• 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

• They'll video tape

• Cancelations, so some one could move to tomorrow

• Python3, Guido's Talk

  • Python 2.5, some improvements

  • Python 3000

    • Language update
    • Stroustroup compatibility
      • C++ backwords, add a new keyword, was a major incompatibility
    • Perl 6 other extreme

  • -Q warn about integer errors, // <- integer division

  • Pep 3100 for info, python.org/dev/peps

  • guidos blog, artima.com/weblogs/

  • big changes

    • kill classic classes
    • Exception derive from single root
    • absolute import ( can be turned on in 2.5 )
    • replacement for d.has_key if x in d
    • interating over file is better than xreadlines

  • smaller changes

    • exec, function again

    • x in favor repr(x)

    • except x,y,z as err instead except e,err

    • generator replaces list comprehension * list comprensions currently leak their name into the surrounding

      System Message: ERROR/3 (<string>, line 38)

      Unexpected indentation.

      scope

    • kill raise E, use raise E(arg) (work away from string exception)

    • xrange has a problem with long ints

      • will change range to do xrange things with lon support

  • string type updates

    • string becomes unicode
    • also introduce a byte type, all conversions from byte to strings require specifying conversion

  • new standard i/o stack

    • replace the c stdio with something a bit more inspired by java * unbuffered io * buffered io built on top
    • see sandbox/sio/sio.py for early prototype

  • print becomes a function

    • easier to change print to something
    • 2.x/3 compatibility requires only printing single string

  • dict views instead of lists

  • drop default <, <=, >, >= for classes (currently does memory)

  • Google python sprint next week

• Understanding NumPy, Travis Oliphant

  • numeric compatibility layer, numpy.oldnumeric
  • dtype object ( defines what the elements of the NumPy array )
    • array scalar ( wraps element returned from cell )
    • dtype code '<i4' (byte order, type, size)
    • isbuiltin, 21 static objects
    • dt.itemsize
    • fields, since array is just chunks of memory, because of alignment issues
    • a.flags ( properties on arrays )
    • a.empty((10,),dtype='int,float,a10') * a.dtype * a.dtype.fields
    • arbitrary structure needed to memmap complicated files

• Extending NumPy, swig, f2py, pyrex, ctypes,

  • swig, first
  • weave, embed C code in python string, kinda fortran like in variable names
    • compiles on the fly
  • pyrex
    • from c_numpy cimport, ... import_array()
  • ctype, calls shared libraries
    • .argtypes allow specifying type checking for c calls

• Python for modern scientific algorithm development, Fernando Perez

• Building a Distributed Component Framework (pyre), Michael Aivazis

  • distributing apps on many machines is hard
  • user space, ssh, scp, pyre services
  • pyGridWare (Kieth jackson)
  • gsl
  • http://www.cacr.caltech.edu/projects/pyre
  • http://pyre.caltech.edu (soon)
  • relase early 2007

• Enthought tool suite

  • What are traits?
    • notification (considered important)
    • visualization

• Synthetic Programming with Python

  • provide low level access to cpu without doing string processing
  • http://www.synthetic-programming.org

• 3D visualization with TVTK and MayaVi2, Prabhu Ramachandran

  • Traited VTK
  • MayaVi2 uses enthought exposes lots of objects and gui tools for playing with them

• Realtime Computing with Python, Andrew Straw

  • introduction to relatime simulation of fly
  • http://dickinson.caltech.edu/Research/Grand_Unified_Fly
  • comedi control measurement device interface

• Lightening Talks

  • Dude from JPL, Mike Ressler
  • Future of IPython, Brian Granger, Tech-X corp
    • planning on extending to ipython to do distributed programming
    • control remote supercomputers from laptop
    • support multiple parallel types
    • focus on interactive work
    • distributed programming in python
      • multiple processes, threads are limited by GIL
      • non-blocking sockets
      • asynchronous error/fault
  • Travis Oliphant, about PEP
    • using trac pages for NumPy http://projects.scipy.org/scipy/numpy
    • table @ dinner about arrays
  • Travis Vaught, Enstaller
    • egg package installation manger
    • has post-install scripts
    • build egg from pointing to a directory
    • code.enthought.com/enthon/enstaller.shtml
    • enthought.com/enthought/wiki/Enstaller
  • The Current State of Vision, Michel Sanner
    • Visual programming tools
    • supports nested graph nodes
    • looks written in tk
    • www.scripts.edu/~sanner/software
  • Quick overview of Chaco, Peter Wang
    • chaco visualization tool
    • http://code.enthought.com/chacho

• SAGE, Alex Clemesha

  • good environment for algebra, number theory, geometry
  • what is it
    • Distribution of math software
    • python library
    • new interface to math software
  • where is it: modular.math.washington.edu/sage
  • their ajax based web notebook looks really impressive

• Mathematica like plotting for SAGE, Alex Clemesha

• BioHub, Diane Trout

• Software Carpentry, Greg Wilson

  • he's a good speaker.
  • debugger for make
  • debugger than can trace back and forth between python & c code
  • Guido pronounced django the web framework.

sometime ago my laptop and phone were paired, but at some point I

deleted one of the connections, and when I tried dialing out the phone wanted a passphrase and kde thought there already was one.

I tried to delete /etc/bluetooth/link_key but that didn't work. Eventually I changed the pin-helper in hcid.conf from the kde one back to the bluez one.

I they started a connection and rand the pin-helper manually. One copy of the helper started up, and then magically another one popped up. I then filled a pin into both the second pin-helper and my phone and was able to make an outbound connection.

Of course then my ppp settings were wrong.

I commented out any fixed address, and the dns server information, and then used the /etc/chatscripts/provider which was setup to dialout to *99***2# (the second dialup profile on my phone)

System Message: WARNING/2 (<string>, line 16); backlink

Inline emphasis start-string without end-string.

I also added

iface ppp0 inet ppp

provider p900-blue

to my /etc/network/interfaces but i don't think that was important in this case.

And now, once again I can connect to tmobile via my phone

I need to make sure i keep my phone better charged.

I got talked into darcs and now want to be able to check out my patches on

my nslu2. Unfortunately darcs requires ghc, and ghc requires itself to compile. This leads us to the joy of making a new port.

http://www.haskell.org/ghc/docs/latest/html/building/sec-porting-ghc.html

I started with the above link and tried to get it to work. So far, the files they tell you to copy includes/(ghcautoconf.h DeriviedConstants.h GHCConstants.h) are not created by the configure step so you need to run make boot in the ghc directory on the target.

Then after copying them over make them read only, as my touches weren't enough to prevent their makefiles from trying to rebuild those files.

i managed to get it to start building, but it died trying to make the compiler with a bunch of cast errors.

I've been trying to setup a VoIP system at home ('cause) and can call

my cordless phone (plugged into a SPA-3000) from a IP Phone (grandstream gxp-2000)

That's all good and works fine. I then decided to go further and plug the SPA-3000's FXO(?) port into my vonage ATA. I can get it to make outgoing calls, and sometimes even incoming calls.

I can't get authentication to work for outgoing, and I can't get caller id to work for incoming.

This thread was rather helpfull on getting the calls working.

..:

[spa_outbound] type=peer secret=<SECRET> port=5061 host=dynamic canreinvite=no nat=no qualify=yes dtmfmod=rfc2833 context=incoming-vonage

is my current outgoing config.

On the SPA I have the PSTN line registering seperately from the ATA line.

If I want to get things to autoforward to the server I need to set PSTN Ring Thru Line 1 to off and to set a dial plan to SO< s:@server.host:5060 > (And of course tell the PSTN which dial plan to use.)

If I set the CID on, asterisk 1.2.1 gets very confused about the source SIP address and chokes. I tried setting things to insecure=very but to no avail.

I'm thinking I might try openser, as its more sip orientated. (Though there documentation is quite sparse).

I found some documentation on the SPA-3000

I've wanted to try to use python & boost for a while, but their tutorial depends on using bjam, which has been a pain to try and figure out. And of course the boost-python developers think that jam is the best thing ever and don't bother providing any documentation of how to use boost-python in a more traditional environment.

Here's my stab.

/* hello.cxx */
#include <boost/python.hpp>
using namespace boost::python;

char const* greet()
{
  return "hello, world";
}

BOOST_PYTHON_MODULE(hello)
{
  def("greet", greet);
}

I compiled it on an amd64 linux box with the following.

$ g++ -c -fpic -I/usr/include/python2.3 hello.cxx -o hello.o
$ g++ -shared -fpic -lpython2.3 -lboost_python hello.o -o hello.so
$ python
>>> import hello
>>> print hello.greet()

It turns out the -fpic is required for the AMD64 box, and on an x86 box, is unnecessary. (Though it doesn't hurt to have leave it in).

Would it have been too hard to show the manual way before extolling the virtues of their build system? Perhaps they were just being lazy as coming up with a simple build script on windows would probably be a lot harder than the above.

