Biowulf High Performance Computing at the NIH
pedcut on Biowulf

A program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size.

References:

Documentation
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 pedcut
[user@cn3144 ~]$ cp $PEDCUT_EXAMPLES/basic2.ped .
[user@cn3144 ~]$ pedcut -p basic2.ped -m 4 -o basic2_o

	#############################
	#  PedCut version 1.19      #
	#  Fan Liu                  #
	#  Erasmus MC Rotterdam     #
	#############################

Following arguments are under consideration:
--pedin         basic2.ped
--maxbit        4
--out           basic2_o

Start 14:07:54-2015/06/29

Computing pair-wise kinship for 6 Subjects Of Interest (SOI) ...	Done
Forming Rij Matrix ...	Done

Recursion 1 ==> analyzing 17 sub-groups of 6 SOI
progress	0%
progress	10%
progress	20%
progress	30%
progress	40%
progress	50%
progress	60%
progress	70%
progress	80%
progress	90%
progress	100%
Selected subpedigree 1 ==>	Bit 3	N SOI 6
Done

Recursion complete!

Selected in total 1 sub pedigrees
Created Output basic2_o
Created Output PedsSummary.csv

Finish 14:07:55-2015/06/29

[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. pedcut.sh). For example:

#!/bin/bash
module load pedcut
pedcut -p my_file.ped -m 4 -o my_file_o

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] pedcut.sh
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. pedcut.swarm). For example:

pedcut -p file1.ped -m 4 -o file1_o
pedcut -p file2.ped -m 4 -o file2_o
pedcut -p file3.ped -m 4 -o file3_o
pedcut -p file4.ped -m 4 -o file4_o

Submit this job using the swarm command.

swarm -f pedcut.swarm [-g #] [-t #] --module pedcut
where
-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 pedcut Loads the pedcut module for each subjob in the swarm