Table of Contents

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General Process

Info

Below demonstrates the general process for:

Setting up your environment to use Conda via a module load.
How to create a conda environment.
How to activate/start your environment and install packages.
How to then use what you’ve installed.
And then how to deactivate/finish using your environment.

Code Block

[salexan5@mblog1 ~]$ module load miniconda3purge
[]$ module load miniconda3/24.3.0
[salexan5@mblog1 ~]$ conda search python
[salexan5@mblog1 ~]$ conda create -n py_env
[salexan5@mblog1 ~]$ conda activate py_env
(py_env) [salexan5@mblog1 ~]$ conda install python=3.12.4
(py_env) [salexan5@mblog1 ~]$ python --version
Python 3.12.4
(py_env) [salexan5@mblog1 ~]$ conda search numpy
(py_env) [salexan5@mblog1 ~]$ conda install numpy
(py_env) [salexan5@mblog1 ~]$ python -c "import numpy; print(numpy.__version__)"
1.26.4
(py_env) [salexan5@mblog1 ~]$ conda deactivate
[salexan5@mblog1 ~]$

...

Search for Packages

Info
Conda enables you look up and search for packages and what versions are available.

Code Block

[salexan5@mblog1 ~]$ 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

(py_env) [salexan5@mblog1 ~

Info

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.

Code Block

...

Create an Environment

Info

Use the create sub command to create your environment.

The -n option will create your environment (which is just a folder) in the default configured location.

Out the box, this will be under: /home/<username>/.conda/envs/

Code Block

[]$ conda searchcreate numpy
Loading channels-n py_env
Channels:
done #- Namedefaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

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

 Version           Build  Channel
numpy             Proceed ([y]/n)? y

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

...

Create an Environment: Proceed

Code Block

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate py_env
#
# To deactivate 1.9.3 py27_nomklhbee5d10_3  pkgs/main
...
numpyan active environment, use
#
#     $                    1.26.4  py39heeff2f4_0  pkgs/main

Create an Environment

Code Block
[salexan5@mblog1 ~conda deactivate

Info

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

Info

Before you can use a conda environment it must be activated.

Every time you want to use it, you must remember to activate it.

Code Block

[]$ conda create -n activate py_env
(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

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

Create an Environment: Proceed

Code Block

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

Info

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

Code Block
[salexan5@mblog1 ~]$ conda activate py_env (py_env) [salexan5@mblog1 ~]$

Info

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

Code Block
(py_env) [salexan5@mblog1 ~]$ conda install python=3.12.4

(py_env) [salexan5@mblog1 ~]$ 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

[]$

Expand

title	Output of what is happening:

Code Block

Info

Note: See 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

Info
Once a conda environment is active, you can start to use it, and one aspect of this is to install conda packages.

Code Block
(py_env) []$ conda install python=3.12.4

Expand

title	Output of what is happening:

Code Block

(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
 build
       ------------------------------------------|-----------------
    pip-24.0
                  |  py312h06a4308_0         3.3 MB     setuptools-69.5.1          |  py312h06a4308_0         1.3 MB
    wheel-0.43.0   Total:         4.7 MB

|The following py312h06a4308_0NEW packages will be INSTALLED:

  _libgcc_mutex 142 KB     ------------------------------------------------------------
  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                Total:pkgs/main/linux-64::expat-2.6.2-h6a678d5_0
  ld_impl_linux-64      4.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutexpkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  libffi             pkgs/main/linux-64::_libgcc_mutex-0.1-mainlibffi-3.4.4-h6a678d5_1
  libgcc-ng    _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
  bzip2 libgcc-ng-11.2.0-h1234567_1
  libgomp             pkgs/main/linux-64::bzip2libgomp-111.2.0.8-h5eee18bh1234567_61
  ca-certificateslibstdcxx-ng       pkgs/main/linux-64::calibstdcxx-certificatesng-202411.32.110-h06a4308h1234567_01
  expat        libuuid      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_1libuuid-1.41.5-h5eee18b_0
  libffincurses             pkgs/main/linux-64::libffincurses-3.46.4-h6a678d5_10
  openssl libgcc-ng           pkgs/main/linux-64::libgccopenssl-ng-113.20.014-h1234567_1h5eee18b_0
  pip    libgomp            pkgs/main/linux-64::libgomppip-11.224.0-h1234567_1py312h06a4308_0
  python      libstdcxx-ng       pkgs/main/linux-64::libstdcxxpython-ng-113.212.04-h1234567h5148396_1
  libuuid readline           pkgs/main/linux-64::libuuidreadline-18.41.52-h5eee18b_0
  ncursessetuptools            pkgs/main/linux-64::ncursessetuptools-669.5.41-h6a678d5py312h06a4308_0
  sqlite openssl            pkgs/main/linux-64::opensslsqlite-3.045.143-h5eee18b_0
  tk pip                pkgs/main/linux-64::piptk-248.6.014-py312h06a4308h39e8969_0
  pythontzdata             pkgs/main/linux-64noarch::python-3.12.4-h5148396_1tzdata-2024a-h04d1e81_0
  wheel   readline           pkgs/main/linux-64::readlinewheel-80.43.20-h5eee18bpy312h06a4308_0
  xz   setuptools              pkgs/main/linux-64::setuptoolsxz-695.54.16-py312h06a4308h5eee18b_01
  zlib  sqlite             pkgs/main/linux-64::sqlitezlib-31.452.313-h5eee18b_01

