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This article will guide you to create an 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/2223.11.10-10.

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

...

0

Unload Mamba module

Use the

...

module unload Mamba command to unload the Mamba.

Code Block
username@lanta:~> condamodule env list
unload Mamba

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

Code Block
username@lanta:~> module purge
Note

Before you use the module unload Mamba 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-2.12.1 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-2.12.1
(tensorflow-2.612.0
1) username@lanta:~>

Deactivate your environment

Use the conda deactivate command to deactivate your environments.

Code Block
(tensorflow-2.612.0)1) 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
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your directory/envs/myenv

Proceed ([y]/n)? y
...
username@lanta:~>

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
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your directory/envs/myenv

  added / updated specs:
    - python=3.9


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    capython-certificates-20233.01.10 |9.19              h06a4308|h0755675_0_cpython        22.7 MB 120 KBconda-forge
    certifiwheel-20220.12.743.0               |   py39h06a4308_0  pyhd8ed1ab_1          57 KB 150 KBconda-forge
    ------------------------------------------------------------
                                           Total:        22.8 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex          Total:conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2      270 KB  The following NEW packages will be INSTALLED: conda-forge/linux-64::bzip2-1.0.8-hd590300_5
   _libgcc_mutexca-certificates       pkgs/mainconda-forge/linux-64::_libgcc_mutex-0.1-mainca-certificates-2024.2.2-hbcca054_0
  ld_openmpimpl_mutexlinux-64      pkgs/main/conda-forge/linux-64::ld_openmpimpl_mutexlinux-64-52.140-1_gnuh41732ed_0
  libffi         ca-certificates    pkgs/mainconda-forge/linux-64::calibffi-certificates-20233.014.102-h06a4308h7f98852_05
  certifilibgcc-ng            pkgs/main/conda-forge/linux-64::certifilibgcc-ng-202213.122.70-py39h06a4308_0h807b86a_5
  libgomp         ld_impl_linux-64   pkgs/mainconda-forge/linux-64::ld_impl_linux-64-libgomp-13.2.380-h1181459h807b86a_15
  libffilibnsl             pkgsconda-forge/main/linux-64::libffilibnsl-32.40.21-h6a678d5hd590300_60
  libgcc-nglibsqlite          pkgsconda-forge/main/linux-64::libgcc-ng-11libsqlite-3.45.2.0-h1234567h2797004_10
  libgomplibuuid            pkgsconda-forge/main/linux-64::libgomplibuuid-112.238.01-h1234567_1h0b41bf4_0
  libxcrypt   libstdcxx-ng       pkgs/mainconda-forge/linux-64::libstdcxxlibxcrypt-ng-114.24.036-h1234567hd590300_1
  ncurseslibzlib            pkgs/mainconda-forge/linux-64::ncurseslibzlib-61.2.413-h6a678d5hd590300_05
  opensslncurses            pkgs/mainconda-forge/linux-64::opensslncurses-16.14.1t20240210-h7f8727eh59595ed_0
  pipopenssl                pkgs/main/conda-forge/linux-64::pipopenssl-223.32.1-py39h06a4308_0hd590300_1
  pip   python             pkgs/main/linux-64conda-forge/noarch::pythonpip-3.924.160-h7a1cb2apyhd8ed1ab_0
  python  readline           pkgsconda-forge/main/linux-64::readlinepython-83.9.219-h5eee18bh0755675_0_cpython
  setuptoolsreadline           pkgs/mainconda-forge/linux-64::setuptoolsreadline-658.6.32-py39h06a4308h8228510_01
  sqlitesetuptools             pkgs/main/linux-64::sqlite-3.40.1-h5082296conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
  tk                 pkgs/mainconda-forge/linux-64::tk-8.6.1213-h1ccaba5noxft_h4845f30_0101
  tzdata             pkgs/mainconda-forge/noarch::tzdata-2022g2024a-h04d1e81h0c530f3_0
  wheel              pkgs/main/linux-64conda-forge/noarch::wheel-0.3843.40-py39h06a4308pyhd8ed1ab_01
  xz                 pkgs/main/linux-64::xz-5.2.10-h5eee18b_1
  zlib               pkgs/mainconda-forge/linux-64::zlibxz-15.2.136-h5eee18bh166bdaf_0

Proceed ([y]/n)? y
...
username@lanta:~>

Use the conda create -n myenv python=3.9 numpy=1.23.5 commands to create the myenv environment with a specific version of python and scipynumpy.

