John Whaley

475 Broadway St 2nd Floor Moka5

Redwood City, CA 94063

Tel: (650) 980-0977

 

Email: jwhaley@alum.mit.edu

URL: http://suif.stanford.edu/~jwhaley

Fax: (650) 596-5743

 

Research Interests

 

Program analysis, compilers, programming languages, software engineering, pointer analysis, virtual machines, operating systems, binary decision diagrams, program transformations.

 

Education

 

Ph.D. Computer Science, 2007. (on leave 2005-2007)

Stanford University, Stanford, CA

Advisor: Monica S. Lam

Thesis: Context-Sensitive Pointer Analysis using Binary Decision Diagrams

 

M.Eng. Electrical Engineering & Computer Science, 1999.

Advisor: Martin Rinard

Massachusetts Institute of Technology,

Cambridge, MA

Thesis: Dynamic Optimization through the Use of Automatic Runtime Specialization

 

B.S. Computer Science and Engineering, 1999.

Minor: East Asian Studies     Concentration: Japanese

Massachusetts Institute of Technology,

Cambridge, MA

Cumulative GPA:  4.9 / 5.0     GPA in major:  5.0 / 5.0

 

Research Experience

 

Founder and CTO, Moka5

June 2005 to present

My advisor, three other Ph.D. students, and I co-founded a company to commercialize a revolutionary computer management solution invented at Stanford. We wrap a complete computing environment in a secure container than can be safely executed on potentially untrusted devices, removing the dependence on hardware and enabling BYO initiatives. The container is centrally managed but executes on the local device, leading to better performance and reduced cost as compared to a server-based approach, as well as the ability to run while offline. Our unique layering technology gives the benefits of single-image management while still allowing users to arbitrarily customize their environment with their own applications and settings. This is a radically different way of doing desktop and mobile management, providing greatly improved security and agility, while simultaneously reducing costs as compared to traditional management approaches. I led the engineering effort to go from rough idea and minimal prototype to actual product in about six months. The product is deployed in production at many large enterprises, governments, and schools.

 

Research Assistant for Prof. Monica Lam, Stanford University

September 2000 to June 2005

I performed research on a wide variety of topics, many of which appeared in top conferences:

         Helped develop Chord, a state-of-the-art static race detection tool for Java that has found hundreds of serious and previously unknown concurrency bugs in several large, widely used open source Java programs [PLDI 2006].

         Developed bddbddb (BDD-Based Deductive DataBase), an implementation of Datalog that represents relations as binary decision diagrams. I used bddbddb to implement context-sensitive pointer analysis, among other analyses [PLDI 2004 Best Paper, APLAS 2005].

         Investigated using machine learning techniques to find effective BDD variable orders for BDD-based program analysis.

         Developed and evaluated a set of heuristics for method-level speculative parallelization [ICPP 2005].

         Designed and wrote Joeq, an advanced compiler and virtual machine infrastructure that is used by numerous researchers throughout the world and as the basis for the compilers course at Stanford [IVME 2003, SCP 2005].

         Implemented a fast inclusion-based context-insensitive pointer analysis for Java [SAS2002].

         Researched techniques for automatically extracting component interfaces using static and dynamic analysis [ISSTA 2002 Distinguished Paper].

         Developed a technique for system checkpointing using reflection and program analysis [Reflection 2001].

 

Visiting Researcher, IBM Tokyo Research Laboratory

August 1999 to August 2000

I worked on the IBM product JIT compiler, interacting with groups in Toronto, New York, Hursley, and Haifa. I implemented a context-sensitive sampling profiler and developed the technique of partial method compilation. [Java Grande 2000, OOPSLA 2001 Best Paper]

 

Internship, IBM Watson Research Laboratory

January 1998 to August 1998

I designed and implemented the optimizing compiler for the Jalapeño Java virtual machine (now called Jikes RVM). I also participated in the design of many other components of the system. My work on Jalapeño culminated into my Masters thesis at MIT. [Java Grande 1999, IBMSJ 2000]

 

Real-Time Manipulation of Objects in a Ray Traced Scene

Fall 1997

I conceived, designed, and implemented an algorithm for real time ray tracing. It runs full screen and real time on a standard Pentium. Submitted to SIGGRAPH 99.

