Northern Colorado Business Report
“A Supercomputing Future”
by Kai Staats
December 2011

Today, November 18, was the closing day of SuperComputing 2011, the conference and trade show for high performance computing research, labs, and industry. For this week the Seattle Washington Convention Center hosted representation of the latest, greatest, and fastest computers in the world, an overwhelming array of blinking lights, whirring fans, and massive LCD, plasma, and projection screens demonstrating human brain power applied to the human quest to learn how all things work.

It was my first time attending since 2008, my ninth or tenth show in total, but as I have been away for three years, I experienced a jump in the otherwise, relatively steady evolution of compute power and associated research results.

As in the movie “Minority Report” there are now fully interactive touch screens the size of a wall. Up to four people may interact, moving, panning, zooming, and annotating documents, photos, and film. I was able to not only resize a movie while it played, but with one hand rotate it 360 degrees, the motion never even hesitating. The immersive 3D worlds are faster, smoother, and of course, much higher resolution. Still a bit awkward for data visualization, but the flight simulators are amazing!

The challenge of building supercomputing clusters has in many respects remained the same, the balance between data storage, bandwidth, calculations per second, and visualization an ongoing battle.

As CPUs get faster, they need to be fed data at a higher rate. The interconnect fabric (network) advances, from 10/100 ethernet to gigabit, from Infiniband to 10g-e and beyond. But then the memory bus is saturated and can’t keep up, so the speed and quantity of RAM and cache must increase too.

As CPU frequencies have for the most part stalled, Moore’s law is maintained by adding more cores, two, four, and eight on a single socket. But even this has its limitation as we reach the boundary of how small we are able to manufacture a transistor and how effectively we may move heat without building quantum machines.

We add more processors in the form of GP/GPUs, advanced accelerators which grew out of the graphics card industry. Nvidia is leading the charge. Ah! A new challenge is presented, for now we have 500 cores in a PCI slot and four slots to fill. But with 2000 cores, a million or more across an entire cluster, we find that our programming models no longer hold up for the message passing interface which moves fragments of a computational problem takes more processing power, diminishing returns due to fabric latency, OS jitters, and kernel interrupts not easily be solved.

IBM builds a rack-mount node which takes four people to carry (let alone install). HP and Dell design higher density blades which require water cooling. Cray reinvents the wheel (it’s a very nice wheel). TI brings to market new digital signal processors while the ARM processor makes enters this industry with a many-core architecture, but the OS platform remains infantile, lacking industry support for compilers and management tools.

Tired yet? I have only just begun. Super computing is super confusing and yet somehow it works. The competition is fierce, new companies claiming fastest and best their second year in the industry. Big guys buy up small guys as the small guys continue to innovate, racing to support the most advanced research in the world: bioinformatics, nuclear physics, brain mapping, three dimensional imaging of the earth beneath our feet, climate modeling, quantum interactions at the event horizon of a black hole.

We now understand more of the universe inside, immediately around, and far beyond ourselves than ever before. Our knowledge of how things work is growing at an exponential rate. We now compare the DNA of a newly discovered species with another, from wet lab to sequencing in a matter of hours, and we know how many millions of years separate the two in their evolutionary tree. We model with incredible accuracy the proteins that make up various parts of our body and the function of individual cells in the human brain. We better predict the movement of hurricanes up coast lines while the mathematical prediction of fluctuations on Wall Street continues uninterrupted.

I watched a 3D model of a protein-ligand interaction, the colors ranging from white to blue to red to represent the heat-energy in various parts of the system. It jumped, danced, and moved in apparently intelligent ways, an “arm” of the protein connecting to itself only to break again where the synthetic drug attempted to bond. The model from start to finish was over a minute in length, and yet it happens millions of times a second throughout our bodies. For a moment I felt alive in a way that is difficult to explain, picturing in my mind these molecular interactions inside of me at a scale I cannot fully comprehend.

I want to know how all of this works, all of it! –but even in ten lifetimes it is impossible to gain this understanding for the people who bring these discoveries to life are experts in increasingly narrow fields.

