Differences

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--- raxml-software [2015/07/27 07:18] – joguya
+++ raxml-software [2018/09/16 07:45] (current) – aorth
@@ Line 2: / Line 2: @@
 RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
-  * Latest Version: 8.2.0
+===== Information =====
+  * Latest Version: 8.2.12
   * Added: June, 2011
-  * Updated: July, 2015
+  * Updated: September, 2018
   * Link: https://github.com/stamatak/standard-RAxML
 === Usage ===
-  * Show all available versions of RAxML<code>module avail RAxML</code>
-  * Load RAxML module: <code>module load RAxML/8.2.0</code>
+Show all available versions of RAxML:
+<code>$ module avail RAxML</code>
+Load one version into your environment and run it:
+<code>$ module load RAxML/8.2.12
+$ raxmlHPC-PTHREADS-AVX</code>
+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:
+<code>$ raxmlHPC-PTHREADS-AVX -T 5</code>
 === Installation ===
-  *Notes from the sysadmin during installation:<code>
+Notes from the sysadmin during installation:
-wget https://github.com/stamatak/standard-RAxML/archive/v8.2.0.tar.gz
-tar -xvf v8.2.0.tar.gz
+<code>$ cd /tmp
-cd standard-RAxML-8.2.0/
+$ wget https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz
-make -f Makefile.AVX.gcc
+$ tar xf v8.2.12.tar.gz
-rm *.o
+$ cd standard-RAxML-8.2.12
-make -f Makefile.AVX.PTHREADS.gcc
+$ make -f Makefile.SSE3.gcc
-rm *.o
+$ make -f Makefile.SSE3.PTHREADS.gcc
-module load openmpi/1.8.2
+$ make -f Makefile.AVX.gcc
-make -f Makefile.MPI.gcc
+$ make -f Makefile.AVX.PTHREADS.gcc
-rm *.o
+$ sudo mkdir -p /export/apps/RAxML/8.2.12/bin
-sudo mkdir -p /export/apps/RAxML/8.2.0/bin
+$ sudo cp raxmlHPC-* /export/apps/RAxML/8.2.12/bin</code>
-sudo cp -v raxmlHPC* /export/apps/RAxML/8.2.0/bin/
-</code>