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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 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
(tensorflow-2.12.1) 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
...

...

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          15057 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        22.8 270MB
KB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgsconda-forge/main/linux-64::_libgcc_mutex-0.1-mainconda_forge
  _openmp_mutex      pkgsconda-forge/main/linux-64::_openmp_mutex-4.5.1-12_gnu
  bzip2         ca-certificates     pkgs/mainconda-forge/linux-64::cabzip2-certificates-20231.010.108-h06a4308hd590300_05
  certifica-certificates            pkgs/main/conda-forge/linux-64::certifica-certificates-20222024.122.72-py39h06a4308hbcca054_0
  ld_impl_linux-64   pkgsconda-forge/main/linux-64::ld_impl_linux-64-2.3840-h1181459h41732ed_10
  libffi             pkgsconda-forge/main/linux-64::libffi-3.4.2-h6a678d5h7f98852_65
  libgcc-ng          pkgsconda-forge/main/linux-64::libgcc-ng-1113.2.0-h1234567h807b86a_15
  libgomp            pkgs/mainconda-forge/linux-64::libgomp-1113.2.0-h1234567_1h807b86a_5
  libnsl      libstdcxx-ng       pkgsconda-forge/main/linux-64::libstdcxx-nglibnsl-11.2.0.1-h1234567hd590300_10
  ncurseslibsqlite            pkgs/main/conda-forge/linux-64::ncurseslibsqlite-63.45.42-h6a678d5h2797004_0
  openssllibuuid            pkgsconda-forge/main/linux-64::openssllibuuid-12.38.1.1t-h7f8727eh0b41bf4_0
  piplibxcrypt                pkgs/main/conda-forge/linux-64::piplibxcrypt-224.34.136-py39h06a4308hd590300_01
  pythonlibzlib             pkgs/main/conda-forge/linux-64::pythonlibzlib-31.92.1613-h7a1cb2ahd590300_05
  readlinencurses            pkgsconda-forge/main/linux-64::readlinencurses-86.24.20240210-h5eee18bh59595ed_0
  openssl   setuptools         pkgs/mainconda-forge/linux-64::setuptoolsopenssl-653.62.31-py39h06a4308_0hd590300_1
  pip   sqlite             pkgs/main/linux-64conda-forge/noarch::sqlitepip-324.40.10-h5082296pyhd8ed1ab_0
  tkpython                 pkgs/mainconda-forge/linux-64::tkpython-83.69.1219-h1ccaba5h0755675_0_cpython
  tzdatareadline             pkgs/main/noarchconda-forge/linux-64::tzdatareadline-2022g8.2-h04d1e81h8228510_01
  wheelsetuptools              pkgs/main/linux-64::wheel-0.38.4-py39h06a4308conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
  xztk                 pkgsconda-forge/main/linux-64::xztk-58.26.1013-h5eee18bnoxft_h4845f30_1101
  zlibtzdata               pkgs/mainconda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/linux-64::zlibxz-15.2.136-h5eee18bh166bdaf_0

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

...

