Install PFLOTRAN on Mac M1
A Guide to Building PFLOTRAN, DFNWorks, and Dakota on Apple Silicon Macs
*This has been tested on an Apple MacBook Pro with M1 Max chip (2021) running MacOS Ventura 13.4
Prerequisites
-
Install Xcode (14.3). Install Xcode command line tools (
xcode-select --install) -
Install Anaconda3: https://www.anaconda.com/download#macos . Mamba is preferred.
conda install python numpy, h5py, scipy, matplotlib, seaborn, networkx
# or
mamba create -n pflotran-short-course python numpy h5py scipy matplotlib seaborn networkx mplstereonet fpdf conda-build -c conda-forge
- Add the following to ~/.bash_profile
export PATH="/opt/homebrew/bin:$PATH"
export PETSC_DIR==/Users/username/path_to_top_level_petsc
export PETSC_ARCH=arch-darwin-c-opt
export PFLOTRAN_DIR=/Users/username/path_to_top_level_pflotran
export dfnworks_PATH=/Users/username/path_to_top_level_dfnworks
export PFLOTRAN_EXE=/Users/username/path_to_top_level_pflotran/src/pflotran/pflotran export LAGRIT_EXE=/Users/username/path_to_top_level_LaGriT/build/lagrit
export DFNGEN_EXE=/Users/username/path_to_top_level_dfnworks/DFNGen/DFNGen
export PATH=/Users/username/path_to_top_level_Dakota/software/dakota/bin:$PATH
Build PFLOTRAN
- Install gcc
brew install gcc
- Set compilers:
cd /opt/homebrew/binand look forgfortran, g++, gcc. - IMPORTANT! Create symbolic links as needed, e.g.,
ln -s g++-13 g++andln -s gcc-13 gcc. This will avoid usingclanginstead, which may fail. export PATH="/opt/homebrew/bin:$PATH"- Create or navigate to your software directory
cd ~/software/
git clone https://gitlab.com/petsc/petsc.git
cd petsc
git checkout v3.19.0
./configure --with-gfortran=/opt/homebrew/bin/gfortran-13 --with-cxx=/opt/homebrew/bin/g++-13 --with-cc=/opt/homebrew/bin/gcc-13 --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-openmpi=yes --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes --download-hypre=yes
export PETSC_DIR=/home/username/path_to_top_level_petsc
export PETSC_ARCH=arch-darwin-c-opt
- Follow on-screen instructions for building and testing your PETSc installation
make all - Potentially: in
~/<path-to-top-level-petsc>/arch-darwin-c-opt/lib/petsc/conf/petscvariables, delete--oversubscribe
# install PFLOTRAN
cd ~/software/
git clone https://bitbucket.org/pflotran/pflotran.git
cd pflotran/src/pflotran
make pflotran
# compile using multiple cores (e.g., 4 cores)
make -j4 pflotran
#install conda-build to use conda develop. conda develop command is to install developmental version
conda install conda-build
conda develop /Users/username/path_to_top_level_pflotran/src/python/
DFNWorks
# install LaGriT
cd ~/software/
git clone https://github.com/lanl/LaGriT.git
cd LaGriT/
mkdir build/ && cd build/
cmake .. && make # make sure cmake is from homebrew/bin
# Install DFNWorks
cd ~/software/
git clone https://github.com/lanl/dfnWorks.git
cd dfnWorks/pydfnworks/bin
git checkout aa02d61
python fix_paths.py
cd ../
conda install -c conda-forge mplstereonet
conda install -c conda-forge fpdf
- Comment out
pyvtkstuff inpydfnworks/dfnGen/meshing/mesh_dfn_helper.py. Perhaps you mean to comment outimport pyvtk?python setup.py bdist_wheel cd ../DFNGen/ make cd ../DFNTrans/ make conda develop /Users/username/path_to_top_level_dfnworks/pydfnworks/Dakota
- Download Dakota (command line only): https://snl-dakota.github.io/docs/6.18.0/users/setupdakota.html#installation
cd ~/software/ tar xzvf /path/to/Dakota-release.platform.tar.gz mv dakota-release.platform dakota conda develop /path/to/Dakota/share/dakota/Python
Other software
- Paraview
- Download Paraview: https://www.paraview.org/download/
- HDFView
- Download HDFView: https://www.hdfgroup.org/downloads/hdfview/
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