Next year I want to attend the show again, and as I have promised myself too many times before, read the posters, interview the grad students and professors who have traveled across the globe to present their latest findings, for their knowledge is our future, a future modeled in supercomputers.

Northern Colorado Business Report
“Taking out the Trash”
By Kai Staats
4 November 2011

As Moore’s law has seen the regular doubling of processor power every two to three years, the cost of storage, both local and on-line, has declined at a steady, rapid pace, giving rise to a tremendous capacity for capturing our digital lives in words, photos, video, and sound.

What has accompanied, even compelled the need for this massive increase in storage space is in part the amount of data we generate. High resolution photos have surpassed print film while lossless audio now carries the quality of the live performance. What’s more, the human tendency to horde everything digital has been compounded by advanced searches which tend to lead to the abandonment of organization.

Many years ago, when Google first introduced Gmail, a battle ensued at my former company, my engineers believed the answer to all their email woes had finally been granted–a single repository coupled with a Google powered search.

However, month after month I witnessed a gradual degradation of response to both internal and customer email. I investigated, and at times, had to intervene.

“I sent an email last week, but have not yet received a response,” became a common theme.

“Are you sure you sent it to me?” was a common reply.

“Yes. Quite certain. Should I forward a copy to you?”

“No, no. Hold on, let me search … oh, here it is. Well, I didn’t see that one ’cause I have more than two thousand email in my Inbox and a few hundred unread,” stated with a grin and a sense of pride, as though the goal of the game was to accumulate the most unread emails.

“That seems like a problem. How about using labels and filters?” I asked.

“Why?! Look, with Gmail I just search and find any thread at any point in time,” and a quick demonstration ensued.

“But you didn’t see my email until just now, and the customer has been waiting for a reply.”

An uncomfortable silence followed, and then recognition of the problem at hand “Right.”

I knew the fight was not about Gmail vs Yahoo! or Kmail vs Apple’s Mail app. This was about implementing a system of organization that was well planned, scalable, and flexible over time.

I defended the use of folders and automated filters which delivered email to unique, associated Inboxes. He was not alone, most of my staff replaced even a minimal sense of organization with Gmail’s paradigm, despite the decrease in response time, and worse, lost communications.

In response, I initiated a competition: my more than twelve thousand email comprising the summary of ten years of communications, archived in the logic of several hundred nested folders against just a few thousand email and Gmail’s search put to good use. The goal? Find a particular email on an exact date sent to a known client about a non-ambiguous subject, granting at least three parameters by which one could search.

Challenge after challenge, I won every time. None of my employees could beat me in accuracy nor timing of information retrieval. Three, at most four mouse clicks and I could locate any email to any customer in just a few seconds.

Yes, I spent thirty minutes every now and again re-organizing my email directory structure to accommodate an increased load, or to gain a greater level of efficiency when I realized that re-sorting directories by one parameter was more effective than by another. But the time I spent in organization was more than compensated by the hours saved in daily operations and what’s more, I gained a strong visual component, a sense of ownership of my data.

What I experienced then, and to this day I believe holds true, is that the most important of all factors in an age of information overload is forming good habits of data organization and of equal importance, taking out the trash. To keep everything, all the time, independent of the number of folders, is to fail to process data on a regular basis, thereby failing to assign value across the board.

No matter where we store things, in a closet, a file drawer, or on-line, the process of managing objects and data is the same:

1. Organize – Create a system of organization which accommodates scalable growth
   and rapid, painless retrieval.
2. Prioritize – Assign dates, names, and/or project titles.
3. Discard – Establish value to the data that remains.

Most methods for teaching data organization seldom discuss deletion. But the process of determining what to throw out is the same as determining what to keep, establishing a mental image that is as effective as any advanced search function.

The next time Gmail responds, “Who needs to delete when you have so much storage?!” consider the clarity of mind you will have gained through managing your data.

