Goal: Demonstrate a basic conda environment creation workflow by creating a Python environment that contains the numpy and pandas packages.

General Process

[]$ module load miniconda3/24.3.0
[]$ conda search python
[]$ conda create -n py_env
[]$ conda activate py_env
(py_env) []$ conda install python=3.12.4
(py_env) []$ python --version
Python 3.12.4
(py_env) []$ conda search numpy
(py_env) []$ conda install numpy
(py_env) []$ python -c "import numpy; print(numpy.__version__)"
1.26.4
(py_env) []$ conda deactivate
[]$

Search for Packages

[]$ conda search python
Loading channels: done
# Name                       Version           Build  Channel
python                        2.7.13     hac47a24_15  pkgs/main
...
python                        3.12.3      h996f2a0_1  pkgs/main
python                        3.12.4      h5148396_1  pkgs/main

Notice: Although Python version 2 has been deprecated, it is still used for old packages/modules/scripts. You can create a conda environment that provides this old, no longer supported version.

This is how ARCC provides this version on the cluster.

(py_env) []$ conda search numpy
Loading channels: done
# Name                       Version           Build  Channel
numpy                          1.9.3 py27_nomklhbee5d10_3  pkgs/main
...
numpy                         1.26.4  py39heeff2f4_0  pkgs/main

Create an Environment

[]$ conda create -n py_env
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##
  environment location: /home/salexan5/.conda/envs/py_env

Proceed ([y]/n)? y

Note the location that the environment will be saved to: environment location: /home/salexan5/.conda/envs/py_env

Create an Environment: Proceed

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate py_env
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Note the command required to activate your environment: conda activate py_env

This will be required every time you wish to use it.

Activate an Environment

[]$ conda activate py_env
(py_env) []$

Note how the command line prompt has changed once the environment has been activated: (py_env) [...]

This indicates the name of the conda environment that is currently active.

Conda Install a Version of Python

(py_env) []$ conda install python=3.12.4

Output of what is happening:

(py_env) []$ conda install python=3.12.4
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/salexan5/.conda/envs/py_env

  added / updated specs:
    - python=3.12.4

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pip-24.0                   |  py312h06a4308_0         3.3 MB
    setuptools-69.5.1          |  py312h06a4308_0         1.3 MB
    wheel-0.43.0               |  py312h06a4308_0         142 KB
    ------------------------------------------------------------
                                           Total:         4.7 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
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6
  ca-certificates    pkgs/main/linux-64::ca-certificates-2024.3.11-h06a4308_0
  expat              pkgs/main/linux-64::expat-2.6.2-h6a678d5_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1
  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
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
  openssl            pkgs/main/linux-64::openssl-3.0.14-h5eee18b_0
  pip                pkgs/main/linux-64::pip-24.0-py312h06a4308_0
  python             pkgs/main/linux-64::python-3.12.4-h5148396_1
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0
  setuptools         pkgs/main/linux-64::setuptools-69.5.1-py312h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0
  tk                 pkgs/main/linux-64::tk-8.6.14-h39e8969_0
  tzdata             pkgs/main/noarch::tzdata-2024a-h04d1e81_0
  wheel              pkgs/main/linux-64::wheel-0.43.0-py312h06a4308_0
  xz                 pkgs/main/linux-64::xz-5.4.6-h5eee18b_1
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Note all the addition dependencies/libraries that are being installed into the environment

Lets check the version installed, within are active environment.

(py_env) []$ python --version
Python 3.12.4

Conda Install the numpy Package

(py_env) []$ conda install numpy

Output of what is happening:

(py_env) []$ conda install numpy
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/salexan5/.conda/envs/py_env

  added / updated specs:
    - numpy

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    mkl-service-2.4.0          |  py312h5eee18b_1          66 KB
    mkl_fft-1.3.8              |  py312h5eee18b_0         204 KB
    mkl_random-1.2.4           |  py312hdb19cb5_0         284 KB
    numpy-1.26.4               |  py312hc5e2394_0          11 KB
    numpy-base-1.26.4          |  py312h0da6c21_0         7.7 MB
    ------------------------------------------------------------
                                           Total:         8.2 MB