 tk  Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing  pkgs/main/linux-64::tk-8.6.14-h39e8969_0
  tzdata             pkgs/main/noarch::tzdata-2024a-h04d1e81_0
  wheeltransaction: done

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

Lets check the version installed, within are active environment.

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

...

Conda Install the numpy Package

Info
Let’s first check if `numpy` is available as a package, and if it is, which versions are available.

Code Block

(py_env) []$ conda search numpy
Loading channels: done
# Name

pkgs/main/linux-64::wheel-0.43.0-py312h06a4308_0

xz

     Version

pkgs/main/linux-64::xz-5.4.6-h5eee18b_1 zlib

Build  Channel
numpy

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

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

Lets check the version installed, within are active environment.

Code Block
(py_env) [salexan5@mblog1 ~]$ python --version Python 3.12.4

...

1.9.3 py27_nomklhbee5d10_3  pkgs/main
...
numpy                         1.26.4  py39heeff2f4_0  pkgs/main

Code Block
(py_env) [

...

]$ conda install numpy

Expand

title	Output of what is happening:

Code Block
(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

Info

...

(Again) Note: See 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.

Code Block
(py_env) [salexan5@mblog1 ~]$ python -c "import numpy; print(numpy.__version__)" 1.26.4

...

Conda Deactivate your Environment

Code Block
(py_env) [salexan5@mblog1 ~]$ conda deactivate [salexan5@mblog1 ~]$

Info

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.

Code Block

[salexan5@mblog1 ~]$ python --version
Python 3.12.2

[salexan5@mblog1 ~]$ python -c "import numpy; print(numpy.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'

...

(Re-)Using the Environment

Info

To re-use a conda environment, you must activate it again.

But, you do not have to re-create it. Creation only happens once.

Code Block

[salexan5@mblog1 ~]$ module purge
[]$ module load miniconda3/24.3.0
[salexan5@mblog1 ~]$ conda activate py_env
(py_env) [salexan5@mblog1 ~]$ python --version
Python 3.12.4
(py_env) [salexan5@mblog1 ~]$ python -c "import numpy; print(numpy.__version__)"
1.26.4
(py_env) [salexan5@mblog1 ~]$ conda deactivate
[salexan5@mblog1 ~]$

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

...

Adding to an Existing Environment

Info

Although we only need to create a conda environment once, we can add/update it every time we use it.

Let’s go back into are existing conda environment and add the pandas package.

Code Block

[salexan5@mblog1 ~]$ module purge
[]$ module load miniconda3/24.3.0
[salexan5@mblog1 ~]$ conda activate py_env
(py_env) [salexan5@mblog1 ~]$ conda install pandas
(py_env) [salexan5@mblog1 ~]$ 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) [salexan5@mblog1 ~]$ conda deactivate

Expand

title	py_test.py

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

Expand

title	Installation Output:

Code Block

(py_env) [salexan5@mblog1 ~]$ 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

...

Versions Compared

Old Version 10

New Version Current

Key

General Process

Search for Packages

Create an Environment

Create an Environment: Proceed

Create an Environment

Activate an Environment

Create an Environment: Proceed

Activate an Environment

Conda Install a Version of Python

Conda Install a Version of Python

Conda Install the numpy Package

Conda Deactivate your Environment

(Re-)Using the Environment

Adding to an Existing Environment

Page Comparison

Versions Compared

Old Version 10

New Version Current

Key

General Process

Search for Packages

Create an Environment

Create an Environment: Proceed

Create an Environment

Activate an Environment

Create an Environment: Proceed

Activate an Environment

Conda Install a Version of Python

Conda Install a Version of Python

Conda Install the numpy Package

Conda Deactivate your Environment

(Re-)Using the Environment

Adding to an Existing Environment