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This article will guide you to create the environment using Miniconda on a LANTA HPC system. An overview of the content can be found in the table of contents below for immediate visualization of the interesting parts.

Table of Contents

Using

...

Mamba on LANTA HPC

Load

...

Mamba module

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

  2. Use the ml Miniconda3Mamba/xx.xx.x command to load the Miniconda Mamba version that you want to use. If you don't specify a version, the default version (D) is loaded, which is Miniconda3Mamba/23.311.10-0.

Code Block
username@lanta:~> ml av MinicondaMamba
---------------------- /lustrefs/disk/modules/easybuild/modules/all -----------------------
   Miniconda3Mamba/2223.11.1-1    Miniconda3/23.3.1-0-0 (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 Miniconda3Mamba/2223.11.10-10

Unload

...

Mamba module

Use the module unload Miniconda3Mamba command to unload the MinicondaMamba.

Code Block
username@lanta:~> module unload Miniconda3Mamba

Use the module purge command to unload all currently loaded modules.

...

Note

Before you use the module unload Miniconda3Mamba or module purge command, you must deactivate your environment with the conda deactivate command.

Activate your environment

  1. Use the conda env list command to view a list of your environments.

  2. If you want to activate your environment such as TensorFlow-2.6.0, you can use the conda activate tensorflow-2.612.01 command.

Code Block
username@lanta:~> conda env list
# conda environments:
#
base                     /lustrefs/disk/modules/easybuild/software/Miniconda3Mamba/2223.11.10-10
netcdf-py39              /lustrefs/disk/modules/easybuild/software/Miniconda3Mamba/2223.11.10-10/envs/netcdf-py39
pytorch-12.112.02            /lustrefs/disk/modules/easybuild/software/Miniconda3Mamba/2223.11.10-10/envs/pytorch-12.112.02
tensorflow-2.612.01         /lustrefs/disk/modules/easybuild/software/Miniconda3Mamba/2223.11.10-10/envs/tensorflow-2.612.01
username@lanta:~> conda activate tensorflow-2.612.01
(tensorflow-2.612.01) username@lanta:~>

Deactivate your environment

Use the conda deactivate command to deactivate your environments.

Code Block
(tensorflow-2.612.01) username@lanta:~> conda deactivate
username@lanta:~>

Creating the environment in the user’s home

Create the environment

Use the conda create -n myenv commands to create the environment with myenv name.

Code Block
username@lanta:~> conda create -n myenv
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your directory/envs/myenv

Proceed ([y]/n)? y
...

Create the environment with a specific version of the packages

Use the conda create -n myenv python=3.9 commands to create the myenv environment with a specific version of python.

...

Code Block
username@lanta:~> conda create -n myenv python=3.9 numpy=1.23.5
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your directory/envs/myenv

  added / updated specs:
    - numpy=1.23.5
    - python=3.9

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-1.0                   |              mkl           6 KB
    ca-certificates-2023.01.10 |       h06a4308_0         120 KB
    certifi-2022.12.7          |   py39h06a4308_0         150 KB
    intel-openmp-2021.4.0      |    h06a4308_3561         4.2 MB
    mkl-2021.4.0               |     h06a4308_640       142.6 MB
    mkl-service-2.4.0          |   py39h7f8727e_0          59 KB
    mkl_fft-1.3.1              |   py39hd3c417c_0         182 KB
    mkl_random-1.2.2           |   py39h51133e4_0         309 KB
    numpy-1.23.5               |   py39h14f4228_0          10 KB
    numpy-base-1.23.5          |   py39h31eccc5_0         6.7 MB
    ------------------------------------------------------------
                                           Total:       154.3 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
  blas               pkgs/main/linux-64::blas-1.0-mkl
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.01.10-h06a4308_0
  certifi            pkgs/main/linux-64::certifi-2022.12.7-py39h06a4308_0
  intel-openmp       pkgs/main/linux-64::intel-openmp-2021.4.0-h06a4308_3561
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  libffi             pkgs/main/linux-64::libffi-3.4.2-h6a678d5_6
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
  mkl                pkgs/main/linux-64::mkl-2021.4.0-h06a4308_640
  mkl-service        pkgs/main/linux-64::mkl-service-2.4.0-py39h7f8727e_0
  mkl_fft            pkgs/main/linux-64::mkl_fft-1.3.1-py39hd3c417c_0
  mkl_random         pkgs/main/linux-64::mkl_random-1.2.2-py39h51133e4_0
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
  numpy              pkgs/main/linux-64::numpy-1.23.5-py39h14f4228_0
  numpy-base         pkgs/main/linux-64::numpy-base-1.23.5-py39h31eccc5_0
  openssl            pkgs/main/linux-64::openssl-1.1.1t-h7f8727e_0
  pip                pkgs/main/linux-64::pip-22.3.1-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.16-h7a1cb2a_0
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0
  setuptools         pkgs/main/linux-64::setuptools-65.6.3-py39h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/linux-64::sqlite-3.40.1-h5082296_0
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
  tzdata             pkgs/main/noarch::tzdata-2022g-h04d1e81_0
  wheel              pkgs/main/linux-64::wheel-0.38.4-py39h06a4308_0
  xz                 pkgs/main/linux-64::xz-5.2.10-h5eee18b_1
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0

