Supercomputing Course: Introduction to Unix, Part I

Back in the dinosaur era of computer science (I can say that since it's before even I was born!), computers were little more than gigantic calculators. They were gigantic because they used vacuum tubes (the transistor had not yet been invented). A computer would be the size of a medium-sized house, yet could perform fewer operations than the calculator on your cheapo digital watch. (Okay, maybe you don't have a watch like that, but I'm sure that somebody reading here does. If I wore a watch, I would totally have one with a calculator. [Yes, I am that nerd-tastic, and proud of it!] But I don't wear a watch.)

Anyhow, the point is, computers in the 1940's and early 1950's were simply gigantic calculators. They had no means of being programmed, except to physically rewire the machine. Eventually punch cards were introduced and that was when you could actually begin to program. The problem was that each computer, even computers built by the same vendor, was different, so if you wrote a program for one computer, you'd have to completely start over for the next computer.

Another problem was the fact that these gigantic calculators cost millions of dollars (for example, the Iliac IV, built by Burroughs and the University of Illinois in 1965, cost $31 million, a princely sum even today), so companies and universities would want to get their money's worth by keeping the computer busy at all times. There were no operating systems to manage users, so what would happen was usually one of two things: 1, You would be assigned a time, let's say 2-4 a.m. on Saturday morning (a particularly inconvenient time that would probably be given to a grad student), during which the computer was all yours; or 2, You would submit your stack of cards, and whenever the operator got around to it, he or she would run your program and you'd get your output several days later.

Well, the thing is that if the computer could automate resource sharing, nobody would have to be hanging around running it at odd hours of the night, or even hanging around the machine much at all. Ken Thompson and Dennis Richie at Bell Labs were kind of annoyed about this inefficient method of resource sharing, so they decided to create an operating system that could handle multiple users on one computer. After a few failures, they developed the UNIX operating system. They freely gave away their code and UNIX became the industry standard operating system on mainframe computers.

In 1991, a Finnish college student by the name of Linus Torvalds decided to create a UNIX-like operating system for personal computers, just for fun. Linux, which started out as simply a hobby, has become a very important operating system in the computing industry. It is used on many servers, clusters, office computers, and even home PCs. Even Microsoft uses Linux for its servers from which you download Windows patches and the like. I have Linux on my desktop machine at work, and my laptop is a Mac running OSX, which is built on top of UNIX.

The vast majority of supercomputers run some flavor of *nix¹; at SC04 (the supercomputing industry conference), we saw that Microsoft was trying to get into the HPC world, but I haven't seen or heard anything about a Windows-based supercomputer. My then-officemate quipped that Microsoft was probably partnering with IBM to make a new supercomputer called "BlueScreen." (This was particularly hilarious because IBM's flagship machine, BlueGene, had just been introduced.)

Anyhow, the point of this whole discussion is that learning *nix commands is necessary before you can use a supercomputer. You don't have to be a *nix whiz kid or anything, but you have to be comfortable getting around and doing what needs to be done. In the next part, I will talk about some important commands in *nix.


¹ The * character is a wildcard character in computer science, so when I say *nix, what I really mean is any word that ends in "nix"; in this case, Linux or Unix. (Yes, I realize that the last vowel in Linux is a u rather than an i, but a lot of people pronounce Linux and Unix as if they rhyme. I am not the originator of this convention so don't blame me!)

Resources:
I got the pictures of Grace Hopper and the punch cards from Lexicon's History of Computing, and the picture of Dennis Ritchie and Ken Thompson from the UNIX/Linux picture gallery.

Arm Woes

Zuska's post on being sick of being sick made me stop being in denial about the condition of my arm. For you new readers, I have a really bad case of medial epicondylitis (a.k.a. golfer's elbow) in my left (dominant) arm, along with some bonus pain up to my shoulder and down to my pinky finger, that has left me unable to do a lot of the activities I was once able to do. It was caused by a number of factors, including playing the violin since the age of three, practicing regularly for several hours at a time in elementary school; the fact that I also use that hand to write; the double-jointedness of my elbow; and probably some sort of natural predisposition to tendonitis.

