Packages in the E3SM Unified conda environment

Owned by Charles Doutriaux (Unlicensed)
Last updated: yesterday at 4:58 am by Naser Mahfouz
3 min read

This page is a catalog of the packages and versions that make up each version of the E3SM-Unified metapackage.  E3SM-Unified is intended to create a single conda environment that includes all of E3SM's analysis and diagnostics software.

The metapackage is maintained by @Xylar Asay-Davis.

Using the metapackage on E3SM supported machines

Please see Diagnostics and Analysis Quickstart#Accessingmetapackagesoftwarebyactivatingacondaenvironment

Installing the metapackage

To install your own version of the metapackage (typically on a machine not supported by E3SM), install miniforge3, typically for Linux and x86_64, then run the following:

conda create -n e3sm-unified -c conda-forge -c e3sm e3sm-unified python=3.10

If you plan to use MPI from conda-forge, you will want to use the mpich or openmpi builds of e3sm-unified.  For example, for mpich:

conda create -n e3sm-unified-mpich -c conda-forge -c e3sm "e3sm-unified=*=mpi_mpich_*" python=3.10

This is only appropriate on Linux and OSX laptops and workstations, as the MPI packages from conda-forge do not work on HPC.

For MacOS M1 users: the MacOS x86 distribution of mambaforge works on M1 and M2 architectures. Apple maintains “Rosetta 2” for backwards compatibility. It should be seamless to the user, but there may be a pop-up asking to install Rosetta if it is not already installed. MacOS Conda installs work better with zsh (updated bash).

Tables of metapackage content

The list of packages installed as required by E3SM (and their pinned stable version) is below. Also listed is the person in charge of maintaining the pinned version.  Contents of previous versions are also listed below.

For previous versions see: https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/3236233332

Current Version

e3sm-unified 1.9.3

Release candidate testing start date: 

Feb 5, 2024 

 

Release date:

Unknown

 

Main Packages

package

version

maintainer(s)

Notes

python

>=3.9,<3.11

@Xylar Asay-Davis

Default python version (used for supported machines) will be 3.10

chemdyg

0.1.5

@Hsiang-He Lee @Qi Tang

 

e3sm_diags

2.11.0

@Jill Chengzhu Zhang

 

e3sm_to_cmip

1.11.2

@Anthony Bartoletti @Tom Vo @Jill Chengzhu Zhang

Includes an Xarray I/O fix for zppy

Changelog

geometric_features

1.3.0

@Xylar Asay-Davis

 

globus-cli

nospec

@Lukasz Lacinski

 

ilamb

2.7

@Michael Kelleher

With system MPI on compute nodes

ipython

nospec

@Jill Chengzhu Zhang

 

jupyter

nospec

@Jill Chengzhu Zhang

 

livvkit

3.0.1

@Michael Kelleher

 

mache

1.21.0

@Xylar Asay-Davis

 

moab

5.5.1

@Vijay M

With system MPI on compute nodes

mpas-analysis

1.10.0

@Xylar Asay-Davis

 

mpas_tools

0.32.0

@Xylar Asay-Davis

 

nco

5.2.2

@Charlie Zender

With system MPI on compute nodes

pcmdi_metrics

2.3.1

@Jill Chengzhu Zhang

 

tempest-remap

2.2.0

@Xylar Asay-Davis

With system compilers on compute nodes

tempest-extremes

2.2.1

@Xylar Asay-Davis
@Jill Chengzhu Zhang

With system MPI on compute nodes

xcdat

0.6.1

@Tom Vo

 

zstash

1.4.2

@Ryan Forsyth

 

zppy

2.4.0

@Ryan Forsyth

 

mkdoc dependencies

package

version

maintainer(s)

 

mkdocs-material

nospec

@Naser Mahfouz

 

pymdown-extensions

nospec

@Naser Mahfouz

 

mkdocs-monorepo-plugin

nospec

@Naser Mahfouz

 

mdutils

nospec

@Naser Mahfouz

 

mkdocs-bibtex

nospec

@Naser Mahfouz

 

Dependencies

package

version

maintainer(s)

 

blas

nospec

@Xylar Asay-Davis

 

bottleneck

nospec

@Xylar Asay-Davis

 

cartopy

>=0.17.0

@Jill Chengzhu Zhang

 

cdat_info

8.2.1

@Jill Chengzhu Zhang

 

cdms2

3.1.5

@Jill Chengzhu Zhang

 

cdtime

3.1.4

@Jill Chengzhu Zhang

 

cdutil

8.2.1

@Jill Chengzhu Zhang

 

cmocean

nospec

@Xylar Asay-Davis

 

dask

2023.6.0

@Xylar Asay-Davis 

 

dogpile.cache

nospec

@Chris Golaz

 

eofs

nospec

@Luke Van Roekel

 

