Anaconda - Revision history

Wwarr@uab.edu: /* Moving conda directory */

2021-03-24T19:50:45Z

Moving conda directory

← Older revision		Revision as of 19:50, 24 March 2021
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	===Moving conda directory===		===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:		As you build new conda environments, you may find that it is taking a lot of space in your $HOME directory, leading to issues with interactive sessions failing to start. Below are 2 methods to resolve the issue.

	Method 1: Move a pre-existing conda directory and create a symlink		Method 1: Move a pre-existing conda directory and create a symlink

Mhanby@uab.edu at 17:11, 22 December 2020

2020-12-22T17:11:30Z

← Older revision		Revision as of 17:11, 22 December 2020
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	## Package Plan ##		## Package Plan ##

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

	added / updated specs:		added / updated specs:
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	# conda environments:		# conda environments:
	#		#
	jupyter_test ~~/home/ravi89~~/.conda/envs/jupyter_test		jupyter_test ~/.conda/envs/jupyter_test
	modeller ~~/home/ravi89~~/.conda/envs/modeller		modeller ~/.conda/envs/modeller
	psypy3 ~~/home/ravi89~~/.conda/envs/psypy3		psypy3 ~/.conda/envs/psypy3
	test ~~/home/ravi89~~/.conda/envs/test		test ~/.conda/envs/test
	test_env ~~/home/ravi89~~/.conda/envs/test_env		test_env ~/.conda/envs/test_env
	test_pytorch ~~/home/ravi89~~/.conda/envs/test_pytorch		test_pytorch ~/.conda/envs/test_pytorch
	tomopy ~~/home/ravi89~~/.conda/envs/tomopy		tomopy ~/.conda/envs/tomopy
	base * /share/apps/rc/software/Anaconda3/5.2.0		base * /share/apps/rc/software/Anaconda3/5.2.0
	DeepNLP /share/apps/rc/software/Anaconda3/5.2.0/envs/DeepNLP		DeepNLP /share/apps/rc/software/Anaconda3/5.2.0/envs/DeepNLP
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	## Package Plan ##		## Package Plan ##

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

	added / updated specs:		added / updated specs:
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	$ conda remove --name test_env --all		$ conda remove --name test_env --all

	Remove all packages in environment ~~/home/ravi89~~/.conda/envs/test_env:		Remove all packages in environment ~/.conda/envs/test_env:


	## Package Plan ##		## Package Plan ##

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

Wwarr@uab.edu: update caveat on source/conda activate usage

2020-11-23T21:37:08Z

update caveat on source/conda activate usage

← Older revision		Revision as of 21:37, 23 November 2020
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	'''IMPORTANT!'''		'''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>'''.		The following only applies to versions prior to 2019.10. '''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>'''.

			From version 2019.10 and on, simply use '''conda activate <env>'''.

	===Locate and install packages===		===Locate and install packages===

Ravi89@uab.edu: /* Moving conda directory */

2020-09-16T18:21:09Z

Moving conda directory

← Older revision		Revision as of 18:21, 16 September 2020
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	cd ~		cd ~
	mv ~/.conda $USER_DATA/		mv ~/.conda $USER_DATA/
	ln -s $USER_DATA/.conda		ln -s $USER_DATA/.conda .conda
	</pre>		</pre>

Mhanby@uab.edu: /* Creating a Conda virtual environment */

2020-03-30T15:49:15Z

Creating a Conda virtual environment

← Older revision		Revision as of 15:49, 30 March 2020
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	</pre>		</pre>

	Load one of the conda environments available on ~~cheaha~~:		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):
	<pre>		<pre>
	$ module avail Anaconda		$ module -t avail Anaconda
			...
			Anaconda3/5.3.0
			Anaconda3/5.3.1
			Anaconda3/2019.10

	~~--------------------------------------------- /share/apps/rc/modules/all ---------------------------------------------~~
	~~Anaconda2/4.0.0 Anaconda2/4.2.0 Anaconda3/4.4.0 Anaconda3/5.0.1 Anaconda3/5.1.0 Anaconda3/5.2.0~~
	</pre>		</pre>
	<pre>		<pre>
	$ module load Anaconda3/5.~~3.1~~		$ module load Anaconda3/2019.10
	</pre>		</pre>
	Once you have loaded Anaconda, you can create an environment using the following command:
			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):
	<pre>		<pre>
	$ conda create --name test_env		$ conda create --name test_env

	Solving environment: done		Solving environment: done

Wwarr@uab.edu: /* Activating a conda virtual environment */

2020-03-24T19:40:59Z

Activating a conda virtual environment

← Older revision		Revision as of 19:40, 24 March 2020
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	===Activating a conda virtual environment===		===Activating a conda virtual environment===
	You can activate your virtual environment for use by running '''source activate ENV_NAME'''		You can activate your virtual environment for use by running '''source activate''' followed by '''conda activate ENV_NAME'''

	<pre>		<pre>
	$ source activate test_env		$ source activate
			$ conda activate test_env
	(test_env) $		(test_env) $
	</pre>		</pre>

	NOTE: Your shell prompt would also include the name of the virtual environment that you activated.		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===		===Locate and install packages===

Mhanby@uab.edu at 15:28, 18 March 2020

2020-03-18T15:28:37Z

Show changes

Mhanby@uab.edu: /* Moving conda directory */

2020-03-18T15:07:31Z

Moving conda directory

← Older revision		Revision as of 15:07, 18 March 2020
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	Method 1: Move a pre-existing conda directory and create a symlink		Method 1: Move a pre-existing conda directory and create a symlink
	<pre>		<pre>
	cd		cd ~
	mv ~/.conda $USER_DATA/		mv ~/.conda $USER_DATA/
	ln -s $USER_DATA/.conda		ln -s $USER_DATA/.conda

Bkomal96@uab.edu: /* Creating a Conda virtual environment */

2020-03-05T21:58:21Z

Creating a Conda virtual environment

← Older revision		Revision as of 21:58, 5 March 2020
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	--------------------------------------------- /share/apps/rc/modules/all ---------------------------------------------		--------------------------------------------- /share/apps/rc/modules/all ---------------------------------------------
	Anaconda2/4.0.0 Anaconda2/4.2.0 Anaconda3/4.4.0 Anaconda3/5.0.1 Anaconda3/5.1.0 Anaconda3/5.2.0		Anaconda2/4.0.0 Anaconda2/4.2.0 Anaconda3/4.4.0 Anaconda3/5.0.1 Anaconda3/5.1.0 Anaconda3/5.2.0
			</pre>
			<pre>
			bkomal96 @ c0003 ➜ ~module load Anaconda3/5.3.1
	</pre>		</pre>
	Once you have loaded Anaconda, you can create an environment using the following command:		Once you have loaded Anaconda, you can create an environment using the following command:

Louistw@uab.edu: /* Create a virtual environment using environment.yml */

2019-04-25T15:55:42Z

Create a virtual environment using environment.yml

← Older revision		Revision as of 15:55, 25 April 2019
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	====Create a virtual environment using environment.yml====		====Create a virtual environment using environment.yml====
	<pre>		<pre>
	conda env create -f environment.yml		conda env create -f environment.yml -n test_env
	</pre>		</pre>