 

Internship, IBM Watson Research Laboratory

Summer 1997

I worked on a clean-room Java virtual machine implementation written in C++. I rewrote the JIT compiler and implemented a real-time profiler, which was featured in an article in Dr. Dobbs.

 

Robotic Dog with Speech Control

Spring 1997

I designed and constructed a robotic dog with an adaptive speech recognition system using only low-cost discrete components. This dog won the Bell Northern Outstanding Research Prize.

 

Internship, IBM Watson Research Laboratory

Summer 1996

I worked in the Mobile Solutions group designing handheld devices. I implemented an extension to Java to support pen input and playback.

 

Research Assistant, MIT AI Laboratory

January 1996

I worked on a robot that used visual-based intelligence with a natural language interface.

 

Teaching Experience

 

Lecturer, Stanford, Winter 2013. CS243: Program Analysis and Optimizations. (Rating: 4.12/5)

Teaching Assistant, Stanford, Winter 2004. CS240: Advanced Topics in Operating Systems.

Teaching Assistant, Stanford, Winter 2002. CS243: Advanced Compiling Techniques.

Teaching Assistant, Stanford, Spring 2001. CS343: Advanced Topics in Compilers.

Teaching Assistant, MIT, Fall 1998. 6.035: Computer Language Engineering.

Grader, MIT, 1997-1998. 1.00: Introduction to Computers and Engineering Problem Solving.

Laboratory Assistant, MIT, 1995-1997. 6.001: Structure and Interpretation of Computer Programs.

 

Refereed Publications

 

Naik, Aiken, Whaley. Effective Static Race Detection for Java. Program Language Design and Implementation (PLDI 2006), Ottawa, Canada.

 

Whaley, Avots, Carbin, Lam. Using Datalog with Binary Decision Diagrams for Program Analysis. Programming Languages and Systems: Third Asian Symposium (APLAS 2005), Tsukuba, Japan.

 

Livshits, Whaley, Lam. Reflection Analysis for Java. Programming Languages and Systems: Third Asian Symposium (APLAS 2005), Tsukuba, Japan.

 

Whaley, Kozyrakis. Heuristics for Dynamic and Profile-Driven Method-Level Speculative Parallelization. International Conference on Parallel Processing (ICPP 2005), Oslo, Norway.

 

Whaley. Joeq: A Virtual Machine and Compiler Infrastructure. Science of Computer Programming Journal (SCP 2005). This is an extended version of my IVME paper.

 

Whaley, Lam. Cloning-Based Context-Sensitive Pointer Alias Analyses Using Binary Decision Diagrams. Programming Languages Design and Implementation (PLDI 2004), Washington, DC.

PLDI Best Paper Award.

 

Whaley. Joeq: A Virtual Machine and Compiler Infrastructure. Workshop on Interpreters, Virtual Machines, and Emulators (IVME 2003), San Diego, CA.

 

Whaley, Lam. An Efficient Inclusion-Based Points-To Analysis for Strictly-Typed Languages. Static Analysis Symposium (SAS 2002), Madrid, Spain.

 

Whaley, Martin, Lam. Automatic Extraction of Object-Oriented Component Interfaces. International Symposium on Software Testing and Analysis (ISSTA 2002), Rome, Italy .

ACM SIGSOFT Distinguished Paper Award.

 

Whaley. Partial Method Compilation using Dynamic Profile Information. Object-Oriented Programming Systems, Languages, and Applications (OOPSLA 2001), Tampa, FL.

OOPSLA Best Paper Award.

 

Whaley. System Checkpointing Using Reflection and Program Analysis. Reflection, 3rd International Conference on Metalevel Architectures and Separation of Crosscutting Concerns, 2001, Kyoto, Japan.

 

Whaley. A Portable Sampling-Based Profiler for Java Virtual Machines. In ACM 2000 Java Grande Conference, San Francisco, CA.

 

Alpern, Attanasio, Barton, Burke, Cheng, Choi, Cocchi, Fink, Grove, Hind, Hummel, Lieber, Litvinov, Ngo, Mergen, Sarkar, Serrano, Shepherd, Smith, Sreedhar, Srinivasan, Whaley. The Jalapeno Virtual Machine. IBM Systems Journal, Java Performance Issue, Vol. 39, No. 1, 2000.

 

Burke, Choi, Fink, Grove, Hind, Sarkar, Serrano, Sreedhar, Srinivasan, Whaley. The Jalapeno Dynamic Optimizing Compiler for Java. ACM 1999 Java Grande Conference.

