Versions Compared

Version Old Version 13 New Version Current
Changes made by

Yutthana Wongnongwa

Yutthana Wongnongwa

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

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:~> module unload Mamba

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

Code Block
username@lanta:~> conda env list
# 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-2.612.01
(tensorflow-2.612.01) username@lanta:~>

Creating an environment in the user’s home

...

Deactivate your environment

Use the conda create -n myenv commands to create the environment with myenv namedeactivate command to deactivate your environments.

Code Block
(tensorflow-2.12.1) username@lanta:~> conda create 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
CollectingChannels:
package metadata (current_- conda-forge
Platform: linux-64
Collecting package metadata (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               |     py39h06a4308pyhd8ed1ab_01          15057 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         270 KB22.8 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/mainconda-forge/linux-64::_libgcc_mutex-0.1-mainconda_forge
  _openmp_mutex      pkgsconda-forge/main/linux-64::_openmp_mutex-4.5.1-12_gnu
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.01.10-h06a4308_0bzip2   certifi            pkgs/mainconda-forge/linux-64::certifibzip2-20221.120.78-py39h06a4308hd590300_05
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0
  ld_impl_linux-64   pkgs/mainconda-forge/linux-64::ld_impl_linux-64-2.3840-h1181459h41732ed_10
  libffi             pkgs/mainconda-forge/linux-64::libffi-3.4.2-h6a678d5h7f98852_65
  libgcc-ng          pkgsconda-forge/main/linux-64::libgcc-ng-1113.2.0-h1234567h807b86a_15
  libgomp            pkgsconda-forge/main/linux-64::libgomp-1113.2.0-h1234567h807b86a_15
  libstdcxx-nglibnsl             pkgs/mainconda-forge/linux-64::libstdcxxlibnsl-ng-11.2.0.1-h1234567hd590300_10
  ncurseslibsqlite            pkgs/mainconda-forge/linux-64::ncurseslibsqlite-63.45.42-h6a678d5h2797004_0
  openssllibuuid            pkgs/mainconda-forge/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
  ncurses readline           pkgs/mainconda-forge/linux-64::readlinencurses-86.4.220240210-h5eee18bh59595ed_0
  openssl setuptools           pkgs/mainconda-forge/linux-64::setuptoolsopenssl-653.62.31-py39h06a4308hd590300_01
  sqlitepip                pkgs/main/linux-64conda-forge/noarch::sqlitepip-324.40.10-h5082296pyhd8ed1ab_0
  tkpython                 pkgs/main/conda-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/main/linux-64conda-forge/noarch::zlib-1.2.13-h5eee18btzdata-2024a-h0c530f3_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 scipy.

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
    --------------------------- wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0

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

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 numpy.

Code Block
username@lanta:~> conda create -n myenv python=3.9 numpy=1.23.5
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (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
    ---------------------------|-----------------
    blaslibblas-13.9.0                   ||21_linux64_openblas          14 KB  conda-forge
mkl    libcblas-3.9.0       6 KB     ca-certificates-2023.01.10 ||21_linux64_openblas       h06a4308_0   14 KB   conda-forge
 120 KB     certifi-2022.12.7libgfortran-ng-13.2.0      |    |   py39h06a4308h69a702a_05          15023 KB  conda-forge
  intel-openmp-2021.4  liblapack-3.9.0       |     h06a4308_3561|21_linux64_openblas          4.2 MB14 KB  conda-forge
    mklnumpy-20211.423.05               |   py39h3d75532_0  h06a4308_640       1425.6 MB  conda-forge
   mkl-service-2.4.0 python-3.9.19           |   py39h7f8727e|h0755675_0_cpython        22.7 MB 59 KBconda-forge
    mklpython_fftabi-1.3.1 9             |   py39hd3c417c_0         182 KB
    mkl_random-1.2.24_cp39           |6 KB  py39h51133e4_0conda-forge
        309 KB
    numpy-1.23.5wheel-0.43.0               |   py39h14f4228  pyhd8ed1ab_01          1057 KB     numpy-base-1.23.5conda-forge
         |   py39h31eccc5_0         6.7 MB
    -------------------------------------------------------------
                                           Total:       154 28.34 MB

