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Documentation Index

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

The Dedalus build scripts provide flexible MPI (Message Passing Interface) configuration options. You can either install OpenMPI from conda-forge or link to a custom system MPI installation.

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Configuration Options

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INSTALL_MPI

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INSTALL_MPI
integer
default:"1"
Controls whether to install OpenMPI from conda-forge.Valid values:
  • 1 - Install OpenMPI from conda-forge (default)
  • 0 - Use custom MPI installation (requires MPI_PATH)

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MPI_PATH

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MPI_PATH
string
required
Path to your custom MPI installation prefix.Must be set when INSTALL_MPI=0. The build script will look for MPI binaries in ${MPI_PATH}/bin.

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Installation Modes

The default configuration installs OpenMPI from conda-forge along with the required compilers and mpi4py.
# Default configuration
INSTALL_MPI=1
This mode:
  • Installs conda-forge compilers
  • Installs OpenMPI and openmpi-mpicc
  • Installs mpi4py from conda
  • Works seamlessly with conda-installed FFTW and HDF5

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Build Behavior

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With INSTALL_MPI=1

From the build script:
conda_install_dedalus3.sh
if [ ${INSTALL_MPI} -eq 1 ]
then
    echo "Installing conda-forge compilers, openmpi, mpi4py"
    conda install "${CARGS[@]}" compilers openmpi openmpi-mpicc mpi4py
The script installs:
  • compilers - Conda-forge compiler toolchain
  • openmpi - OpenMPI library
  • openmpi-mpicc - MPI C compiler wrapper
  • mpi4py - Python MPI bindings

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With INSTALL_MPI=0

From the build script:
conda_install_dedalus3.sh
else
    echo "Not installing openmpi"
    echo "Installing mpi4py with pip"
    # Make sure mpicc will appear on path
    export PATH=${MPI_PATH}/bin:${PATH}
    echo "which mpicc: `which mpicc`"
    # no-cache to avoid wheels from previous pip installs
    python3 -m pip install --no-cache mpi4py
fi
The script:
  1. Adds your custom MPI binaries to PATH
  2. Verifies mpicc is accessible
  3. Builds mpi4py from source against your custom MPI

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Validation

The build script validates MPI configuration before proceeding:
conda_install_dedalus3.sh
if [ ${INSTALL_MPI} -ne 1 ]
then
    if [ -z ${MPI_PATH} ]
    then
        >&2 echo "ERROR: MPI_PATH must be set"
        exit 1
    else
        echo "MPI_PATH set to '${MPI_PATH}'"
    fi
fi
When INSTALL_MPI=0, you must set MPI_PATH or the build will fail with an error.

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Platform Considerations

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HPC Clusters

On HPC systems, you typically want to use the system-provided MPI: 
# Example for SLURM cluster with module system
module load openmpi/4.1.4

# Set in build script
INSTALL_MPI=0
export MPI_PATH="/opt/hpc/openmpi/4.1.4"

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Workstations and Laptops

For local development, the conda-forge OpenMPI is recommended: 
# Default - simplest option
INSTALL_MPI=1

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Compatibility with FFTW

FFFTW from conda-forge is built for OpenMPI. If you use a custom MPI that is not OpenMPI-compatible, you may need to also use a custom FFTW build.From the build script comments:
# Note: FFTW from conda will likely only work with custom MPIs that are OpenMPI

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Common Patterns

# Install everything from conda-forge
INSTALL_MPI=1
INSTALL_FFTW=1
INSTALL_HDF5=1

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