 

Whaley, Rinard. Compositional Pointer and Escape Analysis for Java Programs. Object-Oriented Programming Systems, Languages, and Applications (OOPSLA 1999), Denver, CO.

#93 on Top 10,000 most cited CS articles of 1999.

 


 

Other Publications

 

Lam, Martin, Livshits, Whaley.  Securing Web Applications Using Static and Dynamic Information Flow Tracking.  Partial Evaluation and Program Manipulation (PEPM 2008).  Invited paper.

 

Whaley. Context-Sensitive Pointer Analysis using Binary Decision Diagrams. Ph.D. thesis, Stanford University, March 2007. Winner of Stanford's Arthur L. Samuel Thesis Award for Best Thesis and nominated by Stanford for the ACM Doctoral Dissertation award.

 

Lam, Whaley, Livshits, Martin, Avots, Carbin, Unkel. Context-Sensitive Program Analysis as Database Queries. Principles of Database Systems (PODS 2005). Invited paper.

 

Whaley. Dynamic Optimization through the use of Automatic Runtime Specialization. M.Eng. thesis, Massachusetts Institute of Technology, May 1999.

 

Whaley, Barton. A real-time performance profiler for Java. Dr. Dobbs Journal, March 1998.

 

Invited Talks and Presentations

 

         API CyberSecurity Conference, Dallas, 2013. Mobile Device Management Panel discussion.

         MobileCON, San Jose, 2013. Enterprise AnyWareTM – Ensuring Data Continuity in the BYO World.

         BriForum, Chicago, 2013. Sandboxing Smackdown: Separating Fact from Fiction in Sandboxing Solutions.

         RSA Conference, San Francisco, 2012. Most Innovative Company Finalist: MokaFive BareMetal.

         BriForum, Chicago, 2012. BYO Worst Practices: How to #fail at BYO.

         RSA Conference, San Francisco, 2011. BYOC: Securing Untrusted, Employee-Owned Desktops.

         SINET Conference, Washington DC, 2011. SINET 16 Innovator Finalist.

         BriForum, Chicago, 2011. Best Practices for Windows Layered Management.

         Sansa Corp, Fremont, 2010. Ten Myths About Finding a Software/IT Job.

         RSA Conference, San Francisco, 2010. Managing Your Virtual Desktop with Layers.

         BriForum, Chicago, 2010. BYOPC: IT Panacea or Management Nightmare?

         BriForum, Chicago, 2010. Understanding and Optimizing Disk Access Patterns for Desktop VM Workloads.

         RSA Conference, San Francisco, 2009. Most Innovative Company Finalist: MokaFive Enterprise Suite.

         BriForum, Chicago, 2009. Use of Layers in Desktop Virtualization Management.

         OSCON, Portland, 2008. Leveraging the Power of Virtual Machines for Distributing Linux and Open Source Software.

         ACM MobiVirt Workshop, Breckenridge, 2008. Mobile Virtualization Panel Discussion.

         SYS-con Virtualization Conference, San Jose, 2008. An IT Admin's Dream Come True: The Promise of Desktop Virtualization.

         Flash Memory Summit, Santa Clara, 2008. Throw away your PC – run your desktop from a USB flash drive.

         Morgan Stanley CTO Summit, 2008. MokaFive Virtual Desktop Solution.

         Stanford OSG, 2007. Easy, safe, and available anywhere computing.

         PLDI, Ottawa, 2006. bddbddb: Using Datalog and BDDs for Program Analysis.

         APLAS, Tsukuba, Japan, November 2005. Using Datalog with Binary Decision Diagrams for Program Analysis.

         ICPP, Oslo, Norway, June 2005. Heuristics for Dynamic and Profile-Driven Method-Level Speculative Parallelization.

         Stanford University Broad-Area Seminar, January 2005. Hot Topics in Compilers and Programming Languages.

         Intel Research, Sunnyvale, CA, November 2004. Program Analysis using Binary Decision Diagrams.

         PLDI, Washington DC, June 2004. Cloning-Based Context-Sensitive Pointer Alias Analyses Using Binary Decision Diagrams.

         Stanford University CS343, June 2004. Combining Predicates and Context-Sensitive Pointers.

         Stanford University CS343, May 2004. 0wn3rship Types.

         Stanford Computer Forum, May 2004. Program Analysis with bddbddb.

