Anaconda on Caviness

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

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 Caviness 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/caviness.txt
  • Last modified: 2021-09-30 13:59
  • by anita