Russell D. Fish
   E-Mail: fish@cs.utah.edu      Home Address: 1618 East Meadow Moor Road 
   http://www.cs.utah.edu/~fish                Salt Lake City, Utah  84117
   Cell phone: (801) 953-3778	 Home/work phone: (801) 274-2834

Summary:

My highest skill is leading a technical team in developing and refining systems designs, detailing and producing implementations, and evolving software systems from rapid prototypes to mature products.

Education:

• Graduate studies, 1975-1977, Computer Science Department, University of Utah, Salt Lake City, Utah
• B.S. 1973, Mathematics and Computer Science, The Lindenwood Colleges, St. Charles, Missouri

Computer Knowledge:

• Languages: Python, OpenGL/GLSL, Trolltech Qt, PHP/HTML, Perl, SQL, C++, C, C#(C-Sharp).NET,
  Visual Basic, shell/AWK, TCL/TK, Lisp, APL, Fortran, assembly.
• Databases: MySQL, Oracle, SQL Server, Access, DBASE3/Clipper, IDMS, IMS,
  API's: ADO, OCI, ODBC, JDBC, VDBC, Python-DB.
• Systems: MacOS/FreeBSD/Linux/UNIX (15 varieties), Emacs, Windows XP/2000/NT/98/95/6.22,
  embedded, cross-platform: Cygwin/XFree, VNC, VMWare, Citrix WinDD/Terminal Server.

Professional Experience:

• January 2008 - March 2009: Software Engineer in Computer Aided Design and Modeling, Nanorex, Inc., Bloomfield Hills, Michigan
• March 2004 - December 2007: Computer Science Researcher, Flux Research Group, School of Computing, University of Utah, Salt Lake City, Utah [Emulab] [Emulab XP port] [Robot sensor-net] [SQL vulnerability scanner] [Hyperviewer GUI]
• May, 2003 - February 2004: Software Engineer, Think3 Inc. Industrial Design Applications R&D group, Salt Lake City, Utah
• September, 2001 - December, 2002: Software Engineer, Stabro Laboratories, Inc., Salt Lake City, Utah
• January-August, 2001: Systems Programmer, Halosoft, Inc., Pittsburgh, Pennsylvania
• 1980-2000: Co-founder and Project Technical Lead, GDC (Graphics, Design, and Computation) Project, School of Computing, University of Utah, Salt Lake City, Utah
• 1977-1980: Scientific Applications Programmer, Envirotech Information Systems Division, Salt Lake City, Utah
• 1975-1977: Graduate student, teaching assistant, and research assistant, DARPA 3D Computer Graphics Project, Computer Science Department, University of Utah, Salt Lake City, Utah
• 1973-1975: Computer Center Operations Manager and Systems Programmer, Parks College of Aeronautical Technology, Cahokia, Illinois

January 2008 - March 2009: Software Engineer in Computer Aided Design and Modeling, Nanorex, Inc., Bloomfield Hills, Michigan

Responsibilities:

NanoEngineer-1 is:

• A portable, multi-platform, open-sourced Python and OpenGL program that is freely available to the scientific community.
• A molecular Computer-Aided Design and Analysis system for graphical design and molecular dynamics simulation of nanoscience experiments and developing molecular nanotechnology (atomically-precise manufacturing.)
• A rich, 3D interactive molecular modeling system that includes high-level design operations for Structural DNA and engineered proteins, including automated ordering of synthesized DNA strands for massively self-assembled DNA Origami tiles.

Here's how I did it:

• First, I factored the OpenGL Display List structures to avoid rebuilding them for interactive color changes like mouseover-highlighting, yielding a 4 times speedup. This still gave only 1 frame per second for 20,000 DNA base pseudo-atoms in a DNAO tile, unacceptably slow for interaction, yet it was about as far as the existing OpenGL graphics architecture of NE1 could go.
• In search of a new approach, I developed benchmark drawing test cases to identify and bypass bottlenecks, learning and applying several layers of newer OpenGL extensions. I finally achieved sufficient drawing speed by:
  • moving the data for sphere and cylinder primitives into Vertex Buffer Objects (VBOs) in the Graphics Card RAM;
  • implementing custom Graphics Card GPU ray-tracing primitive shaders for spheres and cylinders in GLSL (the C-like OpenGL Shading Language); and
  • using multi-drawing calls with indexes stored in Graphics Card IBOs to draw the primitives in huge batches for GPU parallelism.
• I collaborated with my co-worker Bruce Smith to design an intermediate-level object-oriented API to encapsulate the management of the shaders, VBOs, and IBOs for the primitive types most used in molecular models, first spheres and then cylinders. Then I implemented it.
• We are now in the process of shifting the top level molecular model interaction in NE1 over onto that foundation and making a final Nanorex release of NanoEngineer-1.

