1. iCER Bioinformatics Support Fall 2010 John B. Johnston HPC Programmer Institute for Cyber Enabled Research © 2010 Michigan State University Board of Trustees.

2. Institute for Cyber Enabled Research (iCER) Hardware (HPCC) Software and Support Education Consulting Collaboration

3. iCER: What is it? The Institute for Cyber Enabled Research (iCER) at Michigan State University (MSU) was established to coordinate and support multidisciplinary resource for computation and computational sciences. The Center's goal is to enhance MSU's national and international presence and competitive edge in disciplines and research thrusts that rely on advanced computing.

4. HPCC: What is it? The HPCC provides computational hardware and support to MSU faculty, students and researchers. The HPCC is contained within iCER; effectively representing the hardware, systems and software “arm” of iCER’s research support mission.

5. Bioinformatics Outreach HPCC hardware Software resources Help Desk Seminars One-on-one Consulting Limited on-site systems setup and configuration Programming and scripting assistance FREE! wiki.hpcc.msu.edu/display/Bioinfo/Bioinformatics+Support+at+MSU

6. HPCC Cluster Overview Linux operating system Primary interface is text based though Secure Shell (ssh) All Machines in the main cluster are binary compatible (compile once, run anywhere) Each user has 50Gigs of personal hard drive space. – /mnt/home/username/ Users have access to 33TB of scratch space. – /mnt/scratch/username/ A scheduler is used to manage jobs running on the cluster A submission script is used to tell the scheduler the resources required and how to run a job A Module system is used to manage the loading and unloading of software configurations

7. Gateway to the System Access to HPCC is primarily though the gateway machine: – ssh username@hpc.msu.eduusername@hpc.msu.edu – ssh username@gateway.hpcc.msu.eduusername@gateway.hpcc.msu.edu – Access to all HPCC services uses MSU username and password. Once in, you can go to the user-oriented destination of choice.

8. HPCC System Diagram

9. Why the HPCC Cluster? Large data sets Lots of number crunching A need to run many simultaneous jobs with different data sets and/or configuration settings You need software you don’t have, don’t want to / can’t setup Comprehensive readymade development environment that is actively administered

10. Linux? OH NOES! If you are a Linux pro, go ahead and take a short nap (you’ve got ~60 seconds) If you’re not, don’t worry! That’s why I get the (not so) big bucks. The Bioinformatics Help Desk is here to get you up and running.

11. Linux Support Client application selection Bring in your laptop (if you have one) Cookbook tutorials and cheat sheets (more on the way) One-on-one consultation Limited on-site support and training We also provide samba support for Windows and Mac boxes so you can map your HPCC account directory to your workstation

12. HPCC Online Resources www.hpcc.msu.edu – HPCC home www.hpcc.msu.edu wiki.hpcc.msu.edu – Public/Private Wiki wiki.hpcc.msu.edu forums.hpcc.msu.edu – User forums forums.hpcc.msu.edu rt.hpcc.msu.edu – Help desk request tracking rt.hpcc.msu.edu mon.hpcc.msu.edu – System Monitors mon.hpcc.msu.edu

13. Available Software Center Supported Development Software – Intel compilers, openmp, openmpi, mvapich, totalview, mkl, pathscale, gnu... Center Supported Research Software – Matlab, R, amber, blast, charmm, emboss... Customer Software (module use.cus) – Clustalw, quest, meme, bowtie, motility, pygr, amos, abyss, tigr, mummer, hmmer, phylip, samtools… – For a more up to date list, see the documentation wiki: http://wiki.hpcc.msu.edu/ http://wiki.hpcc.msu.edu/ Don’t See it Here? Ask for it, we’ll try to help

14. User Software 50GB of initial user space provided Install your own in user space HPCC offers a rich build environment Quota increases can be made available Code installation and (modest) modification support is available through “moi”

15. Cluster Developer Nodes Developer Nodes are accessible from gateway and used for testing. – ssh dev-amd05 – Same hardware as amd05 – ssh dev-intel07 – Same hardware as intel07 – ssh dev-amd09 – Same hardware as amd09 – ssh dev-gfx10 – Same hardware as gfx10 We periodically have some test boxes. These include: – ssh dev-gfx08– Nvidia Graphics Processing Node – ssh dev-cell08 – Playstation 3 Cell processor – ssh dev-intel09 – 8 core Intel Xeon with 24GB of memory Jobs running on the developer nodes should be limited to two hours of walltime. Developer nodes are shared by everyone.

16. HPCC System Diagram

17. Steps in Using the HPCC Connect to HPCC Determine required software Transfer required input files and source code Compile programs (if needed) Test software/programs on a developer node Write a submission script Submit the job Get your results and write a paper!!

18. A couple of examples Biological model – long running, many similar but not identical runs Bioinformatics “data mining” – script to search for gene information in several large very large files In both cases, use of the HPCC cluster was able to produce more results in less time, with little or no active user management

19. But I don’t need a “cluster” Tool selection, setup Scripting assistance Data “browsing”, sharing, group analysis Lab system help or training

20. Scripting Customized, standardized, modify Python, Perl, or ? We have a growing “collection” available as a Git repository. Perhaps you don’t know anything about scripting; or maybe you do, but could use some help?

21. Web-Based Tools GBrowse Custom UCSC Genome Browser Web-Blast Your lab, your setup Not currently supported by the HPCC hardware infrastructure

22. Seminars and Education NextGen Bioinformatics Seminars wiki.hpcc.msu.edu/display/Bioinfo/NextGen+Bioinformatics+Seminars HPCC Mid-Morning Break wiki.hpcc.msu.edu/display/Announce/HPCC+Mid-Morning+Break+Series

23. Setting up an account All account requests must come via a PI. Have your PI fill-in the form at: – www.hpcc.msu.edu/request www.hpcc.msu.edu/request Once received, we will process your request and notify you when your account is ready.

24. Bioinformatics Contact John Johnston, HPC Programmer – M-W, 1449 BPS, 884-2572 – Th-F, 505 BMB, 432-7177 – johnj@msu.edu johnj@msu.edu Ticket requests: – https://rt.hpcc.msu.edu/index.html https://rt.hpcc.msu.edu/index.html – Please include “Bioinformatics Help” in the subject to more quickly route your request.