Installation#

Overview#

SYMFLUENCE installs via pip (the primary, recommended method); the external model binaries are then provided by symfluence binary install. Alternative methods — npm (bundled pre-built binaries), Docker, and a source/bootstrap path for development — are documented below and on the Docker page. HPC environments vary; use the module recipes on your cluster as needed.

Quick Install#

Option 1: pip (recommended)

# Install the Python framework
pip install symfluence

# Install the external model binaries (SUMMA, mizuRoute, FUSE, NGEN, TauDEM, ...)
symfluence binary install

# Verify the binaries
symfluence binary doctor

Note

Python 3.11–3.13 only. Key geospatial dependencies (Fiona, rasterio, GDAL) do not yet ship wheels for Python 3.14+. If you are on 3.14, create a 3.11 or 3.12 environment instead (python3.11 -m venv venv).

Option 2: npm (bundled pre-built binaries)

# Install globally (includes SUMMA, mizuRoute, FUSE, NGEN, TauDEM)
npm install -g symfluence

# Verify installation
symfluence binary info

# Check system compatibility
symfluence binary doctor

Requirements: Linux (Ubuntu 22.04+, RHEL 9+, Debian 12+ x86_64) or macOS 12+ (Apple Silicon). System libraries NetCDF and HDF5 must be installed via your package manager.

Option 3: Docker

Per-method Dockerfiles are provided for reproducible builds across all install paths; see the Docker page.

Development Installation#

For development or custom builds, clone the repository and use the built-in installer:

git clone https://github.com/symfluence-org/SYMFLUENCE.git
cd SYMFLUENCE
./scripts/symfluence-bootstrap --install
source venv/bin/activate

What this does:

Creates/updates venv/ (Python 3.11 recommended)
Installs Python dependencies with pip
Reuses the environment on subsequent runs

Manual Setup (Optional)#

If you prefer to manage the environment yourself:

python3 -m venv venv
source venv/bin/activate
pip install -e .

System Prerequisites#

Build toolchain: GCC/Clang (C/C++), gfortran; CMake >= 3.20; MPI (OpenMPI/MPICH)
Core libs: GDAL, HDF5, NetCDF (C + Fortran), BLAS/LAPACK
Optional tools: R, CDO (when applicable)

For the full list of system dependencies with platform-specific install commands, see docs/SYSTEM_REQUIREMENTS.md. You can verify your environment with:

symfluence binary doctor

CDS API Credentials (CARRA/CERRA)#

If you plan to use CARRA or CERRA forcing datasets, configure CDS API credentials:

Register: https://cds.climate.copernicus.eu/
Get your API key at https://cds.climate.copernicus.eu/user
Create ~/.cdsapirc:

cat > ~/.cdsapirc << EOF
url: https://cds.climate.copernicus.eu/api
key: {UID}:{API_KEY}
EOF

Restrict permissions:

chmod 600 ~/.cdsapirc

Verification:

import cdsapi
c = cdsapi.Client()
print("CDS API configured successfully!")

HPC Module Recipes#

Use your site’s module system, then run the installer:

Anvil (Purdue RCAC):

module load r/4.4.1
module load gcc/14.2.0
module load openmpi/4.1.6
module load gdal/3.10.0
module load conda/2024.09
module load openblas/0.3.17
module load netcdf-fortran/4.5.3
module load udunits/2.2.28

ARC (University of Calgary):

. /work/comphyd_lab/local/modules/spack/2024v5/lmod-init-bash
module unuse $MODULEPATH
module use /work/comphyd_lab/local/modules/spack/2024v5/modules/linux-rocky8-x86_64/Core/

module load gcc/14.2.0
module load cmake
module load netcdf-fortran/4.6.1
module load netcdf-c/4.9.2
module load openblas/0.3.27
module load hdf5/1.14.3
module load gdal/3.9.2
module load netlib-lapack/3.11.0
module load openmpi/4.1.6
module load python/3.11.7
module load r/4.4.1
module load geos

