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BayesTraits
Overview
BayesTraits is a program from the Reading Evolutionary Biology Group for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.
Version 2.0 is installed on the CSF.
Restrictions on use
Details of the licence, restrictions, links to licence docs etc
Set up procedure
To access the software you must first load the modulefile:
# Serial version module load apps/binapps/bayes_traits/2.0 # Parallel (multicore) version module load apps/binapps/bayes_traits/2.0-omp
Running the application
Please do not run BayesTraits on the login node. Jobs should be submitted to the compute nodes via batch. You will need to create a command file which will perform the menu selections needed to run your job.
If you wish to run BayesTraits interactively so that you can check you menu selections, please do so using qrsh which will start an interactive session on a compute node (see below for an example).
Interactive job
To run BayesTraits ineractively so you can make the menu selections, run the following from the CSF login node:
module load apps/binapps/bayes_traits/2.0 qrsh -l inter -l short -cwd -V BayesTraits TreeFile DataFile
This will run BayesTraits on a compute node, not the login node. It will read the input files from the current directory. If no interactive resources are available you will be asked to try again later. Note that interactive jobs can only run for up to one hour.
Batch jobs should be used for longer processing (and parallel processing) – please see the examples below.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings BayesTraitsV2 TreeFile DataFile < CommandFile.txt
The CommandFile.txt should contain your menu selections and any other commands needed by the application. For example:
1 1 run
You can create plain text files on the CSF using gedit on the login node.
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Job will use 8 cores (specify between 2 and 24 here). # Inform BayesTraits how many cores it can use ($NSLOTS automatically set to number given above) export OMP_NUM_THREADS=$NSLOTS BayesTraitsV2_OpenMP TreeFile DataFile < CommandFile.txt
See the serial example above for details of the Command File.
Further info
Updates
None.