Merge pull request #127 from NCAR/main

MUSICA v0.2.0 updates
NCAR · Mar 14, 2023 · 7e3ad6f · 7e3ad6f
2 parents c3bebba + ff001cc
commit 7e3ad6f
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diff --git a/.dockerignore b/.dockerignore
@@ -10,6 +10,7 @@
 !test/
 !examples/
 !etc/
+!cmake/
 
 # exclude generated code
 libs/micm-collection/configured_tags/*

diff --git a/.github/workflows/publish-package.yml b/.github/workflows/publish-package.yml
@@ -0,0 +1,45 @@
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches: ['release']
+    tags:
+      - '*'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Log in to the Container repository
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -14,4 +14,4 @@ jobs:
     - name: build Docker image
       run: docker build -t music-box-test . --build-arg TAG_ID=chapman
     - name: run tests in container
-      run: docker run --name test-container -t music-box-test bash -c 'cd build; make test'
+      run: docker run --name test-container -t music-box-test bash -c 'cd /music-box/build; make test'
diff --git a/.gitmodules b/.gitmodules
@@ -1,18 +1,6 @@
-[submodule "libs/musica-core"]
-	path = libs/musica-core
-	url = https://github.com/NCAR/musica-core.git
 [submodule "libs/micm"]
 	path = libs/micm
 	url = https://github.com/NCAR/micm.git
-[submodule "libs/micm-preprocessor"]
-	path = libs/micm-preprocessor
-	url = https://github.com/NCAR/micm-preprocessor.git
-[submodule "libs/micm-collection"]
-	path = libs/micm-collection
-  url = https://github.com/NCAR/micm-collection.git
-[submodule "libs/music-box-interactive"]
-  path = libs/music-box-interactive
-  url = https://github.com/NCAR/music-box-interactive.git
 [submodule "libs/camp"]
 	path = libs/camp
 	url = https://github.com/open-atmos/camp.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,161 +1,23 @@
-cmake_minimum_required(VERSION 3.12)
+cmake_minimum_required(VERSION 3.21)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE "SetDefaults.cmake")
-project(MUSICA)
+project(musicbox)
 enable_language(Fortran)
 
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 ################################################################################
 # options
 