March 2004 - December 2007: Computer Science Researcher, Flux Research Group, School of Computing, University of Utah, Salt Lake City, Utah

Responsibilities:

Some Emulab details:

• Emulab is time- and space-shared: time-shared in that experiments persist, and can be swapped-in to physical resources on demand; space-shared in that swapped-in experiments co-exist in the testbed with private VLANs, plus a control-net link.
• Researchers use a Web interface, to create logical experiments, "swap in" experiments allocating physical resources, and operate running experiments. The system is implemented in PHP and Perl with XMLRPC, Python, MySQL, C++, and C behind it.
• Logical network topologies and link characteristics for experiments are described in the widely-used "NS" (Network Simulator) language, embedded in TCL. Emulab extensions to NS specify the desired hardware, OS image and software to load, and so on for each node PC in the experiment.
• Emulab cluster hardware consists of 348 rack-mounted PC's, each with 5 or 6 100-Mbps or 1-Gbps network interfaces and remote power and serial console connections, several huge Cisco switches, and several management and server PC's.
• Other Emulab experiment node types include a wireless testbed of 100 802.11 wireless PC's spread through the engineering building, a sensor-net with 30 motes (6 of them mobile), and a PlanetLab portal.

Major Projects:

• Ported the Emulab experiment-node management software to Windows XP

  Each Emulab experiment node runs on a physical PC, on which a saved OS image is rapidly installed using the Emulab "Frisbee" multicast loader. The researcher has root privileges and can install any software they want, then make custom OS images of their own.

  Normally, they start with a base OS image containing Emulab management services that set up:

  • User accounts within a project, including SSH keys and shared project and home directories;
  • Network configuration including interfaces, TCP, DNS, routings, etc;
  • The Emulab event system (control plane), together with many daemons to synchronize the experiment node with the Emulab system and operate the experiment.

  The Emulab experiment-node management software was originally written for FreeBSD and later ported to Linux. I ported it to Windows, scripting the complete setup of Windows XP from the "Out-Of-the-Box-Experience" to full operation in a few minutes.

  I used the Cygwin GNU environment, Resource Kit tools, many Registry hacks, and finally Sysprep to make hardware-independent images. I found race conditions in the XP TCP stack initialization for the multiple NIC's, requiring much check and reconfiguration logic.

• Improved the accuracy of robot location-sensing on a mobile wireless sensor-net testbed

  This work was part of a paper published in the IEEE INFOCOM proceedings, April 2006 . Scroll down for the pictures!

  Mobility is provided for 6 of the Emulab Crossbow "Mica-2" sensor-net nodes. They are mounted on Intel "Stargate" PDA cards, which have an 802.11 control network card and control an Acroname "Garcia" two-wheeled motion platform.

  The Garcias roam in a 60 square meter L-shaped office area, with 6 ceiling-mounted security cameras providing location information for navigation and control. Each Garcia has a "fiducial" marker consisting of orange and blue colored disks mounted on top.

  David Johnson and I surveyed a 1/2 meter measurement grid over the entire robot area to a couple of millimeter accuracy; positioned fiducials at the grid points with pins; and measured that the original location software was accurate to only 10 cm. 1 cm accuracy was determined to be necessary for robot and wireless repeatability.

  We determined that much of the error was due to wide-angle distortion in the lenses, calibrated and corrected for that. I devised an "error cancellation" algorithm to remove the remaining static error, using barycentric triangle coordinates to bilinearly blend corrections from the center and corners of each camera area to its interior points.

  The result was 1.02 cm max error over the whole robot area, and 0.34 cm RMS (Root Mean Squared) error from the surveyed points.

• Implemented a complete automated testing framework and SQL injection vulnerability scanner for the Emulab web interface

  Most web sites are implemented in PHP or ASP code, with a back-end SQL database holding user session and persistent state. Typically, SQL queries are constructed on-the-fly, combining HTML forms inputs from the user with SQL query statement strings. SQL injection attack vulnerability comes from any form inputs that are not checked for SQL metacharacters such as single- or double-quotes, allowing a DB query to be "hijacked" by an attacker.

  Checking forms inputs is generally trivial code, but it must be done on EVERY input without fail, since a single vulnerability can give away control of the whole database. A defender must block everywhere; an attacker only needs to find one hole.

  Researching this problem, I was surprised not to find tools available to do complete, automated checking of web sites. The best I found were manual "penetration testing" tools, random "blind" site-probing tools, and programming toolkits for manually constructing web site test frameworks.

  The Emulab web interface is served from Boss, and it is not desirable to "beat up" the main database for testing. But Emulab has a unique ability to run "inner" copies of itself as "Emulab-in-Emulab" experiments, where the Boss and Ops servers and some experiment nodes are sequestered in an Emulab experiment for testing.

