Beast-Sapelo2 - Revision history

Chelsea: /* Version */

2026-06-16T14:15:55Z

Version

← Older revision		Revision as of 10:15, 16 June 2026
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	<!--1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5-->		<!--1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5-->
	2.7.7		1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0

	== Author / Distributor ==		== Author / Distributor ==

Shtsai at 00:02, 5 April 2026

2026-04-05T00:02:27Z

← Older revision		Revision as of 20:02, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	<!--1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5-->		<!--1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5-->
	2.7.7		2.7.7

	=== Author / Distributor ===		== Author / Distributor ==

	[http://beast2.org/ BEAST2]		[http://beast2.org/ BEAST2]
	[http://beast.community/ BEAST]		[http://beast.community/ BEAST]

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

	BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted,		BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted,
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	More information: http://beast2.org/; http://beast.community/		More information: http://beast2.org/; http://beast.community/

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

	====Versions without GPU support====		===Versions without GPU support===

	* version 2.7.7 installed in /apps/eb/Beast/2.7.7-GCC-12.3.0		* version 2.7.7 installed in /apps/eb/Beast/2.7.7-GCC-12.3.0
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	</pre>		</pre>
	-->		-->
	====Versions with CPU and GPU support====		===Versions with CPU and GPU support===

	* version 2.7.7 with CPU and GPU support, installed in /apps/eb/Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1. This version of Beast is using beagle-lib/4.0.1 with GPU support.		* version 2.7.7 with CPU and GPU support, installed in /apps/eb/Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1. This version of Beast is using beagle-lib/4.0.1 with GPU support.
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	</pre>		</pre>
	-->		-->
	====Run Beast in an interactive session====		===Run Beast in an interactive session===

	Beast is a X window program with graphic interface. It has to be run in an interactive session. Please refer to [[OnDemand#X%20Desktop%20Session%20.28A.K.A.%20The%20Interactive%20X%20login%20app.29\|X Desktop Sessions]] in [https://ondemand.gacrc.uga.edu/pun/sys/dashboard/ Open OnDemand].		Beast is a X window program with graphic interface. It has to be run in an interactive session. Please refer to [[OnDemand#X%20Desktop%20Session%20.28A.K.A.%20The%20Interactive%20X%20login%20app.29\|X Desktop Sessions]] in [https://ondemand.gacrc.uga.edu/pun/sys/dashboard/ Open OnDemand].
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	* beast/beauti in this app is set to '''16GB''' max heap memory. If larger memory is needed, please contact us.		* beast/beauti in this app is set to '''16GB''' max heap memory. If larger memory is needed, please contact us.

	====Run Beast with GPU support in a batch job====		===Run Beast with GPU support in a batch job===

	Example job submission script (sub.sh) to run version 2.7.7 with GPU support in a batch job:		Example job submission script (sub.sh) to run version 2.7.7 with GPU support in a batch job:
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==
	<pre class="gcommand">ml Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1		<pre class="gcommand">ml Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1
	beast -help		beast -help
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source codes download from [http://beast2.org/ BEAST2]		Source codes download from [http://beast2.org/ BEAST2]

	=== System ===		== System ==

	64-bit Linux		64-bit Linux

Chelsea: /* Documentation */

2025-07-07T20:07:14Z

Documentation

@@ Line 200: / Line 200: @@
 : CPU (x86_64)
-     Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
+     Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_CPP THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
 </pre>

Chelsea: /* Version */

2025-07-07T19:36:36Z

Version

← Older revision		Revision as of 15:36, 7 July 2025
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	=== Version ===		=== Version ===

	1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5		<!--1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5-->
			2.7.7

	=== Author / Distributor ===		=== Author / Distributor ===
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	====Versions without GPU support====		====Versions without GPU support====

	* version 1.10.4 installed in /apps/eb/Beast/1.10.4-GCC-11.3.0		* version 2.7.7 installed in /apps/eb/Beast/2.7.7-GCC-12.3.0

