Cluster Information

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Revision as of 18:58, 17 October 2009 by Kay (talk | contribs) (BobSCEd Upgrade)
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Current To-Do

Date represents last meeting where we discussed the item

  • Brad's Graphing Tool (12/Oct/09) -- Brad
 * 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 (12/Oct/09) -- Aaron, Sam, Gus
  • New LittleFe Boards (12/Oct/09) -- Gus
 Board Criteria:
 * mini itx form factor
 * at least 2 core (probably max 2 core)
 * 2 GB ram
 * Cuda Enabled (with chip on board); OpenCL O.K. too
  • BCCD Testing (12/Oct/09) -- Gus, Sam, and Aaron
 * How many node boot up as dhcp servers?  (answer:  just the first one, confirmed 10/13)
 * Liberation testing -- Charlie, Gus, Sam, Aaron -- moved to Tuesday, 10/20 @ 2:30p
  • Travel Plans (12/Oct/09)
 * Send flight info to Jeff Krause -- Charlie
 * Talk to Travel-On -- Brad and Charlie
  • Code Sanity Check (12/Oct/09) -- Aaron and Sam
 * Take exact same set of runs on Sooner
  • EC/SCED Poster Sessions (12/Oct/09) Aaron, Sam, Fitz, and Brad
 * EC -- next Wednesday (10/21)
 * SCEd -- Combine TeraGrid and Fitz posters

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
c13 BRW
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


  • 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 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?


Fix the broken nodes.

(Old) To Do

BCCD Liberation

  • v1.1 release - upgrade procedures

Curriculum Modules

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



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

SC Education

Current Projects

Past Projects

General Stuff

Items Particular to a Specific Cluster

Curriculum Modules

Possible Future Projects