Research Computing Seminar

A discussion of the research computing facilities available at ILRI, Kenya.

Transcript

1. Research Computing at ILRI Alan Orth May 30, 2013 Linux {admin,ninja,plumber}
2. 1. Users! 2. Potential users! 3. Managers of users! The slides aren't technical, but I can't promise I won't start speaking in tongues... Intended audience
3. Harder, Better, Faster, Stronger Work it (harder) Make it (better) Do it (faster) Makes us (stronger) -- Daft Punk Research-oriented computing is different than corporate ICT!
4. History - Few users with "heavy" computing / data requirements (bioinformatics + some GIS) - Etienne de Villiers and the "HPC" (lots of BLAST!) - Other users simply ran analyses on their workstations (small data sets, "first-gen" sequence data, statistics etc)
5. "First-gen" research computing (2010 - 2013) hpc
6. ... servers on fire
7. Things are changing - New platforms (high throughput on all fronts!) - New collaborators (with new toys!) - More users - More projects - Different kinds of data - etc...
8. "Second-gen" research computing (2013)
9. Play nice, use SLURM! - Simple Linux Utility for Resource Management - Everyone is allowed to use a "fair" amount of resources - If you go over, you have to "queue"
10. Why SLURM? - How can I run structure for populations 1.. 10, and repeat each run 3 times? - How can I run newbler for 1 week?! I have to shut my computer down! - How can I get an email when my pipeline finishes? - I want to run R with 4 CPUs right now!
12. Software available - mira, newbler, velvet, trinity - BLAST, bowtie, bwa - figtree, Dendroscope, MEGAN, PhyML - mrbayes, bayescan, R - structure, admixture, apt - CLC Genomics Workbench (kitchen sink) More in /export/apps/*!
13. Where to get help http://hpc.ilri.cgiar.org/wiki/
14. How to get access Talk to Alan, he sits in Lab 2
15. Proposal: HPC Users Group - Meet once a month - Promote community - Share scripts / pipelines / experiences - Yours truly as fearless leader - Promote love of Linux and coffee (?)