1. Katie Antypas NERSC User Services Lawrence Berkeley National Lab 10 February 2012 JGI Compute User Training

2. Today we want to share plans, introduce new services, test workflows, answer questions and hear your feedback New file systems and data management Beta Web documentation JGI User Survey Results Fair share batch systems Crius Rhea Thei a Kronos? Hyperion Oceanus Iapetus Themis

3. 3 Breakdown of NERSC Users’ Science Areas NERSC serves over 4000 users across 500 distinct projects across an array of science areas

4. JGI users are similar to traditional NERSC users in their need for: JGI users have special workflow, throughput, and software needs Stable, reliable systems Large data management and storage Fast queue turn around Access to millions of compute hours

5. 5 Where we have come from … One-on-one collaborations MOU reached for NERSC to support JGI computational and IT systems File system stabilization Cluster Consolidation 2009 Spring 2010 Fall 2010- Fall 2011 May 2011- present Crius Rhea Thei a Kronos? Hyperion Oceanus Iapetus Themis

6. Merge JGI systems into Crius Crius Rhea Thei a Kronos? Hyperion Oceanus Iapetus Themis

7. Next: Move Crius to NERSC Space But … before we do this, we want to make sure all pipelines and workflows are tested so we cause minimum disruption to users Primary benefit: Access to new 2PB file system

8. JGI Sys-ops members have been incorporated into NERSC groups Ilya Malinov Jeremy Brand Matt Dunford Brian Yumae Ravi Cheema Patrick Hajek Fred Loebl Networking, Security, Servers: Brent Draney Continue to contact JGI sys-ops for day to day problems Computational Systems Group: Jay Srinivasan Storage Systems Group: Jason Hick

9. The IT Steering Committee makes policy decisions regarding the cluster JGI Alex Copeland Daniel Rokhsar Harris Shapiro Henrik Nordberg Igor Grigoriev James Bristow Kostas Mavrommatis Len Pennacchio Nikolaos Kyrpidis Ray Turner Rob Egan Victor Markowitz NERSC Brent Draney Jason Hick Jay Srinivasan Jeff Broughton Katie Antypas Shane Canon Contact your representative on the steering committee if you have concerns.

10. 10 The NERSC consultants serve as user advocates Woo-Sun Yang Tools/Math Libraries Richard Gerber Astro/Web Services Helen He Climate Katie Antypas Group Leader Dave Turner Everything Zhengji Zhao Mat. Sci/Chemistry Mike Stewart Compilers Harvey Wasserman Chemistry ? ? Bioinformatics Consultant Yushu Yao Data Analytics Jack Deslippe Mat. Sci/Chemistry Eric Hjort High Energy Physics

11. Logging into Phoebe

12. When you login to Phoebe you will be in your “global home” directory The full UNIX path is stored in the environment variable $HOME Your $HOME quota is 40GB and 1,000,000 inodes We realize most users have a different home directory in /house. Reference your old home directory as $OLD_HOME if you need We use $HOME to initialize environment so do not redefine Note /house is available on Phoebe, NetApps is not

13. Your default shell on Phoebe is bash NERSC sets.bashrc for all users as a read- only file. Do not change your.bashrc file! NERSC uses.bashrc file to make global configuration changes for all users Put your own customizations in.bashrc.ext Want to change your shell? Just let us know.

14. When you login the environment is pre-configured for you /jgi/tools bin and lib directories in your path Batch system environment setup

15. Login to Phoebe ssh username@phoebe.nersc.gov

16. Jason Hick Storage Systems Group Lawrence Berkeley National Lab 10 February 2012 A New 2PB GPFS file system for the JGI “projectb”

17. The new 2PB “projectb” file system is available on Phoebe now Some high level specs for users 2PB XXX

18. File systems best practices Unfortunately disk is still expensive All of the JGI’s data can not be stored on disk within the current budget Archive and delete data you no longer need Disk usage will be controlled through quotas in some cases and purging in others

19. There are two areas of storage within the “project” layout of the “projectb” file system /projectb/ projectdirs/scratch/ PI/ RD/ fungal/ metagenome/ micro/ plant/user/ Group directories Not purged Subject to quota User directories Purged

20. It is important for every group to come up with a data retention policy How long should we keep the raw data? Can the data be deleted or should it be archived? Can we set up an automated way to archive and delete data?