esmf

8.6.0

@Xylar Asay-Davis

With system MPI on compute nodes

esmpy

8.6.0

@Xylar Asay-Davis

 

f90nml

nospec

@Xylar Asay-Davis

 

ffmpeg

nospec

@Xylar Asay-Davis @Luke Van Roekel

 

genutil

8.2.1

@Jill Chengzhu Zhang

 

globus-sdk

nospec

@Lukasz Lacinski

 

gsw

nospec

@Xylar Asay-Davis

 

hdf5

1.14.3

@Jill Chengzhu Zhang

@Xylar Asay-Davis

 

ipygany

nospec

@Erika Roesler

 

libnetcdf

4.9.2

@Xylar Asay-Davis

 

lxml

nospec

@Xylar Asay-Davis

 

matplotlib

3.8.2

@Jill Chengzhu Zhang

@Xylar Asay-Davis

 

metpy

nospec

@Jim Benedict

 

mpi4py

nospec

@Xylar Asay-Davis

With system MPI on compute nodes

nb_conda

nospec

@Jill Chengzhu Zhang

 

ncview

2.1.8

@Jill Chengzhu Zhang

 

ncvis

2023.09.12

@Jill Chengzhu Zhang

 

netCDF4

1.6.4 nompi

@Xylar Asay-Davis

 

numpy

>1.13

@Xylar Asay-Davis

 

output_viewer

1.3.1

@Jill Chengzhu Zhang

@Ryan Forsyth

 

pillow

nospec

@Xylar Asay-Davis

 

plotly

nospec

@Xylar Asay-Davis

 

progessbar2

nospec

@Xylar Asay-Davis

 

proj

9.3.1

@Xylar Asay-Davis

 

pyproj

3.6.1

@Jill Chengzhu Zhang

@Xylar Asay-Davis

 

scikit-image

nospec

@Xylar Asay-Davis

 

scipy

nospec

@Xylar Asay-Davis

 

pyevtk

nospec

@Xylar Asay-Davis

 

pyflann

nospec

@Xylar Asay-Davis

 

pyremap

nospec

@Xylar Asay-Davis

 

pytest

nospec

@Xylar Asay-Davis

 

pywavelets

nospec

@Luke Van Roekel

 

shapely

nospec

@Jill Chengzhu Zhang

 

sympy

nospec

@Xylar Asay-Davis

 

tabulate

nospec

@Xylar Asay-Davis

 

xarray

2023.5.0

@Xylar Asay-Davis

 

xesmf

nospec

@Jill Chengzhu Zhang

 

Next versions

To request changes to package versions, please change the version below and mark them in bold.  

To request a new package, please add a row at the bottom  of either "Main Packages" or "Dependencies" and and mark both the package name and version bold.  

Use "nospec" for packages where conda should automatically choose the version (typically the latest).

e3sm-unified 1.10.0

Release candidate testing start date: 

Apr 15, 2024 

 

Release date:

Apr 29, 2024 

We are pushing this up so it can include new features needed for the E3SM tutorial

Main Packages

package

version

maintainer(s)

Notes

python

>=3.9,<3.11

@Xylar Asay-Davis

Default python version (used for supported machines) will be 3.10

R

no spec

@Sinha, Eva

 

chemdyg

1.0.0

@Hsiang-He Lee @Qi Tang

 

e3sm_diags

2.12.0 not released yet

@Jill Chengzhu Zhang

 

e3sm_to_cmip

1.11.2

@Anthony Bartoletti @Tom Vo @Jill Chengzhu Zhang

 

e3sm-tools

3.0.0

@Xylar Asay-Davis

A set of tools used to integrate new meshes into E3SM:

  • cube_to_target, gen_domain, interpinic, mksurfdata_map, runoff_to_ocn, squadgen

geometric_features

1.3.0

@Xylar Asay-Davis

 

globus-cli

nospec

@Lukasz Lacinski

 

ilamb

2.7

@Michael Kelleher

With system MPI on compute nodes

ipython

nospec

@Jill Chengzhu Zhang

 

jupyter

nospec

@Jill Chengzhu Zhang

 

livvkit

3.0.1

@Michael Kelleher

 

mache

1.21.0

@Xylar Asay-Davis

 

moab

5.5.1

@Vijay M

With system MPI on compute nodes

mpas-analysis

1.11.0

@Xylar Asay-Davis

 

mpas_tools

0.33.0

@Xylar Asay-Davis

 

nco

5.2.4

@Charlie Zender

With system MPI on compute nodes

pcmdi_metrics

2.3.1

@Jill Chengzhu Zhang

 

tempest-remap

2.2.0

@Xylar Asay-Davis

With system compilers on compute nodes

tempest-extremes

2.2.1

@Xylar Asay-Davis
@Jill Chengzhu Zhang

With system MPI on compute nodes

uxarray

>=2024.02.01

@Jill Chengzhu Zhang

Xarray-styled package for reading and directly operating on unstructured grid datasets https://github.com/UXARRAY/uxarray

