• AutoLigand AutoDock, Rodney Harris

  • Tool for "rational" ligand design
  • computes affinity

• GpuPy, Benjamin Eitzen, WashU

  • strengths
    • currently improving faster than traditional cpus
  • weaknesses
    • single precision
    • data must be copied to gpu
  • programmability
    • newer gpus can execute programs in "high level" languages Cg GLSL HLSL
    • programs are called shaders
  • how it works
    • GPU executes program once for each pixel that is drawn to screen
    • overrrides default numpy functions, can be transparent
    • some functions are slower on gpu (like simple add or multiply)
    • some get faster with larger N (pow, arccosh)
    • some are just faster (cos, sin)
    • the more complex you can pass over the faster, correlation
    • not hooked up yet, but have edge detection filter
  • possible future work,
    • autoconfig
  • simulation of double with singles hal.ccssd.cnrs.fr/ccsd-00021443
  • htpp://eecs.wsu.edu/~eitzenb/gpupy

• Boost Graph Library, Douglas Gregor

  • path finding

  • connectivity & clustering

  • network flow

  • coloring

  • layout & visualization

  • motivation

    • python is easier to teach
    • dynamic features of python
    • usabiliy (e.g. c++ error messages)

  • Task: network tolerance

    from boost.graph import * g = read_graphviz("network.dot")

    bicomponent = g.add_edge_property(name='label', type='integer) art_points = biconnected_components(g, bicomponent)

    for v in g.vertices:

    if v in art_points:

  • graph types in python

    • Graph
    • Digraph
    • Graph exploration interface

  • vertex and edge properties

    • attach additional model domain knowledge
      • computer net, vertex(host, ip_addr), edge(bandwidth, latency)

  • Properties in the BGL

    • property map
      • implicity, just access property
      • explicity, allows more specifity, 2 params optional weight = g.add_edge_property(name='weight', type='float')
    • using property maps
      • similar to dictionaries (weight[e], =0.75
      • pass to algorithms dijkstra_shortest_path(g, start_vertex, weight)
    • has visitor model to do something when you hit interesting points in the algorithm. (e.g. debugging, new algorithms)

  • http://www.generic-programming.org/~dgregor/bgl-python/

• summary of research issues with/Fast multipole Algorithm, Idesbald van den Bosch

  • ship signature reduction
  • lots of details about problem and need for optimization
  • gmsh (mesh generation)

• Object Oriented Finite Elements, Andrew Reid

  • OOF2,
    • rapid construction of meshes adapted to irregular microstructural geometriesp

• Parallel PDE solvers in python, Bill Spotz

  • trilinos project
    • provide central repository for sandia's solver
    • http://softwrae.sandia.gov/trilinos

• Python imaging tools for reconstructing magnetic resonance images, make trumpis

  • https://cirl.berkeley.edu/view/BIC/ImagingTools

• PyRoot, Wim Lavrijsen (pronounced more like vim)

  • http://cern.ch/wlav/pyroot/
  • ROOT root.cern.ch
  • reflection for C++ (reflex, http://cern.ch/seal-reflex)
  • they combine reflection based meta-information to generate python wrappers on the fly.
  • also can call python from C++/CINT
  • very impressive looking

• QScimpl, Eric Dobbs

  • personal, dobbse.net
  • Tech-X Corporation, txcorp (scientific physics stuff)
  • mostly decided to advertise the advantage of simplicity

• Genesis SciFlo, Scientific Knowledge Creation on the Grid, Brian Wilson

  • Problem, terabytes of data (years) distributed at several data centers
  • iEarth
  • showed an updating svg diagram showing the execution of their workflow.
    • distributed across many machines via web services
  • data access protocol, retrieve chunks of data over web.
  • used xpath to extract results from amazon soap results
  • software shipped
    • lxml (XPath 1.0)
    • twisted, pyldap, openldap,
    • sleepycat dblxml has xquery and xpath
    • dojo AJAX library
    • openDAP, extract cdf, hdf file
    • globas v4 grid
  • globus v4 is supposed to be soap webservice
  • WSRF (web services resource framework)
  • UDDI universal description discovery and integration, find service
  • grid workflow,
  • rest vs soap, each have advantages/disadvantages
  • UDDI4py from IBM, SOAPpy
  • recommends more XML microformats for "mash ups"
  • publish science algorithms as reusable web services
  • www.opendap.org

• Python Web & Grid Service Tools, Keith R Jackson

  • Globus toolkit
  • decided to simplify system by standardized into webservices
  • helps organize coordinated usage of resources
  • his mac crashed
  • SOAPpy is officially unsported
  • ZSI is hopefully the "new" better way, though they're more complicated than SOAPpy
  • XML schema scary complicated
  • Mapping tool from WSDL to python (wsdl2py)
  • using m2crypto (they thought it was being supported, unlike pySSL)
  • LIGO used it to ship 50 terabytes of data through pyglobus
  • WSRF supposed to define way to hand stateful connections
  • lifecycle, things will die at some point, though can be refreshed.
  • WS-N another webservices spec
  • seems to actually work, java, C, python call all talk.
  • PyCLST
  • GridFTP, implement extra features to handle transfer over highperformance network
  • Visual programming environment, useful for viewing workflow
  • Userinterface
  • planner, condor, dagman
  • exec manager (CBEI)
  • exec context
  • physical resources
  • pyGlobus, http://dsd.lbl.gov/gtg/projects/pyGlobus/
  • ZSI, http://pywebsvcs.sourceforge.net/zsi.html
  • pyGridWare, http://dsd.lbl.gov/gtg/projects/pyGridWare
  • ViCE, http://dsd.lbl.gov/gtg/projects/vice/
  • PythonCLServiceTool, http://dsd.lbl.gov/gtg/projects/PythonCLServiceTrool
  • everything BSD license
  • eclipse has a nice WSDL interface generator
  • python to wsdl would require static type annotation.
  • webservices, text to do control, then binary for shipping data
  • amazon, uses a very efficient xml binary encoding

• Seeing through the MIST, Tripp Lilley

  • interesting point about maliable UIs
    • how do you let a user, know theyre changing their world, and revert.
  • super early project, not even screenshots