build only FVSolver for CMake and CI/CD

Author: jcschaff

.github/workflows/cd.yml

@@ -225,16 +225,7 @@ jobs:
           -DCMAKE_C_COMPILER="clang.exe" \
           -DCMAKE_CXX_COMPILER="clang++.exe" \
           -DOPTION_TARGET_MESSAGING=OFF \
-          -DOPTION_TARGET_PARALLEL=OFF \
-          -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-          -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
           -DOPTION_TARGET_FV_SOLVER=ON \
-          -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
-          -DOPTION_TARGET_NFSIM_SOLVER=ON \
-          -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
-          -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
-          -DOPTION_TARGET_HY3S_SOLVERS=OFF \
           -DOPTION_TARGET_DOCS=OFF \
           -B . -S ..
 
@@ -254,14 +245,6 @@ jobs:
           echo "------ running FiniteVolume_x64 ------"
           ./bin/FiniteVolume_x64 || true
           echo
-          echo "------ running NFsim_x64 ------"
-          ./bin/NFsim_x64 || true
-          echo "------ running SundialsSolverStandalone_x64 ------"
-          ./bin/SundialsSolverStandalone_x64 || true
-          echo "------ running VCellStoch_x64 ------"
-          ./bin/VCellStoch_x64 || true
-          echo "------ running smoldyn_x64 ------"
-          ./bin/smoldyn_x64 || true
           echo "------ running testzip ------"
           ./bin/testzip || true
           echo "------ running ziptool ------"
@@ -293,16 +276,7 @@ jobs:
           cmake \
           -G Ninja \
           -DOPTION_TARGET_MESSAGING=OFF \
-          -DOPTION_TARGET_PARALLEL=OFF \
-          -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-          -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
           -DOPTION_TARGET_FV_SOLVER=ON \
-          -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
-          -DOPTION_TARGET_NFSIM_SOLVER=ON \
-          -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=ON \
-          -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
-          -DOPTION_TARGET_HY3S_SOLVERS=OFF \
           -B . -S ..
 
           ninja
@@ -320,14 +294,6 @@ jobs:
           echo "------ running FiniteVolume_x64 ------"
           ./bin/FiniteVolume_x64 || true
           echo
-          echo "------ running NFsim_x64 ------"
-          ./bin/NFsim_x64 || true
-          echo "------ running SundialsSolverStandalone_x64 ------"
-          ./bin/SundialsSolverStandalone_x64 || true
-          echo "------ running VCellStoch_x64 ------"
-          ./bin/VCellStoch_x64 || true
-          echo "------ running smoldyn_x64 ------"
-          ./bin/smoldyn_x64 || true
           echo "------ running testzip ------"
           ./bin/testzip || true
           echo "------ running ziptool ------"
@@ -340,27 +306,27 @@ jobs:
         run: |
           mkdir build/upload
           cd build/bin
-          rm hello_test TestVCellStoch testzip ziptool || true
+          rm testzip ziptool || true
           ls *_x64   | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
           ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
           ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
           chmod u+w,+x *
           tar czvf ../upload/mac64_bad_paths.tgz .
           ../../.github/scripts/install_name_tool_macos.sh
-          tar czvf ../upload/mac64.tgz --dereference .
+          tar czvf ../upload/fvsolver_mac64.tgz --dereference .
 
       - name: handle shared object paths for Windows native build
         if: matrix.platform == 'windows-latest'
         shell: msys2 {0}
         run: |
           mkdir build/upload
           cd build/bin
-          rm hello_test TestVCellStoch testzip ziptool || true
+          rm testzip ziptool || true
           ls *.exe | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
           ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
           ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
           chmod u+w,+x *
-          zip ../upload/win64.zip ./*
+          zip ../upload/fvsolver_win64.zip ./*
           cd ../..
           # fi
 
@@ -370,41 +336,41 @@ jobs:
         run: |
           mkdir build/upload
           cd build/bin
-          rm hello_test TestVCellStoch testzip ziptool || true
+          rm testzip ziptool || true
           ls *_x64   | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
           ls *.so    | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
           ls *.so    | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
           chmod u+w,+x *
-          tar czvf ../upload/linux64.tgz --dereference .
+          tar czvf ../upload/fvsolver_linux64.tgz --dereference .
           cd ../..
 
