Using the system miniconda 3 install
Using the system miniconda 3 install
I previously wrote about installing your own miniconda install here which I strongly suggest reading. However, after I received many questions about getting the conda set up properly, I decided to make the process of getting conda set up for you a bit easier.
I wrote a script that will:
- Ensure you are not installing to your home directory.
- Eliminate the need to download the miniconda installer.
- Reduce the burden of getting the channels set up and the proper envs and pkgs
settings in your
.condarc
The script will also make sure you have write permissions to the particular directory specified and won’t make changes unless you approve. Lastly, you can say that you’d prefer to run the commands yourself, and then copy/paste the commands into your own terminal.
Running the script
I made a new miniconda3 install here:
/local/cluster/miniconda3_base
This miniconda install will have only ever have the base packages installed and expects you to install any new conda packages in your own environments.
To get this conda setup for you to use, you can run this script:
/local/cluster/miniconda3_base/init_miniconda3 <PATH TO DESIRED CONDA DIR>
e.g.
/local/cluster/miniconda3_base/init_miniconda3 /nfs4/core/home/davised/opt/conda
This will generate the specified dir for you, if necessary, and then set up your
~/.bashrc
to access the new conda bin.
The script will confirm that you actually want to run the listed commands before running them. If you feel better about running the commands yourself, choose option 2 (No) from the list, and feel free to copy/paste them individually into your own terminal.
The script checks for your ~/.condarc
and backs it up, if desired. It also
lets you know if you have already cached environments in the ~/.conda
dir.
If the script is unable to generate the specified conda dir for you, it will not make any changes and instead exit the script.
As an aside, if you’ve accidentally run the conda init
command while in
tcsh
, you may have experienced problems accessing your programs. Just delete
the ~/.tcshrc
file that conda made and you should be good to go. As a
reminder, we don’t support running conda in tcsh
, only bash
.
Regardless of which shell you run init_miniconda3
from, only your ~/.bashrc
will be modified.
One reminder is to check out a node with qrsh
when you want to build a new
conda env, or your conda command will killed after 2 minutes.
To use a conda env over SGE_Batch
, add this to your shell script:
|
|
It also helps to run the SGE_Batch
command while in bash
instead of tcsh
if you happen to have tcsh
as your default shell.
Final tips
Use mamba install
and mamba create
as a stand-in replacements for the
conda install
and conda create
commands. Here is a link to the
mamba docs. mamba
is faster and
will help resolve complex dependencies in a much shorter time than conda
in
some cases.
Also, it’s best practice to install all of your programs with a version number
specified, e.g. mamba create -n python3.8 python=3.8
, and to specify all of
your programs when you create the environment so that all of the dependencies
can be resolved at creation time. Sometimes you can run into issues when
installing programs in different order after creation.
Please join the
CQLS BUG Slack
if you have additional questions regarding conda, and join the #conda
channel.