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RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
Using
Use the module name raxml to discover versions available and to load the application.
Multicore/MultinodeMulti node
The raxmlHPC-MPI application allows you to define multiple cores/threads within calls using the '-N for number of threads allocated to the program' option.
After downloading the example files, a batch script would take the following form where we are defining and using 2 cores and 2 nodes.
| Code Block |
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#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=1
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raxmlHPC-MPI -N 4 -m BINGAMMA -p 12345 -s ./test_data/binary.phy -n T1 |
The best number of cores/threads and memory to use for a particular job will depend on the data and is up to the researcher to explore.
Please feel free to report/share any interesting observations and we can update this page.raxml application has been built with MPI (openmpi) and can run across multiple nodes, as well as across multiple cores, depending on which command you use.
View the options of whichever command you use, specifically reading about the -T and -N options:
Command | Functionality | Use Options: |
|---|---|---|
| Single node, single core. | |
| Single node, multiple cores. |
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| Multiple nodes, single core per task. |
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| Multiple nodes, multiple cores per task. |
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