2024-08-21: We no longer recommend using Anaconda or Miniconda that is
distributed by Anaconda Inc., because of license issues. Anaconda
Inc. argues that using their default package channels requires UCSF to
acquire an enterprise license. If you used module load CBI
miniconda3 in the past, we therefore recommend that you use module
load CBI miniforge3 instead.
Conda is a package manager and an environment management system. It’s popular, because it simplifies installation of many scientific software tools. We recommend to use:
It provides the conda and python commands, among other tools and
libraries.
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 Miniforge distribution are available via the CBI software stack. There is no need for you to install this yourself. To load Miniforge, call:
[alice@dev2 ~]$ module load CBI miniforge3/24.11.0-0
This gives access to:
[alice@dev2 ~]$ conda --version
conda 24.11.0
[alice@dev2 ~]$ python --version
Python 3.12.8
To see what software packages come with this distribution, call:
[alice@dev2 ~]$ conda list
# packages in environment at /wynton/home/boblab/shared/software/CBI/miniforge3-24.11.0-0:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
archspec 0.2.3 pyhd8ed1ab_0 conda-forge
boltons 24.0.0 pyhd8ed1ab_1 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.3 hb9d3cd8_1 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_1 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
conda 24.11.0 py312h7900ff3_0 conda-forge
conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.4.0 pyha770c72_1 conda-forge
conda-package-streaming 0.11.0 pyhd8ed1ab_0 conda-forge
distro 1.9.0 pyhd8ed1ab_0 conda-forge
fmt 11.0.2 h434a139_0 conda-forge
frozendict 2.4.6 py312h66e93f0_0 conda-forge
h2 4.1.0 pyhd8ed1ab_1 conda-forge
hpack 4.0.0 pyhd8ed1ab_1 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_1 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
jsonpatch 1.33 pyhd8ed1ab_1 conda-forge
jsonpointer 3.0.0 py312h7900ff3_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_2 conda-forge
libarchive 3.7.7 h4585015_2 conda-forge
libcurl 8.10.1 hbbe4b11_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.6.4 h5888daf_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libiconv 1.17 hd590300_2 conda-forge
liblzma 5.6.3 hb9d3cd8_1 conda-forge
libmamba 1.5.11 hf72d635_0 conda-forge
libmambapy 1.5.11 py312hf3f0a4e_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsolv 0.7.30 h3509ff9_0 conda-forge
libsqlite 3.47.2 hee588c1_0 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.5 h0d44e9d_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
lzo 2.10 hd590300_1001 conda-forge
mamba 1.5.11 py312h9460a1c_0 conda-forge
menuinst 2.2.0 py312h7900ff3_0 conda-forge
ncurses 6.5 he02047a_1 conda-forge
openssl 3.4.0 hb9d3cd8_0 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pip 24.3.1 pyh8b19718_0 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge
pluggy 1.5.0 pyhd8ed1ab_1 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py312h66e93f0_2 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.12.8 h9e4cc4f_1_cpython conda-forge
python_abi 3.12 5_cp312 conda-forge
readline 8.2 h8228510_1 conda-forge
reproc 14.2.5.post0 hb9d3cd8_0 conda-forge
reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
ruamel.yaml 0.18.6 py312h66e93f0_1 conda-forge
ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge
setuptools 75.6.0 pyhff2d567_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tqdm 4.67.1 pyhd8ed1ab_0 conda-forge
truststore 0.10.0 pyhd8ed1ab_0 conda-forge
tzdata 2024b hc8b5060_0 conda-forge
urllib3 2.2.3 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
zstandard 0.23.0 py312hef9b889_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
A Conda environment is a mechanism for installing extra software tools and versions beyond the base Miniforge distribution in a controlled manner. When using the miniforge3 module, a Conda environment must be used to install extra software. The following command creates a new myjupyter environment:
[alice@dev2 ~]$ conda create -n myjupyter notebook
Channels:
- conda-forge
Platform: linux-64
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 NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
...
zstandard conda-forge/linux-64::zstandard-0.23.0-py312h3483029_0
zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
...
