HPC Users Group

Creating a community around research computing at ILRI

@mralanorth

August 14, 2013

HUG Meetup #2

Infrastructure Hierarchy

HPC

Don't run things here :)

taurus

128 GB of RAM

64 CPUs ("cores")

Great for batch and interactive jobs

mammoth

384 GB of RAM

16 CPUs ("cores")

Great for high-memory jobs

Infrastructure Basics

You are everywhere.

Your data is everywhere.

I am awesome.

SLURM

SLURM, the number-one soft drink of the future!

Simple Linux Utility for Resource Management
Manages allocation of computing resources
Tries to ensure fair distribution of resources
By default, everyone is allowed 20 CPUs total

Sharing resources!

"batch" jobs

Use batch jobs when you:

have tested your parameters (ie, via interactive)
want to leave it running without being connected
want to run many iterations of a job with diff values
want to calculate the answer to:

life, the universe and everything
global warming
what to get your wife for Christmas

Your first batch job

#!/bin/bash
#SBATCH -p batch
#SBATCH -J blastn
#SBATCH -n 4

export BLASTDB=/export/data/bio/ncbi/blast/db

module load blast/2.2.28+

blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4

#SBATCH -p batch -- partition selection
#SBATCH -J blastn -- job name
#SBATCH -n 4 -- number of CPUs for job
export BLASTDB= -- set the path to blast databases
module load blast/2.2.28+ -- load the blast 2.2.28+ module

[aorth@hpc: ~]$ sbatch blastn.sh

Your second batch job

A script that writes batch scripts!

#!/bin/bash
POPULATIONS="1 2 3 4"
REPS="1 2 3 4 5"
STRUCTURE="/export/apps/structure/2.3.3/bin/structure"

for rep in $REPS
do
    for pop in $POPULATIONS
    do  
        sbatch <<BATCH_SCRIPT
#!/bin/bash
#SBATCH -n 1
#SBATCH -p batch

$STRUCTURE -e extraparams.txt -m mainparams.txt -K $pop -i pops_kenya.txt -o pops_kenya_K${pop}_rep${rep}.txt
BATCH_SCRIPT

    done
done

[aorth@hpc: ~]$ ./structure_batch.sh

Stats!

http://hpc.ilri.cgiar.org/ubmod/

New Machine Name Voting!!1

64 GB of RAM

48 CPUs ("cores")

Will share the "batch job" burden with taurus

Getting Help

http://hpc.ilri.cgiar.org

Come back for HUG #3 ;)

September 4, 2013