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           6 KB
    ca-certificates-2023.01.10 |---
      h06a4308_libblas-3.9.0         120 KB     certifi-2022.12.7|21_linux64_openblas          14 |KB  conda-forge
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  142.6 MBconda-forge
     mkl-service-2.4liblapack-3.9.0          |   py39h7f8727e_0|21_linux64_openblas          5914 KB  conda-forge
    mkl_fftnumpy-1.323.15               |   py39hd3c417cpy39h3d75532_0         182 KB5.6 MB  conda-forge
    mkl_randompython-13.29.219           |   py39h51133e4|h0755675_0_cpython        22.7 MB 309 KBconda-forge
    numpypython_abi-1.23.53.9             |        |   py39h14f42284_0cp39           106 KB  conda-forge
    numpywheel-base-10.23.543.0               |   py39h31eccc5_0  pyhd8ed1ab_1          57  6.7 MBKB  conda-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      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2 Total:       154.3 MB  The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main conda-forge/linux-64::bzip2-1.0.8-hd590300_5
  ca-certificates    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-64-52.140-1h41732ed_gnu0
  blaslibblas               pkgs/main/conda-forge/linux-64::blaslibblas-1.0-mkl3.9.0-21_linux64_openblas
  libcblas       ca-certificates    pkgs/mainconda-forge/linux-64::calibcblas-certificates-20233.019.100-h06a4308_021_linux64_openblas
  libffi certifi            pkgs/mainconda-forge/linux-64::certifilibffi-20223.124.72-py39h06a4308h7f98852_05
  intel-openmplibgcc-ng          pkgsconda-forge/main/linux-64::intellibgcc-openmpng-202113.42.0-h06a4308h807b86a_35615
  ld_impl_linux-64libgfortran-ng     pkgs/mainconda-forge/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
  libgomp  liblapack          pkgs/mainconda-forge/linux-64::libgompliblapack-113.29.0-h1234567_121_linux64_openblas
  libnsl      libstdcxx-ng       pkgsconda-forge/main/linux-64::libstdcxxlibnsl-ng-11.2.0.1-h1234567hd590300_10
  mkllibopenblas                pkgs/main/conda-forge/linux-64::mkllibopenblas-20210.43.026-h06a4308_640
  mkl-servicepthreads_h413a1c8_0
  libsqlite          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/mainconda-forge/linux-64::ncurseslibxcrypt-64.4.36-h6a678d5hd590300_01
  numpylibzlib              pkgs/mainconda-forge/linux-64::numpylibzlib-1.232.513-py39h14f4228_0hd590300_5
  ncurses   numpy-base         pkgsconda-forge/main/linux-64::numpyncurses-base-16.234.520240210-py39h31eccc5h59595ed_0
  numpy openssl             pkgsconda-forge/main/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-324.9.160-h7a1cb2apyhd8ed1ab_0
  readlinepython             pkgsconda-forge/main/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                 pkgsconda-forge/main/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                 pkgsconda-forge/main/linux-64::xz-5.2.10-h5eee18b_1
  zlib               pkgs/main/linux-64::zlib-1.2.136-h5eee18bh166bdaf_0

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

Creating the environment in the project’s home

Specify a location for the environment

...

Code Block
username@lanta:~> conda create --prefix /your 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
...

...

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 MB  conda-forge
    wheel-0.43.0 120 KB     certifi-2022.12.7        |  |   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:         270 KB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/mainconda-forge/linux-64::bzip2-1.0.8-hd590300_5
  ca-certificates    conda-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-2022.12.7-py39h06a4308_0
  ld_impl_linux-64   pkgs/main13.2.0-h807b86a_5
  libnsl             conda-forge/linux-64::ld_impl_linux-64-2.38-h1181459_1libnsl-2.0.1-hd590300_0
  libffilibsqlite             pkgs/mainconda-forge/linux-64::libffilibsqlite-3.445.2-h6a678d5h2797004_60
  libuuid libgcc-ng           pkgsconda-forge/main/linux-64::libgcclibuuid-ng-112.238.01-h1234567h0b41bf4_10
  libgomplibxcrypt            pkgs/mainconda-forge/linux-64::libgomplibxcrypt-114.24.036-h1234567hd590300_1
  libzlib   libstdcxx-ng         pkgsconda-forge/main/linux-64::libstdcxxlibzlib-ng-111.2.013-h1234567hd590300_15
  ncurses            pkgsconda-forge/main/linux-64::ncurses-6.4.20240210-h6a678d5h59595ed_0
  openssl            pkgsconda-forge/main/linux-64::openssl-13.2.1.1t-h7f8727ehd590300_01
  pip                pkgs/main/linux-64conda-forge/noarch::pip-2224.3.10-py39h06a4308pyhd8ed1ab_0
  python             pkgs/mainconda-forge/linux-64::python-3.9.1619-h7a1cb2ah0755675_0_cpython
  readline           pkgs/mainconda-forge/linux-64::readline-8.2-h5eee18bh8228510_01
  setuptools         pkgs/main/linux-64::setuptools-65.6.3-py39h06a4308_0
  sqlite             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             pkgsconda-forge/main/noarch::tzdata-2022g-h04d1e81_0
  wheel              pkgs/main/linux-64::wheel-0.38.4-py39h06a43082024a-h0c530f3_0
  xzwheel                 pkgs/main/linux-64::xz-5.2.10-h5eee18b_1
  zlibconda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 pkgs/mainconda-forge/linux-64::zlibxz-15.2.136-h5eee18bh166bdaf_0

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

...

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

...

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

...

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

Removing the environment

Remove the environment in the user’s home

...

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

...

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