I was looking at the log files and discovered that pidentd was throwing error messages about netlink_lookup: write failed: Connection refused

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=305926

Seems to suggest that adding the module should make it shut up.

So I added the following to /etc/modules # tcp_diag may shut pidentd up about netlink_lookup: write failed tcp_diag

idle measurements base 20 watts Via C3 no cards, 44 Amd64 pci-x, 78

I tried getting chilispot working, but it needed to talk to my webserver/radius server which is the main thing i'm trying to protect. Since I also didn't feel like getting radius properly setup, I just punted and went for the simpler WPA-PSK configuration.

However before I went simple I split the wired and wireless networks into two IP address ranges, and I renumbered my IP address space out of 192.168.1

I followed wiki.openwrt.org/HotspotOpenvpnHowto to split the wifi (many nvram commands) Later I discovered that some of my problems getting chillispot working were actually caused by routing issues so I needed to add iptables -A FORWARD -i eth1 -o vlan1 -j ACCEPT # wifi to outside iptables -A FORWARD -i eth1 -o vlan0 -j ACCEPT # wifi to lan iptables -A FORWARD -i vlan0 -o eth1 -j ACCEPT # lan to wifi

I also added slightly more generalized commands to the firewall.user

Eventually I decided I didn't actually need the complexity of chillispot yet, and just started down the WPA-PSK path

http://openwrt.org/OpenWrtDocs/nas Gave some information on setting up the propritary wpa config tool.

I also installed wpasupplicant on my linux laptop. Theoretically it'd be better if I actually got the WPA2/cert mode working, but eh, i'm not ready for that yet.

To get wpa working on the WRT54G I needed to add

nvram set wl0_akm=psk nvram set wl0_crypto=aes+tkip nvram_wpa_psk=<password>

I needed both wl0_akm and wl0_crypto for openwrts nas startup script.

Next I need to move the mini out to the living room, and then set up a some kind of client box in my office. Do I try for getting LDAP authentication working so I can unify the passwords between my mac, my windows partition and all my linux boxen?

Tailor http://nautilus.homeip.net/~lele/projects/tailor/ allows syncing between multiple source code control systems, and since there's several projects in unpleasant sccs's i thought I'd try converting them to darcs

• orange

orange certainly looks promising other than the fact they have bugs, don't have doc strings, and lack unit tests. though their tutorials were pretty straightforward.

Unfortunately they're a bunch of OSS windows developers, so their code is sitting in CVS (blech) so I wanted to convert out of it

My first attempts with earlier versions of tailor didn't work so I upgraded to the latest version, and it had problems as well.

What I ended up doing was checking the HEAD out of cvs first, and then telling tailor to convert it to a darcs repo, I don't know if this'll work when they commit something, but it's worth trying.

I used the following to start creating the config file.

$ tailor --verbose -s cvs -R :pserver:cvs@estelle.fri.uni-lj.si:/CVS --module orange -r INITIAL --subdir orange orange > orange.tailor

the file ended up like this

[DEFAULT] verbose = True

[py] target = darcs:targetpy start-revision = HEAD root-directory = /home/diane/src/orange state-file = orange.state source = cvs:sourcepy subdir = orange.cvs

[darcs:targetpy]

[cvs:sourcepy] module = orange repository = :pserver:cvs@estelle.fri.uni-lj.si:/CVS

[csrc] target = darcs:targetc start-revision = HEAD root-directory = /home/diane/src/orange/orange.cvs state-file = orange.state source = cvs:sourcec subdir = source

[darcs:targetc]

[cvs:sourcec] module = source repository = :pserver:cvs@estelle.fri.uni-lj.si:/CVS

• compclust

both chris and I want to try using darcs with compclust but that'll require 2way syncing.

http://www.darcs.net/pipermail/darcs-users/2005-January/005070.html

debian currently has diskless and lessdisks.

Diskless appears to be an NFS root system where apps run on the client Lessdisks is a terminal based system that runs software on the server.