FIR (Compute Canada):

module load StdEnv/2023
module load gcc/12.3
module load python/3.11.5
module load gdal/3.9.1
module load r/4.5.0
module load cdo/2.2.2
module load mpi4py/4.0.3
module load netcdf-fortran/4.6.1
module load openblas/0.3.24

Then run:

./scripts/symfluence-bootstrap --install

macOS (Intel or Apple Silicon)#

Install Xcode tools and Homebrew:

xcode-select --install
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install core packages:

brew update
brew install cmake gcc open-mpi gdal hdf5 netcdf netcdf-fortran openblas lapack cdo r

Optional compiler pinning:

export CC=$(brew --prefix)/bin/gcc-14
export CXX=$(brew --prefix)/bin/g++-14
export FC=$(brew --prefix)/bin/gfortran-14

Then run:

./scripts/symfluence-bootstrap --install

Verification#

./scripts/symfluence-bootstrap --help

Troubleshooting#

GDAL Installation Issues#

GDAL is the most common source of installation problems. Here are solutions for common scenarios:

macOS Apple Silicon (M1/M2/M3)

The ARM architecture requires special handling:

# Option 1: Homebrew (recommended)
brew install gdal
pip install gdal==$(gdal-config --version)

# Option 2: Conda (if Homebrew fails)
conda create -n symfluence python=3.11
conda activate symfluence
conda install -c conda-forge gdal

# Verify architecture matches
file $(which gdalinfo)  # Should show "arm64"

Version Mismatch Errors

If you see gdal_config_error or version conflicts:

# Check system GDAL version
gdal-config --version

# Install matching Python bindings
pip install gdal==$(gdal-config --version)

# If that fails, try conda-forge
conda install -c conda-forge gdal=$(gdal-config --version)

Windows

Native Windows installation is complex. Use conda-forge:

# Create environment with all geospatial deps
conda create -n symfluence python=3.11
conda activate symfluence
conda install -c conda-forge gdal geopandas rasterio netcdf4 hdf5

# Then install symfluence
pip install symfluence

Linux Build Failures

If GDAL Python bindings fail to compile:

# Ensure development headers are installed
sudo apt-get install -y libgdal-dev

# Set include paths
export CPLUS_INCLUDE_PATH=/usr/include/gdal
export C_INCLUDE_PATH=/usr/include/gdal

# Install with numpy pre-installed
pip install numpy
pip install gdal==$(gdal-config --version)

NetCDF/HDF5 Issues#

Missing libnetcdf or libhdf5

# Ubuntu/Debian
sudo apt-get install -y libnetcdf-dev libhdf5-dev

# macOS
brew install netcdf hdf5

# Verify
nc-config --version
h5cc -showconfig | head -5

HDF5 Version Conflicts

If you see HDF5 header/library version mismatches:

# Force rebuild with system libraries
pip uninstall h5py
HDF5_DIR=/usr/local pip install --no-binary=h5py h5py

rpy2/R Integration Issues#

R Not Found

# Ensure R is in PATH
which R
R --version

# On macOS, you may need to link
export R_HOME=$(R RHOME)

rpy2 Compilation Errors

# Install R development headers
# Ubuntu
sudo apt-get install r-base-dev

# Then reinstall rpy2
pip install --force-reinstall rpy2

Diagnostic Commands#

Run these to diagnose issues:

# Check all dependencies
symfluence binary doctor

# Verify Python environment
python -c "import gdal; print(gdal.__version__)"
python -c "import netCDF4; print(netCDF4.__version__)"
python -c "import rpy2; print(rpy2.__version__)"

# Check system libraries
ldconfig -p | grep -E "(gdal|netcdf|hdf5)"  # Linux
otool -L $(python -c "import gdal; print(gdal.__file__)")  # macOS

Next Steps#

Getting Started — your first run
Configuration — YAML structure and options
Examples — progressive tutorials