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Week of 31 May 2010

Latest Update: Sunday, 6 June 2010 09:44 -0400

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Monday, 31 May 2010
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09:26 - It's Memorial Day here in the U.S., the day set aside to remember those who sacrificed themselves to protect our freedom. Although the official purpose of Memorial Day is to remember those who gave their lives in the service of our country, let's also remember all of those brave men and women, living and dead, who through the years have put their lives on the line to protect all of us. As we have our cookouts and family get-togethers today, let's all take a moment to think about our troops in Iraq and Afghanistan and elsewhere, who can't be with their families. And let's have a thought, not just today but every day of the year, for them and the sacrifices they are making and have made.


Tuesday, 1 June 2010
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09:44 - It's easy to forget that our service members aren't the only ones making sacrifices to protect us. Those lines in the casualty reports also represent profound losses for their wives and husbands, their mothers and fathers, their brothers and sisters, and, most of all, their children.

12:51 - Jasmine's best friend, Ethan Smith, was killed Sunday in a car accident. Barbara and I haven't seen Jas since it happened, but her grandmother says she was and is devastated. Mary said it wasn't a boyfriend/girlfriend thing between them. They were more like brother and sister, hanging out together and teasing each other constantly. Jasmine must be stunned, particularly because she saw him not long before he was killed.

This is the second close friend that Jas has lost in similar circumstances. A couple of years ago, the boy who lives on the street behind us and one house over was killed in a car accident. He was three years or so older than Jas, which is a lot at that age. A 17-year-old boy usually has better things to do than hang out with 14-year olds, but this boy treated the younger kids like brothers and sisters, driving groups of them to the mall and so on. I asked Jas at the time if she'd been close to him, and her reply confused me momentarily. She said, "He was my big brother." And now she's lost another one.


Wednesday, 2 June 2010
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00:00 -


Thursday, 3 June 2010
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10:57 - Still working hard on the book. I should complete the initial passes on the six project chapters in the next few days. I'll post those to the Subscriber page once I have them in reasonably good shape.

I'm also ordering some of the stuff that I need to put together the first batch of 100 microchemistry kits. I won't be ready to ship kits in time for the start of school this autumn, but I'm pushing ahead for next year. My cup runneth over with UPS deliveries. Friday, UPS showed up with a case of 10 mL oral syringes with caps (for gas chemistry experiments). Tuesday, UPS showed up with a large box of chemicals from Elemental Scientific. And today UPS will show up with the six cases I need to complete the component list for the six project systems in the book.

I will be even busier than usual for quite a while.


Friday, 4 June 2010
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08:18 - After years of waiting for the chance, Malcolm finally got to savagely attack the UPS guy yesterday. The poor UPS guy almost got a hernia hauling the stuff up to the front door. Six Antec cases plus a box of miscellaneous stuff I'd ordered from NewEgg. He was walking back and forth from his truck to the front porch, setting boxes on the porch as I carried them into the house. On the last trip, he offered to carry the largest box into the foyer. He then bent down and reached toward Malcolm, who came charging over and viciously licked his hand. Malcolm then did his usual jump in order to get in a quick face slurp as well.

This weekend we'll get all the cases unpacked and sorted out. We also need to shoot a dummy cover image that O'Reilly's marketing folks need to put together marketing promotion materials for the salesforce to use to pre-sell the book. If we have time, we'll also at least get started on the first build. That'll probably be the appliance system, which is an Intel D510MO Atom motherboard with 2 GB of Crucial memory and a 640 GB Seagate notebook hard drive in an Antec ISK300-65 case.


Saturday, 5 June 2010
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09:32 - It looks to me as though anyone who wants to can build an affordable desktop supercomputer. The other night, I looked at the BBC article about the June 2010 Top 500 Supercomputers. The first thing I noticed, of course, is that nearly all of them run Linux, with most of the remainder running AIX or Open Solaris. The next thing I noticed was their LINPACK benchmarks. The slowest of the top 500 is about 24 petaFLOPS.

