Mark Moraes

My background

After a Bachelor's degree in Electrical Engineering at the Indian Institute of Technology, Delhi, I came to University of Toronto for my M.A.Sc in Electrical Engineering which I finished in April 1990 (my thesis was a Hierarchical Design Rule Checker on MIMD multiprocessors, supervised by Martin Snelgrove). I also enjoyed part-time systems admin and programming for the Computer Systems Research Institute.

Till 1991, I worked as a full-time systems programmer, setting up the original cs.toronto.edu systems and networks for the CS Department (AI/Numerical Analysis/Theory), creating a productivity environment for the young X Window System (Versions 11R1-4). Some of the programs I developed in this period (e.g. xpic, xtroff, xplaces, xdrawmap, xplay, malloc, a set of cookbook examples for Xt) can be found in either my CS ftp area or the general CS ftp area. (e.g. programs I hacked on, modified or contributed to like track, ypfake, dvix, host)

I was the the first employee, programmer, sysadmin, customer support person, billing specialist and chief cook & bottlewasher at UUNET Canada and designed, built and supported most of the technology for its original product offering: UUCP feeds, e-mail and netnews as well as dialup and dedicated IP services.

From 1992 to 1995, I worked for D. E. Shaw & Co., a New York City-based investment bank, designing and implementing systems infrastructure for a global trading network spanning Tokyo, London, Boston and New York.

In 1995, I was part of the original team that built Juno Online Services (first free dialup e-mail and then full Internet access) and was CTO there till 2000.

From 2000 to 2003, I was CTO at Teleias International Inc. in Walnut Creek, California, building a neat appliance for server systems management in data centers.

In 2003, I co-founded Pointrex, Inc., purveyors of fine system management tools and best practices for Linux, Solaris and Windows.

I'm presently heading up systems software and computing infrastructure for D. E. Shaw Research (DESRES), a lab doing basic scientific research in computational biochemistry and molecular dynamics. Part of our research includes Anton, a massively parallel supercomputer for biomolecular simulation and Desmond, a scalable molecular dynamics (MD) program for commodity clusters (aka Beowulfs). Some papers that describe some of what we've been working on:

• Anton, a special-purpose machine for molecular dynamics simulation, about the architecture of our massively parallel supercomputer, presented at ISCA 2007
• Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters, about Desmond, a highly parallel program we developed, presented at SuperComputing 2006
• High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation presented at HPCA 2008
• Incorporating Flexibility in Anton, a Specialized Machine for Molecular Dynamics Simulation presented at HPCA 2008
• Anton, a special-purpose machine for molecular dynamics simulation in the Communications of the ACM, July 2008

David Shaw's 2006 talk at Stanford University's Computer Systems Colloquium has both video and slides which provide background, context and elaboration for the papers.

Ron Dror's publications page lists several other papers published by members of our research group on biomolecular simulation, biochemistry research done using molecular dynamics simulation with Desmond, and algorithms for Desmond and Anton

More general articles about D. E. Shaw Research:

• Nature discussed some aspects of the challenge and some of those tackling it in a news feature called Chemistry: Power Play
• The space for the first Anton supercomputer was mentioned in artdaily.org
• The New York Times: John Markoff wrote a brief piece mentioning our CACM paper on Anton

For our research, we deployed a 1056-node cluster (Sun v20z nodes, each with two 2.4Ghz Opteron 250 CPUs) using Infiniband (SDR, PCI-X) as the low-latency interconnect; when deployed, it was the second-largest Infiniband cluster in the world, just behind Virginia Tech's cluster with 1100 Apple Power Mac G5s. I gave a talk on D. E. Shaw Research's experience with that Infiniband cluster at the 2007 OpenFabrics Sonoma Workshop

Other activities

I've been involved with Usenet for a long time; I was part of the original group-advice team and the moderator of news.announce.newusers for many years. The news.answers team has taken over moderation of news.announce.newusers.

I was UUCP Map Coordinator for Canada for several years. Ed Hew now handles that.

John DiMarco has taken over further development of xcpustate. The current version can be obtained via anonymous ftp from his ftp area (ftp.cs.toronto.edu:/pub/jdd/xcpustate).

The latest version of Jove (Jonathan's Own Version of Emacs -- a small, fast, portable Emacs clone) can be found in my ftp area (ftp.cs.toronto.edu:/pub/moraes/jove). Questions about it should be directed to the jove–dev list hosted on cs•toronto•edu.

Other neat things in my ftp area are a program called ptouchlabel that uses ghostscript and a netpbm converter to print to a Brother P-Touch PC labeller, a fast secure unshar written entirely in C, and various little utilities that I hope to document fully one day. Many were written pre-Posix and may need some tweaking to work on modern systems.

Other links

A cool optical illusion

Grandpa Little's Toy Workshop has lovely handcrafted heirloom toy barns