Code Block
username@lanta:~> conda create -n myenv python=3.9 numpy=1.23.5
Channels:
 - conda-forge
Platform: linux-64
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    libblas-3.9.0       6 KB     ca-certificates-2023.01.10 |21_linux64_openblas       h06a4308_0   14 KB  conda-forge
  120 KB     certifi-2022.12.7          |   py39h06a4308_0    libcblas-3.9.0     150 KB     intel-openmp-2021.4.0      |21_linux64_openblas    h06a4308_3561      14 KB  4.2 MBconda-forge
     mkl-2021.4libgfortran-ng-13.2.0      |       h69a702a_5  |     h06a4308_640   23 KB  conda-forge
142.6 MB     mkl-service-2.4liblapack-3.9.0          |   py39h7f8727e_0|21_linux64_openblas          5914 KB  conda-forge
  mkl_fft  numpy-1.323.15               |   py39hd3c417cpy39h3d75532_0         5.6 MB 182 KBconda-forge
    mkl_randompython-13.29.219           |   py39h51133e4|h0755675_0_cpython        22.7 MB 309 KBconda-forge
    numpypython_abi-1.23.53.9             |        |   py39h14f4228_04_cp39           6 KB  conda-forge
    wheel-0.43.0     10 KB     numpy-base-1.23.5    |     pyhd8ed1ab_1 |   py39h31eccc5_0      57 KB  6.7 MBconda-forge
    ------------------------------------------------------------
                                           Total:        28.4 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex       Total:  conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2     154.3 MB  The following NEW packages will be INSTALLED:

  _libgcc_mutex conda-forge/linux-64::bzip2-1.0.8-hd590300_5
  ca-certificates      pkgs/main/conda-forge/linux-64::_libgcc_mutex-0.1-mainca-certificates-2024.2.2-hbcca054_0
  ld_openmpimpl_mutexlinux-64      pkgs/main/conda-forge/linux-64::ld_openmpimpl_mutexlinux-64-52.140-1_gnu
  blash41732ed_0
  libblas            pkgsconda-forge/main/linux-64::blaslibblas-13.9.0-mkl21_linux64_openblas
  libcblas       ca-certificates    pkgsconda-forge/main/linux-64::calibcblas-certificates-20233.019.100-h06a4308_021_linux64_openblas
  libffi certifi            pkgsconda-forge/main/linux-64::certifilibffi-20223.12.7-py39h06a4308_04.2-h7f98852_5
  libgcc-ng   intel-openmp       pkgsconda-forge/main/linux-64::intellibgcc-openmpng-202113.42.0-h06a4308h807b86a_35615
  ld_impl_linux-64libgfortran-ng     pkgsconda-forge/main/linux-64::ld_impl_linux-64-libgfortran-ng-13.2.380-h1181459h69a702a_15
  libffilibgfortran5             pkgs/main/conda-forge/linux-64::libffilibgfortran5-313.42.20-h6a678d5ha4646dd_65
  libgomp  libgcc-ng          pkgs/mainconda-forge/linux-64::libgcclibgomp-ng-1113.2.0-h1234567h807b86a_15
  libgompliblapack            pkgs/mainconda-forge/linux-64::libgompliblapack-113.29.0-h1234567_121_linux64_openblas
  libnsl      libstdcxx-ng       pkgsconda-forge/main/linux-64::libstdcxxlibnsl-ng-11.2.0-h1234567_1
  mkl.1-hd590300_0
  libopenblas             pkgs/mainconda-forge/linux-64::mkllibopenblas-20210.43.026-h06a4308pthreads_h413a1c8_6400
  mkl-servicelibsqlite          pkgsconda-forge/main/linux-64::mkllibsqlite-service-23.445.02-py39h7f8727eh2797004_0
  mkl_fftlibstdcxx-ng            pkgs/main/conda-forge/linux-64::mkl_fft-1.3.1-py39hd3c417c_0libstdcxx-ng-13.2.0-h7e041cc_5
  libuuid   mkl_random         pkgs/mainconda-forge/linux-64::mkl_randomlibuuid-12.238.21-py39h51133e4h0b41bf4_0
  ncurseslibxcrypt            pkgs/main/conda-forge/linux-64::ncurseslibxcrypt-64.4.36-h6a678d5hd590300_01
  numpylibzlib              pkgs/main/conda-forge/linux-64::numpylibzlib-1.232.513-py39h14f4228hd590300_05
  ncurses  numpy-base          pkgsconda-forge/main/linux-64::numpyncurses-base-16.234.520240210-py39h31eccc5h59595ed_0
  numpy openssl             pkgs/mainconda-forge/linux-64::opensslnumpy-1.123.1t5-h7f8727epy39h3d75532_0
  pipopenssl                pkgs/mainconda-forge/linux-64::pipopenssl-223.32.1-py39h06a4308_0hd590300_1
  pip   python             pkgs/main/linux-64conda-forge/noarch::pythonpip-3.924.160-h7a1cb2apyhd8ed1ab_0
  readlinepython             pkgs/mainconda-forge/linux-64::readlinepython-83.9.219-h5eee18bh0755675_0_cpython
  setuptoolspython_abi         pkgsconda-forge/main/linux-64::setuptoolspython_abi-653.6.39-py39h06a43084_0cp39
  sixreadline                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0conda-forge/linux-64::readline-8.2-h8228510_1
  sqlitesetuptools             pkgs/main/linux-64::sqlite-3.40.1-h5082296conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
  tk                 pkgs/mainconda-forge/linux-64::tk-8.6.1213-h1ccaba5noxft_h4845f30_0101
  tzdata             pkgs/main/noarch::tzdata-2022g-h04d1e81_0
  wheel              pkgs/main/linux-64::wheel-0.38.4-py39h06a4308conda-forge/noarch::tzdata-2024a-h0c530f3_0
  xzwheel                 pkgs/main/linux-64::xz-5.2.10-h5eee18bconda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  zlibxz                 pkgs/mainconda-forge/linux-64::zlibxz-15.2.136-h5eee18bh166bdaf_0

