Note that the PAML programs are single-threaded. The only advantage of using Biowulf for PAML jobs is if you can utilize multiple processors by running many simultaneous PAML jobs.
There are several example input files in the directory /usr/local/apps/paml/paml4.7/examples. The scripts below use the MouseLemurs data files from that directory.
First create the command files for the PAML programs you intend to run. (e.g. baseml.ctl, codeml.ctl). Then create a batch script along the following lines:
-------- this file is called run.bat ----------------------- #!/bin/bash #PBS -N PAMLrun #PBS -m be cd $PBS_O_WORKDIR baseml codeml
Submit this job with:
qsub -l nodes=1 run.bat
If this job requires more than the default 1 GB of memory, you should specify a node type with more memory on the qsub command line. (use 'freen' to see available node types). For example, if your job required 10 GB of memory, you would submit to a g24 node (24 GB of memory) with:
qsub -l nodes=1:g24 run.bat
PAML is single-threaded, so the advantage of running PAML jobs on Biowulf is that you can run a large number of them simultaneously. The easiest way to do this is via swarm. Set up a swarm command file like the following:
cd /data/$USER/paml/set1; baseml; codeml cd /data/$USER/paml/set2; baseml; codeml cd /data/$USER/paml/set3; baseml; codeml
Submit this swarm with:
swarm -g 5 -f swarmfile --module paml/4.7
where '-g 5' tells swarm that each command (one line in the file above) requires 5 GB of memory.
PAML User Guide (PDF)
PAML FAQ (PDF)