⚠️ 2022-10-28: Beta version! The instructions on this page are fresh and might be updated soon. That said, they have been validated and approved by a group of experienced Conda users. If you run into issues, please let us know.
⚠️ 2023-06-11: If you’ve used module load CBI miniconda3-py39/4.12.0 in the past, please update to use module load CBI miniconda3/4.12.0-py39 instead. It loads the same Conda version - it’s just the module name structure that has been tidied up.
Conda is a package manager and an environment management system. It’s popular, because it simplifies installation of many scientific software tools. There are two main distributions of Conda:
Both come with Python and conda commands. We recommend working with the smaller Miniconda distribution, especially since it is preinstalled on Wynton. Using Miniconda, you can install additional scientific packages as needed using the conda install ... command.
Note: The aim of this document is to give the essential best-practices for working with Conda on Wynton. It is not meant to be a complete introduction on how to work with Conda in general. A good complement to this document, is the official Conda documentation on Managing environments.
On Wynton HPC, up-to-date versions of the Miniconda distribution are available via the CBI software stack. There is no need for you to install this yourself. To load Miniconda v3 with Python 3.9, call:
[alice@dev1 ~]$ module load CBI miniconda3/23.3.1-0-py39
This gives access to:
[alice@dev1 ~]$ conda --version
conda 23.3.1
[alice@dev1 ~]$ python --version
Python 3.9.16
To see what software packages come with this Miniconda distribution, call:
[alice@dev1 ~]$ conda list
# packages in environment at /wynton/home/cbi/shared/software/CBI/miniconda3-23.3.1-0-py39:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
boltons 23.0.0 py39h06a4308_0
brotlipy 0.7.0 py39h27cfd23_1003
ca-certificates 2023.01.10 h06a4308_0
certifi 2022.12.7 py39h06a4308_0
cffi 1.15.1 py39h5eee18b_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 23.3.1 py39h06a4308_0
conda-content-trust 0.1.3 py39h06a4308_0
conda-package-handling 2.0.2 py39h06a4308_0
conda-package-streaming 0.7.0 py39h06a4308_0
cryptography 39.0.1 py39h9ce1e76_0
idna 3.4 py39h06a4308_0
jsonpatch 1.32 pyhd3eb1b0_0
jsonpointer 2.1 pyhd3eb1b0_0
ld_impl_linux-64 2.38 h1181459_1
libffi 3.4.2 h6a678d5_6
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
ncurses 6.4 h6a678d5_0
openssl 1.1.1t h7f8727e_0
packaging 23.0 py39h06a4308_0
pip 23.0.1 py39h06a4308_0
pluggy 1.0.0 py39h06a4308_1
pycosat 0.6.4 py39h5eee18b_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 23.0.0 py39h06a4308_0
pysocks 1.7.1 py39h06a4308_0
python 3.9.16 h7a1cb2a_2
readline 8.2 h5eee18b_0
requests 2.28.1 py39h06a4308_1
ruamel.yaml 0.17.21 py39h5eee18b_0
ruamel.yaml.clib 0.2.6 py39h5eee18b_1
setuptools 65.6.3 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.41.1 h5eee18b_0
tk 8.6.12 h1ccaba5_0
toolz 0.12.0 py39h06a4308_0
tqdm 4.65.0 py39hb070fc8_0
tzdata 2023c h04d1e81_0
urllib3 1.26.15 py39h06a4308_0
wheel 0.38.4 py39h06a4308_0
xz 5.2.10 h5eee18b_1
zlib 1.2.13 h5eee18b_0
zstandard 0.19.0 py39h5eee18b_0
A Conda environment is a mechanism for installing extra software tools and versions beyond the base Miniconda distribution in a controlled manner. When using the miniconda3 module, a Conda environment must be used to install extra software. The following command creates a new myjupyter environment:
[alice@dev1 ~]$ conda create -n myjupyter notebook
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /wynton/home/boblab/alice/.conda/envs/myjupyter
added / updated specs:
- notebook
The following packages will be downloaded:
package | build
---------------------------|-----------------
anyio-3.5.0 | py311h06a4308_0 214 KB
argon2-cffi-bindings-21.2.0| py311h5eee18b_0 33 KB
...
