Merge pull request #24 from virtualcell/vcellstoch-testing

Vcellstoch testing

.github/scripts/install_name_tool_macos.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+shopt -s -o nounset
+
+#
+# change path to bundled dylibs in executables from absolute path (usr/local/lib/) to same directory
+#
+for exe in `ls *_x64`
+do
+    echo "fixing paths in ${exe}"
+    for libpath in `otool -L ${exe} | grep "/" | grep -v "System" | awk '{print $1}'`
+    do
+		libfilename=${libpath##*/}
+		echo install_name_tool -change $libpath @executable_path/$libfilename  $exe
+		install_name_tool -change $libpath @executable_path/$libfilename  $exe
+  	done
+done
+
+#
+# change path from each dylib to each other (dylibs can refer to other dylibs) from /usr/local/lib to @loader_path (same directory)
+# if there is not dependency, then ignore the errors.
+#
+for libfilename in `ls *.dylib`
+do
+    echo "fixing paths in ${libfilename}"
+	#
+	# set id of dynamic library to @loader_path/libname
+	#
+	echo install_name_tool -id "@loader_path/$libfilename"  $libfilename
+    install_name_tool -id "@loader_path/$libfilename"  $libfilename
+
+	for dependentlibpath in `otool -L ${libfilename} | grep "/" | grep -v "System" | awk '{print $1}'`
+	do
+		dependentlibfilename=${dependentlibpath##*/}
+		#
+		# for each library, change path to dependent libraries to be based on @loader_path
+		#
+		echo install_name_tool -change $dependentlibpath @loader_path/$dependentlibfilename  $libfilename
+		install_name_tool -change $dependentlibpath @loader_path/$dependentlibfilename  $libfilename
+  	done
+done

.github/workflows/cd.yml

@@ -7,44 +7,45 @@ env:
   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@v3
-
-      - name: Log in to the Container registry
-        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 }}
+#  build-and-push-image:
+#    runs-on: ubuntu-latest
+#    permissions:
+#      contents: read
+#      packages: write
+#
+#    steps:
+#      - name: Checkout repository
+#        uses: actions/checkout@v3
+#
+#      - name: Log in to the Container registry
+#        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 }}
 
   native-build:
     name:
       native-build-${{ matrix.platform }}
     strategy:
       fail-fast: false
       matrix:
-        platform: [macos-latest, windows-latest, ubuntu-18.04]
+    #        platform: [macos-latest, windows-latest, ubuntu-18.04]
+        platform: [macos-latest]
     runs-on: ${{ matrix.platform }}
 
     steps:
@@ -92,7 +93,7 @@ jobs:
           -DOPTION_TARGET_FV_SOLVER=ON \
           -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
           -DOPTION_TARGET_NFSIM_SOLVER=ON \
-          -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=ON \
+          -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
           -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
           -DOPTION_TARGET_HY3S_SOLVERS=OFF \
           -B . -S ..
@@ -125,18 +126,213 @@ jobs:
           echo "------ running ziptool ------"
           ./bin/ziptool || true
 
-      - name: Setup tmate session
-        uses: mxschmitt/action-tmate@v3
-        if: ${{ failure() }}
 