I haven't played the violin for more than a year and a half, because I know that it would only make things worse. I do my best not to write with my left hand, either. I've learned to write with my right hand, although it's challenging and slow. I used to be fond of doing calligraphy, but that, like playing the violin, is right out. And a lot of crafts I used to enjoy (well, mostly sewing and cooking, I guess) are also difficult. I have been hesitant to get back into karate because I know that a lot of things in karate (e.g. punching, doing push-ups, etc.) are also damaging.

Last August, my orthopedist gave me another cortisone shot in the elbow, and it helped. But the effects are wearing off, and my daily activities are getting more difficult once again. The worst things for me to do involve gripping with my hand and rotating my arm. Driving the manual transmission car is becoming a challenge, because I can't keep my right hand on the wheel at all times. Opening doors is starting to cause me problems again. And picking up Vinny is becoming painful, especially because he's getting bigger and bigger.

My elbow doesn't hurt as much as it did last year at this time, but I wonder in part if this isn't due to the fact that my pain scale has been recalibrated. Especially because I have new problems, like pain in my pinky when I type. Typing never used to bother me, but now it's starting to.

I just hate to admit that I have a disability, but I decided that I really need some accommodations at work. I had an ergonomic evaluation last year, but I'm going to have another one on Monday, and also discuss the possibility of dictation software and any other tools that they think might help. I also need to make another appointment and go back to the orthopedist.

The worst part of having this problem is that I get so jealous of other people, who don't have to adapt every single activity to their disability. Should I hold the bowl with my left and beat the eggs with my right hand, or vice versa? Can I hold my purse and my lunch bag and open the door, all with my right hand?

So count your blessings if you can use both of your arms freely. I'd give my left arm for that!

Supercomputing Course: Introduction

I am a veritable supercomputer fanatic. So teaching a course on how to use them is almost second nature to me!

Learning how to use them for the first time, however, was decidedly not second-nature. I was woefully computer-ignorant for a computer science graduate student, which I blame on my lack of computer science undergraduate degree. (I majored in Physics.) But I was pretty good at hiding my complete lack of knowledge through obfuscation, procrastination, and general inefficiency.

My extremely observant advisor soon figured out that I didn't know the first thing about computers. But he wasn't upset by that fact! He just gave me a miniature course on Unix and the vi editor. And since I am relatively resourceful and intelligent, I paid attention and consequently caught on rather quickly.

So a lack of computer literacy is nothing to be ashamed of! It's the unwillingness to admit to your ignorance that's a problem. But once you recognize that your ignorance is due to a lack of experience rather than incompetence or any deficiency on your part, you are ready to pick up the skills that are necessary for becoming a supercomputer user!

Over the course of the next few weeks, I will erratically publish posts that I have written based on my supercomputing course. I hope that you will follow along and learn about this subject. If at any point you have questions, feel free to leave them in the comments, and I will do my best to answer!

I've Been Tagged!

So somebody (Twice Tenured) actually tagged me for a meme, scary but true! Here are the rules:

• I have to post these rules before I give you the facts.
  
• Each player starts with eight random facts/habits about themselves.
  
• People who are tagged need to write their own blog about their eight things and post these rules.
  
• At the end of your blog, you need to choose eight people to get tagged and list their names.
  
• Don’t forget to leave them a comment telling them they’re tagged, and to read your blog.

Okay, so eight random facts/habits about myself.  Hmm... let me think... I am kind of boring so this is tricky.