       - name: Upload Intel Macos binaries
         if: matrix.platform == 'macos-13'
         uses: actions/upload-artifact@v4
         with:
-          name: macos_x86_64.tgz
-          path: build/upload/mac64.tgz
+          name: fvsolver_macos_x86_64.tgz
+          path: build/upload/fvsolver_mac64.tgz
 
       - name: Upload ARM Macos binaries
         if: matrix.platform == 'macos-14'
         uses: actions/upload-artifact@v4
         with:
-          name: macos_arm64.tgz
-          path: build/upload/mac64.tgz
+          name: fvsolver_macos_arm64.tgz
+          path: build/upload/fvsolver_mac64.tgz
 
       - name: Upload Windows binaries
         if: matrix.platform == 'windows-latest'
         uses: actions/upload-artifact@v4
         with:
-          name: win64.zip
-          path: build/upload/win64.zip
+          name: fvsolver_win64.zip
+          path: build/upload/fvsolver_win64.zip
 
       - name: Upload Linux binaries
         if: matrix.platform == 'ubuntu-latest'
         uses: actions/upload-artifact@v4
         with:
-          name: linux64.tgz
-          path: build/upload/linux64.tgz
+          name: fvsolver_linux64.tgz
+          path: build/upload/fvsolver_linux64.tgz
 
       - name: Setup tmate session
         if: ${{ failure() }}

Dockerfile

@@ -4,99 +4,27 @@ RUN apt-get -y update && apt-get install -y apt-utils && \
     apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
     libhdf5-dev libcurl4-openssl-dev libboost-dev cmake wget python
 
-#
-# build PETSc with mpich for static linking
-#
-RUN mkdir /usr/local/petsc && \
-    cd /usr/local/petsc && \
-    wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.7.7.tar.gz && \
-    tar xzf petsc-3.7.7.tar.gz && \
-    cd petsc-3.7.7 && \
-    ./configure --with-shared-libraries=0 --download-fblaslapack=1 --with-debugging=1 --download-mpich && \
-    make PETSC_DIR=/usr/local/petsc/petsc-3.7.7 PETSC_ARCH=arch-linux2-c-debug all
-
-ENV PETSC_DIR=/usr/local/petsc/petsc-3.7.7 \
-    PETSC_ARCH=arch-linux2-c-debug
-
 COPY . /vcellroot
 
-#
-# build most solvers, and FiniteVolume without PETSc (FiniteVolume_x64)
-#
 RUN mkdir -p /vcellroot/build/bin
 WORKDIR /vcellroot/build
 
 RUN /usr/bin/cmake \
     -DOPTION_TARGET_MESSAGING=ON \
-    -DOPTION_TARGET_PARALLEL=OFF \
-    -DOPTION_TARGET_PETSC=OFF \
-    -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-    -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-    -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
     -DOPTION_TARGET_FV_SOLVER=ON \
-    -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
-    -DOPTION_TARGET_NFSIM_SOLVER=ON \
-    -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=ON \
-    -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
-    -DOPTION_TARGET_HY3S_SOLVERS=OFF \
     .. && \
     make && \
     ctest
 
