Python-Sapelo2 - Revision history

Shtsai at 01:22, 5 April 2026

2026-04-05T01:22:49Z

← Older revision		Revision as of 21:22, 4 April 2026
Line 212:		Line 212:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	===Examples===		==Examples==

	====Example of using Python3====		===Example of using Python3===

	To use Python 3.10.4, you can use the following in the first line of your Python code:		To use Python 3.10.4, you can use the following in the first line of your Python code:
Line 234:		Line 234:
	</pre>		</pre>

	====Example of using Python2====		===Example of using Python2===

	To use Python 2.7.18, you can use the following in the first line of your Python code:		To use Python 2.7.18, you can use the following in the first line of your Python code:

Shtsai at 01:22, 5 April 2026

2026-04-05T01:22:13Z

← Older revision		Revision as of 21:22, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Programming]]		[[Category:Sapelo2]][[Category:Software]][[Category:Programming]]
	=== Category ===		== Category ==
	Programming		Programming
	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2
	=== Version ===		== Version ==
	2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5		2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5

	=== Author / Distributor ===		== Author / Distributor ==
	[http://www.python.org/ The Python Software Foundation]		[http://www.python.org/ The Python Software Foundation]

	=== Description ===		== Description ==

	Python is a programming language.		Python is a programming language.

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
Line 83:		Line 83:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	===About Python packages===		==About Python packages==

	Some common third-party Python packages are installed individually as separate modules on the cluster.		Some common third-party Python packages are installed individually as separate modules on the cluster.

	====numpy, scipy, pandas====		===numpy, scipy, pandas===

	The numpy, scipy, pandas, mpi4py, mpmath, and deap packages are installed in SciPy-bundle module:		The numpy, scipy, pandas, mpi4py, mpmath, and deap packages are installed in SciPy-bundle module:
Line 132:		Line 132:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	====matplotlib====		===matplotlib===

	The matplotlib package is installed in matplotlib module.		The matplotlib package is installed in matplotlib module.
Line 172:		Line 172:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	====Biopython====		===Biopython===

	The Biopython package is installed in Biopython module.		The Biopython package is installed in Biopython module.
Line 257:		Line 257:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Documentation ===		== Documentation ==
	Please see http://www.python.org/		Please see http://www.python.org/
	=== Installation ===		== Installation ==
	EasyBuild recipes		EasyBuild recipes

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai: /* numpy, scipy, pandas */

2026-01-09T20:07:10Z

numpy, scipy, pandas

← Older revision		Revision as of 16:07, 9 January 2026
Line 101:		Line 101:

	Versions:		Versions:
			SciPy-bundle/2021.10-foss-2021b
	SciPy-bundle/2022.05-foss-2022a		SciPy-bundle/2022.05-foss-2022a
	SciPy-bundle/2023.07-gfbf-2023a		SciPy-bundle/2023.07-gfbf-2023a
			SciPy-bundle/2023.07-iimkl-2023a
	SciPy-bundle/2023.11-gfbf-2023b		SciPy-bundle/2023.11-gfbf-2023b
	SciPy-bundle/2024.05-gfbf-2024a		SciPy-bundle/2024.05-gfbf-2024a
	SciPy-bundle/2024.06-foss-2023a-Python-2.7.18		SciPy-bundle/2024.06-foss-2023a-Python-2.7.18
			SciPy-bundle/2025.06-gfbf-2025a


	------------------------------------------------------------------------------------------------------------------------------------------------------------------		------------------------------------------------------------------------------------------------------------------------------------------------------------------
Line 112:		Line 116:
	For example:		For example:

	$ module spider SciPy-bundle/~~2024~~.06-~~foss~~-~~2023a-Python-2.7.18~~		$ module spider SciPy-bundle/2025.06-gfbf-2025a
	------------------------------------------------------------------------------------------------------------------------------------------------------------------		------------------------------------------------------------------------------------------------------------------------------------------------------------------

