This article will guide you to create an environment using Miniconda on a LANTA HPC system.
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Using Miniconda on LANTA HPC
Load Miniconda module
Use the
ml av Minicondacommand to see which version of Miniconda is available on the LANTA HPC system.Use the
ml Miniconda3/xx.xx.xcommand to load the Miniconda version that you want to use. If you don't specify a version, the default version (D) is loaded, which is Miniconda3/22.11.1-1.
...
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username@lanta:~> conda env list # conda environments: # base /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1 netcdf-py39 /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1/envs/netcdf-py39 pytorch-1.11.0 /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1/envs/pytorch-1.11.0 tensorflow-2.6.0 /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1/envs/tensorflow-2.6.0 username@lanta:~> conda activate tensorflow-2.6.0 (tensorflow-2.6.0) username@lanta:~> |
Creating an environment in the user’s home
Create an environment
Use the conda create -n myenv commands to create the environment with myenv name.
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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
...
username@lanta:~> |
Create an environment with a specific version of the packages
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username@lanta:~> conda create -n myenv python=3.9
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
---------------------------|-----------------
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
...
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.
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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
...
username@lanta:~> |
Creating an environment in the project’s home
Specify a location for an environment
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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
...
username@lanta:~> |
Specify a location for an environment with a specific version of a package
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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
...
username@lanta:~> |
Activate your environment in the project’s home
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username@lanta:~> conda activate /your project directory/envs (/your project directory/envs) username@lanta:~> |
Creating an environment from an requirements.yml file
A simple requirements.yml file
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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
username@lanta:~> |
Create the environment from the requirements.yml file in the project’s home
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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
username@lanta:~> |
Removing the environment
Remove the environment in the user’s home
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username@lanta:~> rm -rf /your project directory/envs |
...
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