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working_with_python [2020/10/05 10:29] – [METHOD 3: easy_install] lenocil | working_with_python [2022/04/04 06:52] – jansen | ||
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export PYTHONUSERBASE=$HOME/ | export PYTHONUSERBASE=$HOME/ | ||
fi | fi | ||
- | For users of the '' | + | For users of the '' |
if (! -f / | if (! -f / | ||
setenv PYTHONUSERBASE $HOME/ | setenv PYTHONUSERBASE $HOME/ | ||
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virtualenv --help | virtualenv --help | ||
</ | </ | ||
+ | |||
==== METHOD 3: easy_install with the `--user' | ==== METHOD 3: easy_install with the `--user' | ||
Easy Install is a python module (easy_install) that lets you automatically download, build, install, and manage Python packages. | Easy Install is a python module (easy_install) that lets you automatically download, build, install, and manage Python packages. | ||
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python -m easy_install --help | python -m easy_install --help | ||
</ | </ | ||
+ | |||
+ | ==== Migrating packages between python versions ==== | ||
+ | Another issue when using personal installs may arrise on operating system upgrades, when a newer version of python is made the default (eg, moving from python 3.7 to python 3.9). | ||
+ | Notes copied from the [[https:// | ||
+ | - Make a list of installed packages in the old python version: | ||
+ | <code bash> | ||
+ | python3.7 -m pip freeze > installed.txt | ||
+ | </ | ||
+ | - Reinstall for the current python version: | ||
+ | <code bash> | ||
+ | python3.9 -m pip install --user -r installed.txt | ||
+ | </ | ||
+ | - Optionally, uninstall the packages from the old python version and/or remove the obsolete directory under $HOME/ | ||
===== Example: how to let python search arbitrary library paths ===== | ===== Example: how to let python search arbitrary library paths ===== | ||
- | Create/edit | + | For instance for python v2.7 installations, |
- | '' | + | '' |
- | by appending the path of your choice, for instance | + | by appending the path of your choice |
< | < | ||
- | echo "/ | + | echo "/ |
</ | </ | ||
All '' | All '' | ||
- | ===== Example: how to create | + | ===== Example: how to create |
- | First enable the module package to search also private module directories | + | Please read [[easybuild_environment|here]]. |
- | <code bash> | + | |
- | module load use.own | + | |
- | </ | + | |
- | the line above will create a $HOME/ | ||
- | |||
- | Let us now install some packages to an arbitrary location and upgrade (__only in $PYTHONUSERBASE__) an already system-wide installed package | ||
- | |||
- | <code bash> | ||
- | export PYTHONUSERBASE=/ | ||
- | pip install --user SomePackage | ||
- | pip install -I --user SomePackageThatWASInstalledSystemwide | ||
- | </ | ||
- | |||
- | Create a file, say `$HOME/ | ||
- | <code bash> | ||
- | #%Module 1.0 | ||
- | # | ||
- | # | ||
- | # | ||
- | prepend-path | ||
- | prepend-path | ||
- | </ | ||
- | |||
- | and type | ||
- | |||
- | <code bash> | ||
- | module load super-module | ||
- | </ | ||
- | and you are ready to use your newly created python environment. Note that is similar procedure can be repeated using python3. | ||
===== Example: numpy with openBLAS ===== | ===== Example: numpy with openBLAS ===== | ||
In this example we create a python2 virtual environment in which we will install the latest version of numpy that will use the openBLAS library. | In this example we create a python2 virtual environment in which we will install the latest version of numpy that will use the openBLAS library. | ||
- | :!: The procedure and paths below will work on any maris node and on the para cluster. | + | :!: The procedure and paths below will work on any maris node. |
<code bash> | <code bash> | ||
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====== Anaconda/ | ====== Anaconda/ | ||
Another way of using a private python install (separate versions etc), is to install and use [[conda|Anaconda/ | Another way of using a private python install (separate versions etc), is to install and use [[conda|Anaconda/ | ||
+ | |||
+ | |||
+ | ====== Jupyter Notebooks ====== | ||
+ | Depending on your operating system (Fedora or RedHat) you might get a different python kernel version as the standard kernel. If you get '' | ||
+ | python3 -m ipykernel install –user | ||
+ | Once this command has run successfully, | ||
+ | |||
+ | After starting '' |