Virtual environment Python 3.4 or higher - Revision history

Vorst0161: /* creating a new virtual environment */

2025-05-19T13:58:29Z

creating a new virtual environment

← Older revision		Revision as of 15:58, 19 May 2025
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	</pre>		</pre>

	And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>~~new_env~~</code>.		And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>/p35_myproj</code>.


	Using the default python (3.12.3):		Using the default python (3.12.3):
	<pre>		<pre>
	python3 -m venv ~/my_envs/~~new_env~~		python3 -m venv ~/my_envs/p35_myproj
	</pre>		</pre>

	when using python 3.4/3.5:		when using python 3.4/3.5:
	<pre>		<pre>
	pyvenv install ~/my_envs/~~new_env~~		pyvenv install ~/my_envs/p35_myproj
	</pre>		</pre>

Vorst0161: /* creating a new virtual environment */

2025-05-19T13:55:32Z

creating a new virtual environment

← Older revision		Revision as of 15:55, 19 May 2025
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	</pre>		</pre>

	~~Then~~, load ~~either~~ Python 3.4 or 3.5 module ~~(Python~~ 3.3.~~3 should also work~~):		Since python 3.12.3 is already the default, you can use that one or load another Python version 3.4 or above. To use python 3.4-3.12.0, you need to load legacy as well:
			<pre>
			module load legacy
			module load python/3.5.0
			</pre>

			And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>new_env</code>.


			Using the default python (3.12.3):
	<pre>		<pre>
	~~module load python~~/~~3.5.0~~		python3 -m venv ~/my_envs/new_env
	</pre>		</pre>
	~~And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>p35_myproj</code>.~~

			when using python 3.4/3.5:
	<pre>		<pre>
	pyvenv install ~/my_envs/~~p35_myproj~~		pyvenv install ~/my_envs/new_env
	</pre>		</pre>

Prins0891: to

 to fix code blocks

2023-06-15T13:45:48Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 15:45, 15 June 2023
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	If you do not already have a directory in your <code>$HOME</code> dir where your virtual environments live, first make one (it is assumed that you will over the course of time create several virtual environments for different projects and different versions of Python side-by-side, best to organise them a bit).		If you do not already have a directory in your <code>$HOME</code> dir where your virtual environments live, first make one (it is assumed that you will over the course of time create several virtual environments for different projects and different versions of Python side-by-side, best to organise them a bit).

	<~~source lang='bash'~~>		<pre>
	mkdir ~/my_envs		mkdir ~/my_envs
	</~~source~~>		</pre>

	Then, load either Python 3.4 or 3.5 module (Python 3.3.3 should also work):		Then, load either Python 3.4 or 3.5 module (Python 3.3.3 should also work):

	<~~source lang='bash'~~>		<pre>
	module load python/3.5.0		module load python/3.5.0
	</~~source~~>		</pre>
	And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>p35_myproj</code>.		And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>p35_myproj</code>.

	<~~source lang='bash'~~>		<pre>
	pyvenv install ~/my_envs/p35_myproj		pyvenv install ~/my_envs/p35_myproj
	</~~source~~>		</pre>

	== activating a virtual environment ==		== activating a virtual environment ==
	Once the environment is created, each time the environment needs to be activated, the following command needs to be issued:		Once the environment is created, each time the environment needs to be activated, the following command needs to be issued:
	<~~source lang='bash'~~>		<pre>
	source ~/my_envs/p35_myproj/bin/activate		source ~/my_envs/p35_myproj/bin/activate
	</~~source~~>		</pre>

	This assumes that the folder that contains the virtual environment documents (in this case called <code>newenv</code>), is in the present working directory.		This assumes that the folder that contains the virtual environment documents (in this case called <code>newenv</code>), is in the present working directory.
	When working on the virtual environment, the virtual environment name will be between brackets in front of the <code>user-host-prompt</code> string.		When working on the virtual environment, the virtual environment name will be between brackets in front of the <code>user-host-prompt</code> string.
	<~~code~~>		<pre>
	(p35_myproj)user@host:~$		(p35_myproj)user@host:~$
	</~~code~~>		</pre>

	Note that like with any command you can make an alias in your <code>~/.bashrc</code>. Just add something like this line to your <code>.bashrc</code>:		Note that like with any command you can make an alias in your <code>~/.bashrc</code>. Just add something like this line to your <code>.bashrc</code>:

	<~~source lang='bash'~~>		<pre>
	alias p35myproj='source ~/my_envs/p35_myproj/bin/activate'		alias p35myproj='source ~/my_envs/p35_myproj/bin/activate'
	</~~source~~>		</pre>

	== installing modules on the virtual environment ==		== installing modules on the virtual environment ==
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	Before you start installing modules, first update pip itself:		Before you start installing modules, first update pip itself:
	<~~source lang='bash'~~>		<pre>
	pip install --upgrade pip		pip install --upgrade pip
	</~~source~~>		</pre>

	you can then install other modules as you like, for instance numpy:		you can then install other modules as you like, for instance numpy:

	<~~source lang='bash'~~>		<pre>
	pip install numpy		pip install numpy
	</~~source~~>		</pre>

	<~~code~~>		<pre>
	(p35_myproj) [user@nfs01 ~]$ pip install numpy		(p35_myproj) [user@nfs01 ~]$ pip install numpy
	Collecting numpy		Collecting numpy
Line 59:		Line 59:
	Running setup.py install for numpy ... done		Running setup.py install for numpy ... done
	Successfully installed numpy-1.10.4		Successfully installed numpy-1.10.4
	</~~code~~>		</pre>

	Similarly, installing packages from source works exactly the same as usual (note: only relevant for modules that can't be pulled through <code>pip</code>).		Similarly, installing packages from source works exactly the same as usual (note: only relevant for modules that can't be pulled through <code>pip</code>).
	<~~source lang='bash'~~>		<pre>
	python setup.py install		python setup.py install
	</~~source~~>		</pre>

	== deactivating a virtual environment ==		== deactivating a virtual environment ==
	Quitting a virtual environment can be done by using the command <code>deactivate</code>, which was loaded using the <code>source</code> command upon activating the virtual environment.		Quitting a virtual environment can be done by using the command <code>deactivate</code>, which was loaded using the <code>source</code> command upon activating the virtual environment.
	<~~source lang='bash'~~>		<pre>
	deactivate		deactivate
	</~~source~~>		</pre>

	== Make IPython work under virtualenv ==		== Make IPython work under virtualenv ==
	IPython can simply be installed through pip.		IPython can simply be installed through pip.

	<~~source lang='bash'~~>		<pre>
	pip install ipython		pip install ipython
	</~~source~~>		</pre>

	== See also ==		== See also ==

Dawes001 at 13:42, 19 March 2019

2019-03-19T13:42:17Z

← Older revision		Revision as of 15:42, 19 March 2019
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	== See also ==		== See also ==
	* [[~~B4F_cluster~~ \| ~~B4F Cluster~~]]		* [[Anunna \| Anunna]]

	== External links ==		== External links ==
	* [https://docs.python.org/3/library/venv.html#module-venv Python docs on virtenv]		* [https://docs.python.org/3/library/venv.html#module-venv Python docs on virtenv]

Megen002 at 08:58, 22 January 2016

2016-01-22T08:58:28Z

← Older revision		Revision as of 10:58, 22 January 2016
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	With many Python packages available, which are often in conflict or requiring different versions depending on application, installing and controlling packages and versions is not always easy. In addition, so many packages are often used only occasionally, that it is questionable whether a system administrator of a centralized server system or a High Performance Compute (HPC) infrastructure can be expected to resolve all issues posed by users of the infrastructure. Even on a local system with full administrative rights managing versions, dependencies, and package collisions is often very difficult. The solution is to use a virtual environment, in which a specific set of packages can then be installed. As many different virtual environments can be created, and used side-by-side, as is necessary.		With many Python packages available, which are often in conflict or requiring different versions depending on application, installing and controlling packages and versions is not always easy. In addition, so many packages are often used only occasionally, that it is questionable whether a system administrator of a centralized server system or a High Performance Compute (HPC) infrastructure can be expected to resolve all issues posed by users of the infrastructure. Even on a local system with full administrative rights managing versions, dependencies, and package collisions is often very difficult. The solution is to use a virtual environment, in which a specific set of packages can then be installed. As many different virtual environments can be created, and used side-by-side, as is necessary.


