Jaspy Software Environments (Python 3, R and other tools)
This page provides details of the "Jaspy" software environments that provide access to Python 3, R and a range of other tools on JASMIN. The article includes:
- Working with Jaspy environments
- Discovering which environments are available
- Jaspy Python (and other tools) environments
- Jaspy R environments (Jasr)
- How Jaspy works
- Changes to software environments
Working with Jaspy environments
Quickstart for Python 3 environment
module load jaspy
Activating the environment in scripts
If you want a particular script to activate a Jaspy environment then add the "module" command to it, e.g.:
#!/bin/bash module load jaspy python do-something.py
Setting your profile to always use a Jaspy environment
If you want all your JASMIN sessions to use a particular Jaspy environment then you can add the "module load jaspy" command to your ".bashrc" file at: $HOME/.bashrc . In order to avoid issues with using "module load" on unsupported servers, please wrap the call in an "if" clause, such as:
if [[ $(hostname) =~ (sci[0-9]|host[0-9]|cylc) ]] ; then module load jaspy fi
Discover which environments are available
$ module avail jaspy ----------- /apps/modulefiles ------------- jaspy/2.7/r20190715 jaspy/3.7/r20181219 jaspy/3.7/r20190612 jaspy/3.7/r20190627 jaspy/3.7/r20200606 jaspy/3.7/r20210320 jaspy/3.8/r20211105
This lists all jaspy modules (i.e. environments) that can be loaded.
Jaspy Python 3.7+ (plus other tools) environments
|Jaspy Python 3.7 Environment||Versioned list of software packages||Default?||Comments / Issues|
|jaspy/3.8/r20211105||List of packages including versions||Yes (from 16/11/2021)||Known problem with NCL rendering Shapefiles (see issue). Some packages were removed in this release due to dependency problems: theano, pymc3, pystan, pyngl, pyferret (see issue).|
|jaspy/3.7/r20210320|| List of packages including versions
|| No (was default:
20/05/2021 - 16/11/2021)
|Known problem with NCL rendering Shapefiles (see issue)|
|jaspy/3.7/r20200606||List of packages including versions||No|
||List of packages including versions||No|
Jaspy Python 2.7 (plus other tools)
This table lists all the Jaspy Python 2.7 environments provided on JASMIN and specifies the current (default) version.
|Jaspy Python 2.7 Environment||Versioned list of software packages||Default?|
|jaspy/2.7/r20190715|| List of packages including versions
Jaspy R environments (Jasr)
Environments for the "R" programming language are packaged into separate software environments, known as "Jasr". This table lists all the Jaspy R environments provided on JASMIN and specifies the current (default) version.
|Jaspy R Environment ("Jasr")||Versioned list of software packages||Default?|
|jasr/4.0/r20211110||List of packages including versions||Yes|
The available R environments can be listed with:
module avail jasr
Understanding Jaspy versioning
module load jaspy/3.7/r20210320
module load jaspy/3.7
module load jaspy
How Jaspy works: managing Python and non-Python packages using conda
Jaspy is a framework for managing multiple Python (and other) environments simultaneously on a single platform. It was created in order to meet the requirements tabulated below.
|Requirement||Details||Jaspy solution||Further info|
|| Conda: https://docs.conda.io
CEDA jaspy environments: https://github.com/cedadev/ceda-jaspy-envs
|Documentation||Provide an appropriate level of documentation detailing which software packages exist in each release.||We use Conda "environment files" to build the environments. These list the packages and versions and are stored in public GitHub repositories so each environment is documented as a collection of packages/versions.|| See: https://github.com/cedadev/jaspy-manager/blob/master/README.md
Example package list: https://github.com/cedadev/ceda-jaspy-envs/blob/master/environments/py3.7/m3-4.5.11/jaspy3.7-m3-4.5.11-r20181219/packages.txt
|Multiple simultaneous environments||Allow multiple, but separate, software environments to co-exist on a single operating system.|| Conda is designed to allow multiple environments to co-exist. Within jaspy it is possible to document each environment. Therefore, multiple environments can be deployed on one system. Key advantages are:
|Manageability||Provide tools to easily construct, test, deploy, document and reproduce software environments.||Jaspy builds upon a set of excellent Conda command-line tools that simplify the package management process. Jaspy wraps the Conda functionality so that command-line tools can be used to build, test, deploy and distribute Conda environments for use by our community.|
Updates and tracking of Jaspy environments
History of Jaspy environments on JASMIN
Which Jaspy environment is "current"?
Please refer to the "Jaspy Python 3.7+ (and other tools)" section above for information about the current release on JASMIN.
Citing Jaspy environments
Can I cite a jaspy (conda) environment?
- E-mail the JASMIN Helpdesk with the subject: "Request for Jaspy update: <package name>"
- Get a GitHub account and add an issue to the `ceda-jaspy-envs` repository at:
Conda method of "activating" Jaspy environments
$ export PATH=/apps/jasmin/jaspy/miniconda_envs/jaspy3.7/m3-4.6.14//bin/conda:$PATH $ source activate jaspy3.7-m3-4.6.14-r20210320
Using Jaspy beyond JASMIN
Jaspy is a versatile and generic tool for managing multiple conda environments. The code is open source and more information is available at: