{"id":3179,"date":"2016-06-27T09:53:01","date_gmt":"2016-06-27T09:53:01","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=3179"},"modified":"2016-07-19T09:03:12","modified_gmt":"2016-07-19T09:03:12","slug":"bayestraits","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/bayestraits\/","title":{"rendered":"BayesTraits"},"content":{"rendered":"

Overview<\/h2>\n

BayesTraits<\/a> is a program from the Reading Evolutionary Biology Group<\/a> for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. <\/p>\n

Version 2.0 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

Details of the licence, restrictions, links to licence docs etc<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

\r\n# Serial version\r\nmodule load apps\/binapps\/bayes_traits\/2.0\r\n\r\n# Parallel (multicore) version\r\nmodule load apps\/binapps\/bayes_traits\/2.0-omp\r\n<\/pre>\n
Running the application<\/h2>\n
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<\/em> which will perform the menu selections needed to run your job.<\/p>\n
If you wish to run BayesTraits interactively so that you can check you menu selections, please do so using qrsh<\/code> which will start an interactive<\/em> session on a compute node (see below for an example).<\/p>\n
Interactive job<\/h3>\n
To run BayesTraits ineractively so you can make the menu selections, run the following from the CSF login node:<\/p>\n
\r\nmodule load apps\/binapps\/bayes_traits\/2.0\r\nqrsh -l inter -l short -cwd -V BayesTraits TreeFile<\/em> DataFile<\/em>\r\n<\/pre>\n
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.<\/p>\n
Batch jobs should be used for longer processing (and parallel processing) – please see the examples below.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\nBayesTraitsV2 TreeFile<\/em> DataFile<\/em> < CommandFile.txt<\/em>\r\n<\/pre>\n
The CommandFile.txt<\/em> should contain your menu selections and any other commands needed by the application. For example:<\/p>\n
\r\n1\r\n1\r\nrun\r\n<\/pre>\n
You can create plain text files on the CSF using gedit<\/code> on the login node.<\/p>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Job will use 8 cores (specify between 2 and 24 here).\r\n\r\n# Inform BayesTraits how many cores it can use ($NSLOTS automatically set to number given above)\r\nexport OMP_NUM_THREADS=$NSLOTS\r\n\r\nBayesTraitsV2_OpenMP TreeFile<\/em> DataFile<\/em> < CommandFile.txt<\/em>\r\n<\/pre>\n
See the serial example above for details of the Command File<\/em>.<\/p>\n
Further info<\/h2>\n