Obtaining dependencies

Obtaining dependencies#

ROMS runs on Unix-like systems. It additionally requires:

  • A Fortran compiler (gfortran and ifx are actively supported)

  • The netcdf-fortran library for netCDF i/o

  • An MPI library (e.g. MPICH, OpenMPI, Intel MPI) for parallelization

… Using ROMS with MARBL biogeochemistry additionally requires MARBL v0.45 (see below section on installing MARBL)

This page details different methods for obtaining these dependencies:

Using containers#

Warning

This is best suited to cloud instances, personal computers, and small-scale scientific computing systems. On high-performance computing systems, running MPI programs inside containers may be nontrivial. You may wish to consult your HPC’s documentation or contact its support team.

The easiest way to obtain a ROMS-ready environment is in a pre-built container. We maintain two container images with pre-configured environments containing all of the above dependencies:

You can fetch and run these images using software like podman or docker, e.g.:

podman pull ghcr.io/cworthy-ocean/marbl_ifx_openmpi:0.0
podman run -it ghcr.io/cworthy-ocean/marbl_ifx_openmpi:0.0

You can then clone ROMS into the container as described on the following page.

Using conda#

Warning

This is best suited to cloud instances, personal computers, and small-scale scientific computing systems. High-performance computing systems typically have internal package management systems that vary between machines and over time. MPI and other libraries installed via conda may have limited compatibility.

The necessary (GNU) dependencies for ROMS can be installed via conda in an environment created from an included yaml file:

conda env create -f environments/conda_environment.yml --name roms_env
conda activate roms_env

NOTE If planning to run ROMS with MARBL biogeochemistry, MARBL will need to be built separately. See the section below on installing MARBL.

You will also need to set some necessary environment variables telling ROMS where to find your conda-installed libraries:

export ROMS_ROOT=⚠️ EDIT ME!<your ROMS clone location>⚠️
export MPIHOME=${CONDA_PREFIX}
export NETCDFHOME=${CONDA_PREFIX}
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$NETCDFHOME/lib"
export PATH="$ROMS_ROOT/Tools-Roms:$PATH"

Verify you set $ROMS_ROOT correctly above with ls $ROMS_ROOT. You should see directories like src,docs, etc. These variables will need to be set every time you wish to use ROMS, so it may be convenient to set their values in a location such as a shell startup file (e.g. ~/.bashrc)

Using LMOD on supported HPC systems.#

The ROMS repo includes a selection of files for configuring the environment for ROMS on supported HPC systems, in the environments directory. If you are on a supported machine, simply run source <machinename>.sh inside that directory (note that paths in these files are relative, so they should not be moved). If you are running ROMS on another system and would like to share your configuration, or to report that one of these configurations is out of date, please open an issue or pull request.

NOTE If planning to run ROMS with MARBL biogeochemistry, MARBL will need to be built separately. See the section below on installing MARBL.

Installing MARBL#

MARBL is an optional dependency used for advanced biogeochemical modeling in ROMS. ROMS works with MARBL v0.45. To install:

  1. Clone MARBL to its own directory and checkout the supported version:

git clone https://github.com/marbl-ecosys/MARBL.git
cd MARBL/
git checkout marbl0.45.0

  1. In this directory (the repo top level), set the MARBL_ROOT environment variable, so ROMS can find MARBL:

export $MARBL_ROOT=$(pwd)

This variable will need to be set every time you wish to use MARBL, so it may be convenient to set its value in a location such as a shell startup file (e.g. ~/.bashrc):

  1. Compile MARBL using the same compiler and environment you set up for ROMS above, e.g.

cd $MARBL_ROOT/src/
make <compiler> USEMPI=TRUE

  1. Where <compiler> is either intel (if your compiler is ifx or ifort) or gnu (if your compiler is gfortran). If you are unsure, your compiler information should be returned by mpifort --version

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