	To use this version of Beast, please first load the module with		To use this version of Beast, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load Beast/1.10.4-GCC-11.3.0		module load Beast/2.7.7-GCC-12.3.0
	</pre>		</pre>
			<!--
	*version 2.5.1 installed in /apps/eb/Beast/2.5.1-GCC-11.3.0		*version 2.5.1 installed in /apps/eb/Beast/2.5.1-GCC-11.3.0

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	module load Beast/2.7.5-GCC-11.3.0		module load Beast/2.7.5-GCC-11.3.0
	</pre>		</pre>
			-->
	====Versions with CPU and GPU support====		====Versions with CPU and GPU support====

	* version 1.10.4 with CPU and GPU support, installed in /apps/eb/Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1. This version of Beast is using beagle-lib/3.1.2 with GPU support.		* version 2.7.7 with CPU and GPU support, installed in /apps/eb/Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1. This version of Beast is using beagle-lib/4.0.1 with GPU support.

	To use this version of Beast, please first load the module with		To use this version of Beast, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1		module load Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1
	</pre>		</pre>
			<!--
	* version 2.6.3 with CPU and GPU support, installed in /apps/eb/Beast/2.6.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.		* version 2.6.3 with CPU and GPU support, installed in /apps/eb/Beast/2.6.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.

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	module load Beast/2.7.3-foss-2021b-CUDA-11.4.1		module load Beast/2.7.3-foss-2021b-CUDA-11.4.1
	</pre>		</pre>
			-->
	====Run Beast in an interactive session====		====Run Beast in an interactive session====

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	# Start an [[OnDemand#X%20Desktop%20Session%20.28A.K.A.%20The%20Interactive%20X%20login%20app.29\|X Desktop Session]] via Open OnDemand		# Start an [[OnDemand#X%20Desktop%20Session%20.28A.K.A.%20The%20Interactive%20X%20login%20app.29\|X Desktop Session]] via Open OnDemand
	# Open the Terminal application in your X Desktop session (icon at the bottom of the Desktop or via the "Applications" button in the top left)		# Open the Terminal application in your X Desktop session (icon at the bottom of the Desktop or via the "Applications" button in the top left)
	# <code>ml Beast/2.7.3-~~foss~~-~~2021b~~-CUDA-11.4.1</code>		# <code>ml Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1</code>
	# <code>beauti</code> ...		# <code>beauti</code> ...
	# <code>beast</code> ...		# <code>beast</code> ...
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	====Run Beast with GPU support in a batch job====		====Run Beast with GPU support in a batch job====

	Example job submission script (sub.sh) to run version 2.6.3 with GPU support in a batch job:		Example job submission script (sub.sh) to run version 2.7.7 with GPU support in a batch job:

	<pre class="gscript">		<pre class="gscript">
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml Beast/2.7.3-~~foss~~-~~2021b~~-CUDA-11.4.1		ml Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1

	beast -threads 4 -beagle -beagle_GPU [options]		beast -threads 4 -beagle -beagle_GPU [options]
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	=== Documentation ===		=== Documentation ===
	<pre class="gcommand">ml Beast/2.7.3-~~foss~~-~~2021b~~-CUDA-11.4.1		<pre class="gcommand">ml Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1
	beast -help		beast -help
	Usage: beast [-window] [-options] [-working] [-seed] [-prefix <PREFIX>] [-statefile <STATEFILE>] [-overwrite] [-resume] [-validate] [-errors <i>] [-threads <i>] [-java] [-noerr] [-loglevel <LEVEL>] [-instances <i>] [-beagle] [-beagle_info] [-beagle_order <order>] [-beagle_CPU] [-beagle_GPU] [-beagle_SSE] [-beagle_single] [-beagle_double] [-beagle_scaling <default\|none\|dynamic\|always>] [-help] [-version] [-strictversions] [-D <DEFINITIONS>] [-DF <DEFINITIONFILE>] [-DFout <DEFINITIONRESULTFILE>] [-sampleFromPrior] [-version_file <VERSIONFILE>] [-packagedir <PACKAGEDIR>] [<input-file-name>]		Usage: beast [-window] [-options] [-working] [-seed] [-prefix <PREFIX>] [-statefile <STATEFILE>] [-overwrite] [-resume] [-validate] [-errors <i>] [-threads <i>] [-java] [-noerr] [-loglevel <LEVEL>] [-instances <i>] [-beagle] [-beagle_info] [-beagle_order <order>] [-beagle_CPU] [-beagle_GPU] [-beagle_SSE] [-beagle_single] [-beagle_double] [-beagle_scaling <default\|none\|dynamic\|always>] [-help] [-version] [-strictversions] [-D <DEFINITIONS>] [-DF <DEFINITIONFILE>] [-DFout <DEFINITIONRESULTFILE>] [-sampleFromPrior] [-version_file <VERSIONFILE>] [-packagedir <PACKAGEDIR>] [<input-file-name>]
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	ml Beast/2.7.3-~~foss~~-~~2021b~~-CUDA-11.4.1		ml Beast/2.7.7-GCC-12.3.0-CUDA-12.1.1
	beast -beagle_info		beast -beagle_info