Northern Colorado Business Report
“Living with Specialization in Userland”
By Kai Staats
7 October 2011

I crossed the U.S. / Canada border on I-5 listening to NPR’s Car Talk, Ray and Tom invoking laughter in the most stoic of listeners, as they always do. A woman called in to ask advice before she traded her beloved 1985 Volkswagon Vanagon for a Subaru Forester. She was understandably reluctant to give up the many years of stories, adventures, and dreams their family had shared driving across the land.

The woman asked about the engine and whether or not her husband could tinker with a new Subaru, doing most of the maintenance himself. Ray and Tom agreed that modern cars do not lend themselves to home mechanics as they have for all the prior years. The stuff under the hood is unfamiliar now, designed to be maintained by trained, industry specialists.

Two hours later I drove into Squamish, British Columbia, the rain washing my windshield clean of more than one thousand five hundred miles since I left home. I walked into the Adventure Center on Canadian HW99 at the edge of town. The young man behind the counter and his manager were discussing the power outage which has disabled all but one VOIP phone and computer terminal.

Neither of them was willing to experiment, fearing they might make it worse. They were waiting for the next day, Monday, when they could call support and talk to an expert.

Last week I stayed with a family friend, a professional photographer, writer, and naturalist with more than thirty years in the field. His life moves through his laptop and cell phone as he is seldom home for more than a few days at a time, and yet, the full capacity for electronic organization and collaboration unrealized.
I assisted him and his wife with switching from Yahoo! to Gmail, synchronizing Google Calendars to their Android phones, configuring email for their Internet domain, expanding their home wireless network with two Apple Airport Extreme adapters, establishing a central repository for sharing files, and connecting their home stereo system to streaming Internet radio.

I transferred user data from an old laptop to one brand new, doubled the capacity of the old laptop, reinstalled Mac OSX, and transferred user data again. They were thrilled, one of their daughters commenting over the phone, “Welcome to the twenty-first century!”

To be honest, I just followed the directions presented to me on-screen, doing little more than what I was told each step of the way. For as much of the effort as they had time, I engaged them in the process. But from their point of view, I am a specialist with many years expertise. Yet compared to code developers and engineers, I am just a layperson, an advanced user in user land. The many levels run deep.

It is not the doing that was the true barrier, for they can point and click as easily as anyone. The challenge is knowing where to start. Apple has not shipped with a printed manual for many years, believing their operating system is so simple anyone can just figure it out. I watched too many people struggle to know this is far from true. Searching Apple’s website is nearly useless and Google yields overwhelming results. You must know what you are looking for before you even begin the search.

Just a few days ago I stayed with a friend a few blocks from the Puget Sound. Their wi-fi went down some time ago. A friend had attempted to swap routers but to no avail for they had lost the passwords and did not know how to reset them. I explained that on the back or bottom of every router is a small button which when pressed with the tip of a ballpoint pen will reset the unit when you plug it in. The factory password will likely be “guest” or “admin” depending upon the brand.

Certainly, there are individuals in each generation willing to explore, to push their boundaries and dive into the depths of what an operating system or applications can do. But how many people have this comfort? I spent three full days upgrading my friends’ digital life, but how many working professionals have this kind of time? What’s more, If you do not know what you are missing, why would you ask for more?

We live in a world of special knowledge applied to special things. Specialization is job security at one level, and yet part of the reason we have so many unemployed.

Personally, I do not see technology as making things easier, for we are only introducing more complexity to our lives, always trying to do more. Placing a record on a turntable requires physical care, but not expertise. Connecting a digital audio archive to a wireless network and home theater requires a specialist. What’s more, the ability for one generation to teach the next is lost, for anything learned is useless in just a few years.
We have no choice but to pick and choose what we will maintain as our expertise, and to have the courage to ask for assistance for everything else. Maybe this brings us together again, or maybe it keeps us apart. What are your thoughts?

