RAxML-Teaching - Revision history

Shtsai at 01:29, 5 April 2026

2026-04-05T01:29:59Z

← Older revision		Revision as of 21:29, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

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

	Teaching		Teaching

	=== Version ===		== Version ==
	8.2.13		8.2.13

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

	[https://github.com/stamatak/standard-RAxML RAxML]		[https://github.com/stamatak/standard-RAxML RAxML]

	=== Description ===		== Description ==
	"RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."		"RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
	More details are at [https://github.com/stamatak/standard-RAxML RAxML]		More details are at [https://github.com/stamatak/standard-RAxML RAxML]

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

	'''Version 8.2.13, MPI enabled'''		'''Version 8.2.13, MPI enabled'''
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

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

	Source code is obtained from [https://github.com/stamatak/standard-RAxML RAxML]		Source code is obtained from [https://github.com/stamatak/standard-RAxML RAxML]

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

Shtsai at 20:41, 9 January 2026

2026-01-09T20:41:12Z

@@ Line 71: / Line 71: @@
 '''2. Running the PTHREADS version:'''
--->
 In the example below the name of the alignment data file in PHYLIP format is primates.phy.
@@ Line 94: / Line 94: @@
 raxmlHPC-PTHREADS-SSE3 -T ${SLURM_CPUS_PER_TASK} -s primates.phy -n testrun -m GTRGAMMA -p 1234 -#1000  <br>
 </div>
 In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
@@ Line 101: / Line 126: @@
 Here is an example of job submission command:
 <pre  class="gcommand">
-sbatch ./subpthreads.sh
+sbatch ./submpi.sh
 </pre>

Shtsai at 20:39, 9 January 2026

2026-01-09T20:39:33Z

← Older revision		Revision as of 16:39, 9 January 2026
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	=== Version ===		=== Version ===
	8.2.12		8.2.13

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

	'''Version 8.2.12, ~~PTHREADS~~ enabled'''		'''Version 8.2.13, MPI enabled'''

	This version is installed in /apps/eb/RAxML/8.2.12-~~foss~~-~~2022a~~-~~pthreads-avx~~		This version is installed in /apps/eb/RAxML/8.2.13-gompi-2023a-avx2

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml RAxML/8.2.12-~~foss~~-~~2022a~~-~~pthreads-avx~~		ml RAxML/8.2.13-gompi-2023a-avx2
	</pre>		</pre>

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	<pre class="gcommand">		<pre class="gcommand">
	ml RAxML/8.2.12-~~foss~~-~~2019b~~-~~PTHREADS-sse3~~		ml RAxML/8.2.13-gompi-2023a-avx2
			raxmlHPC -help
	raxmlHPC-~~PTHREADS-SSE3 -h~~


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	DEFAULT: identical sequences will also be removed in the .reduced file		DEFAULT: identical sequences will also be removed in the .reduced file


	</pre>		</pre>

Chelsea: /* Running Program */

2024-05-14T12:48:12Z

Running Program

← Older revision		Revision as of 08:48, 14 May 2024
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	'''Version 8.2.12, PTHREADS enabled'''		'''Version 8.2.12, PTHREADS enabled'''

	This version is installed in /apps/eb/RAxML/8.2.12-foss-~~2019b~~-~~PTHREADS~~-~~sse3~~		This version is installed in /apps/eb/RAxML/8.2.12-foss-2022a-pthreads-avx

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml RAxML/8.2.12-foss-~~2019b~~-~~PTHREADS~~-~~sse3~~		ml RAxML/8.2.12-foss-2022a-pthreads-avx
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml RAxML/8.2.12-foss-~~2019b~~-~~PTHREADS~~-~~sse3~~<br>		ml RAxML/8.2.12-foss-2022a-pthreads-avx<br>
	raxmlHPC-PTHREADS-SSE3 -T ${SLURM_CPUS_PER_TASK} -s primates.phy -n testrun -m GTRGAMMA -p 1234 -#1000 <br>		raxmlHPC-PTHREADS-SSE3 -T ${SLURM_CPUS_PER_TASK} -s primates.phy -n testrun -m GTRGAMMA -p 1234 -#1000 <br>
	</div>		</div>

Shtsai at 01:46, 28 August 2020

2020-08-28T01:46:05Z

← Older revision		Revision as of 21:46, 27 August 2020
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	<--!		<!--

	'''1. Running the MPI version:'''		'''1. Running the MPI version:'''

Shtsai at 01:45, 28 August 2020

2020-08-28T01:45:43Z

← Older revision		Revision as of 21:45, 27 August 2020
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	=== Version ===		=== Version ===
	8.2.11		8.2.12

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

	'''Version 8.2.11, ~~MPI~~ enabled'''		'''Version 8.2.12, PTHREADS enabled'''

	This version is installed in ~~/usr/local~~/apps/eb/RAxML/8.2.11-foss-~~2016b~~-~~mpi~~-sse3		This version is installed in /apps/eb/RAxML/8.2.12-foss-2019b-PTHREADS-sse3

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml RAxML/8.2.11-foss-~~2016b~~-~~mpi~~-sse3		ml RAxML/8.2.12-foss-2019b-PTHREADS-sse3
	</pre>		</pre>


	~~'''Version 8.2.11, PTHREADS enabled'''~~

	~~This version is installed in /usr/local/apps/eb/RAxML/8.2.11-foss-2016b-pthreads-sse3~~

	~~To use this version, please load the module with~~
	~~<pre class="gscript">~~
	~~ml RAxML/8.2.11-foss-2016b-pthreads-sse3~~
	~~</pre>~~

			<--!

