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Anaconda

On ManaKoa, modules for Anaconda exist.  These modules are provided so that users do not need to install their own copy of anaconda or miniconda.  While this may provide convenience  to many users, for those that require full control over their conda version, please look at the MiniConda guide.

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To build an conda environment on ManaKoa, one would first start an interactive session and then load the specific Anaconda module they wish to use.  Take note of the module you use, since you will need to load the anaconda module each time you wish to use anaconda and you may want to use the same or newer version.

[user@login001 ~]$ srun -p sandbox --mem=6G -c 2 -t 60 --pty /bin/bash
[user@node-0005 ~]$ module load  lang/Anaconda3/2019.07
[user@node-0005 ~]$ condamamba create -n ipyrad -c conda-forge -c bioconda ipyrad

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[user@node-0005 ~]$ condamamba create -n test -c conda-forge -c conda  python=3.8 matplotlib scipy ipython

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While a base anaconda module exists for users to access and build their own conda environments, this is not the only way.  Below you will find instructions created by Eric Firing covering an alternate method in which you can use miniconda on Mana Koa instead of the Anaconda module.

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1. The user has no ability to install system-level packages. Instead, the administrators install packages together with modules that the user can load to put those packages on the user’s path, thereby making them accessible.

2. The user cannot write to the user’s own .bashrc file, even though the standard Linux permissions for the file show the file as user-writable. Writing is blocked at a different level.

3. Some libraries must be compiled specifically for HPC use, so packages from conda-forge using the Message Passing Interface (MPI) might not work correctly. See this note on MPI in conda-forge. I don’t know how this applies to the ManaKoa.

The Mana Koa admins have created a module giving access to a base Anaconda environment at the system level, meaning the user cannot change anything in that environment. It is possibly, however, to use that as a base environment for the creation of new working environments in the user’s directory tree (specifically, hidden in the ~/.conda/ subdirectory). This still has some disadvantages compared to using a normal Miniconda installation; primarily, that conda itself (which must live in the base environment) cannot be updated, and that the newer method of activating and deactivating environments with conda is unavailable.

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. /optusr/ohpcshare/admin/lmod/lmod/init/zsh # Needed to run modules in zsh.

Now log out completely, log back in, and start an interactive session on a compute node. Download the Miniconda installer:

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