Northern Colorado Business Report
“Astronomy keeps amateurs, pros looking up”
By Kai Staats
9 September 2011

When I was in my final year of high school and first two years of college I presided over the Phoenix Astronomical Society. In those years I was privileged to meet Eugene Shoemaker and David Levy, co-discoverers of the Shoemaker-Levy comet which later plunged into the atmosphere of Jupiter.

Now more than twenty years later, Gene has passed away, his ashes scattered on the surface of the moon while David and I had long ago lost contact. This summer, I dove headfirst into a documentary film project about astronomers and astrophysicists, my desire to capture their motivation to ask where did we come from, and why? A passion for knowledge expressed through looking up.

The second day of August I joined David, his wife Wendee, and three dozen amateur astronomers at the annual Adirondack Astronomy Retreat, hosted by SUNY in the mountains of upstate New York. It was a long overdue reunion with David and a wonderful learning experience for me, having been away from amateur astronomy for far too long.

In the process of working on my film and my return to astronomy, I came to appreciate two aspects which are both compelling and complimentary to each other. Astronomy, more than any other science, offers an accessible, functional bridge between amateurs and professionals, a gateway for the next generation to be compelled to learn.

Amateur astronomy enables anyone with some experience, patience, and a little luck to happen upon an event in the night sky which aids the professional community. While professional astronomers have at their disposal more advanced telescopes, the amount of time they have with them is limited by a long cue of researchers around the world. Furthermore, professional astronomers and professors often visit local astronomy club meetings to share their latest findings, young astronomers, as I once was, are inspired by direct interaction with professional scientists.

The sheer number of amateur astronomers world-wide is astounding, literally thousands of scopes peering into the sky every night. This makes for a world-wide network of data collection devices, some manually operated, some automated through computer driven tracking systems. What’s more, the opportunity for a budding astronomer to capture his or her first photograph of a colorful nebulae or the bands and moons of Jupiter is literally at their fingertips.

For the years I have been away from astronomy the industry has changed. Certainly, motor drives and tracking systems were in use, but we found our way around the night sky using hand held maps, large, many-page star charts printed in black and white. Now, micro-computers, stepper motors, and laptops attached by USB cables enable anyone with curiosity to engage in the oldest science of humankind.

As with the discussion around GPS versus topographical maps, one can argue that to know only how to use GPS units in the wilderness is a tremendous risk, for the batteries may die, or the lost in a creek. With aviation too, pilots are trained in the original, non-electronic means of navigation before working with on-board GPS and radar guidance.

There is part of me that says the same should be true with astronomy, learn it the hard way so that it becomes ingrained and a part of you. But when I consider the excitement of a child viewing the rings of Saturn for the first time, their mouth and eyes open wide, “Wow! Did you see that? Come look!” There is no right or wrong way to open the door to a lifelong passion for learning.

If in our instant gratification world a child can be turned on to the sciences, then by any means possible, point, click, and be thrilled. If they stick with it long enough, they will eventually know their way around the night sky and be able to tell their friends, “Right there, see that fuzzy thing? It’s a galaxy that if we could see it with our naked eye would be six times larger than the moon!”

While I am now just a bit over forty, I was a kid again for those three nights, staying awake ’till 4:30 AM, barely making it to breakfast hours after dawn. I was the recipient of patient assistance for astronomers are a generous lot, each generation offering something to the next. I spent an entire night taking my first photographs of Jupiter and M27, the Dumbbell nebulae, my new Canon 60D DSLR attached directly to a 13” Meade scope. Ah! The clarity, the color—it was amazing!

Even without assistance, someone new to astronomy can attach a USB cable to a relatively inexpensive telescope, train it on the North Star, and see on-screen a map of what lies overhead while the scope automagically moves to any object chosen by the mouse. Photographs can be logged, archived, and correlated to the map, an interactive show-n-tell.

With astronomy, every night is an adventure, an exploration of some one hundred billion stars, nebulae, and gaseous birthing chambers for the next generation of solar engines, pulsars, super novae, and black holes. The mind has no choice but to open when one looks through a telescope, to look up and ask, “Why?”