Anaconda on DARWIN

$ vpkg_versions anaconda
Available versions in package (* = default version):
anaconda           Open Enterprise Python
* 5.3.1:python2    Anaconda Python2
  5.3.1:python3    Anaconda Python3
  2020.11:python3  Anaconda Python3 (Python 2 deprecated)

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

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/5.2.0:python3
Adding package `anaconda/5.2.0: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
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.5.11
  latest version: 4.8.1

Please update conda by running

    $ conda update -n base -c defaults conda

## 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:
# > source activate /home/1201/fenicsproject
# To deactivate an active environment, use:
# > source deactivate

[traine@login00 ~]$ workgroup -g it_css
[(it_css:traine)@login00 ~]$ salloc --partition=devel
salloc: Pending job allocation 5434421
salloc: job 5434421 queued and waiting for resources
salloc: job 5434421 has been allocated resources
salloc: Granted job allocation 5434421
salloc: Waiting for resource configuration
salloc: Nodes r00n56 are ready for job
[traine@r00n56 ~]$ vpkg_devrequire anaconda/5.2.0:python3
Adding package `anaconda/5.2.0:python3` to your environment
[traine@r00n56 ~]$ source activate ~/fenicsproject
(/home/1201/fenicsproject) [traine@r00n56 ~]$ python3 -c "import mshr"
(/home/1201/fenicsproject) [traine@r00n56 ~]$ source deactivate
[traine@r00n56 ~]$ exit
salloc: Relinquishing job allocation 5434421
[(it_css:traine)@login00 ~]$

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.

  • software/anaconda/darwin.txt
  • Last modified: 2021-09-30 14:02
  • by anita