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(Created page with "{| cellspacing="5" cellpadding="0" style="margin: 0em 0em 1em 0em; border: 1px solid #1DA0E7; background: #e03a3a; width: 100%" | '''''Hello UAB Research Computing Community! We have created a new streamlined and user-friendly set of documentation for our services. Please visit https://uabrc.github.io/ for our new documentation site. Please bear in mind the documentation is still a work in progress and subject to change. As part of the process we are deprecating, an...")
 
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[https://conda.io/docs/user-guide/overview.html Conda] is a powerful package manager and environment manager. Conda allows you to maintain distinct environments for your different projects, with dependency packages defined and installed for each project.
{| cellspacing="5" cellpadding="0" style="margin: 0em 0em 1em 0em; border: 1px solid #1DA0E7;  background: #e03a3a; width: 100%"
| '''''Hello UAB Research Computing Community!


===Creating a Conda virtual environment===
First step, direct conda to store files in $USER_DATA to avoid filling up $HOME. Create the '''$HOME/.condarc''' file by running the following code:
<pre>
cat << "EOF" > ~/.condarc
pkgs_dirs:
  - $USER_DATA/.conda/pkgs
envs_dirs:
  - $USER_DATA/.conda/envs
EOF
</pre>


Load one of the conda environments available on Cheaha (Note, starting with Anaconda 2018.12, Anaconda releases changed to using YYYY.MM format for version numbers):
We have created a new streamlined and user-friendly set of documentation for our services. Please visit https://uabrc.github.io/ for our new documentation site. Please bear in mind the documentation is still a work in progress and subject to change.
<pre>
$ module -t avail Anaconda
...
Anaconda3/5.3.0
Anaconda3/5.3.1
Anaconda3/2019.10


</pre>
<pre>
$ module load Anaconda3/2019.10
</pre>


Once you have loaded Anaconda, you can create an environment using the following command (change '''test_env''' to whatever you want to name your environment):
As part of the process we are deprecating, and eventually retiring, the current documentation site here at https://docs.uabgrid.uab.edu/.
<pre>
$ conda create --name test_env


Solving environment: done


## Package Plan ##
Thank you for your continued use and support.


  environment location: /home/ravi89/.conda/envs/test_env


  added / updated specs:
The Research Computing Team'''''
    - setuptools
|}
 
 
The following packages will be downloaded:
 
    package                    |            build
    ---------------------------|-----------------
    python-3.7.0              |      h6e4f718_3        30.6 MB
    wheel-0.32.1              |          py37_0          35 KB
    setuptools-40.4.3          |          py37_0        556 KB
    ------------------------------------------------------------
                                          Total:        31.1 MB
 
The following NEW packages will be INSTALLED:
 
    ca-certificates: 2018.03.07-0
    certifi:        2018.8.24-py37_1
    libedit:        3.1.20170329-h6b74fdf_2
    libffi:          3.2.1-hd88cf55_4
    libgcc-ng:      8.2.0-hdf63c60_1
    libstdcxx-ng:    8.2.0-hdf63c60_1
    ncurses:        6.1-hf484d3e_0
    openssl:        1.0.2p-h14c3975_0
    pip:            10.0.1-py37_0
    python:          3.7.0-h6e4f718_3
    readline:        7.0-h7b6447c_5
    setuptools:      40.4.3-py37_0
    sqlite:          3.25.2-h7b6447c_0
    tk:              8.6.8-hbc83047_0
    wheel:          0.32.1-py37_0
    xz:              5.2.4-h14c3975_4
    zlib:            1.2.11-ha838bed_2
 
Proceed ([y]/n)? y
 
Downloading and Extracting Packages
python-3.7.0        | 30.6 MB  | ########################################################################### | 100%
wheel-0.32.1        | 35 KB    | ########################################################################### | 100%
setuptools-40.4.3    | 556 KB    | ########################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate test_env
#
# To deactivate an active environment, use:
# > source deactivate
#
</pre>
 
You can also specify the packages that you want to install in the conda virtual environment:
<pre>
$ conda create --name test_env PACKAGE_NAME
</pre>
 
===Listing all your conda virtual environments===
In case you forget the name of your virtual environments, you can list all your virtual environments by running '''conda env list'''
<pre>
$ conda env list
# conda environments:
#
jupyter_test            /home/ravi89/.conda/envs/jupyter_test
modeller                /home/ravi89/.conda/envs/modeller
psypy3                  /home/ravi89/.conda/envs/psypy3
test                    /home/ravi89/.conda/envs/test
test_env                /home/ravi89/.conda/envs/test_env
test_pytorch            /home/ravi89/.conda/envs/test_pytorch
tomopy                  /home/ravi89/.conda/envs/tomopy
base                  *  /share/apps/rc/software/Anaconda3/5.2.0
DeepNLP                  /share/apps/rc/software/Anaconda3/5.2.0/envs/DeepNLP
ubrite-jupyter-base-1.0    /share/apps/rc/software/Anaconda3/5.2.0/envs/ubrite-jupyter-base-1.0
</pre>
NOTE: Virtual environment with the asterisk(*) next to it is the one that's currently active.
 