+#      - name: Install Windows Dependencies
+#        if: matrix.platform == 'windows-latest'
+#        uses: msys2/setup-msys2@v2
+#        with:
+#          msystem: CLANG64
+#          update: true
+#          install: >
+#            git
+#            mingw-w64-clang-x86_64-toolchain
+#            mingw-w64-clang-x86_64-flang
+#            mingw-w64-clang-x86_64-cmake
+#            mingw-w64-clang-x86_64-boost
+#            mingw-w64-clang-x86_64-hdf5
+#            mingw-w64-clang-x86_64-libzip
+#            mingw-w64-clang-x86_64-netcdf
+#
+#      - name: Build Windows
+#        if: matrix.platform == 'windows-latest'
+#        shell: msys2 {0}
+#        run: |
+#          platform=windows
+#          echo "working dir is $PWD"
+#
+#          mkdir build
+#          cd build
+#
+#          PATH="/c/Program Files/LLVM/bin:$PATH"
+#
+#          cmake \
+#          -G Ninja \
+#          -DCMAKE_C_COMPILER=clang \
+#          -DCMAKE_CXX_COMPILER=clang++ \
+#          -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 \
+#          -B . -S ..
+#
+#          ninja -j 1
+#
+#      - name: Test Windows
+#        if: matrix.platform == 'windows-latest'
+#        shell: msys2 {0}
+#        run: |
+#          platform=windows
+#          echo "working dir is $PWD"
+#
+#          cd build
+#
+#          ctest -VV
+#
+#          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 ------"
+#          ./bin/ziptool || true
 
-# Uncomment to debug Windows builds
-#      - name: Setup tmate session
-#        uses: mxschmitt/action-tmate@v3
-#        if: ${{ matrix.platform == 'windows-latest' }}
+#      - name: Install Linux Dependencies
+#        if: matrix.platform == 'ubuntu-18.04'
+#        run: |
+#          sudo apt-get update
+#          sudo apt-get install -y libboost-all-dev
+#          sudo apt-get install -y libhdf5-dev
+#          sudo apt-get install -y ninja-build
+#
+#          gcc --version
+#          gfortran --version
+#          cmake --version
+#          dpkg -s libboost-all-dev
+#          dpkg -s libhdf5-dev
+#
+#      - name: Build Linux
+#        if: matrix.platform == 'ubuntu-18.04'
+#        run: |
+#          platform=linux
+#          echo "working dir is $PWD"
+#
+#          mkdir build
+#          cd build
+#
+#          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=OFF \
+#          -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
+#          -DOPTION_TARGET_HY3S_SOLVERS=OFF \
+#          -B . -S ..
+#
+#          ninja
+#
+#      - name: Test Linux
+#        if: matrix.platform == 'ubuntu-18.04'
+#        run: |
+#          platform=linux
+#          echo "working dir is $PWD"
+#
+#          cd build
+#
+#          ctest -VV
+#
+#          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 ------"
+#          ./bin/ziptool || true
+#
 
+      - name: fix Macos shared object paths
+        if: matrix.platform == 'macos-latest'
+        shell: bash
+        run: |
+          mkdir build/upload
+          cd build/bin
+          rm hello_test TestVCellStoch 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 .
+
+#      - name: handle shared object paths for Windows native build
+#        if: matrix.platform == 'windows-latest'
+#        shell: msys2 {0}
+#        run: |
+#          cd build/bin
+#          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 ../linux64.tgz --dereference .
+#          cd ../..
+#          fi
+#
+#      - name: handle shared object paths for Linux native build
+#        if: matrix.platform == 'ubuntu-18.04'
+#        shell: bash
+#        run: |
+#          cd build/bin
+#          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 ../linux64.tgz --dereference .
+#          cd ../..
+#          fi
+#
+      - name: Upload Macos binaries
+        if: matrix.platform == 'macos-latest'
+        uses: actions/upload-artifact@v3
+        with:
+          name: mac64.tgz
+          path: build/upload/mac64.tgz
+
+      - name: Upload Windows binaries
+        if: matrix.platform == 'windows-latest'
+        uses: actions/upload-artifact@v3
+        with:
+          name: win64.tgz
+          path: build/upload/win64.tgz
+
+      - name: Upload Linux binaries
+        if: matrix.platform == 'ubuntu-18.04'
+        uses: actions/upload-artifact@v3
+        with:
+          name: linux64.tgz
+          path: build/upload/linux64.tgz
+
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
+        with:
+          limit-access-to-actor: false
 
-# Uncomment to debug Linux builds
-#      - name: Setup tmate session
-#        uses: mxschmitt/action-tmate@v3
-#        if: ${{ matrix.platform == 'ubuntu-18.04' }}