Biowulf High Performance Computing at the NIH
sumtrees on Biowulf

The sumtrees program summarize non-parameteric bootstrap or Bayesian posterior probability support for splits or clades on phylogenetic trees.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load sumtrees
[user@cn3144 ~]$ --help
[user@cn3144 ~]$ --min-clade-freq=0.95 --burnin=200 --output-tree-filepath=result.tre treefile1.tre treefile2.tre treefile3.tre
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load sumtrees -m4 -f0.95 -b200 -o result.tre treefile1.tre treefile2.tre treefile3.tre treefile4.tre

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=2g
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. sumtrees.swarm). For example:

cd dir1; -f0.95 -b200 -o result.tre treefile1.tre treefile2.tre treefile3.tre
cd dir2; --summary-target=mcct --burnin=200 --support-as-labels --output-tree-filepath=result2.tre treefile1.tre treefile2.tre treefile3.tre

Submit this job using the swarm command.

swarm -f sumtrees.swarm [-t #] [-g #] --module sumtrees
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module sumtrees Loads the sumtrees module for each subjob in the swarm