	BEAST v2.7.3, 2002-~~2022~~		BEAST v2.7.7, 2002-2024
	Bayesian Evolutionary Analysis Sampling Trees		Bayesian Evolutionary Analysis Sampling Trees
	Designed and developed by		Designed and developed by

Moses: /* Version */

2024-07-12T14:10:56Z

Version

← Older revision		Revision as of 10:10, 12 July 2024
Line 10:		Line 10:
	=== Version ===		=== Version ===

	1.10.4, 2.6.3, 2.7.3, 2.7.5		1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5

	=== Author / Distributor ===		=== Author / Distributor ===
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	<pre class="gscript">		<pre class="gscript">
	module load Beast/1.10.4-GCC-11.3.0		module load Beast/1.10.4-GCC-11.3.0
			</pre>
			*version 2.5.1 installed in /apps/eb/Beast/2.5.1-GCC-11.3.0

			To use this version of Beast, please first load the module with
			<pre class="gscript">
			module load Beast/2.5.1-GCC-11.3.0
	</pre>		</pre>
	* version 2.7.5 installed in /apps/eb/Beast/2.7.5-GCC-11.3.0		* version 2.7.5 installed in /apps/eb/Beast/2.7.5-GCC-11.3.0

Chelsea at 14:00, 9 May 2024

2024-05-09T14:00:25Z

← Older revision		Revision as of 10:00, 9 May 2024
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	====Versions without GPU support====		====Versions without GPU support====

	* version 1.10.4 installed in /apps/eb/Beast/1.10.4-GCC-11.3.0<pre class="gscript">		* version 1.10.4 installed in /apps/eb/Beast/1.10.4-GCC-11.3.0

			To use this version of Beast, please first load the module with
			<pre class="gscript">
	module load Beast/1.10.4-GCC-11.3.0		module load Beast/1.10.4-GCC-11.3.0
	</pre>		</pre>
	* version 2.7.5 installed in /apps/eb/Beast/2.7.5-GCC-11.3.0<pre class="gscript">		* version 2.7.5 installed in /apps/eb/Beast/2.7.5-GCC-11.3.0

			To use this version of Beast, please first load the module with
			<pre class="gscript">
	module load Beast/2.7.5-GCC-11.3.0		module load Beast/2.7.5-GCC-11.3.0
	</pre>		</pre>
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	====Versions with CPU and GPU support====		====Versions with CPU and GPU support====

	* version 1.10.4 with CPU and GPU support, installed in /apps/eb/Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1. This version of Beast is using beagle-lib/3.1.2 with GPU support.<pre class="gscript">		* version 1.10.4 with CPU and GPU support, installed in /apps/eb/Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1. This version of Beast is using beagle-lib/3.1.2 with GPU support.

			To use this version of Beast, please first load the module with
			<pre class="gscript">
	module load Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1		module load Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1
	</pre>		</pre>
	* version 2.6.3 with CPU and GPU support, installed in /apps/eb/Beast/2.6.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.<pre class="gscript">		* version 2.6.3 with CPU and GPU support, installed in /apps/eb/Beast/2.6.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.