-################################################################################
-# NetCDF library
-
-find_path(NETCDF_INCLUDE_DIR netcdf.mod NETCDF.mod
-  DOC "NetCDF include directory (must contain netcdf.mod)"
-  PATHS
-    $ENV{NETCDF_HOME}/include
-    /usr/lib/gfortran/modules
-    /usr/lib64/gfortran/modules
-    /opt/local/include)
-find_library(NETCDF_C_LIB netcdf
-  DOC "NetCDF C library"
-  PATHS
-    $ENV{NETCDF_HOME}/lib
-    $ENV{NETCDF_HOME}/lib64
-    opt/local/lib)
-find_library(NETCDF_FORTRAN_LIB netcdff
-  DOC "NetCDF Fortran library"
-  PATHS
-    $ENV{NETCDF_HOME}/lib
-    $ENV{NETCDF_HOME}/lib64
-    /opt/local/lib)
-set(NETCDF_LIBS ${NETCDF_C_LIB})
-if(NETCDF_FORTRAN_LIB)
-  set(NETCDF_LIBS ${NETCDF_LIBS} ${NETCDF_FORTRAN_LIB})
-endif()
-include_directories(${NETCDF_INCLUDE_DIR})
-
-################################################################################
-# json-fortran library
-
-find_path(JSON_INCLUDE_DIR json_module.mod
-  DOC "json-fortran include directory (must include json_*.mod files)"
-  PATHS
-    $ENV{JSON_FORTRAN_HOME}/lib
-    /opt/local/lib
-    /usr/local/lib
-    /usr/local/lib64)
-find_library(JSON_LIB jsonfortran
-  DOC "json-fortran library"
-  PATHS
-    $ENV{JSON_FORTRAN_HOME}/lib
-    /opt/local/lib
-    /usr/local/lib
-    /usr/local/lib64)
-include_directories(${JSON_INCLUDE_DIR})
-
-################################################################################
-# GSL
-
-find_path(GSL_INCLUDE_DIR gsl/gsl_math.h
-  DOC "GSL include directory (must have gsl/ subdir)"
-  PATHS $ENV{GSL_HOME}/include /opt/local/include)
-find_library(GSL_LIB gsl
-  DOC "GSL library"
-  PATHS $ENV{GSL_HOME}/lib /opt/local/lib)
-find_library(GSL_CBLAS_LIB gslcblas
-  DOC "GSL CBLAS library"
-  PATHS $ENV{GSL_HOME}/lib /opt/local/lib)
-find_library(M_LIB m
-  DOC "standard C math library")
-set(GSL_LIBS ${GSL_LIB} ${GSL_CBLAS_LIB} ${M_LIB})
-include_directories(${GSL_INCLUDE_DIR})
-
-################################################################################
-# SUNDIALS
-
-find_path(SUITE_SPARSE_INCLUDE_DIR klu.h
-  DOC "SuiteSparse include directory (must have klu.h)"
-  PATHS $ENV{SUITE_SPARSE_HOME}/include $ENV{SUNDIALS_HOME}/include
-        /opt/local/include /usr/local/include)
-find_library(SUITE_SPARSE_KLU_LIB klu
-  DOC "SuiteSparse klu library"
-  PATHS $ENV{SUITE_SPARSE_HOME}/lib $ENV{SUNDIALS_HOME}/lib
-        /opt/local/lib /usr/local/lib)
-find_library(SUITE_SPARSE_AMD_LIB amd
-  DOC "SuiteSparse amd library"
-  PATHS $ENV{SUITE_SPARSE_HOME}/lib $ENV{SUNDIALS_HOME}/lib
-        /opt/local/lib /usr/local/lib)
-find_library(SUITE_SPARSE_BTF_LIB btf
-  DOC "SuiteSparse btf library"
-  PATHS $ENV{SUITE_SPARSE_HOME}/lib $ENV{SUNDIALS_HOME}/lib
-        /opt/local/lib /usr/local/lib)
-find_library(SUITE_SPARSE_COLAMD_LIB colamd
-  DOC "SuiteSparse colamd library"
-  PATHS $ENV{SUITE_SPARSE_HOME}/lib $ENV{SUNDIALS_HOME}/lib
-        /opt/local/lib /usr/local/lib)
-find_library(SUITE_SPARSE_CONFIG_LIB suitesparseconfig
-  DOC "SuiteSparse config library"
-  PATHS $ENV{SUITE_SPARSE_HOME}/lib $ENV{SUNDIALS_HOME}/lib
-        /opt/local/lib /usr/local/lib)
-find_path(SUNDIALS_INCLUDE_DIR cvode/cvode.h
-  DOC "SUNDIALS include directory (must have cvode/, sundials/, nvector/ subdirs)"
-  PATHS $ENV{SUNDIALS_HOME}/include /opt/local/include /usr/local/include)
-find_library(SUNDIALS_NVECSERIAL_LIB sundials_nvecserial
-  DOC "SUNDIALS serial vector library"
-  PATHS $ENV{SUNDIALS_HOME}/lib /opt/local/lib /usr/local/lib)
-find_library(SUNDIALS_CVODE_LIB sundials_cvode
-  DOC "SUNDIALS CVODE library"
-  PATHS $ENV{SUNDIALS_HOME}/lib /opt/local/lib /usr/local/lib)
-find_library(SUNDIALS_KLU_LIB sundials_sunlinsolklu
-  DOC "SUNDIALS KLU library"
-  PATHS $ENV{SUITE_SPARSE_HOME}/lib $ENV{SUNDIALS_HOME}/lib
-        /opt/local/lib /usr/local/lib)
-find_library(SUNDIALS_SUNMATRIX_SPARSE_LIB sundials_sunmatrixsparse
-  DOC "SUNDIALS SUNMatrixSparse library"
-  PATHS $ENV{SUITE_SPARSE_HOME}/lib $ENV{SUNDIALS_HOME}/lib
-        /opt/local/lib /usr/local/lib)
-set(SUNDIALS_LIBS ${SUNDIALS_NVECSERIAL_LIB} ${SUNDIALS_CVODE_LIB}
-  ${SUNDIALS_KLU_LIB} ${SUNDIALS_SUNMATRIX_SPARSE_LIB} ${SUITE_SPARSE_KLU_LIB}
-  ${SUITE_SPARSE_COLAMD_LIB} ${SUITE_SPARSE_AMD_LIB} ${SUITE_SPARSE_BTF_LIB}
-  ${SUITE_SPARSE_CONFIG_LIB})
-include_directories(${SUNDIALS_INCLUDE_DIR} ${SUITE_SPARSE_INCLUDE_DIR})
-
-################################################################################
-# CAMP library
-
-find_path(CAMP_INCLUDE_DIR camp_core.mod
-  DOC "CAMP include directory (must include camp_*.mod files)"
-  PATHS
-    /opt/local/lib
-    /usr/local/lib
-    /usr/local/lib64)
-  find_library(CAMP_LIB camp
-    DOC "CAMP library"
-  PATHS
-    /opt/local/lib
-    /usr/local/lib
-    /usr/local/lib64)
-include_directories(${CAMP_INCLUDE_DIR})
-
 ################################################################################
 # Create a directory to hold input data
 
 add_custom_target(data-directory ALL COMMAND ${CMAKE_COMMAND} -E make_directory
   ${CMAKE_BINARY_DIR}/data)
 
