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Loading Mamba module

  1. Use the ml av Mamba command to see which version of Mamba is available on the LANTA HPC system.

  2. Use the ml Mamba/xx.xx.x command to load the Mamba version that you want to use. If you don't specify a version, the default version (D) is loaded, which is Mamba/23.11.0-0.

Code Block
username@lanta:~> ml av Mamba
---------------------- /lustrefs/disk/modules/easybuild/modules/all -----------------------
   Mamba/23.11.0-0 (D)
Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
username@lanta:~> ml Mamba/23.11.0-0

Selecting the channels for package installation

In the Mamba module, you can use only the following free channels, such as:

  • conda-forge

  • bioconda

Note

The channels provided by Anaconda, Inc. (default and anaconda channels) have a service fee.

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You can specify channels in the package installation with the -c conda-forge command.

Code Block
username@lanta:~> conda install -c conda-forge matplotlib

Verifying the default channel URLs within your conda module

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Code Block
username@lanta:~> ml Mamba/23.11.0-0
username@lanta:~> conda info
     active environment : None
            shell level : 0
       user config file : /home/username/.condarc
 populated config files : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.10.13.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen3
                          __conda=23.11.0=0
                          __glibc=2.31=0
                          __linux=5.14.21=0
                          __unix=0=0
       base environment : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0  (read only)
      conda av data dir : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/pkgs
                          /home/ywongnon/.conda/pkgs
       envs directories : /home/ywongnon/.conda/envs
                          /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/envs
               platform : linux-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Linux/5.14.21-150400.24.81_12.0.86-cray_shasta_c sles/15.4 glibc/2.31 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5
                UID:GID : 1980400170:1980400170
             netrc file : None
           offline mode : False

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However, if you found the URLs in this format, you need to check your user config file. To access the below channels, a license from Anaconda, Inc. is required.

Code Block
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
               https://repo.anaconda.com/pkgs/main/noarch
               https://repo.anaconda.com/pkgs/r/linux-64
               https://repo.anaconda.com/pkgs/r/noarch

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Note

If the default and anaconda channels are present in your user config file, kindly remove them.

Expand
titleExample
Code Block
username@lanta:~> cat /home/username/.condarc
channels:
  - conda-forge
  - bioconda
  - defaults  ## delete this line
channel_priority: strict

Installing package with specified channels

You can specify channels in the package installation with the -c option command.

For example,

Code Block
username@lanta:~> ml Mamba/23.11.0-0
username@lanta:~> conda activate your_env
username@lanta:~> conda install -c conda-forge matplotlib