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Readme_windows.md

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Contents

  1. Requirements
  2. MinGW and dependencies
  3. Build solvers via MinGW
    1. Building all solvers
    2. Building NFSim
  4. Build solvers via PowerShell
    1. Building all solvers
    2. Building NFSim

Requirements

1. git
    check typing git at command prompt
2. MinGW
    windows search for mingw, should find win 64 version

Installing MinGW and dependencies

  1. Download and install the latest MinGW for windows
  2. Open MinGW
    • Download and install these dependencies
    pacman -S git
    pacman --noconfirm -Syu
    pacman --noconfirm -Syyu python mingw-w64-x86_64-gcc
    pacman --noconfirm -S msys/git
    pacman --noconfirm -S mingw64/mingw-w64-x86_64-gcc-fortran
    pacman --noconfirm -S mingw64/mingw-w64-x86_64-cmake
    pacman --noconfirm -S mingw64/mingw-w64-x86_64-doxygen
    pacman --noconfirm -S msys/make
    pacman --noconfirm -S mingw-w64-x86_64-pkg-config
    pacman --noconfirm -S mingw-w64-x86_64-hdf5
    pacman --noconfirm -S mingw-w64-x86_64-libzip
    pacman --noconfirm -S mingw-w64-x86_64-netcdf

For building solvers manually from MinGW

  1. Open MinGW and redirect to vcell-solvers cloned directory
  2. mkdir -p build/bin
  3. cd build

For building all solvers via MinGW

    cmake -G "Unix Makefiles" \
    -DCMAKE_BUILD_TYPE="Release" \
    -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 \
    ..

make

❗**Note: Remove wrongly built NFSim solver and build seperately

For building NFSim via MinGW

    cmake -G "Unix Makefiles" \
    -DBUILD_SHARED_LIBS=OFF \
    -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
    -DCMAKE_EXE_LINKER_FLAGS="-static" \
    -DOPTION_TARGET_MESSAGING=OFF \
    -DOPTION_TARGET_PARALLEL=OFF \
    -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
    -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
    -DOPTION_TARGET_FV_SOLVER=OFF \
    -DOPTION_TARGET_STOCHASTIC_SOLVER=OFF \
    -DOPTION_TARGET_NFSIM_SOLVER=ON \
    -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
    -DOPTION_TARGET_SUNDIALS_SOLVER=OFF \
    -DOPTION_TARGET_HY3S_SOLVERS=OFF \
    ..

make

For building solvers manually from Powershell

  1. Open powershell and redirect to vcell-solvers cloned directory
  2. Export the path $Env:Path = "c:\msys64\mingw64\bin" + ";" + "c:\msys64\usr\bin" + ";" + $Env:Path
  3. mkdir -p build/bin
  4. cd build

Building all solvers via Powershell

    cmake -G "Unix Makefiles" `
    -DCMAKE_BUILD_TYPE="Release" `
    -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 `
    ..

make

❗**Note: Remove wrongly built NFSim solver if you want build in same directory

For building NFSim via Powershell

    cmake -G "Unix Makefiles" `
    -DBUILD_SHARED_LIBS=OFF `
    -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" `
    -DCMAKE_EXE_LINKER_FLAGS="-static" `
    -DOPTION_TARGET_MESSAGING=OFF `
    -DOPTION_TARGET_PARALLEL=OFF `
    -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF `
    -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF `
    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF `
    -DOPTION_TARGET_FV_SOLVER=OFF `
    -DOPTION_TARGET_STOCHASTIC_SOLVER=OFF `
    -DOPTION_TARGET_NFSIM_SOLVER=ON `
    -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF `
    -DOPTION_TARGET_SUNDIALS_SOLVER=OFF `
    -DOPTION_TARGET_HY3S_SOLVERS=OFF `
    ..

make