NERSCPowering Scientific Discovery Since 1974

JGI Compute User Training Series



NERSC and IT staff will host a series training sessions and open office hours to introduce new services and review best practices for using the Crius cluster.  All sessions are hands on, so please bring your laptop.  If you are or were a user of any of the following systems, Crius, Rhea, Kronos, Theia, Oceanus or Phoebe, it will be beneficial for you to attend these training sessions.  And if you plan to use JGI compute resources in the future, we also encourage you to attend. 

It will also be an opportunity for JGI compute users to ask questions and give NERSC and IT staff feedback on your requirements.

Session 3: February 24th, 2012 1:30-5pm rm 100-101


1:30-1:45 - Intro and presentation of the transition schedule we talked about at the last SysOps meeting.


1:45 - 2:15  - Best practices when using the shared batch system on Crius and Phoebe.


2:15 - 2:30 - More detail on Job arrays, use, control and monitoring of jobs  

2:30 - 2:45 - Review of queue policies (long jobs, highmem jobs)


2:45 - 3:00 - Data transfer from DTN nodes including moving data off NetApps (/home) to /house or /projectb


3:00 - 5:00 - Open question hours, drop by, ask questions, trouble shoot problems with NERSC and IT staff.


Session 2: February 17th, 2012 1:30-5pm

In session 2 we will go over a few new topics but dedicate most of the afternoon to open office hours where users can drop by and ask questions.  There is no need to register for this session.


1:30-1:50 - Introduction to the NIM (NERSC Information Management) System.

Learn how to change your password, set your security questions, change your shell, and create an HPSS token with NIM (

1:50 - 2:15 - Backing up your data faster

Last week we covered authentication to HPSS and basic commands.  Now that you know the basics, learn how to transfer large amounts of data efficiently with NERSC's high bandwidth "Data Transfer Nodes"

2:15 - 2:30 - Using the new "projectb" file system

Move data and start using the new JGI GPFS 2PB file system. 

2:30 - 2:45 - Review of job submission and job monitoring commands

Learn more about the commands used to submit and monitor your jobs like, qsub, qstat, qalter.

2:45 - 5pm - Open Office Hours

Drop by, ask questions, trouble shoot problems with NERSC and IT staff.


Session 1: February 10th, 2012 1:30-5pm


1:30-1:45pm - Welcome and purpose of training - Katie Antypas


1:45-2:15pm - Using NERSC's "global homes" environment - Katie Antypas & Nick Cardo

     Topics:  /home environment, dotfiles, user customizations, quotas
     Hands on - Login to phoebe, Matt Dunford standing by for account support help

2:15-3pm - Transferring data to HPSS - Nick Balthaser

     20 min lecture
     20 min hands on period

3-3:15pm - Break


3:15 - 4pm - Using the batch system - Ilya Malinov, Jay Srinivasan, Iwona Sakrejda

     Topics: review of job submission, shares, large memory nodes, best practices
      Hands on - submit your job/workflow on Phoebe

4-4:15pm  - Information on the new 2PB JGI file system, projectb - Jason Hick & Katie Antypas

     Topics: size and purpose of new file system, proposed layout

4:15-4:30pm - JGI Survey results  - Katie Antypas


4:30pm - Reveal new web documentation - Katie Antypas