	'''1. Running the MPI version:'''		'''1. Running the MPI version:'''
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	'''2. Running the PTHREADS version:'''		'''2. Running the PTHREADS version:'''
			-->

	In the example below the name of the alignment data file in PHYLIP format is primates.phy.		In the example below the name of the alignment data file in PHYLIP format is primates.phy.
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml RAxML/8.2.11-foss-~~2016b~~-~~pthreads~~-sse3<br>		ml RAxML/8.2.12-foss-2019b-PTHREADS-sse3<br>
	raxmlHPC-PTHREADS-SSE3 -T ${SLURM_CPUS_PER_TASK} -s primates.phy -n testrun -m GTRGAMMA -p 1234 -#1000 <br>		raxmlHPC-PTHREADS-SSE3 -T ${SLURM_CPUS_PER_TASK} -s primates.phy -n testrun -m GTRGAMMA -p 1234 -#1000 <br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml RAxML/8.2.11-foss-~~2016b~~-~~pthreads~~-sse3		ml RAxML/8.2.12-foss-2019b-PTHREADS-sse3

	raxmlHPC-PTHREADS-SSE3 -~~help~~		raxmlHPC-PTHREADS-SSE3 -h


	This is RAxML version 8.2.11 released by Alexandros Stamatakis on ~~June 2017~~.		This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.

	With greatly appreciated code contributions by:		With greatly appreciated code contributions by:

Shtsai at 20:24, 13 August 2018

2018-08-13T20:24:35Z

Show changes

Yhuang at 18:07, 10 August 2018

2018-08-10T18:07:01Z

← Older revision		Revision as of 14:07, 10 August 2018
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	<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>		<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>
	<nowiki>#</nowiki>SBATCH --output=RAxML.%j.out<br>		<nowiki>#</nowiki>SBATCH --output=RAxML.%j.out<br>
			<nowiki>#</nowiki>SBATCH --error=RAxML.%j.err<br>

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
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	<pre class="gcommand">		<pre class="gcommand">
	ml RAxML/8.2.11-foss-2016b-mpi-sse3		ml RAxML/8.2.11-foss-2016b-mpi-sse3
	~~raxmlHPC-PTHREADS-AVX~~ raxmlHPC-PTHREADS-AVX -help		raxmlHPC-PTHREADS-AVX -help

	</pre>		</pre>

Yhuang at 17:46, 10 August 2018

2018-08-10T17:46:23Z

← Older revision		Revision as of 13:46, 10 August 2018
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	The last version of this application is at /usr/local/apps/eb/RAxML/8.2.11-foss-2016b-mpi-sse3		The last version of this application is at /usr/local/apps/eb/RAxML/8.2.11-foss-2016b-mpi-sse3

	To use this version, please ~~loads~~ the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml RAxML/8.2.11-foss-2016b-mpi-sse3		ml RAxML/8.2.11-foss-2016b-mpi-sse3
	</pre>		</pre>

	Here is an example of a shell script, sub.sh, to run on at the batch queue:		Here is an example of a shell script, sub.sh, to run on the batch queue:

	<div class="gscript2">		<div class="gscript2">

Yhuang at 15:35, 10 August 2018

2018-08-10T15:35:49Z

← Older revision		Revision as of 11:35, 10 August 2018
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	To use this version, please loads the module with		To use this version, please loads the module with
	<pre class="gscript">		<pre class="gscript">
	ml RAxML/8.2.11-foss-2016b-mpi-sse3		ml RAxML/8.2.11-foss-2016b-mpi-sse3

	~~raxmlHPC-PTHREADS-AVX~~
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
			ml RAxML/8.2.11-foss-2016b-mpi-sse3<br>
	ml <!-- ~~TEST_COMMAND BEGIN~~ -->~~<!-- TEST_COMMAND END~~ --> <u>[options]</u><br>		raxmlHPC-PTHREADS-AVX <u>[options]</u><br>
	</div>		</div>
	In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values ~~or be reviewed~~ .		In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

	Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application \| Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] for more details of running jobs at Teaching cluster.		Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application \| Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] for more details of running jobs at Teaching cluster.
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	<pre class="gcommand">		<pre class="gcommand">
	RAxML/8.2.11-foss-2016b-mpi-sse3		ml RAxML/8.2.11-foss-2016b-mpi-sse3
	raxmlHPC-PTHREADS-AVX -help		raxmlHPC-PTHREADS-AVX raxmlHPC-PTHREADS-AVX -help

	</pre>		</pre>