Shtsai at 20:05, 9 January 2026

2026-01-09T20:05:57Z

← Older revision		Revision as of 16:05, 9 January 2026
Line 5:		Line 5:
	Sapelo2		Sapelo2
	=== Version ===		=== Version ===
	2.7.18~~, 3.7.4, 3.8.6~~, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3		2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5

	=== Author / Distributor ===		=== Author / Distributor ===
Line 18:		Line 18:
	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

	There is no default python command on the system. The OS comes with ~~a default /usr/bin/python2 (v. 2.7.18) and~~ a default /usr/bin/python3 (v. 3.6.8). Scripts that have the first line:		There is no default python command on the system. The OS comes with a default /usr/bin/python3 command that provides Python v. 3.9.21. Scripts that have the first line:
	<pre class="gscript">		<pre class="gscript">
	#!/usr/bin/python		#!/usr/bin/python
	</pre>		</pre>
	will not work on Sapelo2 (with the Rocky 8 OS). We recommend that you change this line to		will not work on Sapelo2 (with the Rocky 9 OS). We recommend that you change this line to
	<pre class="gscript">		<pre class="gscript">
	#!/usr/bin/env python		#!/usr/bin/env python
Line 45:		Line 45:

	Versions:		Versions:
	~~Python/2.7.18-GCCcore-11.2.0-bare~~
	~~Python/2.7.18-GCCcore-11.2.0~~
	Python/2.7.18-GCCcore-11.3.0-bare		Python/2.7.18-GCCcore-11.3.0-bare
	Python/2.7.18-GCCcore-11.3.0		Python/2.7.18-GCCcore-11.3.0
	Python/3.7.4-GCCcore-8.3.0		Python/2.7.18-GCCcore-12.3.0
	Python/3.8.6-GCCcore-10.2.0		Python/2.7.18-GCCcore-13.2.0
			Python/2.7.18-GCCcore-13.3.0
	Python/3.9.6-GCCcore-11.2.0-bare		Python/3.9.6-GCCcore-11.2.0-bare
	Python/3.9.6-GCCcore-11.2.0		Python/3.9.6-GCCcore-11.2.0
Line 57:		Line 56:
	Python/3.10.8-GCCcore-12.2.0-bare		Python/3.10.8-GCCcore-12.2.0-bare
	Python/3.10.8-GCCcore-12.2.0		Python/3.10.8-GCCcore-12.2.0
			Python/3.11.3-GCCcore-12.3.0-eb520
	Python/3.11.3-GCCcore-12.3.0		Python/3.11.3-GCCcore-12.3.0
	Python/3.11.5-GCCcore-13.2.0		Python/3.11.5-GCCcore-13.2.0
	Python/3.12.3-GCCcore-13.3.0		Python/3.12.3-GCCcore-13.3.0
			Python/3.13.1-GCCcore-14.2.0
			Python/3.13.5-GCCcore-14.3.0
	Other possible modules matches:		Other possible modules matches:
	Biopython Boost.Python GitPython IPython bx-python flatbuffers-python ...		Biopython Boost.Python Brotli-python GitPython IPython Python-bundle-PyPI bx-python flatbuffers-python graphviz-python intervaltree-python libxml2-python ...

	----------------------------------------------------------------------------------		----------------------------------------------------------------------------------

Shtsai: /* matplotlib */

2025-08-01T16:08:37Z

matplotlib

← Older revision		Revision as of 12:08, 1 August 2025
Line 141:		Line 141:

	Versions:		Versions:
	matplotlib/2.2.5-foss-~~2021b~~-Python-2.7.18		matplotlib/2.2.5-foss-2023a-Python-2.7.18
	~~matplotlib/2.2.5-foss-2022a-Python-2.7.18~~
	~~matplotlib/3.4.3-foss-2021b~~
	~~matplotlib/3.5.2-foss-2021b~~
	matplotlib/3.5.2-foss-2022a		matplotlib/3.5.2-foss-2022a
			matplotlib/3.7.2-gfbf-2023a
			matplotlib/3.8.2-gfbf-2023b
			matplotlib/3.9.2-gfbf-2024a

	----------------------------------------------------------------------------------		----------------------------------------------------------------------------------
Line 152:		Line 152:
	For example:		For example:

