Differences

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--- raxml-software [2014/12/08 10:12] – [Installation Notes] joguya
+++ raxml-software [2025/05/14 12:03] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== RAxML ======
+RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
-===== RAxML 8.0.23 =====
+===== Information =====
-==== Information ====
-  * Version: 8.0.23
+  * Latest Version: 8.2.12
   * Added: June, 2011
-  * Updated: May 27, 2014
+  * Updated: May, 2025
   * Link: https://github.com/stamatak/standard-RAxML
-==== Usage ====
+=== Usage ===
-=== See versions of RAxML which are available ===
+Show all available versions:
-<code>module avail RAxML</code>
-==== Installation =====
+<code>$ module avail RAxML</code>
-Notes from the sysadmin during installation:
-<code>git clone https://github.com/stamatak/standard-RAxML.git
+Load one version into your environment and run it:
-cd standard-RAxML
-scl enable devtoolset-1.1 bash
-git checkout v8.0.23
-make -f Makefile.AVX.gcc
-rm *.o
-make -f Makefile.AVX.PTHREADS.gcc
-sudo mkdir -p /export/apps/RAxML/8.0.23/bin
-sudo cp raxmlHPC-* /export/apps/RAxML/8.0.23/bin/</code>
-===== RAxML 8.1.9 =====
-Information:
-  * Version: 8.1.9
-  * Added: December, 2014
-  * Link: https://github.com/stamatak/standard-RAxML/releases/tag/v8.1.9
-==== Installation Notes ====
+<code>$ module load RAxML/8.2.12
-  * Download pandaseq 2.8.1, create version specific dir in /export/apps/pandaseq/, compile & install it.<code>
+$ raxmlHPC-PTHREADS-AVX2</code>
-git clone https://github.com/stamatak/standard-RAxML.git
-cd standard-RAxML
-scl enable devtoolset-1.1 bash
-git checkout v8.1.9
-make -f Makefile.gcc
-rm *.o
-make -f Makefile.SSE3.gcc
-rm *.o
-make -f Makefile.AVX.gcc
-rm *.o
-make -f Makefile.PTHREADS.gcc
-rm *.o
-make -f Makefile.AVX.PTHREADS.gcc
-rm *.o
-make -f Makefile.SSE3.PTHREADS.gcc
-rm *.o
-module load openmpi/1.8.2
-make -f Makefile.MPI.gcc
-rm *.o
-make -f Makefile.SSE3.MPI.gcc
-rm *.o
-make -f Makefile.AVX.MPI.gcc
-rm *.o
-sudo mkdir -p /export/apps/RAxML/8.1.9/bin
-sudo cp raxmlHPC* /export/apps/RAxML/8.1.9/bin/
-</code>
-  * RAxML/8.1.9 module file:<code>#%Module1.0
+Note: you should set the number of concurrent CPU threads using the ''-T'' option. For example, if you have requested five CPUs in your SLURM batch script, you can tell RAxML to use five threads:
-#####################################################################
-##
-## RAxML Modulefile
-## by James Oguya, <j.oguya@cgiar.org>
-## December, 2014
-##
-set     appname         RAxML
+<code>$ raxmlHPC-PTHREADS-AVX2 -T 5</code>
-set     version         8.1.9
-set     prefix          /export/apps/${appname}/${version}
-set     exec_prefix     ${prefix}/bin
-conflict    RAxML
-prepend-path    PATH            ${exec_prefix}
-</code>
+=== Installation ===
+Notes from the sysadmin during installation:
+<code>$ cd /tmp
+$ wget https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz
+$ tar xf v8.2.12.tar.gz
+$ cd standard-RAxML-8.2.12
+$ make -f Makefile.SSE3.gcc
+$ make -f Makefile.SSE3.PTHREADS.gcc
+$ make -f Makefile.AVX.gcc
+$ make -f Makefile.AVX.PTHREADS.gcc
+$ make -f Makefile.AVX2.gcc
+$ make -f Makefile.AVX2.PTHREADS.gcc
+$ sudo mkdir -p /export/apps/RAxML/8.2.12/bin
+$ sudo cp raxmlHPC-* /export/apps/RAxML/8.2.12/bin</code>