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Note

This page relates to if users wish to install Miniconda3 locally, instead of using the provide module on our clusters.

Table of Contents
stylenone

...

Info

Yes. You can install miniconda3 (and other applications) yourself. There is nothing wrong or against policy with this.

Note

If you do install it, please make sure you:

  • understand what

your

  • you are doing

,

  • .

  • how it affects your environment

,

  • .

  • and track/record what you’ve done and why.

Warning

Since you are intentionally effecting your environment, you need to take a level of responsibility to mange and work with this.

Expand
titleGeneral Installation Process
Code Block

[<username>@mblog2 ~]$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
[<username>@mblog2 ~]$ bash Miniconda3-latest-Linux-x86_64.sh
Welcome to Miniconda3 py312_24.7.1-0
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
...
Do you accept the license terms? [yes|no]
>>> yes

Miniconda3 will now be installed into this location:
/home/<username>/miniconda3

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/home/<username>/miniconda3] >>>
PREFIX=/home/<username>/miniconda3
Unpacking payload ...
Installing base environment...
Downloading and Extracting Packages:
## Package Plan ##
  environment location: /home/<username>/miniconda3
...
installation finished.

Do you wish to update your shell profile to automatically initialize conda?
This will activate conda on startup and change the command prompt when activated.
If you'd prefer that conda's base environment not be activated on startup,
   run the following command when conda is activated:

conda config --set auto_activate_base false

You can undo this by running `conda init --reverse $SHELL`? [yes|no]
[no] >>> yes
no change     /home/<username>/miniconda3/condabin/conda
no change     /home/<username>/miniconda3/bin/conda
no change     /home/<username>/miniconda3/bin/conda-env
no change     /home/<username>/miniconda3/bin/activate
no change     /home/<username>/miniconda3/bin/deactivate
no change     /home/<username>/miniconda3/etc/profile.d/conda.sh
no change     /home/<username>/miniconda3/etc/fish/conf.d/conda.fish
no change     /home/<username>/miniconda3/shell/condabin/Conda.psm1
no change     /home/<username>/miniconda3/shell/condabin/conda-hook.ps1
no change     /home/<username>/miniconda3/lib/python3.12/site-packages/xontrib/conda.xsh
no change     /home/<username>/miniconda3/etc/profile.d/conda.csh
modified      /home/<username>/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

Thank you for installing Miniconda3!
[<username>@mblog2 ~]$

Should I Install Miniconda3 Locally?

...

Ask yourself “what does a local installation benefit me over using the provided miniconda3 module?”

Info

There are might be reasons why you might need to install this yourself, just make sure you can communicate why, and that you understand what you are doing to your environment - and take responsibility for this.

If you can not answer this, then use the version that ARCC provides as a module.

Note

If you can answer this, please be prepared to answer the next question.

...

If you can not answer this, then ARCC will suggest that your uninstall this and use the provide miniconda3 module.

We support this module and understand how it should be working and can typically resolve your issues.

...

How Do I Know if Miniconda3 Has Been Installed Locally?

...

Info

Step 3: On the start of your next session, the command prompt should return to normal:

Code Block
[<username>@mblog2 ~]$

...

Job Submission Error

Note

We can not guarantee that what ever conda environments you have activate on the login nodes will be inherited when you submit a job using sbatch.

You will errors of the form:

Code Block
# Within Submission Script:
...
conda activate <path-to-conda-environment>
...

within the slurm output you will see:

Code Block
...
CondaError: Run 'conda init' before 'conda activate'
...

...

Info

ARCC recommends using the versions of miniconda3 provided as a module, and use a submission script of the form:

Code Block
...
module purge
module load miniconda3/<version>
conda activate <path-to-conda-environment>
...

...

ARCC Related Conda Workshops

Before moving forward, ARCC has the following workshops

We would highly recommend working through at least the first one to understand how to use conda effectively.