Proceed ([y]/n)? y
...

Creating the environment in the project’s home

Specify a location for the environment

Use the conda create --prefix /your project directory/envs commands to create the environment on the specific location.

Code Block
username@lanta:~> conda create --prefix /your project directory/envs
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your project directory/envs

Proceed ([y]/n)? y
...

Specify a location for the environment with a specific version of a package

Use the conda create --prefix /your project directory/envs python=3.9 commands to create the environment with a specific version of a package on a specific location.

Code Block
username@lanta:~> conda create --prefix /your project directory/envs python=3.9
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your project directory/envs

  added / updated specs:
    - python=3.9

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2023.01.10 |       h06a4308_0         120 KB
    certifi-2022.12.7          |   py39h06a4308_0         150 KB
    ------------------------------------------------------------
                                           Total:         270 KB

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
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.01.10-h06a4308_0
  certifi            pkgs/main/linux-64::certifi-2022.12.7-py39h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  libffi             pkgs/main/linux-64::libffi-3.4.2-h6a678d5_6
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
  openssl            pkgs/main/linux-64::openssl-1.1.1t-h7f8727e_0
  pip                pkgs/main/linux-64::pip-22.3.1-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.16-h7a1cb2a_0
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0
  setuptools         pkgs/main/linux-64::setuptools-65.6.3-py39h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.40.1-h5082296_0
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
  tzdata             pkgs/main/noarch::tzdata-2022g-h04d1e81_0
  wheel              pkgs/main/linux-64::wheel-0.38.4-py39h06a4308_0
  xz                 pkgs/main/linux-64::xz-5.2.10-h5eee18b_1
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0

Proceed ([y]/n)? y
...

Activate your environment in the project’s home

If you want to activate your environment in the project’s home, you can use the conda activate /your project directory/envs command.

Code Block
username@lanta:~> conda activate /your project directory/envs
(/your project directory/envs) username@lanta:~>

Creating the environment from an requirements.yml file

A simple requirements.yml file

In the requirements.yml file, you need to specify the environment name and packages that you want to use.

Code Block
name: envs
dependencies:
  - python=3.9
  - numpy=1.23.5
  - pandas

Create the environment from the requirements.yml file in the user’s home

Use the conda env create -f requirements.yml commands to create the environment from the requirements.yml file in the user’s home.

Code Block
username@lanta:~> conda env create -f requirements.yml
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Create the environment from the requirements.yml file in the project’s home

Use the conda env create -f requirements.yml --prefix /your project directory/envs commands to create the environment from the requirements.yml file on the specific location.

Code Block
username@lanta:~> conda env create -f requirements.yml --prefix /your project directory/envs
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Removing the environment

Remove the environment in the user’s home

If you want to remove the myenv environment, you can use the conda remove --name myenv --all command.

Code Block
username@lanta:~> conda remove --name myenv --all

Remove the environment in the project’s home

If you want to remove the environment in /your project directory/envs, you can use the rm -rf /your project directory/envs command.

Code Block
username@lanta:~> rm -rf /your project directory/envs

...

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