Installation on macOS (via MacPorts)

This section will guide you through installing and compiling NextGenPB from source using MacPorts, a package manager for macOS.

Homebrew can be used too.

✅ Step 1: Install Core Dependencies

We’ll begin by installing necessary packages via MacPorts. This may take a while.

sudo port install openmpi cmake onetbb boost cgal5 nlohmann-json jansson octave
sudo port install mumps +openmpi -mpich
sudo port install lis +openmpi -mpich
sudo port install p4est +openmpi -mpich

• +openmpi ensures compatibility with the MPI implementation NextGenPB expects.
• -mpich avoids conflicts from having multiple MPI stacks.

✅ Step 2: Install External Libraries

These libraries are not managed by MacPorts and must be installed manually.

NanoShaper: Generate molecular surfaces

NanoShaper is required to compute molecular surfaces.

git clone https://gitlab.iit.it/SDecherchi/nanoshaper.git
cd nanoshaper
cp CMakeLists_so.txt CMakeLists.txt
cd build_lib
cmake .. -DCGAL_DIR=/opt/local/ -DCMAKE_BUILD_TYPE=Release
make

• CGAL is required for NanoShaper’s surface triangulation.
• The library will be used later by the main NextGenPB build.

octave_file_io: Required for .octbin handling

Needed to interface with .octbin files generated by GNU Octave.

git clone https://github.com/carlodefalco/octave_file_io.git
cd octave_file_io
./autogen.sh
mkdir build
cd build
../configure CXX=mpicxx --prefix=/opt/octave_file_io/1.0.91 --with-octave-home=/opt/local/bin 'LDFLAGS=-Wl,-rpath -Wl,/opt/local/lib/libgcc -Wl,-rpath -Wl,/opt/local/lib/gcc13 -ld_classic'
make
sudo make install

bim++ (NextGenPB branch)

Download and configure the custom FEM library:

wget https://github.com/carlodefalco/bimpp/archive/refs/tags/NextGenPB-v0.0.01.tar.gz
tar -xvzf NextGenPB-v0.0.01.tar.gz
cd bimpp-NextGenPB-v0.0.01
./autogen.sh
mkdir build && cd build

Configure build options carefully:

../configure --prefix=/opt/bimpp \
  LDFLAGS="-L/opt/local/lib -Wl,-rpath,/opt/local/lib/libgcc -Wl,-rpath,/opt/local/lib/gcc14" \
  CPPFLAGS="-I/opt/local/include/ -I/opt/local/include/gcc14 -DOMPI_SKIP_MPICXX -DHAVE_OCTAVE_44 -DBIM_TIMING" \
  --with-blas-lapack="-lopenblas" \
  --with-octave_file_io-home=/opt/octave_file_io/1.0.91 \
  --with-octave-home=/opt/local/bin \
  --with-p4est-home=/opt/local \
  --with-lis-home=/opt/local \
  --with-mumps-home=/opt/local \
  --with-mumps-extra-libs="-L/opt/local/lib -lptscotch -lscotch -lmpi -Wl,-flat_namespace -Wl,-commons,use_dylibs \
  -L/opt/local/lib/openmpi-mp -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lopenblas -L/opt/local/lib/gcc14 -lgfortran" \
  F77=mpif90 CXX=mpicxx MPICC=mpicc CC=mpicc \
  CXXFLAGS="-std=c++17 -O3 -mtune=native -march=native"

Then compile and install:

make
sudo make install

✅ Step 3: Build NextGenPB

Prepare Build Settings

Copy the appropriate local_settings.mk file from the local_setting/ directory:

cp local_setting/local_settings_mac.mk src/local_settings.mk

Edit this file as needed for macOS-specific paths and compiler flags.

Compile the executable

From the src directory:

make clean all

This will create the binary ngpb inside the src directory.

✅ Step 4: (Optional) Add ngpb to Your Path

To call ngpb from any directory:

echo 'export PATH=/path/to/ngpb/src:$PATH' >> ~/.zshrc
source ~/.zshrc

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✅ You’re now ready to run simulations with NextGenPB!

➡️ Go to running section to learn out to run the solver.