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Anaconda

On Mana, modules for Anaconda

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Installing/creating a ipyrad virtual environment

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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.

While the modules for Anaconda can simplify using conda install software, it does have at least two things that you should be aware of:

1. The conda version is updated using newer modules, so some packages may be out of date compared to the latest available version
2. Not all of the latest commands work with the Anaconda modules.  The most visible case of this is how one activates and deactivates a conda environment.

To build an conda environment on Mana, 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

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 /bin/bash

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Loading & executing the ipyrad environment

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srun -p sandbox --mem=6G -c 2 -t 60 --pty /bin/bash
module load lang/Anaconda2
source activate ipyrad
export HOME=/tmp/ (ipyrad specific)
ipcluster start --n ${SLURM_CPUS_PER_TASK} --daemonize (ipyrad specific)
sleep 200 (ipyrad specific)
ipyrad -p params.txt -s 1234567 -c ${SLURM_CPUS_PER_TASK} --ipcluster (ipyrad specific)

NOTE: Contrary to what Anaconda might say after you create a new environment you need to use source activate and NOT conda activate on Mana.

[user@node-0005 ~]$ module load  lang/Anaconda3/2019.07
[user@node-0005 ~]$ conda create -n ipyrad -c ipyrad ipyrad

Once anaconda is loaded, you will now be able to create an anaconda environment, using the conda  create command.  In the example below, we will be naming our conda environment "test" and temporarily adding the conda channel of "conda-forge", while trying to install "

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

Once the environment is installed, it can be activated using "source activate test", or the generic form of "source activate [name of conda environment ]".

[user@node-0005 ~]$ source activate test
(test) [user@node-0005 ~]$ conda deactivate
[user@node-0005 ~]$ 

MiniConda

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 instead of the Anaconda module.

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conda create -n py38 python=3.8 matplotlib scipy ipython 
conda activate py38

Of course, any time you can use conda to add more packages, use pip to install packages that are not available from conda-forge, make and populate new environments, etc. Just be careful to activate whichever environment you want to work with.

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