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https://github.com/weiji14/pyissm

Experimental code on running the Ice Sheet System Model (ISSM) via Python instead of the default Matlab interface.
https://github.com/weiji14/pyissm

antarctica ice-sheet-models issm python

Last synced: 22 days ago
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Experimental code on running the Ice Sheet System Model (ISSM) via Python instead of the default Matlab interface.

Host: GitHub
URL: https://github.com/weiji14/pyissm
Owner: weiji14
License: lgpl-3.0
Created: 2020-03-22T22:40:09.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2020-12-22T02:31:27.000Z (almost 4 years ago)
Last Synced: 2024-10-23T04:26:51.597Z (23 days ago)
Topics: antarctica, ice-sheet-models, issm, python
Language: Python
Homepage:
Size: 124 KB
Stars: 5
Watchers: 2
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE.md

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README

# PyISSM

Experimental code on running the [Ice-sheet and Sea-level System Model (ISSM)](https://issm.jpl.nasa.gov) via Python instead of the default Matlab interface.
Focusing on Pine Island Glacier (based on this [tutorial](https://issm.jpl.nasa.gov/documentation/tutorials/pig/)).

## Quickstart

Launch in [Pangeo Binder](https://pangeo-binder.readthedocs.io) (Interactive jupyter lab environment in the cloud).

[![Binder](https://binder.pangeo.io/badge_logo.svg)](https://binder.pangeo.io/v2/gh/weiji14/pyissm/master)

## Installation

Start by cloning this [repo-url](/../../)

git clone

Then I recommend [using conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) to install the dependencies.

cd pyissm
conda env create -f environment.yml

Activate the conda environment first.

conda activate pyissm

Then clone the ISSM svn trunk repository.
You will need to have [subversion](https://subversion.apache.org/) installed.

echo 'anon' | svn checkout --username anon --password-from-stdin -r 25855 https://issm.ess.uci.edu/svn/issm/issm/trunk

After that, you will need to compile some of the dependencies shipped with ISSM.

export ISSM_DIR=/path/to/pyissm/trunk
source $ISSM_DIR/etc/environment.sh && cd $ISSM_DIR/externalpackages/m1qn3 && ./install.sh
source $ISSM_DIR/etc/environment.sh && cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh

Setup some environment variables and configuration settings,
and patch the configure file to remove the 'm' for minimal (Python 3.8 and above only).

export CONDA_DIR=/path/to/.conda/envs/pyissm
cd $ISSM_DIR && source $ISSM_DIR/etc/environment.sh && autoreconf -ivf
cd $ISSM_DIR && \
./configure \
--prefix="$ISSM_DIR" \
--disable-static \
--enable-debugging \
--enable-development \
--with-numthreads=8 \
--with-python-version=3.7 \
--with-python-dir="$CONDA_DIR" \
--with-python-numpy-dir="$CONDA_DIR/lib/python3.7/site-packages/numpy/core/include/numpy" \
--with-fortran-lib="-L$CONDA_DIR/lib/gcc/x86_64-conda-linux-gnu/7.5.0/ -lgfortran" \
--with-mpi-include="$CONDA_DIR/lib/include" \
--with-mpi-libflags="-L$CONDA_DIR/lib -lmpi -lmpicxx -lmpifort" \
--with-metis-dir="$CONDA_DIR/lib" \
--with-scalapack-dir="$CONDA_DIR/lib" \
--with-mumps-dir="$CONDA_DIR/lib" \
--with-petsc-dir="$CONDA_DIR" \
--with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
--with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install"
# sed -i 's/-lpython${PYTHON_VERSION}m/-lpython${PYTHON_VERSION}/g' $ISSM_DIR/configure

For completeness, here's the equivalent commands for compiling under MATLAB.
The 'with-matlab-dir' filepath needs to be set to where MATLAB is installed.

cd $ISSM_DIR && \
./configure \
--prefix="$ISSM_DIR" \
--disable-static \
--enable-debugging \
--enable-development \
--with-numthreads=8 \
--with-matlab-dir="/opt/Matlab/R2019a/" \
--with-fortran-lib="-L$CONDA_DIR/lib/gcc/x86_64-conda-linux-gnu/7.5.0/ -lgfortran" \
--with-mpi-include="$CONDA_DIR/lib/include" \
--with-mpi-libflags="-L$CONDA_DIR/lib -lmpi -lmpicxx -lmpifort" \
--with-metis-dir="$CONDA_DIR/lib" \
--with-scalapack-dir="$CONDA_DIR/lib" \
--with-mumps-dir="$CONDA_DIR/lib" \
--with-petsc-dir="$CONDA_DIR" \
--with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
--with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install"

Finally compile ISSM!

cd $ISSM_DIR
make --jobs=8
make install

You'll need to export some more environment variables for things to work.
Plus add a line into your .bashrc file to apply the settings each time you restart.
See also official instructions at https://issm.jpl.nasa.gov/documentation/addpath/

export PYTHONPATH=$ISSM_DIR/bin:$PYTHONPATH
export PYTHONPATH=$ISSM_DIR/lib:$PYTHONPATH
echo "source $ISSM_DIR/etc/environment.sh" >> $HOME/.bashrc

### Syncing/Updating to new dependencies

conda env update -f environment.yml
cd $ISSM_DIR && svn update
make clean
# now recompile ISSM following instructions above

## Running jupyter lab

conda activate pyissm
python -m ipykernel install --user --name pyissm # to install conda env properly
jupyter kernelspec list --json # see if kernel is installed
jupyter lab &

## TODO

- [x] Use newer dataset inputs (e.g. BedMachine, ALBMAPv1, MEaSUREs Phase Map of Antarctic Ice Velocity)
- [x] Go from Python 2.7 to Python 3
- [x] Get reproducible [binder](https://mybinder.readthedocs.io) build to work (using Dockerfile)
- [x] [PyGMT](https://pygmt.org) plots!

## Notes

- ISSM installed in $ISSM_DIR which is /home/user/pyissm/trunk, activated by running `source $ISSM_DIR/etc/environment.sh`
- Pine Island Tutorial located in $ISSM_DIR/examples/Pig, and can be copied to /home/user/pyissm/Pig
- Datasets found under /home/user/pyissm/Data

## References

- Larour, E., Seroussi, H., Morlighem, M., & Rignot, E. (2012). Continental scale, high order, high spatial resolution, ice sheet modeling using the Ice Sheet System Model (ISSM). Journal of Geophysical Research: Earth Surface, 117(F1). https://doi.org/10.1029/2011JF002140