The following NEW packages will be INSTALLED:

  blas               pkgs/main/linux-64::blas-1.0-mkl
  intel-openmp       pkgs/main/linux-64::intel-openmp-2023.1.0-hdb19cb5_46306
  mkl                pkgs/main/linux-64::mkl-2023.1.0-h213fc3f_46344
  mkl-service        pkgs/main/linux-64::mkl-service-2.4.0-py312h5eee18b_1
  mkl_fft            pkgs/main/linux-64::mkl_fft-1.3.8-py312h5eee18b_0
  mkl_random         pkgs/main/linux-64::mkl_random-1.2.4-py312hdb19cb5_0
  numpy              pkgs/main/linux-64::numpy-1.26.4-py312hc5e2394_0
  numpy-base         pkgs/main/linux-64::numpy-base-1.26.4-py312h0da6c21_0
  tbb                pkgs/main/linux-64::tbb-2021.8.0-hdb19cb5_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Again, note all the addition dependencies/libraries that are being installed into the environment

If no package version is defined, typically it’ll install the latest version.

Lets check the version installed, within are active environment.

(py_env) []$ python -c "import numpy; print(numpy.__version__)"
1.26.4

Packages are being updated on a frequent basis.
When this workshop was created numpy/1.26.4 was the latest version.
As of 20240815, version 2.0.1 is available, and in a few weeks a newer version will likely be available.
If you do not define a version, then the latest will be installed.

Conda Deactivate your Environment

(py_env) []$ conda deactivate
[]$

Note how the command line prompt has changed, reverting back to before being activated: [...]

The conda environment is no longer activate and can not be used.

[]$ python --version
Python 3.12.2

[]$ python -c "import numpy; print(numpy.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'

Using the Environment

[]$ module load miniconda3/24.3.0
[]$ conda activate py_env
(py_env) []$ python --version
Python 3.12.4
(py_env) []$ python -c "import numpy; print(numpy.__version__)"
1.26.4
(py_env) []$ conda deactivate
[]$

Note how the conda environment must be activated to use it.

Adding to an Existing Environment

[]$ module load miniconda3/24.3.0
[]$ conda activate py_env
(py_env) []$ conda install pandas
(py_env) []$ python py_test.py
Python: 3.12.4 | packaged by Anaconda, Inc. | (main, Jun 18 2024, 15:12:24) [GCC 11.2.0]
Numpy: 1.26.4
Pandas: 2.2.2
(py_env) []$ conda deactivate

py_test.py

import sys
import numpy
import pandas

print("Python: " + str(sys.version))
print("Numpy: " + str(numpy.__version__))
print("Pandas: " + str(pandas.__version__))

Installation Output:

(py_env) []$ conda install pandas
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/salexan5/.conda/envs/py_env

  added / updated specs:
    - pandas


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bottleneck-1.3.7           |  py312ha883a20_0         140 KB
    numexpr-2.8.7              |  py312hf827012_0         149 KB
    pandas-2.2.2               |  py312h526ad5a_0        15.4 MB
    python-dateutil-2.9.0post0 |  py312h06a4308_2         318 KB
    pytz-2024.1                |  py312h06a4308_0         220 KB
    ------------------------------------------------------------
                                           Total:        16.2 MB

The following NEW packages will be INSTALLED:

  bottleneck         pkgs/main/linux-64::bottleneck-1.3.7-py312ha883a20_0
  numexpr            pkgs/main/linux-64::numexpr-2.8.7-py312hf827012_0
  pandas             pkgs/main/linux-64::pandas-2.2.2-py312h526ad5a_0
  python-dateutil    pkgs/main/linux-64::python-dateutil-2.9.0post0-py312h06a4308_2
  python-tzdata      pkgs/main/noarch::python-tzdata-2023.3-pyhd3eb1b0_0
  pytz               pkgs/main/linux-64::pytz-2024.1-py312h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

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What is Conda? Using Miniconda3 on the Cluster

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Intro to Using Conda

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Conda Configuration and Environments

Example 01: Python, Numpy and Pandas Environment