         Sun Microsystems, Mountain View, CA, August 2003. Design and Implementation of the Joeq Virtual Machine.

         IVME Workshop, San Diego, CA, June 2003. Joeq: A Virtual Machine and Compiler Infrastructure.

         Stanford University EE392C, April 2003. Emerging Applications: Verification.

         Stanford University CS243, March 2003. Dynamic Compilation.

         SAS, Madrid, Spain. September 2002. An Efficient Inclusion-Based Points-To Analysis for Strictly-Typed Languages.

         ISSTA, Rome, Italy. July 2002. Automatic Extraction of Object-Oriented Component Interfaces.

         Stanford University CS343, May 2002. Context-Sensitive Analysis.

         Stanford University CS343, May 2002. Context-Sensitive Flow Analysis Using Instantiation Constraints.

         Stanford University CS243, January 2002. The Joeq Compiler System.

         Stanford University Seminar, December 2001. An Application for Flow- and Context-Sensitive Pointer Analysis.

         OOPSLA, Tampa, FL, October 2001. Partial Method Compilation using Dynamic Profile Information.

         Reflection, Kyoto, Japan, September 2001. System Checkpointing using Reflection and Program Analysis.

         Stanford University CS343, June 2001. Scalable, Precise Pointer Analysis (and other oxymorons)

         Stanford University CS343, May 2001. Pointer Analysis That Works.

         Stanford University CS343, May 2001. What's so hard about pointers?

         ACM Java Grande, San Francisco, CA, June 2000. A Portable Sampling-Based Profiler for Java Virtual Machines.

         OOPSLA, Denver, CO, November 1999. Compositional Pointer and Escape Analysis for Java Programs.

         University of Tokyo. July 2000. Effectively gathering and using dynamic profile data.

         Tokyo Institute of Technology. July 2000. Analysis and Optimizations of Multithreaded Programs.

         IBM Japan, 1999. December 1999. Pointer and Escape Analysis for Java.

         Tokyo Institute of Technology. December 1999. Automatic Dynamic Specialization.

         University of Tokyo. September 1999. Compositional Pointer and Escape Analysis for Java Programs.

         Silicon Graphics. December 1998. The Makings of a Seamless Java Virtual Machine.

         MIT 6.892, December 1998. Escape Analysis in Java.

         MIT 6.892, November 1998. Jalapeño: The Makings of a Seamless Java Virtual Machine.

         IBM T.J. Watson Research Center, March 1998. Porting IBvM to x86.

         IBM T.J. Watson Research Center, August 1997. Single-Pass Java Bytecode to IR.

 

 

 

 

Professional Activities

 

Programming Language Design and Implementation (PLDI) Program Committee, 2008.

Parallel and Distributed Embedded Systems (PDES) Program Committee, 2005.

Compiler Optimization Meets Compiler Verification (COCV) Program Committee, 2002.

Reviewer for POPL, PLDI, OOPSLA, ECOOP, TOPLAS, FSE, CGO, USENIX.

 

Open Source Projects

 

Joeq virtual machine and compiler infrastructure. http://joeq.sourceforge.net

JavaBDD binary decision diagram library. http://javabdd.sourceforge.net

bddbddb: BDD-Based Deductive DataBase. http://bddbddb.sourceforge.net

Eclipse KeepResident plugin. http://suif.stanford.edu/pub/keepresident

BuDDy BDD package. http://buddy.sourceforge.net

 

Honors and Awards

 

Arthur L. Samuel Thesis Award for Best Thesis, Computer Science Department, Stanford, 2007.

Nominated by Stanford for ACM Doctoral Dissertation Award, 2007.

Intel Graduate Fellowship Award, 2004-2005.

Stanford Engineering Fellowship, 2003-2004.

NSF Graduate Student Fellowship Award, 1999-2003.

Paper Awards at PLDI 2004, ISSTA 2002, OOPSLA 2001.

Bell Northern Outstanding Undergraduate Research Prize, 1997.

Faculty Letters for outstanding performance in MIT courses:

Structure and Interpretation of Computer Programs (6.001), Computation Structures (6.004), Artificial Intelligence (6.034), Compiler Design (6.035), Software Engineering Lab (6.170)

USA Computer Olympiad '93: Went to national finals as one of the Top 15 programmers in US.

 

Languages

 

English (native speaker), Japanese (fluent speaker)