Table of Contents

Anaconda on DARWIN

$ vpkg_versions anaconda
 
Available versions in package (* = default version):
 
[/opt/shared/valet/2.1/etc/anaconda.vpkg_yaml]
anaconda           Open Enterprise Python
* 5.3.1:python2    Anaconda Python2
  5.3.1:python3    Anaconda Python3
  2020.11:python3  Anaconda Python3 (Python 2 deprecated)
  2022.05:python3  Anaconda Python3 (Python 2 deprecated)
  2023.03:python3  Anaconda Python3 (Python 2 deprecated)
  2024.02:python3  Anaconda Python3 (Python 2 deprecated)

See Recipes for examples of building virtual environments for specific packages.

Virtual Environment

If you are going to follow the instructions for creating an Anaconda virtual environment on DARWIN consider using a slight modification to the documentation provided by each software package and use VALET to load the proper version of Anaconda for Python 2 or Python 3, specify a path in your home ($HOME) or workgroup ($WORKDIR) directory not in the system path for Anaconda, and also ignore the warnings to update conda as it is building your virtual environment.

See the example below which creates a virtual Anaconda environment based on Python 3 for FEniCS called fenicsproject in the traine home directory and installs all the fenics packages and mshr. Once the environment is created, then a simple interactive test is done on a compute node via the devel partition to verify the new fenicsproject Anaconda environment is working properly. 

[traine@login00 ~]$ vpkg_devrequire anaconda/2024.02:python3
Adding package `anaconda/2024.02:python3` to your environment
[traine@login00 ~]$ conda create -p ~/fenicsproject -c conda-forge fenics fenics-dijitso fenics-dolfin fenics-ffc fenics-fiat fenics-libdolfin fenics-ufl mshr
Retrieving notices: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/1201/fenicsproject

  added / updated specs:
    - fenics
    - fenics-dijitso
    - fenics-dolfin
    - fenics-ffc
    - fenics-fiat
    - fenics-libdolfin
    - fenics-ufl
    - mshr


The following packages will be downloaded:
...
...
...
Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
...
...
...
#
# To activate this environment, use:
# > conda activate /home/1201/fenicsproject
#
# To deactivate an active environment, use:
# > conda deactivate
#

[traine@login00 ~]$ workgroup -g it_css
[(it_css:traine)@login00 ~]$ salloc --partition=idle
salloc: Pending job allocation 5275439
salloc: job 5275439 queued and waiting for resources
salloc: job 5275439 has been allocated resources
salloc: Granted job allocation 5275439
salloc: Waiting for resource configuration
salloc: Nodes r1n00 are ready for job
[traine@r1n00 ~]$ vpkg_devrequire anaconda/2024.02:python3
Adding package `anaconda/2024.02:python3` to your environment
[traine@r1n00 ~]$ conda activate ~/fenicsproject
(/home/1201/fenicsproject) [traine@r1n00 ~]$ python3 -c "import mshr"
(/home/1201/fenicsproject) [traine@r1n00 ~]$ conda deactivate
[traine@r1n00 ~]$ exit
logout
salloc: Relinquishing job allocation 5275439
[(it_css:traine)@login00 ~]$

Recipes

Examples documented as recipes to be used for specific installations including using a workgroup directory as well as creating VALET packages for these environments and job scripts setup for batch runs, but can also perhaps help others in solving similar installation dilemmas.