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)
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/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
exit
salloc: Relinquishing job allocation 5434421
[(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.
- Gurobi Python Virtual Environments