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Tutorial

Overview

The VIMS group is migrating most pre/post-precessing utiliies to Python-based tools, e.g., PySCHISM and Pylibs. Setting up a python environment enables you to take advantage of these readily-made tools.

We recommend using conda or mamba to manage your python environment.

Example for W&M’s Sciclone

Install Mamba from scratch

We don’t recommend using the conda module provided by SciClone, because you may run into permission issues or get confused with different conda versions on different subclusters.

Follow these steps to set up Mamba from scratch:

  • Select a subcluster (femto is the latest; the environment will be usable on all subclusters after installation)

  • Get the installer from mambaforge:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh

Install (e.g., under your home directory):

./Mambaforge-Linux-x86_64.sh

chmod +x Mambaforge-Linux-x86_64.sh if necessary; yes to all installer questions

Autoload Mamba base environment upon logon

  • Append the content of this file /sciclone/home10/feiye/conda_init_rc to the end of your ~/.cshrc This step is required because Mamba does not have the option to write the ‘.cshrc’ directly.

  • Add one more line conda activate base at the end of the .cshrc file,

Install tool set

Select the ones you need:

Install ipython

mamba install ipython

Install PySCHISM

Test Installation: type ipython, then in ipython: from pyschism.mesh import Hgrid

If warnings appear, you can try these steps to fix them (or leave them be):

pip uninstall shapely

conda install -c conda-forge- geos

pip install shapely --no-binary shapely

Install Pylibs

Test Installation: type ipython, then in ipython: import pylib