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Merge branch '36-fix-unloading-of-anaconda-environments-mixing-bash-tcl-in-unloader' into 'master'

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Resolve "fix unloading of anaconda environments (mixing bash & tcl in unloader)"

Closes #36

See merge request Pmodules/buildblocks!42
This commit is contained in:
feichtinger
2019-09-09 17:09:18 +02:00
parent 3ba6ea2254 9e2060c297
commit 27dcc1e535
2 changed files with 17 additions and 9 deletions
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6
Programming/anaconda/README.md
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@@ -3,7 +3,7 @@
## Concepts
* The anaconda module just provides the **conda** package management tool together with its directory infrastructure which contains *conda environments* and a cache of downloaded packages
* Python and user software is provided in **conda environments**. These environments are located within the directory tree belonging to the anaconda module, e.g. `/afs/psi.ch/sys/psi.merlin/Programming/anaconda/2019.03/conda/envs/`
* Python and user software is provided in **conda environments**. These environments are located within the directory tree belonging to the anaconda module, e.g. `/afs/psi.ch/sys/psi.merlin/Programming/anaconda/2019.07/conda/envs/`
* The software in these environments can be accessed by users through
1) loading the anaconda module and then using `conda activate somemodule_py36`
1) a seperate pmodule that transparently switches to that installed environment by just setting the correct PATH to the python binary.
@@ -21,14 +21,14 @@
In the simplest case, the environment can be created by conda alone. First load the anaconda module to get access to the conda package installer and the install environment.
```
module load anaconda/2019.03
module load anaconda/2019.07
```
Define your installation in a `conda YAML` file and place it inside the buildblock
tree
```
cd buildblocks/Programming/anaconda/2019.03/conda-env-defs
cd buildblocks/Programming/anaconda/2019.07/conda-env-defs
mkdir datascience_36
vim datascience_36/datascience_36.yml
```

20
Programming/anaconda/modulefile
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@@ -69,14 +69,22 @@ switch [module-info mode] {
if { [dict get $option -code] != 0 } {
puts stderr "Error: cannot cleanly unload anaconda: conda is not in the PATH"
} else {
# if the user has invoked this from a subshell, the conda functions may
# not be defined, so we need to reload the environment
puts stdout {if [[ x$(command -v conda) != xconda ]];then source $(conda info --base)/etc/profile.d/conda.sh; fi;}
# if the user has invoked this from a subshell, the conda
# functions may not be defined even though a conda
# executable is still in the path ! One could try the
# following, but currently we leave it commented.
# puts stdout {if [[ x$(command -v conda) != xconda ]];then source $(conda info --base)/etc/profile.d/conda.sh; fi;}
# Deactivate all layers of active conda environments
puts stdout {while [[ "${CONDA_SHLVL:-0}" -gt 0 ]]; do conda deactivate; done;}
# If the conda env is intact (conda defined as a function), then
# deactivate all layers of active conda environments
puts stdout {if [[ x$(command -v conda) == xconda ]]; then while [[ "${CONDA_SHLVL:-0}" -gt 0 ]]; do [[ $PMODULES_DEBUG == 1 ]] && echo "unloading conda env $CONDA_DEFAULT_ENV..." >&2; conda deactivate; [[ $PMODULES_DEBUG == 1 ]] && echo $PATH >&2; done; fi;}
# the path cleaning cannot use tcl remove-path, since at this point tcl
# is not aware that the above bash statements will have modified the path
# upon the eval that is done by the outer "module" function.
puts stdout {PATH=$(echo $PATH| tr ':' '\n' | grep -v "$mydel" | tr '\n' ':'); export PATH=${PATH%:};}
remove-path PATH $PREFIX/conda/condabin
# remove the conda function definitions
unsetenv __conda_activate
unsetenv __conda_hashr