	$ module spider matplotlib/3.5.2-~~foss~~-~~2022a~~		$ module spider matplotlib/3.9.2-gfbf-2024a
	----------------------------------------------------------------------------------		----------------------------------------------------------------------------------
	</pre>		</pre>

	Same as SciPy-bundle, when you load matplotlib module, a specific version of Python that matplotlib is built for will be loaded at first, which means you don't have to load the Python module separately from loading matplotlib module. For example:		Same as SciPy-bundle, when you load matplotlib module, a specific version of Python that matplotlib is built for will be loaded at first, which means you don't have to load the Python module separately from loading matplotlib module. For example:

	*Python/3.9.6-GCCcore-11.2.0 will be automatically loaded when you load matplotlib/3.4.3-foss-2021b or matplotlib/3.5.2-foss-2021b.

	*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when you load matplotlib/3.5.2-foss-2022a.		*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when you load matplotlib/3.5.2-foss-2022a.

	*Python/2.7.18-GCCcore-11.2.0 will be automatically loaded when you load matplotlib/2.2.5-foss-~~2021b~~-Python-2.7.18.		*Python/2.7.18-GCCcore-12.3.0 will be automatically loaded when you load matplotlib/2.2.5-foss-2023a-Python-2.7.18.

	*Python/2.7.18-GCCcore-11.3.0 will be automatically loaded when you load matplotlib/2.2.5-foss-2022a-Python-2.7.18.

	----		----

Shtsai: /* Biopython */

2025-08-01T16:05:54Z

Biopython

← Older revision		Revision as of 12:05, 1 August 2025
Line 184:		Line 184:

	Versions:		Versions:
	~~Biopython/1.79-foss-2021b~~
	Biopython/1.79-foss-2022a		Biopython/1.79-foss-2022a
			Biopython/1.83-foss-2023a
			Biopython/1.84-foss-2023b
			Biopython/1.84-foss-2024a

	----------------------------------------------------------------------------------		----------------------------------------------------------------------------------
Line 192:		Line 194:
	For example:		For example:

	$ module spider Biopython/1.79-foss-~~2022a~~		$ module spider Biopython/1.84-foss-2024a
	----------------------------------------------------------------------------------		----------------------------------------------------------------------------------
	</pre>		</pre>
Line 198:		Line 200:
	Same as above SciPy-bundle and matplotlib, when you load Biopython module, a specific version of Python that the package is built for will be loaded at first. You don't have to load the Python module separately from loading Biopython module. For ecample:		Same as above SciPy-bundle and matplotlib, when you load Biopython module, a specific version of Python that the package is built for will be loaded at first. You don't have to load the Python module separately from loading Biopython module. For ecample:

	*Python/3.9.6-GCCcore-11.2.0 will be automatically loaded when Biopython/1.79-foss-2021b is loaded.

	*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when Biopython/1.79-foss-2022a is loaded.		*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when Biopython/1.79-foss-2022a is loaded.

			*Python/3.12.3-GCCcore-13.3.0 will be automatically loaded when Biopython/1.84-foss-2024a is loaded.

Shtsai: /* Example of using Python3 */

2025-08-01T16:04:19Z

Example of using Python3

← Older revision		Revision as of 12:04, 1 August 2025
Line 210:		Line 210:
	====Example of using Python3====		====Example of using Python3====

	To use Python 3.9.6, you can use the following in the first line of your Python code:		To use Python 3.10.4, you can use the following in the first line of your Python code:

	<pre class="gscript">		<pre class="gscript">
	#!/apps/eb/Python/3.9.6-GCCcore-11.2.0/bin/python3		#!/apps/eb/Python/3.10.4-GCCcore-11.3.0/bin/python3
	</pre>		</pre>

Line 223:		Line 223:

	<pre class="gcommand">		<pre class="gcommand">
	module load Python/3.9.6-GCCcore-11.2.0		module load Python/3.10.4-GCCcore-11.3.0

	python myProgram.py		python myProgram.py

Shtsai: /* Example of using Python2 */

2025-08-01T16:02:46Z

Example of using Python2

← Older revision		Revision as of 12:02, 1 August 2025
Line 233:		Line 233:

	<pre class="gscript">		<pre class="gscript">
	#!/apps/eb/Python/2.7.18-GCCcore-11.2.0/bin/python		#!/apps/eb/Python/2.7.18-GCCcore-11.3.0/bin/python
	</pre>		</pre>

Line 243:		Line 243:

	<pre class="gcommand">		<pre class="gcommand">
	module load Python/2.7.18-GCCcore-11.2.0		module load Python/2.7.18-GCCcore-11.3.0

	python myProgram.py		python myProgram.py

Shtsai: /* numpy, scipy, pandas */

2025-08-01T16:00:28Z

numpy, scipy, pandas

← Older revision		Revision as of 12:00, 1 August 2025
Line 98:		Line 98:
	Bundle of Python packages for scientific software		Bundle of Python packages for scientific software

	Versions:		Versions:
	~~SciPy-bundle/2021.10-foss-2021b-Python-2.7.18~~
	~~SciPy-bundle/2021.10-foss-2021b~~
	~~SciPy-bundle/2021.10-foss-2022a-Python-2.7.18~~
	SciPy-bundle/2022.05-foss-2022a		SciPy-bundle/2022.05-foss-2022a
			SciPy-bundle/2023.07-gfbf-2023a
			SciPy-bundle/2023.11-gfbf-2023b
			SciPy-bundle/2024.05-gfbf-2024a
			SciPy-bundle/2024.06-foss-2023a-Python-2.7.18

	----------------------------------------------------------------------------------		------------------------------------------------------------------------------------------------------------------------------------------------------------------
	For detailed information about a specific "SciPy-bundle" package (including how to load the modules) use the module's full name.		For detailed information about a specific "SciPy-bundle" package (including how to load the modules) use the module's full name.
	Note that names that have a trailing (E) are extensions provided by other modules.		Note that names that have a trailing (E) are extensions provided by other modules.
	For example:		For example:

	$ module spider SciPy-bundle/~~2022~~.05-foss-~~2022a~~		$ module spider SciPy-bundle/2024.06-foss-2023a-Python-2.7.18
	----------------------------------------------------------------------------------		------------------------------------------------------------------------------------------------------------------------------------------------------------------

	</pre>		</pre>

	Note that, when you load SciPy-bundle module, a specific version of Python that the package is built for will be loaded at first. This means that you don't have to load the Python module separately from loading SciPy-bundle module. For example:		Note that, when you load SciPy-bundle module, a specific version of Python that the package is built for will be loaded at first. This means that you don't have to load the Python module separately from loading SciPy-bundle module. For example:

	*Python/3.9.6-GCCcore-11.2.0 will be automatically loaded when SciPy-bundle/2021.10-foss-2021b is loaded.

	*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when SciPy-bundle/2022.05-foss-2022a is loaded.		*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when SciPy-bundle/2022.05-foss-2022a is loaded.

	*Python/2.7.18-GCCcore-11.2.0 will be automatically loaded when SciPy-bundle/~~2021~~.10-foss-~~2021b~~-Python-2.7.18 is loaded.		*Python/2.7.18-GCCcore-12.3.0 will be automatically loaded when SciPy-bundle/2024.06-foss-2023a-Python-2.7.18 is loaded.

	*Python/2.7.18-GCCcore-11.3.0 will be automatically loaded when SciPy-bundle/~~2021~~.~~10-foss-2022a~~-~~Python~~-~~2.7.18~~ is loaded.		*Python/3.12.3-GCCcore-13.3.0 will be automatically loaded when SciPy-bundle/2024.05-gfbf-2024a is loaded.

	----		----

Shtsai: /* Running Program */

2025-08-01T15:56:34Z

Running Program

← Older revision		Revision as of 11:56, 1 August 2025
Line 73:		Line 73:
	For example:		For example:

	$ module spider Python/3.11.5-GCCcore-13.2.0		$ module spider Python/3.12.3-GCCcore-13.3.0
	----------------------------------------------------------------------------------		----------------------------------------------------------------------------------