1. I chew gum every afternoon, and my flavor of choice is wintergreen.  Jeff and I have a joke that all gum is actually wintergreen flavor, so when he pulls out his cinnamon gum, I always say, "Mmm... wintergreen!"
2. I love bad puns and what most people would call groaners.  Some people, such as my boss, appreciate this sort of humor.  Others don't, so I keep my humor to myself with them.
3. I had a pedicure from hell about a year ago, where the person giving the pedicure accidentally took off a chunk of my right heel.  The gash healed very slowly, and I still have a scar there that hurts if I rub it the wrong way.
4. Since we're on the subject of injuries, when I was in college I fractured my right radius (arm bone) right near the elbow by gracefully falling in the shower.  That was quite humiliating.  I tried to tell my friends that I'd done it during my Olympic ski trials but somehow nobody was convinced.
5. And since we're on the subject of elbows, I am double-jointed in the elbows.  I can open my arms out to more than 180º.  This is what caused my arm to break, because it bent backwards instead of bending the right way when I tried to catch myself.  It's also something that has exacerbated my very serious medial epicondylitis (golfer's elbow) in my left arm.
6. I keep all my fingernails except for my left thumbnail very short.  This is residual from playing the violin.  The only nail that could be long was the left thumbnail.  I used to keep fingernail clippers in my violin case just in case one of my nails had gotten too long.
7. I am one of a small minority of people at my workplace who dresses up to go to work.  I don't get too dressed up.  It's just that I never wear jeans and I always wear a blouse.  Most of "the guys" wear t-shirts.  I dress up because I feel like I have to look professional in order to be taken seriously.  Does it work? Maybe.
8. I've always been very tall.  I was taller than my teacher in the fifth grade.  By the age of twelve, I had grown to almost my adult height.  One nice thing about being tall is that I can reach the top shelf at the grocery store.  A woman asked me to reach something for her at the store the other day, and it felt good to be able to help.

Now I have to tag people.  Well, I'm definitely tagging my better half, my sister Rachel, my sister-in-law Ginger, my cousin Susie, my blogfriends Tony, Flicka Mawa, Doctor Pion, and anyone else who wants to play along.  

This Day in History

On this day two years ago, I defended my dissertation!

It was a very hot day in Illinois, unusually hot for June. Jeff, Dad, Marvis, and Laura were in the audience. I brought all kinds of treats for the committee and the rest of the audience, including pirozhkis specially baked by the nice Russian lady at the Farmer's Market. My dad was the only person to ask a question before the committee kicked out the audience to grill me in private. They didn't actually ask me any really hard questions or anything. I did have to show one committee member where a certain proof was within the dissertation, and then they asked me to add a section with some more results at the end, which I dutifully did.

That evening, we all went out to dinner with my aunt and uncle and cousins as a family celebration, and then the next day I had a huge party, to which I invited basically everyone whom I knew and could tolerate, although with the exception of a few relatives and my parents-in-law and a friend from way back when, it was mostly just locals who attended. I held it at a city park on a lake, and my guests got to paddle on the lake in canoes and paddleboats. In addition, I had a sheet cake saying "Congratulations, Dr. Rebecca!" on it. The invite list, the location, and the cake were the only requirements I had for my party. It was a lot of fun to celebrate the accomplishment of a lifetime with my friends and family.

Of course life carries on even after you've accomplished something wonderful. Unlike a book, which would have spent maybe a few more pages summing things up, or a movie, which probably would have cut to credits right after the party, in real life this was just one event in the course of time. Since then we have moved to a new state, I started an actual job, and we had a baby, amongst other things. But that was still a great two days and it felt like such a relief to finally be done with school, even if it only meant I was moving on to something else.

Supercomputing Course

My supercomputing course on Tuesday went really well. I think I had about 30-35 students, mostly undergraduate and graduate students, along with a couple of staff members. I felt really energized and inspired that day, and I think I did a really good job. I got a couple of very nice e-mails from students who felt like they had learned a lot.

I had a request from a fearless reader to adapt the course for this blog. I'll see what I can do about that.

Father's Day Celebrations

We had a good Father's Day here. I made a nice dinner for Jeff, which we ate outside on our deck while sitting at his present (a picnic table and benches). We had veal parmesan, spaghetti, fruit plate, and Texas sheet cake. Vinny and I both gave him Father's Day cards, which I think he appreciated a great deal. We tried to make it the best Father's Day possible, under the circumstances.

You see, Jeff had a huge boil that was cut and drained on Thursday, and in a great deal of pain because of it. He was on narcotic pain killers and still feeling a lot of pain. But I think our Father's Day celebration at least distracted him a bit.