===Activating a conda virtual environment===
You can activate your virtual environment for use by running '''source activate''' followed by '''conda activate ENV_NAME'''
 
<pre>
$ source activate
$ conda activate test_env
(test_env) $
</pre>
 
NOTE: Your shell prompt would also include the name of the virtual environment that you activated.
 
 
'''IMPORTANT!'''
 
'''source activate <env>''' is not idempotent. Using it twice with the same environment in a given session can lead to unexpected behavior. The recommended workflow is to use '''source activate''' to source the '''conda activate''' script, followed by '''conda activate <env>'''.
 
===Locate and install packages===
Conda allows you to search for packages that you want to install:
<pre>
(test_env) $ conda search BeautifulSoup4
Loading channels: done
# Name                  Version          Build  Channel
beautifulsoup4            4.4.0          py27_0  pkgs/free
beautifulsoup4            4.4.0          py34_0  pkgs/free
beautifulsoup4            4.4.0          py35_0  pkgs/free
...
beautifulsoup4            4.6.3          py35_0  pkgs/main
beautifulsoup4            4.6.3          py36_0  pkgs/main
beautifulsoup4            4.6.3          py37_0  pkgs/main
(test_env) $
</pre>
NOTE: Search is case-insensitive
 
You can install the packages in conda environment using
<pre>
(test_env) $ conda install beautifulsoup4
Solving environment: done
 
## Package Plan ##
 
  environment location: /home/ravi89/.conda/envs/test_env
 
  added / updated specs:
    - beautifulsoup4
 
 
The following packages will be downloaded:
 
    package                    |           build
    ---------------------------|-----------------
    beautifulsoup4-4.6.3      |          py37_0        138 KB
 
The following NEW packages will be INSTALLED:
 
    beautifulsoup4: 4.6.3-py37_0
 
Proceed ([y]/n)? y
 
 
Downloading and Extracting Packages
beautifulsoup4-4.6.3 | 138 KB    | ########################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(test_env) $
</pre>
 
===Deactivating your virtual environment===
You can deactivate your virtual environment using '''source deactivate'''
<pre>
(test_env) $ source deactivate
$
</pre>
 
===Sharing an environment===
You may want to share your environment with someone for testing or other purposes. Sharing the environemnt file for your virtual environment is the most starightforward metohd which allows other person to quickly create an environment identical to you.
====Export environment====
* Activate the virtual environment that you want to export.
* Export an environment.yml file
<pre>
conda env export -n test_env > environment.yml
</pre>
* Now you can send the recently created environment.yml file to the other person.
 
====Create a virtual environment using environment.yml====
<pre>
conda env create -f environment.yml -n test_env
</pre>
 
===Delete a conda virtual environment===
You can use the '''remove''' parameter of conda to delete a conda virtual environment that you don't need:
<pre>
$ conda remove --name test_env --all
 
Remove all packages in environment /home/ravi89/.conda/envs/test_env:
 
 
## Package Plan ##
 
  environment location: /home/ravi89/.conda/envs/test_env
 
 
The following packages will be REMOVED:
 
    beautifulsoup4:  4.6.3-py37_0
    ca-certificates: 2018.03.07-0
    certifi:        2018.8.24-py37_1
    libedit:        3.1.20170329-h6b74fdf_2
    libffi:          3.2.1-hd88cf55_4
    libgcc-ng:      8.2.0-hdf63c60_1
    libstdcxx-ng:    8.2.0-hdf63c60_1
    ncurses:        6.1-hf484d3e_0
    openssl:        1.0.2p-h14c3975_0
    pip:            10.0.1-py37_0
    python:          3.7.0-h6e4f718_3
    readline:        7.0-h7b6447c_5
    setuptools:      40.4.3-py37_0
    sqlite:          3.25.2-h7b6447c_0
    tk:              8.6.8-hbc83047_0
    wheel:          0.32.1-py37_0
    xz:              5.2.4-h14c3975_4
    zlib:            1.2.11-ha838bed_2
 
Proceed ([y]/n)? y
</pre>
 
===Moving conda directory===
As you build new conda environments, you may find that it is taking a lot of space in your $HOME directory. Here are 2 methods:
 
Method 1: Move a pre-existing conda directory and create a symlink
<pre>
cd ~
mv ~/.conda $USER_DATA/
ln -s $USER_DATA/.conda
</pre>
 
Method 2: Create a "$HOME/.condarc" file in the $HOME directory by running the following code
<pre>
cat << "EOF" > ~/.condarc
pkgs_dirs:
  - $USER_DATA/.conda/pkgs
envs_dirs:
  - $USER_DATA/.conda/envs
EOF
</pre>

Revision as of 18:37, 4 August 2022

Hello UAB Research Computing Community!


We have created a new streamlined and user-friendly set of documentation for our services. Please visit https://uabrc.github.io/ for our new documentation site. Please bear in mind the documentation is still a work in progress and subject to change.


As part of the process we are deprecating, and eventually retiring, the current documentation site here at https://docs.uabgrid.uab.edu/.


Thank you for your continued use and support.


The Research Computing Team