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Create an Example Environment

Info

To help demonstrate the various concepts, lets create the following environment:

Code Block
[] cd /project/<project-name>/<username>/conda
[]$ module purge
[]$ module load miniconda3/24.3.0
[]$ conda create -p py_conda_pip_env python=3.12
[]$ conda activate /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ python --version
Python 3.12.4
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ which python
/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/bin/python
# Create a self contined environment i.e don't install anything into the local home folder.
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ export PYTHONUSERBASE=$CONDA_PREFIX
# Use conda to install: numpy
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ conda install numpy
# Use pip to install: nltk
# has dependencies: click, joblib, regex and tqdm
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ pip install nltk

...

What is Installed? conda list

Info

The conda list command will provide details of all packages as well as conda environment libraries:

Code Block
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ conda list
...
click                     8.1.7                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
nltk                      3.8.1                    pypi_0    pypi
numpy                     2.0.1           py312h1103770_0    conda-forge
regex                     2024.7.24                pypi_0    pypi
tqdm                      4.66.4                   pypi_0    pypi
Expand
titlefull conda list
Code Block
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ conda list
# packages in environment at /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
click                     8.1.7                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
libblas                   3.9.0           23_linux64_openblas    conda-forge
libcblas                  3.9.0           23_linux64_openblas    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 14.1.0               h77fa898_0    conda-forge
libgfortran-ng            14.1.0               h69a702a_0    conda-forge
libgfortran5              14.1.0               hc5f4f2c_0    conda-forge
libgomp                   14.1.0               h77fa898_0    conda-forge
liblapack                 3.9.0           23_linux64_openblas    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.27          pthreads_hac2b453_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libstdcxx-ng              14.1.0               hc0a3c3a_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
ncurses                   6.5                  h59595ed_0    conda-forge
nltk                      3.8.1                    pypi_0    pypi
numpy                     2.0.1           py312h1103770_0    conda-forge
openssl                   3.3.1                h4bc722e_2    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
python                    3.12.4          h194c7f8_0_cpython    conda-forge
python_abi                3.12                    4_cp312    conda-forge
readline                  8.2                  h8228510_1    conda-forge
regex                     2024.7.24                pypi_0    pypi
setuptools                71.0.4             pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tqdm                      4.66.4                   pypi_0    pypi
tzdata                    2024a                h0c530f3_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge

...

What is Installed? pip list -v

Info

The pip list command will only list the explicitly installed pip python packages.

Look at the Installer column to identify what was installed via conda install, pip install, by default.

Code Block
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ pip list -v
Package    Version   Location                                                                                  Installer
---------- --------- ----------------------------------------------------------------------------------------- ---------
click      8.1.7     /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages pip
joblib     1.4.2     /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages pip
nltk       3.8.1     /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages pip
numpy      2.0.1     /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages conda
pip        24.0      /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages
regex      2024.7.24 /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages pip
setuptools 71.0.4    /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages
tqdm       4.66.4    /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages pip
wheel      0.43.0    /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages
Info

Check under the python related lib folder.

Expand
titleList what's in: /project/arcc/salexan5/conda/py_conda_pip_env/lib/python3.12/site-packages/
Code Block
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ ls /project/<project-name>/<username>/conda/py_conda_pip_env/lib/python3.12/site-packages/
click                     joblib                  numpy                     pkg_resources              setuptools                         wheel
click-8.1.7.dist-info     joblib-1.4.2.dist-info  numpy-2.0.1.dist-info     README.txt                 setuptools-71.0.4-py3.12.egg-info  wheel-0.43.0.dist-info
_distutils_hack           nltk                    pip                       regex                      tqdm
distutils-precedence.pth  nltk-3.8.1.dist-info    pip-24.0-py3.12.egg-info  regex-2024.7.24.dist-info  tqdm-4.66.4.dist-info

...

What is Installed? conda env export

Info

The output of the conda env export command you can use to recreate.

Identify what was install via conda install vs pip install:

Code Block
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ conda env export > env.yml
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ cat env.yml
name: /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env
...
dependencies:
...
  - numpy=2.0.1=py312h1103770_0
...
  - python=3.12.4=h194c7f8_0_cpython
...
  - pip:
      - click==8.1.7
      - joblib==1.4.2
      - nltk==3.8.1
      - regex==2024.7.24
      - tqdm==4.66.4
prefix: /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env
Expand
titlefull output:
Code Block
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ conda env export > env.yml
(/cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env) []$ cat env.yml
name: /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - bzip2=1.0.8=h4bc722e_7
  - ca-certificates=2024.7.4=hbcca054_0
  - ld_impl_linux-64=2.40=hf3520f5_7
  - libblas=3.9.0=23_linux64_openblas
  - libcblas=3.9.0=23_linux64_openblas
  - libexpat=2.6.2=h59595ed_0
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=14.1.0=h77fa898_0
  - libgfortran-ng=14.1.0=h69a702a_0
  - libgfortran5=14.1.0=hc5f4f2c_0
  - libgomp=14.1.0=h77fa898_0
  - liblapack=3.9.0=23_linux64_openblas
  - libnsl=2.0.1=hd590300_0
  - libopenblas=0.3.27=pthreads_hac2b453_1
  - libsqlite=3.46.0=hde9e2c9_0
  - libstdcxx-ng=14.1.0=hc0a3c3a_0
  - libuuid=2.38.1=h0b41bf4_0
  - libxcrypt=4.4.36=hd590300_1
  - libzlib=1.3.1=h4ab18f5_1
  - ncurses=6.5=h59595ed_0
  - numpy=2.0.1=py312h1103770_0
  - openssl=3.3.1=h4bc722e_2
  - pip=24.0=pyhd8ed1ab_0
  - python=3.12.4=h194c7f8_0_cpython
  - python_abi=3.12=4_cp312
  - readline=8.2=h8228510_1
  - setuptools=71.0.4=pyhd8ed1ab_0
  - tk=8.6.13=noxft_h4845f30_101
  - tzdata=2024a=h0c530f3_0
  - wheel=0.43.0=pyhd8ed1ab_1
  - xz=5.2.6=h166bdaf_0
  - pip:
      - click==8.1.7
      - joblib==1.4.2
      - nltk==3.8.1
      - regex==2024.7.24
      - tqdm==4.66.4
prefix: /cluster/medbow/project/<project-name>/<username>/conda/py_conda_pip_env

...

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