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
  blasbzip2               pkgs/main/conda-forge/linux-64::blasbzip2-1.0.8-mklhd590300_5
  ca-certificates    pkgsconda-forge/main/linux-64::ca-certificates-20232024.012.102-h06a4308hbcca054_0
  certifild_impl_linux-64            pkgs/main/conda-forge/linux-64::certifi-2022.12.7-py39h06a4308_0
  intel-openmpld_impl_linux-64-2.40-h41732ed_0
  libblas            pkgs/mainconda-forge/linux-64::intellibblas-openmp-20213.49.0-h06a4308_356121_linux64_openblas
  libcblas        ld_impl_linux-64   pkgsconda-forge/main/linux-64::ld_impl_linux-64-2.38-h1181459_1libcblas-3.9.0-21_linux64_openblas
  libffi             pkgs/mainconda-forge/linux-64::libffi-3.4.2-h6a678d5h7f98852_65
  libgcc-ng          pkgsconda-forge/main/linux-64::libgcc-ng-1113.2.0-h1234567h807b86a_15
  libgomplibgfortran-ng            pkgs/main/conda-forge/linux-64::libgomplibgfortran-ng-1113.2.0-h1234567h69a702a_15
  libstdcxx-nglibgfortran5       pkgs/mainconda-forge/linux-64::libstdcxxlibgfortran5-ng-1113.2.0-h1234567ha4646dd_15
  mkllibgomp                pkgs/mainconda-forge/linux-64::mkllibgomp-202113.42.0-h06a4308h807b86a_6405
  liblapack mkl-service         pkgsconda-forge/main/linux-64::mklliblapack-service-23.49.0-py39h7f8727e21_linux64_0openblas
  mkl_fftlibnsl             pkgsconda-forge/main/linux-64::mkl_fftlibnsl-12.30.1-py39hd3c417chd590300_0
  mkl_randomlibopenblas         pkgs/mainconda-forge/linux-64::mkl_randomlibopenblas-10.23.226-py39h51133e4pthreads_h413a1c8_0
  ncurseslibsqlite            pkgs/main/conda-forge/linux-64::ncurseslibsqlite-63.45.42-h6a678d5h2797004_0
  numpylibstdcxx-ng              pkgs/mainconda-forge/linux-64::numpylibstdcxx-ng-113.232.50-py39h14f4228_0h7e041cc_5
  libuuid   numpy-base         pkgs/mainconda-forge/linux-64::numpylibuuid-base-12.2338.51-py39h31eccc5h0b41bf4_0
  openssllibxcrypt            pkgs/main/conda-forge/linux-64::openssllibxcrypt-14.14.1t36-h7f8727ehd590300_01
  piplibzlib                pkgs/mainconda-forge/linux-64::piplibzlib-221.32.113-py39h06a4308hd590300_05
  pythonncurses             pkgs/main/conda-forge/linux-64::pythonncurses-36.94.1620240210-h7a1cb2ah59595ed_0
  numpy  readline            pkgs/mainconda-forge/linux-64::readlinenumpy-81.23.25-h5eee18bpy39h3d75532_0
  setuptoolsopenssl            pkgsconda-forge/main/linux-64::setuptoolsopenssl-653.62.31-py39h06a4308hd590300_01
  sixpip                pkgs/mainconda-forge/noarch::sixpip-124.16.0-pyhd3eb1b0pyhd8ed1ab_10
  sqlitepython             pkgsconda-forge/main/linux-64::sqlitepython-3.409.119-h5082296h0755675_0_cpython
  tkpython_abi                 pkgs/main/conda-forge/linux-64::tkpython_abi-83.6.129-h1ccaba54_0cp39
  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/main/conda-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
...
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
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-20233.019.1019 |       h06a4308_0      |h0755675_0_cpython   120 KB     certifi-2022.12.722.7 MB  conda-forge
    wheel-0.43.0               |     py39h06a4308pyhd8ed1ab_01          15057 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         270 KB22.8 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/mainconda-forge/linux-64::_libgcc_mutex-0.1-mainconda_forge
  _openmp_mutex      pkgsconda-forge/main/linux-64::_openmp_mutex-4.5.1-12_gnu
  ca-certificatesbzip2        pkgs/main/      conda-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       pkgs/mainconda-forge/linux-64::libstdcxxlibnsl-ng-11.2.0.1-h1234567hd590300_10
  ncurseslibsqlite            pkgs/main/conda-forge/linux-64::ncurseslibsqlite-63.45.42-h6a678d5h2797004_0
  openssllibuuid            pkgs/mainconda-forge/linux-64::openssllibuuid-12.38.1.1t-h7f8727eh0b41bf4_0
  piplibxcrypt                pkgs/main/conda-forge/linux-64::piplibxcrypt-224.34.136-py39h06a4308hd590300_01
  pythonlibzlib             pkgs/mainconda-forge/linux-64::pythonlibzlib-31.92.1613-h7a1cb2ahd590300_05
  ncurses readline           pkgs/mainconda-forge/linux-64::readlinencurses-86.4.220240210-h5eee18bh59595ed_0
  setuptoolsopenssl         pkgs/main/   conda-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/main/conda-forge/linux-64::tkpython-83.69.1219-h1ccaba5h0755675_0_cpython
  tzdatareadline             pkgs/mainconda-forge/linux-64::readline-8.2-h8228510_1
  setuptools         conda-forge/noarch::tzdata-2022g-h04d1e81_0setuptools-69.2.0-pyhd8ed1ab_0
  tk   wheel              pkgsconda-forge/main/linux-64::wheeltk-08.386.413-py39h06a4308_0noxft_h4845f30_101
  tzdata        xz     conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_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
Channels:
 - conda-forge
Platform:  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
...
username@lanta:~>

Activate your environment in the project’s home

Code Block
username@lanta:~> conda activate
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

Creating an environment from an environment.yml file

A simple environment.yml file

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

...


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

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

Code Block
username@lanta:~> conda env create -f environment.yml

...

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:~> conda envrm create -f environment.yml --prefix-rf /your project directory/envs

...

Related articles

Filter by label (Content by label)
showLabelsfalse
max5
spacescom.atlassian.confluence.content.render.xhtml.model.resource.identifiers.SpaceResourceIdentifier@48ae393
showSpacefalse
sortmodified
showSpacetypefalsepage
reversetrue
typelabelspagesingularity python container
cqllabel in ( "vir-env" , "python-script" , "jupyter" ) and space = currentSpace ( )labelssingularity python container