Getting Started

A number of pieces of software must be installed to run ModelE successfully — not just ModelE and ModelE-Control, but also ModelE dependencies, as well as key post-processing tools. These tools have already been installed on some systems, allowing users to get started immediately simply by making changes to .bashrc.

Check below to see if the ModelE environment has been installed on your favorite computer. If not, head to the full Installation instructions below.

Quick Start: NCCS Discover

The ModelE environment has already been installed on NCCS Discover, allowing users to get started quickly with ModelE. To use this environment:

1. Remove all module load commands from your .bashrc file.

2. Add the following to your .bashrc file:

   .. code-block:: console
   

   source /home/rpfische/env/modele-ksx-gcc

Use the following instead for Intel compilers (not yet implemented):

.. code-block:: console

   source /home/rpfische/env/modele-ksx-intel

3. Set MODELE_FILE_PATH in your .bashrc, modifying depending on where you wish to keep user-generated input files. For example:

   export MODELE_FILE_PATH=/discover/nobackup/projects/giss/prod_input_files:$HOME/modele_input/local
   

That’s it, you are now ready to use ModelE, along with all the latest tools, NetCDF, etc.

Installation

ModelE and ModelE-Control have a number of dependencies, which are automatically handled by Spack. The following instructions may be used to install ModelE, modele-control and Spack startin from a clean machine:

Install Spack

If you are not using discover, then here is how to build a ModelE environment on your machine.

1. Download:

   cd ~
   # git clone git@github.com:citibeth/spack.git -b efischer/develop
   git clone https://github.com/citibeth/spack.git -b efischer/develop
   

2. Add to your .bashrc file:

   export SPACK_ROOT=$HOME/spack
   . $SPACK_ROOT/share/spack/setup-env.sh
   

3. Remove non-system stuff from your PATH, LD_LIBRARY_PATH and other environment variables, which can cause strange errors when building with Spack.

Setup Spack

See Spack docs for more info on setting up compilers, bootstrapping, etc.

Actuallyxx… give instructions here on Intel, etc. compilers

Setup Packages

Copy the following to your ~/.spack/packages.yaml file:

packages:
    python:
        # Lie about the version in the system, so it's new enough for Spack to recognize.
        paths:
            python@2.7.8: /        # Spack can't install Python2, I don't know why
        version: [3.5.2,2.7.8]

    py-cython:
        version: [0.23.5]
    py-proj:
        version: [1.9.5.1.1]    # Normal released version 1.9.5.1 is buggy
    py-matplotlib:
        variants: +gui +ipython
    py-numpy:
        variants: +blas +lapack

    ibmisc:
        version: [develop]
        variants: +python +netcdf
    icebin:
        version: [develop]
        variants: +gridgen +python ~coupler ~pism

    # Running without dynamic ice
    modele:
        version: [landice]

#    # Running with dynamic ice
#    modele:
#        version: [glint2]
#        variants: [+couler +pism]

    pism:
        version: [glint2]
    glint2:
        version: [glint2]
        variants: +coupler +pism

    everytrace:
        version: [develop]
    eigen:
        variants: ~suitesparse
    netcdf:
        variants: +mpi


    # Recommended for security reasons
    # Do not install OpenSSL as non-root user.
    openssl:
        paths:
            openssl@system: /usr
        version: [system]
        buildable: False

    # Recommended, unless your system doesn't provide Qt4
    qt:
        paths:
            qt@system: /usr
        version: [system]
        buildable: False

    all:
        compiler: [gcc@4.9.3]
        providers:
            mpi: [openmpi]
            blas: [openblas]
            lapack: [openblas]

Install ModelE Environment

This installs all the prerequisites needed to run ModelE, along with basic tools to analyze its output.

spack install modele-utils
spack install --dependencies-only modele
spack install ncview
spack install nco
spack install modele-control

Generate the Module Loads

Run the following script, to generate the file ~/env/modele. This will load the modules you just created:

#!/bin/sh
#
# Generate commands to load the Spack environment


SPACKENV=$HOME/env/modele
FIND='spack module loads'

echo '#!/bin/sh -f' >$SPACKENV
echo '# ---- Machine generated; do not edit!' >>$SPACKENV
#echo 'module purge' >>$SPACKENV

# --- ModelE Stuff
$FIND ncview >>$SPACKENV
$FIND nco >>$SPACKENV
$FIND modele-control >>$SPACKENV
$FIND modele-utils >>$SPACKENV

NOTES:

1. Remember to include any bootstrapping modules you might need as well: for example, pre-existing compilers sometimes must be loaded to run anything built with them.

2. Depending on how your system’s environment modules are configured, you might need to add --prefix to the spack module loads command. See spack module loads --help.

Update .bashrc

Add the following to your .bashrc file, modifying accordingly:

export SPACK_ROOT=$HOME/spack
. $SPACK_ROOT/share/spack/setup-env.sh
export MODULEPATH=$SPACK_ROOT/share/spack/modules:$MODULEPATH
export PATH=$PATH:$HOME/spack/bin
alias spack='nice spack'
export SPACK_DIRTY=
export LESS='-R'
source $HOME/env/modele