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.
Using Mamba on LANTA HPC
Load Mamba module
Use the
ml av Mambacommand to see which version of Mamba is available on the LANTA HPC system.Use the
ml Mamba/xx.xx.xcommand 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.
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
Unload Mamba module
Use the module unload Mamba command to unload the Mamba.
username@lanta:~> module unload Mamba
Use the module purge command to unload all currently loaded modules.
username@lanta:~> module purge
Before you use the module unload Mamba or module purge command, you must deactivate your environment with the conda deactivate command.
Activate your environment
Use the
conda env listcommand to view a list of your environments.If you want to activate your environment such as TensorFlow-2.6.0, you can use the
conda activate tensorflow-2.12.1command.
username@lanta:~> conda env list # conda environments: # base /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0 netcdf-py39 /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/envs/netcdf-py39 pytorch-2.2.2 /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/envs/pytorch-2.2.2 tensorflow-2.12.1 /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/envs/tensorflow-2.12.1 username@lanta:~> conda activate tensorflow-2.12.1 (tensorflow-2.12.1) username@lanta:~>
Deactivate your environment
Use the conda deactivate command to deactivate your environments.
(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.
username@lanta:~> conda create -n myenv Channels: - conda-forge Platform: linux-64 Collecting package metadata (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.
username@lanta:~> conda create -n myenv python=3.9
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:
- python=3.9
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-3.9.19 |h0755675_0_cpython 22.7 MB conda-forge
wheel-0.43.0 | pyhd8ed1ab_1 57 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 conda-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_impl_linux-64-2.40-h41732ed_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_5
libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_5
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.45.2-h2797004_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.4.20240210-h59595ed_0
openssl conda-forge/linux-64::openssl-3.2.1-hd590300_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.19-h0755675_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata 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
...
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.
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
---------------------------|-----------------
libblas-3.9.0 |21_linux64_openblas 14 KB conda-forge
libcblas-3.9.0 |21_linux64_openblas 14 KB conda-forge
libgfortran-ng-13.2.0 | h69a702a_5 23 KB conda-forge
liblapack-3.9.0 |21_linux64_openblas 14 KB conda-forge
numpy-1.23.5 | py39h3d75532_0 5.6 MB conda-forge
python-3.9.19 |h0755675_0_cpython 22.7 MB conda-forge
python_abi-3.9 | 4_cp39 6 KB conda-forge
wheel-0.43.0 | pyhd8ed1ab_1 57 KB 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 conda-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_impl_linux-64-2.40-h41732ed_0
libblas conda-forge/linux-64::libblas-3.9.0-21_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-21_linux64_openblas
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_5
libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_5
libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_5
libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_5
liblapack conda-forge/linux-64::liblapack-3.9.0-21_linux64_openblas
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libopenblas conda-forge/linux-64::libopenblas-0.3.26-pthreads_h413a1c8_0
libsqlite conda-forge/linux-64::libsqlite-3.45.2-h2797004_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_5
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.4.20240210-h59595ed_0
numpy conda-forge/linux-64::numpy-1.23.5-py39h3d75532_0
openssl conda-forge/linux-64::openssl-3.2.1-hd590300_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.19-h0755675_0_cpython
python_abi conda-forge/linux-64::python_abi-3.9-4_cp39
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata 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
...
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.
username@lanta:~> conda create --prefix /your project directory/envs Channels: - conda-forge Platform: linux-64 Collecting package metadata (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.
username@lanta:~> conda create --prefix /your project directory/envs python=3.9
Channels:
- conda-forge
Platform: linux-64
Collecting package metadata (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
---------------------------|-----------------
python-3.9.19 |h0755675_0_cpython 22.7 MB conda-forge
wheel-0.43.0 | pyhd8ed1ab_1 57 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 conda-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_impl_linux-64-2.40-h41732ed_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_5
libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_5
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.45.2-h2797004_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.4.20240210-h59595ed_0
openssl conda-forge/linux-64::openssl-3.2.1-hd590300_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.19-h0755675_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata 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.
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.
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.
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
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.
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
If you want to remove the myenv environment, you can use the conda remove --name myenv --all command.
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.
username@lanta:~> rm -rf /your project directory/envs