	== creating a new virtual environment ==		== creating a new virtual environment ==
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	pyvenv install ~/my_envs/p35_myproj		pyvenv install ~/my_envs/p35_myproj
	</source>		</source>


	== activating a virtual environment ==		== activating a virtual environment ==

Megen002: /* activating a virtual environment */

2016-01-22T08:57:44Z

activating a virtual environment

← Older revision		Revision as of 10:57, 22 January 2016
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	</code>		</code>

	Note that like with any command you can make an alias in your ~/.bashrc. Just add something like this line to your .bashrc:		Note that like with any command you can make an alias in your <code>~/.bashrc</code>. Just add something like this line to your <code>.bashrc</code>:

	<source lang='bash'>		<source lang='bash'>

Megen002: /* activating a virtual environment */

2016-01-22T08:56:28Z

activating a virtual environment

← Older revision		Revision as of 10:56, 22 January 2016
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	(p35_myproj)user@host:~$		(p35_myproj)user@host:~$
	</code>		</code>

			Note that like with any command you can make an alias in your ~/.bashrc. Just add something like this line to your .bashrc:

			<source lang='bash'>
			alias p35myproj='source ~/my_envs/p35_myproj/bin/activate'
			</source>

	== installing modules on the virtual environment ==		== installing modules on the virtual environment ==

Megen002: /* External links */

2016-01-22T08:50:25Z

External links

← Older revision		Revision as of 10:50, 22 January 2016
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	== External links ==		== External links ==
	* [https://docs.python.org/3/library/venv.html#module-venv \| Python docs on virtenv]		* [https://docs.python.org/3/library/venv.html#module-venv Python docs on virtenv]

Megen002: /* External links */

2016-01-22T08:50:13Z

External links

← Older revision		Revision as of 10:50, 22 January 2016
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	== External links ==		== External links ==
	* [https://docs.python.org/3/library/venv.html#module-venv]		* [https://docs.python.org/3/library/venv.html#module-venv \| Python docs on virtenv]

Megen002 at 08:49, 22 January 2016

2016-01-22T08:49:47Z

← Older revision		Revision as of 10:49, 22 January 2016
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	== creating a new virtual environment ==		== creating a new virtual environment ==

	If you do not already have a directory in your <code>)$HOME</code>) dir where your virtual environments live, first make one (it is assumed that you will over the course of time create several virtual environments for different projects and different versions of Python side-by-side, best to organise them a bit).		If you do not already have a directory in your <code>$HOME</code> dir where your virtual environments live, first make one (it is assumed that you will over the course of time create several virtual environments for different projects and different versions of Python side-by-side, best to organise them a bit).

	<source lang='bash'>		<source lang='bash'>
Line 15:		Line 15:
	module load python/3.5.0		module load python/3.5.0
	</source>		</source>
	And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>)p35_myproj</code>).		And then simply create an environment with a reasonably descriptive name (remember, you may accumulate as many as you desire), in this example <code>p35_myproj</code>.

	<source lang='bash'>		<source lang='bash'>
Line 35:		Line 35:

	== installing modules on the virtual environment ==		== installing modules on the virtual environment ==
	Installing modules is the same as usual. The difference is that modules are in <code>/path/to/virtenv/lib</code>, which may be living somewhere on your home directory. An easy way of installing modules is using <code>)pip</code>).		Installing modules is the same as usual. The difference is that modules are in <code>/path/to/virtenv/lib</code>, which may be living somewhere on your home directory. An easy way of installing modules is using <code>pip</code>.

	Before you start installing modules, first update pip itself:		Before you start installing modules, first update pip itself:
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	deactivate		deactivate
	</source>		</source>

	== Make IPython work under virtualenv ==		== Make IPython work under virtualenv ==
	IPython ~~may not work initially under a virtual environment~~. ~~It may produce an error message like below:~~		IPython can simply be installed through pip.

	~~<code>~~
	~~File "/usr/bin/ipython", line 11~~
	~~print "Could not start qtconsole. Please install ipython-qtconsole"~~
	^
	~~</code>~~

	~~This can be resolved by adding a soft link with the name <code>ipython</code> to the <code>bin</code> directory in the virtual environment folder.~~
	<source lang='bash'>		<source lang='bash'>
	~~ln -s /path/to/virtenv/bin/ipython3 /path/to/virtenv/bin/~~ipython		pip install ipython
	</source>		</source>

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	== External links ==		== External links ==
	* [https://~~pypi~~.python.org/~~pypi~~/~~virtualenv Python3 documentation for virtualenv]~~		* [https://docs.python.org/3/library/venv.html#module-venv]
	* [http:/~~/cemcfarland~~.~~wordpress.com/2013/03/09/getting~~-~~ipython3-working-inside-your-virtualenv/ Solving the IPython hickup under virtual environment~~]