xz-5.4.2 | h5eee18b_0 642 KB
yaml-0.2.5 | h7b6447c_0 75 KB
------------------------------------------------------------
Total: 67.6 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
...
zeromq pkgs/main/linux-64::zeromq-4.3.4-h2531618_0
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
...
jupyterlab_pygments- | 8 KB | #################################### | 100%
jupyter_client-7.3.5 | 194 KB | #################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate myjupyter
#
# To deactivate an active environment, use
#
# $ conda deactivate
[alice@dev1 ~]$
By default, the environment is created in your home directory under ~/.conda/. To create the environment at a specific location, see Managing environments part of the official Conda documentation. That section covers many useful topics such as removing a Conda environment, and creating an environment with a specific Python version.
After an environment is created, the next time you log in to a development node, you can set myjupyter (or any other Conda environment you’ve created) as your active environment by calling:
[alice@dev1 ~]$ module load CBI miniconda3
[alice@dev1 ~]$ conda activate myjupyter
(myjupyter) [alice@dev1 ~]$ jupyter notebook --version
6.5.4
(myjupyter) [alice@dev1 ~]$
Note how the command-line prompt is prefixed with (myjupyter); it highlights that the Conda environment myjupyter is activated. To deactivate an environment and return to the base environment, call:
(myjupyter) [alice@dev1 ~]$ conda deactivate
[alice@dev1 ~]$ jupyter notebook --version
jupyter: command not found
[alice@dev1 ~]$
We highly recommend configuring Conda environment to be automatically staged only on the local disk whenever activated. This results in your software running significantly faster. Auto-staging is straightforward to configure using the conda-stage tool, e.g.
[alice@dev1 ~]$ module load CBI miniconda3
[alice@dev1 ~]$ module load CBI conda-stage
[alice@dev1 ~]$ conda activate myjupyter
(myjupyter) [alice@dev1 ~]$ conda-stage --auto-stage=enable
INFO: Configuring automatic staging and unstaging of original Conda environment ...
INFO: Enabled auto-staging
INFO: Enabled auto-unstaging
For the complete, easy-to-follow instructions, see the conda-stage documentation.
Once you have your Conda environment built, we recommend that you back up its core configuration. The process is quick and straightforward, and fully documented in the official Conda Managing environments documentation. For example, to back up the above myjupyter environment, call:
[alice@dev1 ~]$ conda env export --name myjupyter | grep -v "^prefix: " > myjupyter.yml
[alice@dev1 ~]$ ls -l myjupyter.yml
-rw-rw-r-- 1 alice boblab 3597 Jun 11 03:48 myjupyter.yml
This configuration file is useful:
when migrating the environment from Wynton to another Conda version, another computer, or another HPC environment
for sharing the environment with collaborators
for making a snapshot of the software stack used in a project
for disaster recovery, e.g. if you remove the Conda environment by mistake
for updating the dependencies in a Conda environment
To restore a backed up Conda environment from a yaml file, on the target machine:
download the yaml file, e.g. myjupyter.yml
make sure there is no existing environment with the same name, i.e. check conda env list
create a new Conda environment from the yaml file
For example, assume we have downloaded myjupyter.yml to our local machine. Then we start by getting the name of the backed-up Conda environment and making sure it does not already exist;
{local}$ grep "name:" myjupyter.yml
name: myjupyter
{local}$ conda env list
# conda environments:
#
sandbox /wynton/home/boblab/alice/.conda/envs/sandbox
base /path/to/anaconda3
When have confirmed that there is no name clash, we can restore the backed up environment on our local machine using:
{local}$ conda env create -f myjupyter.yml
This will install the exact same software versions as when we made the backup.
Warning: This is not a fool-proof backup method, because it depends on packages to be available from the package repositories also when you try to restore the Conda environment. To lower the risk for failure, keep your environments up to date with the latest packages and test frequently that your myjupyter.yml file can be restored.
