Miniforge - Conda and Mamba

The Miniforge tool provides access to versions of the conda and mamba utilities. These come pre-configured to use the open-source conda-forge community software channels. We reccomend the use of Miniforge in all cases where you need to create a conda or mamba environment.

For more information: https://github.com/conda-forge/miniforge

Running Miniforge on Comet

Simply load the Miniforge module, and this will set up the conda and mamba tools for you:

$ module load Miniforge
$ which conda
conda ()
{ 
    \local cmd="${1-__missing__}";
    case "$cmd" in 
        activate | deactivate)
            __conda_activate "$@"
        ;;
        install | update | upgrade | remove | uninstall)
            __conda_exe "$@" || \return;
            __conda_reactivate
        ;;
        *)
            __conda_exe "$@"
        ;;
    esac
}

$ module load Miniforge
$ which mamba
mamba ()
{ 
    \local cmd="${1-__missing__}";
    case "$cmd" in 
        activate | deactivate)
            __conda_activate "$@"
        ;;
        install | update | upgrade | remove | uninstall)
            __mamba_exe "$@" || \return;
            __conda_reactivate
        ;;
        *)
            __mamba_exe "$@"
        ;;
    esac
}

Environment Location

By default, both conda and mamba will create new environments under /mnt/nfs/home/$USER/miniforge3. Do not delete this directory or you will need to recreate your environments.

conda

Create a new conda environment on Comet:

$ module load Miniforge
$ conda create -n mycondaenv -c conda-forge
Retrieving notices: done
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /mnt/nfs/home/n1234/miniforge3/envs/mycondaenv

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate mycondaenv
#
# To deactivate an active environment, use
#
#     $ conda deactivate
$

Install software into the environment:

$ module load Miniforge
$ conda activate mycondaenv
(mycondaenv) $
(mycondaenv) $ conda install python=3.9.23
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##
  environment location: /mnt/nfs/home/n1234/miniforge3/envs/mycondaenv

  added / updated specs:
    - python=3.9.23

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libnsl-2.0.1               |       hb9d3cd8_1          33 KB  conda-forge
    pip-25.2                   |     pyh8b19718_0         1.1 MB  conda-forge
    python-3.9.23              |hc30ae73_0_cpython        22.6 MB  conda-forge
    setuptools-80.9.0          |     pyhff2d567_0         731 KB  conda-forge
    wheel-0.45.1               |     pyhd8ed1ab_1          61 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        24.5 MB

The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-20_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hda65f42_9 
  ca-certificates    conda-forge/noarch::ca-certificates-2026.1.4-hbd8a1cb_0 
  icu                conda-forge/linux-64::icu-78.2-h33c6efd_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.45.1-default_hbd61a6d_101 
  libexpat           conda-forge/linux-64::libexpat-2.7.4-hecca717_0 
  libffi             conda-forge/linux-64::libffi-3.5.2-h3435931_0 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-he0feb66_18 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_18 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-he0feb66_18 
  liblzma            conda-forge/linux-64::liblzma-5.8.2-hb03c661_0 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1 
  libsqlite          conda-forge/linux-64::libsqlite-3.51.2-hf4e2dac_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_18 
  libuuid            conda-forge/linux-64::libuuid-2.41.3-h5347b49_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.6.1-h35e630c_1 
  pip                conda-forge/noarch::pip-25.2-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.9.23-hc30ae73_0_cpython 
  readline           conda-forge/linux-64::readline-8.3-h853b02a_0 
  setuptools         conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h366c992_103 
  tzdata             conda-forge/noarch::tzdata-2025c-hc9c84f9_1 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb78ec9c_6 

Proceed ([y]/n)?

Downloading and Extracting Packages:
                                                                                                                                   
Preparing transaction: done                                                                                                        
Verifying transaction: done                                                                                                        
Executing transaction: done
(mycondaenv) $

Run software in the environment:

$ module load Miniforge
$ conda activate mycondaenv
(mycondaenv) $ conda run python -V
Python 3.9.23
(mycondaenv) $

For more information: https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html

mamba

Create a new mamba environment on Comet:

$ module load Miniforge
$ mamba create -n my_mamba_env -c conda-forge
Empty environment created at prefix: /mnt/nfs/home/n1234/miniforge3/envs/my_mamba_env
$

Install software into your new mamba environment:

$ module load Miniforge
$ mamba activate my_mamba_env
(my_mamba_env) $
(my_mamba_env) $ mamba install python=3.14.3
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache

Transaction
  Prefix: /mnt/nfs/home/n1234/miniforge3/envs/my_mamba_env

  Updating specs:
   - python=3.14.3

  Package              Version  Build                 Channel           Size
──────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────

  + _openmp_mutex          4.5  20_gnu                conda-forge     Cached
  + bzip2                1.0.8  hda65f42_9            conda-forge     Cached
  + ca-certificates   2026.1.4  hbd8a1cb_0            conda-forge     Cached
  + icu                   78.2  h33c6efd_0            conda-forge     Cached
  + ld_impl_linux-64    2.45.1  default_hbd61a6d_101  conda-forge      726kB
  + libexpat             2.7.4  hecca717_0            conda-forge     Cached
  + libffi               3.5.2  h3435931_0            conda-forge     Cached
  + libgcc              15.2.0  he0feb66_18           conda-forge     Cached
  + libgomp             15.2.0  he0feb66_18           conda-forge     Cached
  + liblzma              5.8.2  hb03c661_0            conda-forge     Cached
  + libmpdec             4.0.0  hb03c661_1            conda-forge     Cached
  + libsqlite           3.51.2  hf4e2dac_0            conda-forge     Cached
  + libstdcxx           15.2.0  h934c35e_18           conda-forge     Cached
  + libuuid             2.41.3  h5347b49_0            conda-forge     Cached
  + libzlib              1.3.1  hb9d3cd8_2            conda-forge     Cached
  + ncurses                6.5  h2d0b736_3            conda-forge     Cached
  + openssl              3.6.1  h35e630c_1            conda-forge     Cached
  + pip                 26.0.1  pyh145f28c_0          conda-forge        1MB
  + python              3.14.3  h32b2ec7_101_cp314    conda-forge       37MB
  + python_abi            3.14  8_cp314               conda-forge     Cached
  + readline               8.3  h853b02a_0            conda-forge     Cached
  + tk                  8.6.13  noxft_h366c992_103    conda-forge     Cached
  + tzdata               2025c  hc9c84f9_1            conda-forge     Cached
  + zstd                 1.5.7  hb78ec9c_6            conda-forge     Cached

  Summary:
  Install: 24 packages
  Total download: 39MB

──────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n]
..
...
...
Transaction finished
(my_mamba_env) $

Run software in the mamba environment:

$ module load Miniforge
$ mamba activate my_mamba_env
(my_mamba_env) $ mamba run python -V
Python 3.14.3
(my_mamba_env) $

For more information: https://mamba.readthedocs.io/en/latest/user_guide/mamba.html

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