So I ran LINPACK on my den system, an old Core2 Duo. It scored just under one gigaFLOPS, so the current #500 supercomputer on the planet is only about 25,000 times faster than my old den system. That got me to wondering about the new Extreme System we'll be building, which uses an Intel Core i7-980X processor. That processor benchmarks at just over 100 gigaFLOPS in double-precision mode, which means the world's #500 top supercomputer is only about 250 times faster than the main CPU in the new Extreme System.

But, as the old commercial used to say, wait, there's more! General-purpose processors are really rotten at floating-point operations. That's why serious gamers buy high-end video adapters, which are optimized for floating-point ops. The fastest GPU on the planet is the ATi RADEON HD 5970, which reaches nearly 5 teraFLOPS in single-precision floating-point ops. Unfortunately, like all GPUs, it's much less efficient in double-precision floating-point ops, where it turns in benchmarks just under 1 teraFLOPS.

Of course, we're not limited to just one RADEON HD 5970. Installing two of them in a CrossFireX motherboard takes us up to nearly 2 teraFLOPS, and installing four would take us to nearly 4 teraFLOPS. Even allowing for scaling inefficiencies, that system should have potential performance of around 10% of the #500 supercomputer on the planet. That, to my mind, definitely qualifies as a desktop supercomputer. As to "affordable", definitions obviously vary. Those video cards cost $700 each, and you'd need an expensive motherboard and a very expensive 1000W or higher power supply. You'd probably also want to install liquid cooling, particularly for the video adapters. Still, all told, for a few grand you end up with a real supercomputer. And, in not all that many years, this level of performance will be the norm for a budget system.

Of course, by then the world's fastest supercomputers will be much faster than today's. But at some point, absolute speed begins to become more important than relative speed. So what if in ten years a $1,000 desktop system no longer places in the world's Top Million Supercomputers? It's still extremely fast in absolute terms, and able to do all of the things that today's top supercomputers are doing now. I think this has profound implications in many respects, but particularly for science, and more particularly for endeavors like total organic syntheses and designing synthetic lifeforms. It's going to be an interesting decade.

I'd intended to write something about this myself, but Pat Condell says it all.

12:03 - There may be hope for us yet.  CNN reports a Pew study that says interracial marriages are at an all-time high. And why not?

My generation can take credit for this, I think. My parents' generation were not all racists by any means; certainly my parents were not, nor my mother's mother, although my father's mother was. And yet, when I dated a black girl I don't doubt my parents were concerned, not because she was black but because young married couples have enough pressures on them without having to deal with the then-prevailing taboo on racially-mixed marriages. Had I married one of those girls, I don't doubt that some family members, on both sides, would have shunned us, as would a significant fraction of society. And that would have been true in the Northeast, where I lived then. It would have been much, much worse in the South. The Woodstock Generation changed that, or at least started the change.

There are certainly still racists of all colors out there, but they've been marginalized, at least among the middle- and upper classes and the well-educated in general. Most of that group, seeing the photograph in that article, see only an attractive young couple that are obviously delighted to have found each other. I'm sure they'll still have to deal with some racist crap here and there, but it'll be an order of magnitude less than a mixed-race couple of my generation would have had to deal with. There may be hope for us yet.


Sunday, 6 June 2010
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09:44 - Happy Birthday to me. Today I turn 57, although I prefer to think of it as 0x39. Or, as Elayne Boosler would say, twenty-thirty-seven.

We started a new tradition today: my annual birthday haircut. Back when was in college, I just let my hair grow. My hair was extremely curly, so as it grew it simply expanded outward in a red Afro. Then, a couple of months ago, I was watching one of Martyn Poliakoff's videos (he of the white Afro) and wondered if I could still do that. So I've let my hair grow for the last couple of months, and found that it indeed does still curl up well enough that I could still grow it out as an Afro. Since we're just entering the hottest months of the year, I thought it made sense to start with my hair short as of my birthday and see how far it'll grow out in the coming weeks and months.


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