Applications/RaXML - Revision history

Pysdlb: /* Further Information */

2022-11-16T10:56:58Z

‎Further Information

Pysdlb: /* Navigation */

2022-11-16T10:56:51Z

‎Navigation

Pysdlb at 13:39, 24 May 2019

2019-05-24T13:39:12Z

Pysdlb at 14:17, 7 June 2018

2018-06-07T14:17:47Z

Seif: /* Interactive */

2017-11-16T17:11:02Z

‎Interactive

Seif: /* Batch Session */

2017-11-16T17:10:52Z

‎Batch Session

Seif: /* Interactive */

2017-11-16T17:05:52Z

‎Interactive

Seif: Created page with "===Interactive=== While logged into viper login node: you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example..."

2017-11-16T17:05:07Z

Created page with "===Interactive=== While logged into viper login node: you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example..."

New page

===Interactive===

While logged into viper login node:
you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example.phy copy it to the location where you would like to run the below steps

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ interactive
salloc: Granted job allocation 296769
Job ID 296769 connecting to c170, please wait...
Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246
[username@c170 ~]$ module add openmpi/gcc/1.10.2
[username@c170 ~]$ /trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause

</pre>

====Batch Session====

Below is how to submit the same example using our scheduler slurm.
please replace /home/USERNAME/PATH/OF/DIR to the path of the directory where you copied the example.phy file or to the file that you want to use.
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J raxml_example # Job name, you can change it to whatever you want
#SBATCH -o %N.%j.out # Standard output will be written here
#SBATCH -e %N.%j.err # Standard error will be written here
#SBATCH -n 14 # number of cores
#SBATCH -N 1 # Number of nodes
#SBATCH -p highmem # Slurm partition, where you want the job to be queued
#SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module load openmpi/gcc/1.10.2
cd /home/USERNAME/PATH/OF/DIR
/trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause

</pre>

Then the next step is to submit the above script to slurm
for example if you name the above text file raxml.sh
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[user@login01 ~]$ sbatch raxml.sh
Submitted batch job 409671

</pre>

← Older revision		Revision as of 10:56, 16 November 2022
Line 52:		Line 52:

	* https://sco.h-its.org/exelixis/web/software/raxml/cluster.html		* https://sco.h-its.org/exelixis/web/software/raxml/cluster.html
−
−

	{{Modulepagenav}}		{{Modulepagenav}}

← Older revision		Revision as of 10:56, 16 November 2022
Line 55:		Line 55:


−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 55: / Line 55: @@
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 4: / Line 4: @@
 *Licence:  Open source
 ===Interactive===
@@ Line 47: / Line 48: @@
 </pre>
 ==Further Information==

← Older revision		Revision as of 17:10, 16 November 2017
Line 47:		Line 47:

	</pre>		</pre>
		+	==Further Information==
		+
		+	* https://sco.h-its.org/exelixis/web/software/raxml/cluster.html
		+
		+
		+
		+	{\|
		+	\|style="width:5%; border-width: 0" \| [[File:icon_home.png]]
		+	\|style="width:95%; border-width: 0" \|
		+	* [[Main_Page\|Home]]
		+	* [[Applications\|Application support]]
		+	* [[General\|General]]
		+	* [[Training\|Training]]
		+	* [[Programming\|Programming support]]
		+	\|-
		+	\|}

@@ Line 34: / Line 34: @@
 #SBATCH --exclusive         # Request exclusive access to a node (all 28 cores, 128GB of RAM)
-module load openmpi/gcc/1.10.2
+module add openmpi/gcc/1.10.2
 cd /home/USERNAME/PATH/OF/DIR
 /trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause

← Older revision		Revision as of 17:05, 16 November 2017
Line 1:		Line 1:
		+	==Application Details==
		+	*A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
		+	*Version: MPI AVX 8.2.11
		+	*Licence: Open source
		+
	===Interactive===		===Interactive===