First off we want a version of grub that has has pxegrub apt-get source grub

I then edited the debian/rules file and added the following --enable-diskless (several net cards)

apt-get install lessdisks

I mostly followed along the lessdisks-doc/install

On the router I added the following to dnsmasq.conf (I really should back that bugger up)

# configure network booting #dhcp-vendorclass=pxe,PXEClient dhcp-boot=net:/tftpboot/pxegrub,dara,192.168.1.13

dhcp-option=17,/var/lib/lessdisks #root-path dhcp-option=42,192.168.1.1 #ntp-server dhcp-option=48,192.168.1.13 #font-server dhcp-option=49,192.168.1.13 #x-display-manager dhcp-option=66,dara.ghic.org # tftp-server-name dhcp-option=pxe,67,pxegrub #bootfile-name dhcp-option=69,192.168.1.13 #smtp-server

sigh the pxe client wasn't smart enough to boot off of a different computer than what we started with. So i tried with dara being the dhcp server, i got further but then ran into problems with not being able to load pxegrub from things other than /tftpboot

pxegrub had problems, when i switched to pxelinux.0, installed the default file into pxelinux.cfg (and then copied all of /var/lib/lessdisks/boot into /tftpboot I was able to boot. Unfortunately the kernel they installed doesn't support the ethernet card on my amd64 box.

What do i have to do to get a tftp server to server files off of something other than /tftpboot (or is just the pxeclient that has trouble with it?)

Whee

Spent some time browsing through the linux howtos http://fiona/cgi-bin/dwww?type=file&location=/usr/share/doc/HOWTO/en-html/LDAP-HOWTO/sasl.html

it looks like sasl ships with a number of different auth types with the kerberos stuff split out into sperate modules. The above link documents some information about getting MD5-Digest working with ldap, which should be useful for setting up an ldap auth server.

I forgot to update my xlibs package when upgrading to Xorg so its missing the keymaps necessary to change keyboard settings :( (no caps lock to control mapping)

Another question is should my home net have the wireless VPNed? and if so which protocol? IPSec or OpenVPN

http://openwrt.org/HotspotOpenvpnHowto?highlight=%28Howto%29 Talks about setting up openvpn on the wrt54

One interesting thing that I did do was http://thinkwiki.org/wiki/How_to_make_use_of_Graphics_Chips_Power_Management_features Enable power management of the graphics chips.

Hopefully I the library has free wifi

Home net: what do i want

priority routing for my traffic control / monitering of guest access securing wireless traffic

So I was able to get extensions working in both asterisk and ser.

Asterisk is designed as a PBX so all calls are routed through it, SER is designed like the internet and the router is just a location service. Once a SIP call is initiated through SER it's just the two clients talking to each other.

adding a user in asterisk at the simplest involves adding a sip user for authentication and then binding that user identity to an extension.

In sip the user identity is the extension, however if you want to make it easy for phones to dial the user id you can create aliases using the serctl command.

One major difficulty I had with getting ser working was the registration kept failing. It turns out that its really important for SER to know what all the hostnames its using are so it can know if a request is actualy being sent to itself.

Because my dns server reverse name lookup was broken it wasn't able to determine its FQDN. (there's a reason why you should always list names as "host.domain.name." in the reverse name tables, because if you don't know what you're doing its easy for the default domain to be wrong.

Once I got that fixed SER worked correctly

call transfer worked right too...

• Meta classses for fun and profit

  www.highenergymagic.org/presentations/metaclasses/

  • are there issues with using __new__ in metaclass?
  • __init__ is much more limited than __new__?
  • do remember to call base class options.

• Quixote 2.0 tutorial

  s = StringForm("foo",

  if request.form:

  value = s.parse(request) retuern "value", value

  else:

  return "<form>%s</form>" % (s.render()

# keywords: exim mail debian

Debian tried changing exim's group and user from mail:adm to Debian-exim:Debian-exim however my old config isn't setting that properly

To get things working temporarily, I changed /etc/logrotate.d/exim4, the group in /var/log/exim4/* and the keys *.crt *.key in /etc/exim4

Howto i'm using

https://alioth.debian.org/docman/view.php/30192/21/debian-amd64-howto.html#id258638

I downloaded the netinstall iso, killed my old root partition

I needed to grab nvidia-kernel-common from an x86-32 box that has access to the all architecture and built that package

i installed using the "desktop system" prompt from the installer, and then have installed emacs21, vim, and kde (and everything those things depended on)

installed x-window-system at completion Xprt had a segfault

I built my own nvidia driver, but it wanted to be in 2.6.9 instead of debians 2.6.9-9-amd64, so I symlinked /lib/modules/2.6.9/nvidia to /lib/modules/2.6.9-9-amd64/nvidia

installed nvidia-glx nvidia-glx-dev

the nvidia driver cant find my card, first "nv" is not the nvidia driver, "nvidia" is the nvidia closed soruce drivers

hmm it's also important to make sure that the version of gcc used to compile the kernel matches that of the version used to build the module. (I used gcc-3.3 by default and the debian kernel was built with gcc-3.4)

I went with the ia32 chroot system for running ia32 binaries as hopefully i can still use apt to manage the packages