+
+#RUN apt-get update && \
+#    apt-get install -y apt-utils && \
+#    apt-get install -q -y --no-install-recommends curl dnsutils
 #
-# build FiniteVolume with PETSc (FiniteVolume_PETSc_x64)
+#RUN apt-get install -qq -y -o=Dpkg::Use-Pty=0 gcc gfortran zlib1g \
+#    libhdf5-103 libhdf5-cpp-103 libcurl4-openssl-dev zip
+#
+#COPY --from=build /vcellroot/build/bin /vcellbin
+#WORKDIR /vcellbin
+#ENV PATH=/vcellbin:$PATH
 #
-RUN mkdir -p /vcellroot/build_PETSc/bin
-WORKDIR /vcellroot/build_PETSc
-
-RUN /usr/bin/cmake \
-    -DOPTION_TARGET_MESSAGING=ON \
-    -DOPTION_TARGET_PARALLEL=OFF \
-    -DOPTION_TARGET_PETSC=ON \
-    -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-    -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
-    -DOPTION_TARGET_FV_SOLVER=ON \
-    -DOPTION_TARGET_STOCHASTIC_SOLVER=OFF \
-    -DOPTION_TARGET_NFSIM_SOLVER=OFF \
-    -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
-    -DOPTION_TARGET_SUNDIALS_SOLVER=OFF \
-    -DOPTION_TARGET_HY3S_SOLVERS=OFF \
-    .. && \
-    make && \
-    ctest
-
-
-FROM eclipse-temurin:17 as jre-build
-
-# Create a custom Java runtime
-RUN $JAVA_HOME/bin/jlink \
-         --add-modules ALL-MODULE-PATH \
-         --strip-debug \
-         --no-man-pages \
-         --no-header-files \
-         --compress=2 \
-         --output /javaruntime
-
-# Define base image and copy in jlink created minimal Java 17 environment
-FROM python:3.9.7-slim
-ENV JAVA_HOME=/opt/java/openjdk
-ENV PATH "${JAVA_HOME}/bin:${PATH}"
-COPY --from=jre-build /javaruntime $JAVA_HOME
-
-# now we have Java 17 and Python 3.9
-ENV DEBIAN_FRONTEND noninteractive
-ENV LANG=en_US.UTF-8
-
-RUN apt-get update && \
-    apt-get install -y apt-utils && \
-    apt-get install -q -y --no-install-recommends curl dnsutils
-
-RUN apt-get install -qq -y -o=Dpkg::Use-Pty=0 gcc gfortran zlib1g \
-    libhdf5-103 libhdf5-cpp-103 libcurl4-openssl-dev zip
-
-COPY --from=build /vcellroot/build/bin /vcellbin
-COPY --from=build /vcellroot/build_PETSc/bin/FiniteVolume_PETSc_x64 /vcellbin/
-WORKDIR /vcellbin
-ENV PATH=/vcellbin:$PATH
-

README.md

@@ -7,50 +7,11 @@
 ---
 ![CI](https://github.com/virtualcell/vcell-solvers/actions/workflows/cd.yml/badge.svg)
 
-# vcell-solvers
+# vcell-fvsolver
 Virtual Cell solvers [virtualcell/vcell-solvers](https://github.com/virtualcell/vcell-solvers) is a collection of numerical simulation codes used in the Virtual Cell framework [virtualcell/vcell](https://github.com/virtualcell/vcell)).
 
 
 ## The Virtual Cell Project
 The Virtual Cell is a modeling and simulation framework for computational biology.  For details see http://vcell.org and http://github.com/virtualcell.
 
-## Building VCell Solvers
-### Using VirtualBox and Vagrant
-* git clone https://github.com/virtualcell/vcell.git
-* cd vcell/VagrantBoxes
-### Building for Linux (64 bit)
-[details](VagrantBoxes/linux64/README.md)
-
-```bash
-$ cd linux64
-$ vagrant up
-$ vagrant ssh -c /vagrant_numerics/build.sh
-$ vagrant halt
-```
-### Building for Linux (32 bit)
-[details](VagrantBoxes/linux32/README.md)
-
-```bash
-$ cd linux32
-$ vagrant up
-$ vagrant ssh -c /vagrant_numerics/build.sh
-$ vagrant halt
-```
-### Building for Macos on a Mac **Apple only allows a Mac VM to run on Apple hardware**
-[details}(VagrantBoxes/mac64/README.md)
-
-```bash
-$ cd mac64
-$ vagrant up
-$ vagrant ssh -c /vagrant/build.sh
-$ vagrant halt
-```
-### Building for Windows (64 bit) on Windows
-[details: including building on other platforms](VagrantBoxes/win64/README.md)
-
-```bash
-$ cd win64
-$ vagrant up
-$ vagrant powershell -c \vagrant\build.sh
-$ vagrant halt
-```
+## Python Bindings (more to come)