Note: holoview visualization library is one of uxarray’s dependencies

xcdat

0.7.0

@Tom Vo

 

zstash

1.4.3

@Ryan Forsyth

 

zppy

2.5.0 not released yet

@Ryan Forsyth

 

mkdoc dependencies

package

version

maintainer(s)

 

mkdocs-material

nospec

@Naser Mahfouz

 

pymdown-extensions

nospec

@Naser Mahfouz

 

mkdocs-monorepo-plugin

nospec

@Naser Mahfouz

 

mdutils

nospec

@Naser Mahfouz

 

mkdocs-bibtex

nospec

@Naser Mahfouz

 

mkdocs-redirects

nospec

@Naser Mahfouz

 

markdownlint-cli2

nospec

@Naser Mahfouz

NOTE: only available through mahf708 channel now (PR into conda-forge pending). Use -c mahf708 to get it. The package was uploaded from the conda-forge/staged-recipes PR (not build locally). https://anaconda.org/mahf708/markdownlint-cli2. I verified it worked on my local machine as well as on chrysalis as expected.

Dependencies

package

version

maintainer(s)

 

blas

nospec

@Xylar Asay-Davis

 

bottleneck

nospec

@Xylar Asay-Davis

 

cartopy

>=0.17.0

@Jill Chengzhu Zhang

 

cdat_info

8.2.1

@Jill Chengzhu Zhang

 

cdms2

3.1.5

@Jill Chengzhu Zhang

 

cdtime

3.1.4

@Jill Chengzhu Zhang

 

cdutil

8.2.1

@Jill Chengzhu Zhang

 

cmocean

nospec

@Xylar Asay-Davis

 

dask

2023.6.0

@Xylar Asay-Davis 

 

dogpile.cache

nospec

@Chris Golaz

 

eofs

nospec

@Luke Van Roekel

 

esmf

8.6.0

@Xylar Asay-Davis

With system MPI on compute nodes

esmpy

8.6.0

@Xylar Asay-Davis

 

f90nml

nospec

@Xylar Asay-Davis

 

ffmpeg

nospec

@Xylar Asay-Davis @Luke Van Roekel

 

genutil

8.2.1

@Jill Chengzhu Zhang

 

globus-sdk

nospec

@Lukasz Lacinski

 

gsw

nospec

@Xylar Asay-Davis

 

hdf5

1.14.3

@Jill Chengzhu Zhang

@Xylar Asay-Davis

 

ipygany

nospec

@Erika Roesler

 

libnetcdf

4.9.2

@Xylar Asay-Davis

 

lxml

nospec

@Xylar Asay-Davis

 

matplotlib

3.8.2

@Jill Chengzhu Zhang

@Xylar Asay-Davis

 

metpy

nospec

@Jim Benedict

 

mpi4py

nospec

@Xylar Asay-Davis

With system MPI on compute nodes

nb_conda

nospec

@Jill Chengzhu Zhang

 

ncview

2.1.8

@Jill Chengzhu Zhang

 

ncvis

2023.09.12

@Jill Chengzhu Zhang

 

nc-time-axis

nospec

@Naser Mahfouz

Nifty package to correctly plot the time axis with xarray

netCDF4

1.6.4 nompi

@Xylar Asay-Davis

 

numpy

>1.13

@Xylar Asay-Davis

 

output_viewer

1.3.1

@Jill Chengzhu Zhang

@Ryan Forsyth

 

pillow

nospec

@Xylar Asay-Davis

 

plotly

nospec

@Xylar Asay-Davis

 

progessbar2

nospec

@Xylar Asay-Davis

 

proj

9.3.1

@Xylar Asay-Davis

 

pyproj

3.6.1

@Jill Chengzhu Zhang

@Xylar Asay-Davis

 

scikit-image

nospec

@Xylar Asay-Davis

 

scipy

nospec

@Xylar Asay-Davis

 

pyevtk

nospec

@Xylar Asay-Davis

 

pyflann

nospec

@Xylar Asay-Davis

 

pyremap

nospec

@Xylar Asay-Davis

 

pytest

nospec

@Xylar Asay-Davis

 

pywavelets

nospec

@Luke Van Roekel

 

r-tidyverse

nospec

@Sinha, Eva

 

r-dplyr

1.0.10

@Sinha, Eva

 

r-ggplot2

nospec

@Sinha, Eva

 

shapely

nospec

@Jill Chengzhu Zhang

 

sympy

nospec

@Xylar Asay-Davis

 

tabulate

nospec

@Xylar Asay-Davis

 

windpharm

nospec

@Jill Chengzhu Zhang

https://pypi.org/project/windspharm/ spherical harmonic vector wind analysis in Python

xarray

2023.5.0

@Xylar Asay-Davis

 

xesmf

nospec

@Jill Chengzhu Zhang