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habrok:examples:mamba [2024/12/12 07:08] – fokkehabrok:examples:mamba [2024/12/12 07:21] (current) – [Manual Mamba initialization] fokke
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 Mamba (https://mamba.readthedocs.io/en/latest/index.html) is an alternative to Anaconda, which is released under an open source license. In order to use it on Hábrók you can install it into your home directory. This can be done following the instructions on their website. There is an important **caveat**, however, which is that you should **NOT** let it start up the base environment on log in, as that would break any other Python software on the cluster. Mamba (https://mamba.readthedocs.io/en/latest/index.html) is an alternative to Anaconda, which is released under an open source license. In order to use it on Hábrók you can install it into your home directory. This can be done following the instructions on their website. There is an important **caveat**, however, which is that you should **NOT** let it start up the base environment on log in, as that would break any other Python software on the cluster.
 +
 +In general Mamba and conda environments cannot be used together with **any** of our preinstalled software modules that depend on Python.
  
 Please also note, that you should only use mamba/conda repositories that have licenses that allow your intended usage. Please also note, that you should only use mamba/conda repositories that have licenses that allow your intended usage.
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 <code> <code>
 mamba config --set auto_activate_base false mamba config --set auto_activate_base false
 +</code>
 +  * In case you want to use the base environment, you can reactivate it using:
 +<code>
 +mamba activate base
 </code> </code>
  
-==== Tips and tricks ====+==== Manual Mamba initialization ====
  
-  * In case you did not let Mamba change your login scripts, manual activation of the initial mamba/conda environment can be achieved using the following commands:+In case you did **not** let Mamba change your login scripts during the installation, manual activation of the initial mamba/conda environment can be achieved using the following commands:
 <code> <code>
-. $HOME/miniforge3/etc/profile.d/conda.sh +. ~/miniforge3/etc/profile.d/conda.sh 
-. $HOME/miniforge3/etc/profile.d/mamba.sh+. ~/miniforge3/etc/profile.d/mamba.sh
 </code> </code>
-  * You can activate the base environment using: +Note that you have to run these every time you want to use Mamba. 
-<code> + 
-mamba activate base +==== Modifying the login profile ===== 
-</code> + 
-  * In order to undo the login profile modifications for mamba you can use the following command, where bash is your actual command line shell:+In order to undo the login profile modifications for mamba you can use the following command, where bash is your actual command line shell:
 <code> <code>
 mamba init --reverse bash mamba init --reverse bash
 </code> </code>
-You can reverse this, to have mamba available on login, using:+ 
 +You can reverse the previous step, to have mamba available on login, using:
 <code>  <code> 
 ~/miniforge3/bin/mamba init ~/miniforge3/bin/mamba init
 </code> </code>