Cluster Information
Revision as of 13:35, 1 March 2010 by Amweeden06 (talk | contribs)
Contents
Current To-Do
Date represents last meeting where we discussed the item
- 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
- TeraGrid Runs (28/Feb/10)
B = builds, R = runs, D = reports back to database, F = "finished" -- there is a good set of runs (10 per data point) in the database that appear on a graph
area under curve | GalaxSee | |||||||
---|---|---|---|---|---|---|---|---|
Serial | MPI | OpenMP | Hybrid | Serial | MPI | OpenMP | Hybrid | |
ACLs | ||||||||
BobSCEd | ||||||||
BigRed | ||||||||
Sooner | ||||||||
pople |
- New cluster (5/Feb/10)
* wiki page * Decommission Cairo * Figure out how to mount on Telco Rack * Get pdfs of all materials -- post them on wiki
- BCCD Testing (5/Feb/10)
* Get Fitz's liberation instructions into wiki * Get Kevin's VirtualBox instructions into wiki * pxe booting -- see if they booted, if you can ssh to them, if the run matrix works * Send /etc/bccd-revision with each email * Send output of netstat -rn and /sbin/ifconfig -a with each email * Run Matrix * For the future: scripts to boot & change bios, watchdog timer, 'test' mode in bccd, send emails about errors * USB scripts -- we don't need the "copy" script
- SIGCSE Conference -- March 10-13 (28/Feb/10)
* Leaving 8:00 Wednesday * Brad, Sam, or Gus pick up the van around 7, bring it by loading dock outside Noyes * Posters -- new area runs for graphs, start implementing stats collection and OpenMP
- Spring Cleaning (Noyes Basement) (5/Feb/10)
* Next meeting: Saturday 6/Feb @ 3 pm
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
area under curve | GalaxSee (standalone) | |||||||
---|---|---|---|---|---|---|---|---|
Serial | MPI | OpenMP | Hybrid | Serial | MPI | OpenMP | Hybrid | |
acls | BRW | BRW | BRW | BRW | BR | |||
bobsced0 | BRW | BRW | BRW | BRW | BR | |||
c13 | BR | |||||||
BigRed | BRW | BRW | BRW | BRW | ||||
Sooner | BRW | BRW | BRW | BRW | ||||
pople | ||||||||
Charlie's laptop | BR |
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:
- 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
- Firmware update?
- C3 tools and configuration [v4.0.1]
- Ganglia and configuration [v3.1.2]
- PBS and configuration [v2.3.16]
- /cluster/bobsced local to bs0
- /cluster/... passed-through to compute nodes
- Large local scratch space on each node
- Gaussian09
- WebMO and configuration [v9.1] - Gamess, Gaussian, Mopac, Tinker
- Infiniband and configuration
- GNU toolchain with OpenMPI and MPICH [GCC v4.4.0], [OpenMPI v1.3.2] [MPICH v1.2.7p1]
- Intel toolchain with OpenMPI and native libraries
- Sage with do-dads (see Charlie)
- Systemimager for the client nodes?
Installed:
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)
- SC10 brainstorming
Current Projects
Past Projects
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
Curriculum Modules
Possible Future Projects
Archive
- TeraGrid '06 (Indianapolis, June 12-15, 2006)
- 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)