Getting started

Activate e3sm_unified environment

If you have an account on one of the E3SM supported machines (NERSC, Compy, Acme1, LCRC, Cooley, Rhea), you can access zstash by activating e3sm_unified, which is a conda environment that pulls together Python and other E3SM tools such as e3sm_diags.

The paths to e3sm_unified activation scripts are machine dependent:

Compy
source /share/apps/E3SM/conda_envs/load_latest_e3sm_unified_compy.sh
NERSC
source /global/common/software/e3sm/anaconda_envs/load_latest_e3sm_unified_cori-haswell.sh
Anvil
source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_anvil.sh
Chrysalis
source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh
Cooley
source /lus/theta-fs0/projects/ccsm/acme/tools/e3sm-unified/load_latest_e3sm_unified_cooley.sh
acme1
source /usr/local/e3sm_unified/envs/load_latest_e3sm_unified_acme1.sh
Andes
source /ccs/proj/cli900/sw/rhea/e3sm-unified/load_latest_e3sm_unified_andes.sh

Change .sh to .csh for csh shells.

Note that e3sm_unified’s development cycle is not in phase with zstash, therefore the version of zstash included may not be the latest. To install the latest stable release, refer to the following:

Installation in a Conda Environment

If the E3SM Unified environment doesn’t serve your needs, you can alternatively install the latest version in your own custom conda environment.

First, activate conda or install it if it’s not available. Details vary amongst machines.

Compy

module load anaconda3/2019.03
source /share/apps/anaconda3/2019.03/etc/profile.d/conda.sh

NERSC

module load python/3.7-anaconda-2019.10
source /global/common/cori_cle7/software/python/3.7-anaconda-2019.10/etc/profile.d/conda.sh

Others/Local

If the system doesn’t come with conda pre-installed, follow these instructions:

  1. Download Conda

    Linux
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    MacOS (note that zstash is not supported on MacOS, but it may be useful to contribute to the documentation on MacOS)
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

  2. Install Conda

    Linux
    bash ./Miniconda3-latest-Linux-x86_64.sh
    MacOS
    bash ./Miniconda3-latest-MacOSX-x86_64.sh

    • Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] yes

3. If you are working on a machine/network that intercepts SSL communications (such as acme1), you will get an SSL error unless you disable the SSL verification:

conda config --set ssl_verify false
binstar config --set ssl_verify False

4. Once conda is properly working, you can install the (a) Latest Stable Release or create a (b) Development Environment.

(a) Latest Stable Release

Installation using conda

First, make sure that you’re using bash.

$ bash

You must have Anaconda installed as well. See “Installation in a Conda Environment” section above for installing conda. Create a new Anaconda environment with zstash installed and activate it:

$ conda create -n zstash_env -c e3sm -c conda-forge zstash
$ source activate zstash_env

Or you can install zstash in an existing environment.

$ conda install zstash -c e3sm -c conda-forge

Installation on NERSC

After installing on NERSC, you may see improved performance running zstash on the data transfer nodes (dtn{01..15}.nersc.gov). However, modules are not directly available there, so you will need to manually activate Anaconda:

$ bash
$ source /global/common/cori_cle7/software/python/3.7-anaconda-2019.10/etc/profile.d/conda.sh
$ conda activate zstash_env

Updating

If you installed via Anaconda (e.g., not through the unified environment), you can update zstash by doing the following:

conda update zstash -c e3sm -c conda-forge

(b) Development Environment

Unlike the latest stable release (i.e., the user environment), the development environment does not include zstash. Instead, the developer will pip install . to build zstash with changes (see step 6 below).

Furthermore, the dev environment includes quality assurance (QA) tools such as code formatters, linters, and pre-commit. NOTE: These QA tools are enforced using pre-commit checks in the continuous integration/continuous delivery (CI/CD) build, so you must use the dev environment for all contributions.

  1. Follow “Others/Local” section for installing conda.

  2. Clone your fork and keep it in sync with the main repo’s master

    # Go to https://github.com/E3SM-Project/zstash
# Click "Fork" in the upper right hand corner. This will fork the main repo.
# Click the green "Code" button
# Choose the HTTPS or SSH option.
# (To use the SSH option, you need to have a SSH connection to GitHub set up).
# Click the clipboard icon to copy the path.
# On your command line:
git clone <path>
git remote -v
# You should see your fork listed as `origin`

    or if you already have a clone of your fork, rebase your fork on the main repo’s master to keep it in sync:

    # Add the main repo as a remote.
# You can call it anything but "upstream" is recommended.
# We'll use `<upstream-origin>` here.
git remote add <upstream-origin> <path from the green "Code" button mentioned above>

# Fetch all the branches of that remote into remote-tracking branches
git fetch <upstream-origin>

# Make sure that you're on your master branch:
git checkout master

# Rewrite your master branch so that any of your commits that
# aren't already in <upstream-origin>/master are replayed on top of that branch:
git rebase <upstream-origin>/master

# Push your master branch to your GitHub fork:
# Note that <fork-origin> should be `origin` if you cloned your fork as above.
git push -f <fork-origin> master

    Checkout a new branch from master:

    git checkout -b <branch-name> <remote-origin>/master

  3. Remove any cached conda packages. This will ensure that you always get the latest packages.

    conda clean --all

  4. Enter the fork’s clone.

    cd zstash

5. Use conda to create a new dev environment. (zstash is not included in this environment).

  • Tip: Add the flag -n <name_of_env> to customize the name of the environment

conda env create -f conda/dev.yml
conda activate zstash_dev

  1. Install pre-commit.

    pre-commit install

  2. Make the desired changes to zstash, then rebuild and install with:

    pip install .

  3. Commit changes and make sure pre-commit checks pass

    git commit -m "commit-message"
    pre-commit Output

    pre-commit Output

Archiving

For archiving E3SM simulations, we recommend following the Best practices for E3SM.