			To use this version of Beast, please first load the module with
			<pre class="gscript">
	module load Beast/2.6.3-foss-2021b-CUDA-11.4.1		module load Beast/2.6.3-foss-2021b-CUDA-11.4.1
	</pre>		</pre>

Chelsea: /* Version */

2024-05-09T13:58:39Z

Version

← Older revision		Revision as of 09:58, 9 May 2024
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	=== Version ===		=== Version ===

	2.7.3		1.10.4, 2.6.3, 2.7.3, 2.7.5

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

			====Versions without GPU support====

			* version 1.10.4 installed in /apps/eb/Beast/1.10.4-GCC-11.3.0<pre class="gscript">
			module load Beast/1.10.4-GCC-11.3.0
			</pre>
			* version 2.7.5 installed in /apps/eb/Beast/2.7.5-GCC-11.3.0<pre class="gscript">
			module load Beast/2.7.5-GCC-11.3.0
			</pre>

	====Versions with CPU and GPU support====		====Versions with CPU and GPU support====

			* version 1.10.4 with CPU and GPU support, installed in /apps/eb/Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1. This version of Beast is using beagle-lib/3.1.2 with GPU support.<pre class="gscript">
			module load Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1
			</pre>
			* version 2.6.3 with CPU and GPU support, installed in /apps/eb/Beast/2.6.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.<pre class="gscript">
			module load Beast/2.6.3-foss-2021b-CUDA-11.4.1
			</pre>
	* version 2.7.3 with CPU and GPU support, installed in /apps/eb/Beast/2.7.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.		* version 2.7.3 with CPU and GPU support, installed in /apps/eb/Beast/2.7.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.

Moses at 16:10, 5 September 2023

2023-09-05T16:10:27Z

Show changes

Ben: Document how to use this in OOD rather than xqlogin

2021-12-09T14:53:56Z

Document how to use this in OOD rather than xqlogin

← Older revision		Revision as of 10:53, 9 December 2021
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	====Run Beast in an interactive session====		====Run Beast in an interactive session====

	Beast is a X window program with graphic interface. It has to be run in an interactive session. Please refer to [[~~Running_Jobs_on_Sapelo2~~#~~How_to_open_an_interactive_session~~ \| ~~Run interactive Jobs~~]] ~~and [~~[~~Running_Jobs_on_Sapelo2#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]~~].		Beast is a X window program with graphic interface. It has to be run in an interactive session. Please refer to [[OnDemand#X%20Desktop%20Session%20.28A.K.A.%20The%20Interactive%20X%20login%20app.29\|X Desktop Sessions]] in [https://ondemand.gacrc.uga.edu/pun/sys/dashboard/ Open OnDemand].

	Start X Terminal ~~(Mac),~~ X ~~window~~ (~~Windows)~~ at the ~~local computer first, then~~		# Start an [[OnDemand#X%20Desktop%20Session%20.28A.K.A.%20The%20Interactive%20X%20login%20app.29\|X Desktop Session]] via Open OnDemand
			# Open the Terminal application in your X Desktop session (icon at the bottom of the Desktop or via the "Applications" button in the top left)
	<~~pre class="gcommand"~~>		# <code>ml Beast/2.6.3-foss-2019b</code>
	~~xqlogin~~		# <code>beauti</code> ...
	~~module load~~ Beast/2.6.3-foss-2019b		# <code>beast</code> ...
	beauti
	...
	beast
	...
	~~exit~~
	~~</pre>~~

	* beast/beauti in this app is set to '''16GB''' max heap memory. If larger memory is needed, please contact us.		* beast/beauti in this app is set to '''16GB''' max heap memory. If larger memory is needed, please contact us.

Moses: /* Versions with CPU and GPU support */

2020-12-03T15:41:41Z

Versions with CPU and GPU support

← Older revision		Revision as of 11:41, 3 December 2020
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	<pre class="gscript">		<pre class="gscript">
	module load Beast/2.6.3-fosscuda-2019b		module load Beast/2.6.3-fosscuda-2019b

	</pre>		</pre>