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Fetch the complete documentation index at: https://mintlify.com/DedalusProject/dedalus_conda/llms.txt

Use this file to discover all available pages before exploring further.

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Overview

FFTW (Fastest Fourier Transform in the West) is a critical dependency for Dedalus spectral methods. The build scripts allow you to install FFTW from conda-forge or link to a custom FFTW installation.

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Configuration Options

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INSTALL_FFTW

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INSTALL_FFTW
integer
default:"1"
Controls whether to install FFTW from conda-forge.Valid values:
  • 1 - Install FFTW from conda-forge (default)
  • 0 - Use custom FFTW installation (requires FFTW_PATH)

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FFTW_PATH

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FFTW_PATH
string
required
Path to your custom FFTW installation prefix.Must be set when INSTALL_FFTW=0. The build will link against FFTW libraries in this location.

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FFTW_STATIC

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FFTW_STATIC
integer
Controls whether to statically link FFTW.Automatically set based on BLAS choice:
  • 0 - Dynamic linking (when BLAS="openblas")
  • 1 - Static linking (when BLAS="mkl")
You typically should not set this manually.

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Installation Modes

The default configuration installs FFTW from conda-forge, specifically the OpenMPI variant.
# Default configuration
INSTALL_FFTW=1
From the build script:
conda_install_dedalus3.sh
if [ ${INSTALL_FFTW} -eq 1 ]
then
    echo "Installing conda-forge fftw"
    # no-deps to avoid pulling openmpi
    conda install "${CARGS[@]}" --no-deps "fftw=*=*openmpi*"
The --no-deps flag prevents conda from pulling OpenMPI as a dependency, allowing the script to manage MPI separately.

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FFTW Linking Behavior

The FFTW_STATIC variable is automatically set based on your BLAS configuration:

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With OpenBLAS (Dynamic Linking)

conda_install_dedalus3.sh
case "${BLAS}" in
"openblas")
    echo "Installing conda-forge openblas, numpy, scipy"
    # Pin openblas on apple silicon since 0.3.20 causes ggev errors
    if [ ${APPLE_SILICON_BUILD_ARM} -eq 1 ]
    then
        conda install "${CARGS[@]}" "libopenblas<0.3.20"
    fi
    conda install "${CARGS[@]}" "libblas=*=*openblas" numpy scipy
    # Dynamically link FFTW
    export FFTW_STATIC=0
With OpenBLAS, FFTW is dynamically linked.

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With MKL (Static Linking)

conda_install_dedalus3.sh
"mkl")
    echo "Installing conda-forge mkl, numpy, scipy"
    conda install "${CARGS[@]}" "libblas=*=*mkl" numpy scipy
    # Statically link FFTW to avoid MKL symbols
    export FFTW_STATIC=1
Static linking is used with MKL to avoid symbol conflicts between FFTW and MKL libraries.

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Validation

The build script validates FFTW configuration:
conda_install_dedalus3.sh
if [ ${INSTALL_FFTW} -ne 1 ]
then
    if [ -z ${FFTW_PATH} ]
    then
        >&2 echo "ERROR: FFTW_PATH must be set"
        exit 1
    else
        echo "FFTW_PATH set to '${FFTW_PATH}'"
    fi
fi
When INSTALL_FFTW=0, you must set FFTW_PATH or the build will fail.

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MPI Compatibility

Important compatibility note from the build script:
# Note: FFTW from conda will likely only work with custom MPIs that are OpenMPI
The conda-forge FFTW package is built against OpenMPI. If you use a custom MPI implementation that is not OpenMPI-compatible, you should also use a custom FFTW build.

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Platform Considerations

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Standard Conda Build

For most users, the conda-forge FFTW works well: 
INSTALL_MPI=1      # Use conda OpenMPI
INSTALL_FFTW=1     # Use conda FFTW (built for OpenMPI)

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HPC Clusters

On HPC systems, you may need to use optimized system libraries: 
# Use system MPI and FFTW
INSTALL_MPI=0
export MPI_PATH="/opt/mpi/openmpi-4.1.4"

INSTALL_FFTW=0
export FFTW_PATH="/opt/fftw/3.3.10-openmpi"

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Building Custom FFTW

If you need to build FFTW yourself (e.g., for a non-OpenMPI MPI): 
# Download and build FFTW
wget http://www.fftw.org/fftw-3.3.10.tar.gz
tar -xzf fftw-3.3.10.tar.gz
cd fftw-3.3.10

# Configure with MPI support
./configure --prefix=/opt/fftw/3.3.10 \
            --enable-mpi \
            --enable-openmp \
            --enable-threads \
            --enable-shared
make -j
make install

# Use in build script
INSTALL_FFTW=0
export FFTW_PATH="/opt/fftw/3.3.10"

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Common Patterns

# Simplest configuration
INSTALL_MPI=1
INSTALL_FFTW=1
BLAS="openblas"
# FFTW_STATIC will be automatically set to 0

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Troubleshooting

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Symbol conflicts with MKL

If you see symbol conflicts between FFTW and MKL: 
# Ensure FFTW is statically linked when using MKL
BLAS="mkl"
INSTALL_FFTW=1
# FFTW_STATIC=1 will be set automatically

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Custom MPI with conda FFTW

If using custom MPI with conda FFTW fails: 
# Use custom FFTW built against your MPI
INSTALL_MPI=0
export MPI_PATH="/path/to/custom/mpi"

INSTALL_FFTW=0  # Don't use conda FFTW
export FFTW_PATH="/path/to/fftw/built/with/custom/mpi"

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