  So I built an automated testing framework for the Emulab web interface, with an SQL injection scanner on top of it. An inner Emulab is started and "activated" by scripted creation of "one of everything" in the DB. This causes all Emulab web pages to be presented to a "spider" pass over the whole site. The saved pages are then mined for forms input arguments; the inputs are combined with a small test values dictionary; and test scripts are generated to drive the web interface.

  There are two test modes, one to just verify operation of each of the forms through setup, control, and teardown of each managed object type. Another probes each of the forms inputs individually by substituting in a labeled SQL injection probe string.

  A "probe catcher" pattern check on the way into DB query-handling code reports the labels of uncaught probes that could compromise the database. It's then trivial to fix up the input checking code, sealing off the vulnerabilities. Since the process is automated, it can be repeated regularly with little cost as the web site is evolved.

• Created hypview, an interactive GUI tool for interactive three-dimensional exploration of network experiment topologies.

  It became difficult to understand Emulab Testbed network experiments as they grew from tens to hundreds of router and hardware nodes, and then to thousands of virtual nodes. Emulab experiments are specified in a programming language, an extension of the widely-used ns network simulation language which is in turn based on TCL. Besides needing to look for bugs in their ns programs, experimenters began using and building their own topology generators, so they needed to examine the generated network topologies.

  Links:

  • A comparison of visualization in GraphViz and hypview.
  • The hypview online tutorial.
  • An example of hypview in action.

  The main OpenGL display pane in hypview is based on the C++ HyperViewer software from Tamara Munzner at Stanford. I SWIGed it into Python and built controls for it with the wxWidgets/GTK2 GUI Python toolkit, using wxGlade as a user interface editor.

  hypview is packaged for installation on FreeBSD, Windows, and Linux user workstations, and is open-sourced along with the rest of the Emulab software.

May, 2003 - February 2004: Software Engineer, Think3 Inc. Industrial Design Applications R&D group, Salt Lake City, Utah

Responsibilities:

As a software developer, I used C++, STL and ATL/COM, together with a proprietary GUI environment and OpenGL, to implement new functionality for the ThinkDesign product.

As the local system integrator, I did the final merge of software changes and additions flowing from the seven programmers in Salt Lake City, checked them in to the weekly world-wide build cycle in Italy via ClearCase Attache, downloaded and compiled the next official build of the system and prepared it for the developers, and ran the official regression test suites. To support this process, I used and enhanced a suite of Perl programs developed in the French R&D office of Think3, extended by my own automation using Cygwin/Bash. I also introduced software power tools for use by the whole group, including WinMerge and WinCvs.

September, 2001 - December, 2002: Software Engineer, Stabro Laboratories, Inc. (Now a division of Simco Electronics), Salt Lake City, Utah

Responsibilities:

Stabro Laboratories is the only calibration service in the state of Utah which is accredited by the A2LA under the ISO Guide 17025 standard. Companies which use many kinds of measuring tools (electronic, dimensional, pressure-force, temperature/humidity, light...) send them to Stabro to be calibrated against standards which are traceable to NIST standards or physical constants.

Stabro uses software to track and schedule calibration work and maintain the necessary history and standards traceability in an accredited Quality environment. Just to make things interesting, calibration work is done at a main lab, satellite labs, and by mobile technicians at customer sites.

We architected and implemented an evolution to the new C# (C-Sharp) CLR .Net environment for visual client programs. This incrementally replaces the legacy stand-alone Visual Basic and DOS applications programs, front-ending DBASE/Clipper and Access/ADO databases on a Novell server. In the new system, distributed calibrations are handled by Web Services client connections to Debian Linux Zope servers, using XML-RPC/SOAP over HTTP, authenticated by OpenSSH public keys and encrypted by OpenSSL. Server-side business logic is written in Zope/Python and runs against MySQL databases.

We also implemented a Web Application server for calibration work status queries by Stabro customers. This was done using the FCGI-Python interface to Zope from the company web site on an Apache/HTTP server. Python code processes data which was submitted by customer forms and queries the MySQL database tables, dynamically generating HTML/JavaScript pages in response.

January-August, 2001: Systems Programmer, Halosoft, Inc., Pittsburgh, Pennsylvania

Responsibilities:

Our first two goals were to prove Viva on its own as a very high-speed applications server, and to implement very high-speed Java J2SE applications code compatibility.

Viva is the brain-child of Professor Levent Gursoz of CMU, who is the founder and CEO of Halosoft. Viva is a remarkable technology including a powerful, elegant programming language named V, together with a network-distributed, platform-independent operating system environment. V includes the ability to define language syntaxes as a low-level part of its own self-bootstrapping, as well as native language-specific datastructure primitives. It can thus naturally be used to implement multi-language compatible development and runtime systems for a networked virtual computer.

