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Merge branch 'anaconda-docu-upd-20201019' into 'master'

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Update anaconda README.md with information on logging

See merge request Pmodules/buildblocks!127
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feichtinger
2020-10-19 10:59:44 +02:00
parent b453afe51e 2ed35423d2
commit 1ccc73bf65
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Programming/anaconda/README.md
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@@ -75,14 +75,15 @@ This works if the python package has a correct setup.py build
cd /opt/psi/Programming/anaconda/2019.07/xxxx/mypackage
pip install .
```
## Building for use with jupyter
Jupyter can discover conda environments if the environment contains the **nb_conda_kernels** package.
Jupyter can discover conda environments if the environment contains the **nb_conda_kernels** package.
Regrettably the environment activation by this package does not run through the full process as compared to the command line functions. The activation scripts that can be placed in an environment do not get executed (q.v. my bug report https://github.com/Anaconda-Platform/nb_conda_kernels/issues/145).
In order to fix this, we must use a workaround which involves modifying the kernel spec configuration file of the environment to wrap the call to the python kernel like in this example for `.../envs/mpi-test/share/jupyter/kernels/python3/kernel.json`:
```
```
{
"argv": [
"/opt/psi/Programming/anaconda/2019.07/admintools/kernelwrapper.sh",
@@ -96,13 +97,25 @@ In order to fix this, we must use a workaround which involves modifying the kern
"display_name": "Python 3",
"language": "python"
}
```
```
In order to modify an environment easily I wrote a tool found in the `admintools` of this buildblock which you can use as follows:
```
files/admintools/install-kernelwrapper.py -v /opt/psi/Programming/anaconda/2019.07/conda/envs/hep_root
```
```
files/admintools/install-kernelwrapper.py -v /opt/psi/Programming/anaconda/2019.07/conda/envs/hep_root
```
### Logging of environment activation information
The logging of information for the usage of central environments is
important, because it allows to do lifetime management of the conda
environments. We can find out whether a particular environment is used at all
and by whom, and can so plan the decommissioning.
Logging is currently implemented by an activation hook script that gets placed
in each environment. This is done by running the script `.../files/admintools/install-env-loggers.sh`
which will loop over all central environments of this anaconda pmodule.