We can also use myjupyter.yml to update an existing environment. The gist is to edit the file to reflect what we want to be updated, and then run conda env update .... See Managing environments part of the official Conda documentation for exact instructions.
If you updated or installed new packages in your Conda environment and need to roll back to a previous version, it is possible to do this using Conda’s revision utility. To list available revisions in the current Conda environment, use:
[alice@dev1 ~]$ CONDA_STAGE=false conda activate myjupyter
(myjupyter) [alice@dev1 ~]$ conda list --revisions
2023-06-11 03:46:03 (rev 0)
+_libgcc_mutex-0.1 (defaults/linux-64)
+_openmp_mutex-5.1 (defaults/linux-64)
+anyio-3.5.0 (defaults/linux-64)
+argon2-cffi-21.3.0 (defaults/noarch)
...
2023-06-11 03:52:03 (rev 1)
+conda-pack-0.7.0 (conda-forge/noarch)
+python_abi-3.11 (conda-forge/linux-64)
To roll back to a specific revision, say revision zero, use:
(myjupyter) [alice@dev1 ~]$ conda install --revision 0
Warning: This only works with packages installed using conda install. Packages installed via python3 -m pip install will not be recorded by the revision system. In such cases, we have to do manual backup snapshots (as explained above).
If you previously have installed Conda yourself, there is a risk that it installed itself into your ~/.bashrc file such that it automatically activates the ‘base’ environment whenever you start a new shell, e.g.
{local}$ ssh alice@log1.wynton.ucsf.edu
alice1@log1.wynton.ucsf.edu:s password: XXXXXXXXXXXXXXXXXXX
(base) [alice@log1 ~]$
If you see a (base) prefix in your prompt, then you have this set up and the Conda ‘base’ environment is active. You can verify this by querying conda info as:
[alice@dev1 ~]$ conda info | grep active
conda info | grep active
active environment : base
active env location : /wynton/home/boblab/alice/miniconda3
This auto-activation might sound convenient, but we strongly recommend against using it, because Conda software stacks have a great chance to cause conflicts (read: wreak havoc) with other software tools installed outside of Conda. For example, people that have Conda activated and then run R via module load CBI r, often report on endless, hard-to-understand problems when trying to install common R packages. Instead, we recommend to activate your Conda environments only when you need them, and leave them non-activated otherwise. This will give you a much smoother day-to-day experience. To clarify, if you never installed Conda yourself, and only used module load CBI miniconda3-py39/23.3.1-0-py39, then you should not have this problem.
To reconfigure Conda to no longer activate the ‘base’ Conda environment by default, call:
(base) [alice@dev1 ~]$ conda config --set auto_activate_base false
(base) [alice@dev1 ~]$
Next time you log in, the ‘base’ environment should no longer be activated by default.
If you want to completely retire you personal Conda installation, and move on to only using module load CBI miniconda3, you can uninstall the Conda setup code that were injected to your ~/.bashrc file by calling:
[alice@dev1 ~]$ conda init --reverse
no change /wynton/home/boblab/alice/miniconda3/condabin/conda
no change /wynton/home/boblab/alice/miniconda3/bin/conda
no change /wynton/home/boblab/alice/miniconda3/bin/conda-env
no change /wynton/home/boblab/alice/miniconda3/bin/activate
no change /wynton/home/boblab/alice/miniconda3/bin/deactivate
no change /wynton/home/boblab/alice/miniconda3/etc/profile.d/conda.sh
no change /wynton/home/boblab/alice/miniconda3/etc/fish/conf.d/conda.fish
no change /wynton/home/boblab/alice/miniconda3/shell/condabin/Conda.psm1
no change /wynton/home/boblab/alice/miniconda3/shell/condabin/conda-hook.ps1
no change /wynton/home/boblab/alice/miniconda3/lib/python3.9/site-packages/xontrib/conda.xsh
no change /wynton/home/boblab/alice/miniconda3/etc/profile.d/conda.csh
modified /wynton/home/boblab/alice/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
[alice@dev1 ~]$