1980-2000: Co-founder and Project Technical Lead, GDC (Graphics, Design, and Computation) Project, School of Computing, University of Utah, Salt Lake City, Utah

Responsibilities:

Alpha_1 is an extensible, portable, object-oriented, research software testbed for Computer Aided Design and Manufacturing, Geometric Computing, and Computer Graphics applications. Within that framework, I personally advised the software portions of at least thirty M.S. and Ph.D. research projects, as well as the continuous software evolution work of a staff of up to eight full-time programmers.

Major Projects:

1986-1995 - Led research developing a feature-object based mechanical engineering language and manufacturing process plan representation, together with automatic CNC machining program generation methods. Sub-projects included CIDAM: Concurrent Integrated Design and Manufacture , RaDEO-MIND: Multiphase Integrated eNgineering Design , and MADE/MadeFast . This work culminated in the FeatureCAM commercial product of our tech-transfer company, Engineering Geometry Systems. I am one of the four inventors granted U.S. Patent number 5,726,896 for a real-time CNC machining servo-control method which added NURBS curves and surfaces to the usual lines and arcs handled by embedded machining controllers.

1982-2000 - Created and led the evolution of the Shape_edit interactive design and geometric modeling environment, featuring:

• A hierarchy of object vocabularies such as constructive and sculptured geometry, volumetric primitives, and mechanical engineering design and manufacturing process planning.
• Parametric procedural modeling and incremental user extensibility, including the definition of new design vocabularies which inter-operate smoothly with the rest of the system.
• Automatic model object relationship capture and dataflow incremental change propagation algorithms, which automatically maintain consistency in the model with minimal recomputation.
• Integrated procedural and graphical user interfaces, where either interface representation may be used to evolve the underlying model object graph, and the changes are automatically reflected in the other.

1980-2000 - With Beth Cobb, created StructGen, an object-oriented class definition system on top of the C language, and used it as the basis for evolving Alpha_1. The initial version was based on the system design developed in my Masters thesis and predated C++ by at least five years. StructGen is based on a meta-definition of the object structures similar to the current C++ dossiers or Java reflection. It includes generic method dispatching and polymorphic services such as deep copying, and very efficient interprocess serialized binary communication of structures of objects. Converted to C++ by Robert Mecklenburg in 1990, the higher levels are still the basis of distributed client-server interaction and persistent model state storage in Alpha_1. This has all been portable across more than a dozen Unix platforms, including Linux and Windows XP/Cygwin ports.

1990-2000 - Contributed to telecollaborative design research in our five-university NSF Science and Technology Center. This has included multi-way teleconferencing with H.263 over T1 lines and H.323 over IP, combined with real-time design refinement on networked computers. Concurrent distributed engineering design and CNC machining projects using our Alpha_1 and FeatureCAM software have included creation of a series of immersive augmented-reality research instruments with the UNC group, and development of a combined version of our design system with a post-WIMP gestural interface with the Brown group.

1977-1980: Scientific Applications Programmer, Envirotech Information Systems Division, Salt Lake City, Utah

Responsibilities:

Major Projects:

• NC programming support for the Eimco Process Machinery and Tunnel Mining Equipment Divisions: selected and installed an APT processor, terminals, and plotters. Developed post processor programs, an NC tape translator for an NC controller retrofit, and an automatic part nesting program for NC flame cutters.
• Co-authored Sketch, a graphical editor/front-end for an in-house structural analysis and automatic member sizing program for frame and truss structures, as well as commercial analysis codes.
• Supported the Sap-4 and STRUDL finite-element engineering analysis programs.
• Evaluated CAD/CAM systems for engineering design and NC programming user groups within the corporation.
• Installed and maintained the DCLASS group technology (GT) part classification system.
• Participated in the design of a distributed shop-floor data entry system.
• In collaboration with a computer hardware engineer, architected, designed, and implemented a single-board process control microcomputer system for water treatment and chemical process installations. Bootstrapped all system software: cross assembler, I/O kernel, and an interpreted high-level process control program with a simple-English natural language process specification parser.

1975-1977: Graduate student, teaching assistant, and research assistant, DARPA 3D Computer Graphics Project, Computer Science Department, University of Utah, Salt Lake City, Utah

Research Area:

Thesis title:

Advisors:

1973-1975: Computer Center Operations Manager and Systems Programmer, Parks College of Aeronautical Technology, Cahokia, Illinois

Responsibilities:

Major Projects:

• Maintained and directed operations of the college-wide Registration System, supporting the data cycle from class registration and classroom scheduling, through tuition billing and report card generation.
• Data analysis programming in support of contracts to evaluate military aircraft parts maintenance records.
• Aeronautical engineering computing support, including wind tunnel data collection.
• Instructional computing support, with computing instructor John Lamb.