Proceed ([y]/n)? y
...
username@lanta:~>

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 project directory/envs
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your project directory/envs

Proceed ([y]/n)? y
...
username@lanta:~>

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
Channels:
 - conda-forge
Platform: linux-64
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
    ---------------------------|-----------------
    capython-certificates-20233.01.10 |9.19              h06a4308|h0755675_0_cpython        22.7 120 KBMB  conda-forge
    certifiwheel-2022.12.70.43.0               |     py39h06a4308pyhd8ed1ab_01          15057 KB  conda-forge
    ------------------------------------------------------------------------
                                           Total:        22.8 MB

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
  bzip2                Total:conda-forge/linux-64::bzip2-1.0.8-hd590300_5
  ca-certificates      270 KB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/mainconda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0
  ld_impl_linux-64   conda-forge/linux-64::ld_libgccimpl_mutexlinux-64-02.1-main40-h41732ed_0
  libffi       _openmp_mutex      pkgsconda-forge/main/linux-64::_openmp_mutex-5.1-1_gnulibffi-3.4.2-h7f98852_5
  ca-certificateslibgcc-ng          pkgsconda-forge/main/linux-64::calibgcc-certificatesng-202313.012.100-h06a4308h807b86a_05
  certifilibgomp            pkgsconda-forge/main/linux-64::certifilibgomp-202213.122.70-py39h06a4308_0h807b86a_5
  libnsl          ld_impl_linux-64   pkgs/mainconda-forge/linux-64::ld_impl_linux-64-libnsl-2.380.1-h1181459hd590300_10
  libffilibsqlite             pkgs/main/conda-forge/linux-64::libffilibsqlite-3.445.2-h6a678d5h2797004_60
  libgcc-nglibuuid            pkgsconda-forge/main/linux-64::libgcclibuuid-ng-112.238.01-h1234567h0b41bf4_10
  libgomplibxcrypt            pkgs/main/conda-forge/linux-64::libgomplibxcrypt-114.24.036-h1234567hd590300_1
  libzlib   libstdcxx-ng         pkgs/mainconda-forge/linux-64::libstdcxxlibzlib-ng-111.2.013-h1234567hd590300_15
  ncurses            pkgs/mainconda-forge/linux-64::ncurses-6.4.20240210-h6a678d5h59595ed_0
  openssl            pkgs/mainconda-forge/linux-64::openssl-13.2.1.1t-h7f8727ehd590300_01
  pip                pkgs/main/linux-64conda-forge/noarch::pip-2224.3.10-py39h06a4308pyhd8ed1ab_0
  python        
    pkgs/main/linux-64::python-3.9.16-h7a1cb2a_0
  readline python             pkgsconda-forge/main/linux-64::readlinepython-83.9.219-h5eee18bh0755675_0_cpython
  readline setuptools          pkgs/mainconda-forge/linux-64::setuptoolsreadline-658.6.32-py39h06a4308h8228510_01
  sqlitesetuptools             pkgs/main/linux-64::sqlite-3.40.1-h5082296conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
  tk                 pkgsconda-forge/main/linux-64::tk-8.6.1213-h1ccaba5noxft_h4845f30_0101
  tzdata             pkgsconda-forge/main/noarch::tzdata-2022g2024a-h04d1e81h0c530f3_0
  wheel              pkgs/main/linux-64conda-forge/noarch::wheel-0.3843.40-py39h06a4308pyhd8ed1ab_01
  xz                 pkgs/mainconda-forge/linux-64::xz-5.2.10-h5eee18b_1
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b6-h166bdaf_0

Proceed ([y]/n)? y
...
username@lanta:~>

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
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
username@lanta:~>

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
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
username@lanta:~>

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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