 ################################################################################
-# MUSICA library
-
-add_subdirectory(libs/musica-core/src)
-include_directories(${CMAKE_BINARY_DIR}/libs/musica-core/src)
-
-################################################################################
-# MICM library
+# Dependencies
 
-add_subdirectory(libs/micm/src)
-include_directories(${CMAKE_BINARY_DIR}/libs/micm/src)
+include(cmake/dependencies.cmake)
 
 ################################################################################
 # MusicBox application

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM fedora:33
+FROM fedora:37
 
 RUN dnf -y update \
     && dnf -y install \
@@ -13,30 +13,18 @@ RUN dnf -y update \
         cmake \
         make \
         wget \
-        python \
+        git \
+        postgresql-devel \
         python3 \
         python3-pip \
-        texlive-scheme-basic \
-        'tex(type1cm.sty)' \
-        'tex(type1ec.sty)' \
-        dvipng \
-        git \
-        nodejs \
-        ncview \
     && dnf clean all
 
-# python modules needed in scripts
-RUN dnf -y install python3-pandas
-
-RUN pip3 install requests numpy scipy matplotlib ipython jupyter nose Django pillow \
-                 django-crispy-forms pyvis django-cors-headers drf-yasg
-
 # Build the SuiteSparse libraries for sparse matrix support
 RUN curl -LO http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.1.0.tar.gz \
     && tar -zxvf SuiteSparse-5.1.0.tar.gz \
     && export CXX=/usr/bin/cc \
     && cd SuiteSparse \
-    && make install INSTALL=/usr/local BLAS="-L/lib64 -lopenblas"
+    && make -j 8 install INSTALL=/usr/local BLAS="-L/lib64 -lopenblas"
 
 # install json-fortran
 RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
@@ -46,24 +34,15 @@ RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz
     && mkdir build \
     && cd build \
     && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
-    && make install
+    && make -j 8 install
 
-# copy the MusicBox code
-COPY . /music-box/
-
-# move the change mechanism script to the root folder
-RUN cp /music-box/etc/change_mechanism.sh /
-
-# move the example configurations to the build folder
-RUN mkdir /build \
-    && cp -r /music-box/examples /build/examples
-
-# nodejs modules needed Mechanism-To-Code
-RUN cd /music-box/libs/micm-preprocessor; \
-    npm install
+# copy the interactive server code
+COPY . /music-box
 
 # Install a modified version of CVODE
-RUN tar -zxvf /music-box/libs/camp/cvode-3.4-alpha.tar.gz \
+RUN mkdir cvode_build \
+    && cd cvode_build \
+    && tar -zxvf /music-box/libs/camp/cvode-3.4-alpha.tar.gz \
     && cd cvode-3.4-alpha \
     && mkdir build \
     && cd build \
@@ -90,38 +69,13 @@ RUN mkdir camp_build \
              /music-box/libs/camp \
     && make
 
-# command line arguments
-ARG TAG_ID=false
-
-# get a MICM mechanism if one has been specified
-RUN if [ "$TAG_ID" = "false" ] ; then \
-      echo "No mechanism specified" ; else \
-      echo "Grabbing mechanism $TAG_ID" \
-      && cd /music-box/libs/micm-preprocessor \
-      && nohup bash -c "node combined.js &" && sleep 4 \
-      && mkdir /data \
-      && cd /music-box/libs/micm-collection \
-      && if [ "$TAG_ID" = "chapman" ] ; then \
-           python3 preprocess_tag.py -c configured_tags/$TAG_ID/config.json -p localhost:3000 \
-        && python3 stage_tag.py -source_dir_kinetics configured_tags/$TAG_ID/output -target_dir_data /data \
-        ; else \
-           echo "Only Chapman chemistry is currently available for MusicBox-MICM" \
-        && exit 1 \
-        ; fi \
-      ; fi
-
-# build the model
-RUN cd /build \
-      && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
-      && cmake -D CAMP_INCLUDE_DIR="/camp_build/include" \
-               -D CAMP_LIB="/camp_build/lib/libcamp.a" \
-               /music-box \
-      && make
-
-# Prepare the music-box-interactive web server
-RUN mv music-box/libs/music-box-interactive .
-ENV MUSIC_BOX_BUILD_DIR=/build
-
-EXPOSE 8000
-
-CMD ["python3", "music-box-interactive/interactive/manage.py", "runserver", "0.0.0.0:8000" ]
+# build music-box
+RUN cd music-box \
+    && mkdir build \
+    && cd build \
+    && export FC=gfortran \
+    && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
+    && cmake -D CAMP_INCLUDE_DIR="/camp_build/include" \
+              -D CAMP_LIB="/camp_build/lib/libcamp.a" \
+              .. \
+    && make -j 8