Cluster Information

Current To-Do

Date represents last meeting where we discussed the item

• Writeups for Jeff Krause (3/Nov/09)
• Brad's Graphing Tool (19/Oct/09)

 * 2 y-axis scales (runtime and problem size)
 * error bars for left and right y-axes with checkboxes for each
 * eps file for the poster

• TeraGrid Runs (1/Dec/09)

 * Check new GalaxSee on BobSCEd
 * Update configure.ac based on Fitz's notes from Kraken
 * Status on pople?
 * Remember Big Red has a debug queue
 * GalaxSee -- after stats changes, GalaxSee slowed down by a lot.
   * Double check on BobSCEd, find the algorithm problem

• New LittleFe Boards (19/Oct/09)
• BCCD Testing (1/Dec/09)

 * Liberation testing
 * pxe booting
 * Test all boot options
 * Test CUDA boot options
 * Send /etc/bccd-revision with each email
 * Send output of netstat -rn and /sbin/ifconfig -a with each email
 * Test MPICH2 on Life, paramspace, GalaxSee, etc.
   * module unload openmpi && module load mpich2 && make clean && make
   * for MPICH2, machines file must be in current directory
   * do -np 2, 4, etc.

Summer of Fun (2009)

An external doc for GalaxSee
Documentation for OpenSim GalaxSee

What's in the database?

	GalaxSee (MPI)			area-under-curve (MPI, openmpi)			area-under-curve (Hybrid, openmpi)
	acl0-5	bs0-5 GigE	bs0-5 IB	acl0-5	bs0-5 GigE	bs0-5 IB	acl0-5	bs0-5 GigE	bs0-5 IB
np X-XX	2-20	2-48	2-48	2-12	2-48	2-48	2-20	2-48	2-48

What works so far? B = builds, R = runs, W = works

B-builds, R-runs	area under curve				GalaxSee (standalone)
	Serial	MPI	OpenMP	Hybrid	Serial	MPI	OpenMP	Hybrid
acls	BRW	BRW	BRW	BRW		BRW
bobsced0	BRW	BRW	BRW	BRW		BRW
c13						BRW
pople
Charlie's laptop						BRW

To Do

• Fitz/Charlie's message
• Petascale review
• BobSCEd stress test

Implementations of area under the curve

• Serial
• OpenMP (shared)
• MPI (message passing)
• MPI (hybrid mp and shared)
• OpenMP + MPI (hybrid)

GalaxSee Goals

• Good piece of code, serves as teaching example for n-body problems in petascale.
• Dials, knobs, etc. in place to easily control how work is distributed when running in parallel.
• Architecture generally supports hybrid model running on large-scale constellations.
• Produces runtime data that enables nice comparisons across multiple resources (scaling, speedup, efficiency).
• Render in BCCD, metaverse, and /dev/null environments.
• Serial version
• Improve performance on math?

GalaxSee - scale to petascale with MPI and OpenMP hybrid.

• GalaxSee - render in-world and steer from in-world.
• Area under a curve - serial, MPI, and OpenMP implementations.
• OpenMPI - testing, performance.
• Start May 11th

LittleFe

• Testing
• Documentation
• Touch screen interface

Notes from May 21, 2009 Review

• Combined Makefiles with defines to build on a particular platform
• Write a driver script for GalaxSee ala the area under the curve script, consider combining
• Schema
  • date, program_name, program_version, style, command line, compute_resource, NP, wall_time
• Document the process from start to finish
• Consider how we might iterate over e.g. number of stars, number of segments, etc.
• Command line option to stat.pl that provides a Torque wrapper for the scripts.
• Lint all code, consistent formatting
• Install latest and greatest Intel compiler in /cluster/bobsced

BobSCEd Upgrade

Build a new image for BobSCEd:

1. One of the Suse versions supported for Gaussian09 on EM64T [v11.1] - Red Hat Enterprise Linux 5.3; SuSE Linux 9.3, 10.3, 11.1; or SuSE Linux Enterprise 10 (see G09 platform list) <-- CentOS 5.3 runs Gaussian binaries for RHEL ok
2. Firmware update?
3. C3 tools and configuration [v4.0.1]
4. Ganglia and configuration [v3.1.2]
5. PBS and configuration [v2.3.16]
6. /cluster/bobsced local to bs0
7. /cluster/... passed-through to compute nodes
8. Large local scratch space on each node
9. Gaussian09
10. WebMO and configuration [v9.1] - Gamess, Gaussian, Mopac, Tinker
11. Infiniband and configuration
12. GNU toolchain with OpenMPI and MPICH [GCC v4.4.0], [OpenMPI v1.3.2] [MPICH v1.2.7p1]
13. Intel toolchain with OpenMPI and native libraries
14. Sage with do-dads (see Charlie)
15. Systemimager for the client nodes?

Installed:

• New BobSCEd Install Log
• New BobSCEd LDAP Log
• Sage Chroot

Fix the broken nodes.

(Old) To Do

BCCD Liberation

• v1.1 release - upgrade procedures

Curriculum Modules

• POVRay
• GROMACS
• Energy and Weather
• Dave's math modules
• Standard format, templates, how-to for V and V

LittleFe

• Explore machines from first Intel donation (notes and pictures)
• Build 4 SCED units

Infrastructure

• Masa's GROMACS interface on Cairo
• gridgate configuration, Open Science Grid peering
• hopper'

SC Education

• Scott's homework (see the message)

Current Projects

• BCCD
• LittleFe
• Folding@Clusters
• Benchmarking OpenMPI

Past Projects

• Big-FE
• Low Latency Linux Kernel

General Stuff

• Todo
• General
• Hopper
• Howto's
• Networking
• 2005-11-30 Meeting
• 2006-12-12 Meeting
• 2006-02-02 Meeting
• 2006-03-16 Meeting
• 2006-04-06 Meeting
• Node usage
• Numbers for Netgear switches
• Latex Poster Creation
• Bugzilla Etiquette
• Modules

Items Particular to a Specific Cluster

• ACL
• Athena
• Bazaar
• Cairo
• Bobsced

Curriculum Modules

• Curriculum
• Fluid Dynamics
• Population Ecology
• GROMACS Web Interface
• Wiki Life for Academics

Possible Future Projects

• Realtime Parallel Visualization

Archive

• TeraGrid '06 (Indianapolis, June 12-15, 2006)
  • Conference webpage
  • Student poster guidelines
  • Big-FE abstract

• SIAM Parallel Processing 2006 (San Fransisco, February 22-24, 2006)
  • Conference webpage
  • Little-Fe abstract
  • Low Latency Kernal abstract
  • Folding@Clusters
  • Best practices for teaching parallel programming to science faculty (Charlie only)

• College Avenue