HPC Users Group


Creating a community around research computing at ILRI



@mralanorth

August 14, 2013

HUG Meetup #2

Infrastructure Hierarchy

HPC



Login node
"Master" of the slaves
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



--

Come back for HUG #3 ;)
September 4, 2013

HPC Users Group 2

By Alan Orth

HPC Users Group 2

A discussion of research computing facilities available at ILRI, including examples of how to use them!

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