{"id":4444,"date":"2018-02-19T15:52:02","date_gmt":"2018-02-19T15:52:02","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4444"},"modified":"2018-02-19T15:52:23","modified_gmt":"2018-02-19T15:52:23","slug":"pbmpi","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/pbmpi\/","title":{"rendered":"Phylobayes MPI (PBMPI)"},"content":{"rendered":"

Overview<\/h2>\n

Phylobayes MPI<\/a> is a Bayesian software for phylogenetic reconstruction using mixture models which can run in parallel using MPI.<\/p>\n

Version 1.8 is installed on the CSF. It has been compiled with the Intel 15.0.3 compiler.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing this software on the CSF. It is release under the GNU GPL v2<\/a> license and all use must adhere to that license.<\/p>\n

Set up procedure<\/h2>\n

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

\r\n# Single node (2-24 cores) parallel jobs\r\nmodule load apps\/intel-15.0\/pbmpi\/1.8\r\n\r\n# Multi node (48 cores or more in multiples of 24) parallel jobs\r\nmodule load apps\/intel-15.0\/pbmpi\/1.8-ib\r\n\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run pbmpi tools on the login node. Jobs should be submitted to the compute nodes via batch. There are a number of command-line tools available:<\/p>\n
\r\nbpcomp    cvrep    pb_mpi    readpb_mpi    tracecomp\r\n<\/pre>\n
You may<\/em> run each command without any args \/ parameters on the login node to see the help text. For example:<\/p>\n
\r\npb_mpi\r\n\r\nmpirun -np  pb_mpi -d  [options] \r\n\tcreates a new chain, sampling from the posterior distribution, conditional on specified data\r\n\r\nmpirun -np  pb_mpi \r\n\tstarts an already existing chain\r\n\r\n\tmpirun -np      : number of parallel processes (should be at least 2)\r\n\r\n\t-cat -dp            : infinite mixture (Dirichlet process) of equilibirium frequency profiles\r\n\t-ncat         : finite mixture of equilibirium frequency profiles\r\n\r\n...\r\n<\/pre>\n
Single node 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     # Number of cores for single node jobs (2-24)\r\n\r\nmpirun -n $NSLOTS pb_mpi inputfile<\/em>\r\n                            #\r\n                            # Will load inputfile<\/em>.param from the current dir\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Multi-node Parallel batch job submission<\/h3>\n
For larger multinode jobs ensure you have the -ib<\/code> modulefile loaded, then submit a jobscript similar to:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -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 orte-24-ib.pe 48     # Must be 48 or more cores in multiples of 24\r\n\r\nmpirun -n $NSLOTS pb_mpi inputfile<\/em>\r\n                            #\r\n                            # Will load inputfile<\/em>.param from the current dir\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n