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@dev2 ~]$
By default, the environment is created in your home directory under ~/.conda/envs/. 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@dev2 ~]$ module load CBI miniforge3
[alice@dev2 ~]$ conda activate myjupyter
(myjupyter) [alice@dev2 ~]$ jupyter notebook --version
7.2.1
(myjupyter) [alice@dev2 ~]$
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@dev2 ~]$ conda deactivate
[alice@dev2 ~]$ jupyter notebook --version
jupyter: command not found
[alice@dev2 ~]$
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@dev2 ~]$ module load CBI miniforge3
[alice@dev2 ~]$ module load CBI conda-stage
[alice@dev2 ~]$ conda stage --auto-stage=enable myjupyter
INFO: Configuring automatic staging and unstaging of original Conda environment ...
INFO: [ONCE] Packaging Conda environment, because it hasn't been done before ...
Collecting packages...
Packing environment at '/wynton/home/boblab/alice/.conda/envs/myjupyter' to
'/wynton/home/boblab/alice/.conda/envs/.tmp.myjupyter.tar.gz'
[########################################] | 100% Completed | 4min 5.6s
INFO: Total 'conda-pack' time: 274 seconds
INFO: Created conda-pack tarball: /wynton/home/boblab/alice/.conda/envs/myjupyter.tar.gz
(140099022 bytes; 2025-03-02 19:33:08.108806755 -0800)
INFO: Enabled auto-staging
INFO: Enabled auto-unstaging
[alice@dev2 ~]$
That’s it. 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@dev2 ~]$ conda env export --name myjupyter | grep -v "^prefix: " > myjupyter.yml
[alice@dev2 ~]$ ls -l myjupyter.yml
-rw-rw-r-- 1 alice boblab 4982 Aug 21 17:56 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:
#
myjupyter /wynton/home/boblab/alice/.conda/envs/myjupyter
base /path/to/miniforge3
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@dev2 ~]$ CONDA_STAGE=false conda activate myjupyter
(myjupyter) [alice@dev2 ~]$ 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@dev2 ~]$ 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@log2.wynton.ucsf.edu
alice1@log2.wynton.ucsf.edu:s password: XXXXXXXXXXXXXXXXXXX
(base) [alice@log2 ~]$
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@dev2 ~]$ conda info | grep active
conda info | grep active
active environment : base
active env location : /wynton/home/boblab/alice/.conda
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 miniforge3, then you should not have this problem.
To reconfigure Conda to no longer activate the ‘base’ Conda environment by default, call:
(base) [alice@dev2 ~]$ conda config --set auto_activate_base false
(base) [alice@dev2 ~]$
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 miniforge3, you can uninstall the Conda setup code that were injected to your ~/.bashrc file by calling:
[alice@dev2 ~]$ conda init --reverse
no change /wynton/home/boblab/alice/.conda/condabin/conda
no change /wynton/home/boblab/alice/.conda/bin/conda
no change /wynton/home/boblab/alice/.conda/bin/conda-env
no change /wynton/home/boblab/alice/.conda/bin/activate
no change /wynton/home/boblab/alice/.conda/bin/deactivate
no change /wynton/home/boblab/alice/.conda/etc/profile.d/conda.sh
no change /wynton/home/boblab/alice/.conda/etc/fish/conf.d/conda.fish
no change /wynton/home/boblab/alice/.conda/shell/condabin/Conda.psm1
no change /wynton/home/boblab/alice/.conda/shell/condabin/conda-hook.ps1
no change /wynton/home/boblab/alice/.conda/lib/python3.9/site-packages/xontrib/conda.xsh
no change /wynton/home/boblab/alice/.conda/etc/profile.d/conda.csh
modified /wynton/home/boblab/alice/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
[alice@dev2 ~]$