LIVVkit Extensions (LIVVext)

This repository holds a collection of extensions to LIVVkit for validation and custom analyses of ice sheet models and their associated Earth system models.

LIVVext (LEX) was first described in Evans, et al., 2019¹

Dependencies

The Python dependencies are listed in requirements.txt and requirements-dev.txt but this suite depends on a set of reanalysis and observational datasets, which are part of E3SM-Diags, available on several DOE supported machines, including Perlmutter at NERSC, and Chrysalis at ANL's LCRC.

The Python package itself is described in pyproject.toml, which is used by pip to install this package

Currently, LIVVext is designed to run on NERSC's Perlmutter, and ANL-LCRC's Chrysalis, but future work is planned to support other machines where E3SM runs.

Environment setup

For setting up an environment to which LIVVext and dependencies will be installed, Pixi and conda are documented here. NB this will only currently work on Perlmutter and Chrysalis, the environment should be created there.

Pixi environment

pixi is a package management tool, and the primary environment management tool for LIVVext.

First, pixi must be installed locally following these instructions, then an enviornment for LIVVext development can be created:

$ git clone https://github.com/LIVVkit/LIVVext.git
$ cd LIVVext
$ pixi install          # This will install the default environment
$ pixi shell -e default # To activate the default (runtime) environment

If development tools are needed (e.g. pytest), install and activate the dev environment:

$ pixi install -e dev   # Installs the environment
$ pixi shell -e dev     # Activates the dev environment (for code testing and checks)

N.B. it is not recommended to do pixi install --all, as this will install the environment versions used for testing.

Conda environment

$ git clone https://github.com/LIVVkit/LIVVext.git
$ cd LIVVext
$ {conda, mamba} env create -n lex_env python --file env.yml
$ {conda, mamba} activate lex_env
$ pip install -e .    # Installs the LIVVext module as an editable Python package to the lex_env environment.

Basic usage

Within the LIVVext/config directory there are templates for ELM r05 and r025 resolutions, as well as pre-existing configurations for several current runs.

To execute any of these analyses, point livv (LIVVkit's command line interface) to any of these extensions via the the -V/--validate option.

For example, to run the minimal example extension, place the output website in the vv_test directory, and serve the output website you'd run this command:

$ livv -V config/example/example.yml -o vv_test -s

This will create a directory in the current directory called vv_test (~7.5 MB), and spawn an HTTP server, which should only be used for testing purposes. (This works best if the output is in the current directory)

Note: All the extension configurations files assume you are working from the top level LIVVext directory. You can run any of these extensions from any directory, but you will need to edit the paths in the YAML configuration files so that livv can find the required files.

Likewise, you can also apply these analyses to any new model run² by adjusting the paths to point to your model run.

Running existing cases on PM-CPU

The LIVVext/run_livv.sh script will run all the currently available analyses on pm-cpu for a particular case, e.g.:

$ cd $HOME/LIVVext
$ ./run_livv.sh v2.1.r025.IGERA5ELM_MLI-deep_firn_1980_2020

Will create a web output at /global/cfs/projectdirs/e3sm/www/${USER}/v2.1.r025.IGERA5ELM_MLI-deep_firn_1980_2020, viewable at https://portal.nersc.gov/project/e3sm/${USER}/v2.1.r025.IGERA5ELM_MLI-deep_firn_1980_2020

The batch script provided will run all current cases on Perlmutter on a compute node in parallel

$ cd LIVVext
$ sbatch run_lex_pm-cpu.sbatch

Running new cases on PM-CPU

Generate a single timeseries file from ELM h0 outputs

• CASE="The case name"
• ncrcat -v topo,landfrac,QSNOFRZ,FSRND,FSRVD,FSDSVD,FSDSND,EFLX_LH_TOT,FIRA,FLDS,FSA,FSDS,FSH,QICE,QRUNOFF,QSNOMELT,QSOIL,RAIN,SNOW,TSA,SNOWICE,SNOWLIQ,H2OSNO ${CASE}.elm.h0*.nc -o ${CASE}.nc

Perform post-processing on a single time series ELM h0 output

• Edit the LIVVext/LIVVext/postproc/e3sm/postproc.sbatch batch file to mach the new run

  Key variables:

  • INDIR: Path which contains single output time series file
  • OUTCASE: Name of the new case which is the name of the netCDF file without extension (e.g. v2.1.r025.IGERA5ELM_MLI-deep_firn_1980_2020)
  • RES: ELM output resolution (currently accepts R05 and R025)
  • OUTDIR: Scratch directory into which climatology files will be written, defaults to ${SCRATCH}/LIVVext/data/e3sm/${OUTCASE}

• Run the post-processing script:

  • cd LIVVext/LIVVext/postproc/e3sm; sbatch postproc.sbatch

NB: the postproc.sbatch script will create the configuration for your case (based on OUTCASE and OUTDIR), then run LIVVkit on it with LIVVext/run_livv.sh

Developing a custom extension

See the LIVVkit documentation for details on how to develop an extension. Briefly, a absolute minimum working example is provided by the example/ extension, which should be copied to provide the basis for your new extension. All extensions are required to contain a minimal working example set of data such that they can be run an executed on any machine.

For extensions that require data for which re-host permission cannot be granted, they must include documentation on how to acquire and use the data as well as either a small set of processed data or a set of "fake" example data.

Issues, questions, comments, etc.?

If you would like to suggest features, request tests, discuss contributions, report bugs, ask questions, or contact us for any reason, use the LIVVkit issue tracker. LIVVext issue tracker.

Want to send us a private message?

Michael E. Kelleher :github: @mkstratos

Joseph H. Kennedy :github: @jhkennedy

Katherine J. Evans :github: @kevans32

Footnotes

1. Evans, K.J., J.H. Kennedy, D. Lu, M.M. Forrester, S. Price, J. Fyke, A.R. Bennett, M.J. Hoffman, I. Tezaur, C.S. Zender, and M. Vizcaino (2019). LIVVkit 2.1: Automated and extensible ice sheet model validation. Geoscientific Model Development. https://gmd.copernicus.org/articles/12/1067/2019/ ↩

2. This assumes the new data files conform to the format of the included data files. That is, an extension that analyses output from the CISM-Albany ice sheet model will likely be able to analyze any similar CISM-Albany simulation, but likely would not be able to analyze output from the PISM ice sheet model without "massaging" the PISM files into a CISM-Albany like structure, or adjusting the extension. This is a problem we are working on for future LIVVext releases. ↩