wiki:access/BomAccessDocumentation/bom-conda

Version 7 (modified by Vinod Kumar, 4 months ago) (diff)

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BoM Conda Package and Environment Management

Motivation

An effort to set up a centralised, consultative, consolidated python-conda environment has been undertaken in the BoM/NWP (Atmospheric Modelling and Data Assimilation) section, which encompass all the packages we use for our work. This shared conda environment can be an entirely new one or an environment layered upon an existing one (conda/analysis27-18.07 or conda/analysis3-18.04). Some of the potential advantages of having such a shared environment is:

  1. Writing codes which are transferrable between team members.
  2. Eliminate potential for duplicate personal python environments
  3. Implicit sharing of information. Allows you to dodge issues that has been already tackled by someone else earlier (i.e., compatible packages already installed and tested).
  4. Save you from loading multitudes of python modules and figuring out compatibilities.
  5. Prevent further proliferation of python modules available under ~access/modules (as it stands there are about 141 python packages under ~access/modules).
  6. Possibly easy for ITOs to manage.
  7. Allows you to set up, test and use your own new/additional packages, on top of this environment. This allow you to still get on with your work, until an ITO find some time to install the requested package.

Current problems encountered when using Python, Python packages, Python tools

PS global suites

  • PS global suites use scitools for some tasks. Some examples of how scitools versions are used,
PS scitools version used
PS41 global standard suite production-os41-1
PS42 global standard suite scitools/production_legacy-os42-1

We have no way of knowing what Python version, Python packages and their versions and other Python tools and their versions were used.

ACCESS-C (UKV) suites

PS scitools version used
PS43 MOGREPS-UK component trial suite scitools/production_legacy-os42-1

Global Evaluation Suite (GES)

  • GES uses Python and its standard packages in addition to some UKMO-developed Python tools such as VerPy and BoiteNoire (a part of VarPy)
  • The GES suite sets up Python environment using either,
module load scitools

or

module load scitools/default-previous

But this gives no indication what packages are in the UKMO mofulefile, scitools. It's often an educated guess or trial-and-error when we port GES trying to figure out which versions of packages are used

  • UKMO GES suite developers use these Python packages and tools quite indepedently of RES suite developers and so the Python environment in GES is different to the Python environment in RES

Regional Evaluation Suite (RES)

The current version of RES in MetOffice uses the following module

scitools/production-os41-1

After lengthy testing in relation to RES porting, Vinod/Wenming? has set up the following module consisting of various python packages to run RES at NCI

rmedtools/1.0.0

obsmon

  • Apart from standard library packages, direct use is made of numpy, matplotlib, netCDF4, cartopy and odbserver. odbserver is not available through conda download, it is installed separately.
  • odbserver is sensitive to the compiler environment. If the version of gcc (for the underlying C++ code) is not compatible with the installation version then a Exception: Can't find libOdb.so error is raised.
  • Cartopy is usually made available through iris and that has some compatibility issues as noted elsewhere. Some versions of cartopy have issues with some versions of matplotlib. See varpy ticket 67 and varpy ticket 185 for examples.
  • Cartopy requires data files that are automatically downloaded into a user's .local directory if the are not found in a pre-installed location. This must be avoided as it will break any suites that do not run cartopy on a data-mover node (i.e., all of them) as shared and compute nodes do not have external access. A shared location for these files (that is defined in the installed package) is essential.
  • The sphinx package, pep8, and associated modules are used for automatic documentation generation and code tidying respectively. These are not required in the operation of the code but they are for admin purposes in varpy. Sphinx and pep8 are part of the Met Office scitools environment.

Vision

Our Python environment will be identical to UKMO scitools and so Python, Python packages and Python tools within GES, RES and obsmon will work at NCI without any modifications and tweaking.

A possible solution

There's a discussion going on within UKMO and across the partnership about a portable Python environment (see the section under the heading, "Useful information" below). One of the ideas proposed is some kind of containerised environment, but whatever solution UKMO comes up it will take some time before we can take advantage. As an interim solution we propose that,

At each release of a suite the relevant UKMO suite developer publishes following information (preferrably in a yml file),

  • Python version used
  • a list of Python packages and their versions
  • a list of Python tools and their versions

The agreement to do this and a new working practice can be discussed through TISD workpackage.

Installations and Related Documentations

Base installations

Various family of environments

Useful information

Things to do

  • Ask Mike Thurlow and Adam Martins what version of scitools were used in global and GES suites