak4Foam && \
+    cd /root/source/openfoam/swak4Foam && \
+    hg update develop && \
+    ./AllwmakeAll
+
+#clean up
+RUN apt-get clean && rm -rf /var/lib/apt/lists/*
+
+#======================================================================
+#2nd build stage.  build container without unncesary build artifacts
+#to keep final image smaller
+#======================================================================
+#if user doesnt want to build first stage, they can pull HEATbuilder from
+#dockerhub using the following command (need to comment out first stage too):
+#FROM plasmapotential/HEATbuilder:<tag> as HEATbuilder
+
+FROM ubuntu:22.04
+LABEL maintainer="[email protected]"
+ARG DEBIAN_FRONTEND=noninteractive
+ENV runMode docker
+
+#update layer
+RUN apt-get -yqq update && apt-get -yqq upgrade
+
+#python layer
+RUN apt-get -yqq install python3 && \
+    apt-get -yqq install python3-pip && \
+    apt-get -yqq install python3-pkg-resources && \
+    apt-get -yqq install python3-distutils && \
+    apt-get -yqq install python3-paraview
+
+#RUN apt-get -yqq install mdsplus-python
+
 # freecad layer
 #RUN apt-get -yqq install libfreecad-python3-0.20 #22.04
 #RUN apt-get -yqq install libfreecad-python3-0.19 #22.10
@@ -66,30 +161,88 @@ RUN apt-get -yqq install software-properties-common && \
     apt-get update && \
     apt-get install -yqq freecad-python3
 
-#utility tools/libs layers
-RUN apt-get -yqq install coreutils libnglib-6.2 libcurl4 libunwind-dev nano git gfortran iputils-ping iproute2 htop
+# elmer layer / OF layer
+RUN apt-get -yqq update && \
+    apt-add-repository ppa:elmer-csc-ubuntu/elmer-csc-ppa && \
+    apt-get update && \
+    apt-get install -yqq elmerfem-csc libglu1 libscotch-dev libptscotch-dev python-is-python3
+
+#RUN apt-get -yqq libnglib-6.2 
+RUN apt-get -yqq install coreutils libcurl4 libunwind-dev nano git gfortran iputils-ping iproute2 htop
 
 #3D plasmas layer
 RUN apt-get -yqq install libopenmpi-dev libhdf5-openmpi-dev libnetcdf-dev libnetcdff-dev
 
 #linking layer
 RUN ln -s /usr/lib/x86_64-linux-gnu/libunwind.so /usr/lib/x86_64-linux-gnu/libunwind.so.1
 
-# copy context
-WORKDIR /root
-COPY . .
+#clone EFIT
+RUN git clone https://github.com/ORNL-Fusion/EFIT.git /root/source/EFIT
 
-# fetch app specific deps
+#clone HEAT (note v4.1 branch can be changed)
+RUN git clone -b v4.1 --single-branch https://github.com/plasmapotential/HEAT.git /root/source/HEAT
+
+# fetch HEAT specific python dependencies
 RUN python3 -m pip install --upgrade pip && \
     python3 -m pip install --ignore-installed blinker && \
-    python3 -m pip install -r requirements.txt
-
-#clean up
-RUN apt-get clean && rm -rf /var/lib/apt/lists/*
+    python3 -m pip install -r /root/source/HEAT/docker/requirements.txt
+
+#make build dirs
+RUN mkdir -p /root/builds/M3DC1 && \
+    mkdir -p /root/builds/MAFOT && \
+    mkdir -p /root/builds/openfoam && \
+    mkdir -p /root/builds/swak4foam
+
+#copy M3DC1 fusion-io bins / libs
+COPY --from=HEATbuilder /root/source/M3DC1/build/bin /root/builds/M3DC1/bin
+COPY --from=HEATbuilder /root/source/M3DC1/build/lib /root/builds/M3DC1/lib
+COPY --from=HEATbuilder /root/source/M3DC1/build/include /root/builds/M3DC1/include
+COPY --from=HEATbuilder /root/source/M3DC1/build/modules /root/builds/M3DC1/modules
+
+#copy MAFOT bins / libs
+COPY --from=HEATbuilder /root/source/MAFOT/build/bin /root/builds/MAFOT/bin
+COPY --from=HEATbuilder /root/source/MAFOT/build/lib /root/builds/MAFOT/lib
+
+#copy openFOAM bin / libs
+ENV OFversion 2306 
+COPY --from=HEATbuilder /root/source/openfoam/OpenFOAM-v${OFversion}/platforms /root/builds/openfoam/platforms
+COPY --from=HEATbuilder /root/source/openfoam/OpenFOAM-v${OFversion}/build /root/builds/openfoam/build
+COPY --from=HEATbuilder /root/source/openfoam/OpenFOAM-v${OFversion}/bin /root/builds/openfoam/bin
+COPY --from=HEATbuilder /root/source/openfoam/OpenFOAM-v${OFversion}/etc /root/builds/openfoam/etc
+
+#copy swak4foam bins / libs
+COPY --from=HEATbuilder /root/OpenFOAM/user-v2306/platforms/linux64GccDPInt32Opt/bin /root/builds/swak4Foam/bin
+COPY --from=HEATbuilder /root/OpenFOAM/user-v2306/platforms/linux64GccDPInt32Opt/lib /root/builds/swak4Foam/lib
+
+#paths for libs
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/qt5
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/netgen
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/builds/MAFOT/lib
+#ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/opt/paraview/lib #comment to prevent qt5 conflicts
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/builds/openfoam/lib
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/builds/openfoam/platforms/linux64GccDPInt32Opt/lib
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/builds/openfoam/platforms/linux64GccDPInt32Opt/lib/sys-openmpi
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/builds/openfoam/platforms/linux64GccDPInt32Opt/lib/dummy
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/builds/swak4Foam/lib
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/root/builds/M3DC1/lib
+ENV PYTHONPATH $PYTHONPATH:/root/builds/M3DC1/lib
 
+#set up paths for bins
+ENV PATH $PATH:/root/builds/MAFOT/bin
+#ENV PATH $PATH:/root/builds/paraview/bin
+ENV PATH $PATH:/root/builds/openfoam/bin
+ENV PATH $PATH:/root/builds/openfoam/platforms/linux64GccDPInt32Opt/bin
+ENV PATH $PATH:/root/builds/swak4foam/bin
+ENV PATH $PATH:/root/builds/M3DC1/bin
+ENV PYTHONPATH $PYTHONPATH:/usr/lib/freecad-python3/lib
 
 # expose port
 EXPOSE 8050
 
+WORKDIR /root
+
+#clean up
+RUN apt-get clean && rm -rf /var/lib/apt/lists/*
+
 # start app
 CMD [ "python3", "./source/HEAT/source/launchHEAT.py", "--a", "0.0.0.0", "--p", "8050", "--m", "g" ]

docker/buildDocker

@@ -1,4 +1,5 @@
 #!/bin/bash
+#THIS FILE IS NO LONGER USED.  LEGACY LEFT FOR REFERENCE UNTIL v5.0
 #Engineer: T Looby
 #Date: 12/27/2023
 #Description:  prepares docker context, then creates docker container

docker/buildM3DC1

@@ -0,0 +1,12 @@
+#!/bin/bash
+#builds M3DC1 Fusion-io libs inside the container
+echo "Building M3DC1 fusion-io..."
+#sets up environment and builds fusion-io libs
+export FIO_ROOT=/root/source/M3DC1/fusion-io
+export FIO_ARCH="ubuntu_x86"
+export FIO_INSTALL_DIR=/root/source/M3DC1/build
+export PYTHON=python3
+
+cd /root/source/M3DC1/fusion-io
+make
+make install

docker/buildMAFOT

@@ -0,0 +1,15 @@
+#!/bin/bash
+#builds MAFOT inside the container
+echo "Building Blitz..."
+cd ./source/MAFOT/blitz++
+tar -xvzf blitz-0.9_cstdlibPatched.tar.gz
+cd blitz-0.9
+./configure 
+make lib
+make install
+cd /root/source/MAFOT
+rm make.inc
+ln -s install/make.inc.HEAT make.inc
+ls /
+echo "Building MAFOT..."
+make heat