Fun with Friends

On Saturday, Vinny and I went over to my colleague's house to meet his nine-week-old son. We had a good time. Vinny got to play with some of the toys they had that were for babies older than their son, and I got to hold the baby. He's a cute little dude and took well to me even though I was a stranger.

I also passed along a bunch of baby clothes that Vinny had outgrown. I kept some of my favorite of his clothes, but I was able to give away most of them without feeling too nostalgic about it.

It's amazing the contrast between a nine-week-old and an eight-month-old baby! It's also kind of hard to believe that Vinny was that small and inactive. Vinny stole the show. He was funny, active, and cheerful, and he giggled and smiled a lot while we were there. After we got home, however, he was superbly cranktastic, having evidently used up all his cheerfulness and charm at my colleague's house!

Supercomputing!

Today I am teaching my special one-day course in supercomputing to the student interns. It is becoming an annual event. (I taught it last year at about this time too.)

This year it is going to be even better. The people at the lab's supercomputing center offered me the use of one of their smaller machines for the students. Also, they're going to give them a 45-minute tour of the facility. How cool is that?!?!

Happy Father's Day!

I wrote the following tribute to my dad a couple of years ago, but the words still ring true today as much as ever.

It is said that a man’s hands reflect his personality. Join me in this look at my father’s hands, and you will see him as I do.

I have always admired my dad and his hands. In fact, my first memories of him are more aptly described as memories of his hands. I remember grasping his finger as a toddler, his patient presence guiding me as we walked together. His pinky finger was a handful for my young hands! While my own hands have grown larger, they still aren’t as large as his. I believe his hands are larger than most. He has thick, broad fingers and wide palms. His hands are powerful, yet gentle and nurturing; rough and scarred but strong and caring; sometimes dirty and sometimes clean.

Despite his office job, my father’s hands are powerful, working hands. Dad built a playroom, jungle gym, and even bedroom furniture for his three daughters. He was handy about the house and made most of the improvements himself, from bricklaying to installing a wood stove. Yet these powerful hands turned gentle in the presence of his daughters. He was active in our young lives, playing with us after he got home from work, and holding us on his lap as he read the Sunday comics aloud. And I have seen him cradle my infant nephew in his nurturing hands. In fact, it was in my father’s hands that my nephew gave his first smile.

My father’s hands bear scars and rough spots. Some of these result from the sort of handyman work he performs at home, but others are the result of accidents. But the strength in those hands has remained consistent over time. Recently we went through a difficult time as a family. Some of Dad’s scars originated in this trying time: a Cuisinart accident injuring his finger required stitches. But Dad’s hands didn’t fail him -- he soon learned the cooking skills he’d never needed before, and remains a safe and skilled chef to this day. During this time, I suffered from deep despair that bordered on self-destruction. But my father’s strong hands never let go of me, supporting me through my trials and saving me in the depths of my anguish.

Sometimes Dad’s hands are dirty, but this is because my father is a man who gets involved. I have fond memories of many projects with Dad: changing the oil, patching the car’s muffler, installing the home electrical outlets, planting a garden, taking photographs of nature, balancing the checkbook, watching the Packers on TV. He actually slogged through my calculus textbook in an effort to help me learn calculus, even though he knew next to nothing about it. It was thanks to his helping and encouraging hands that I became a scientist.

Yet his hands are clean when it is important. I have memories of him coming inside from some outdoor project before dinner and washing his hands. The dirty water swirling down the drain would be so dark with soil! He would sit down at the table, this wild man smelling of sweat, with mussed-up hair and flecks of dirt caught in the moisture of his brow -- but spotless hands. His hands are clean when it counts. My dad is a man of integrity, who rises above the petty and picayune. He has an even temper and an easy-going disposition, and confidence without a hint of cockiness. He exhibits respect for others even when they disrespect him. His hands have never been used to threaten or harm or to make rude gestures. During the difficult times, he was careful to treat all parties with respect and avoid doing anything he would later regret. He tried to keep his hands clean in a situation where most people would dig into the mud.

According to Red Green, “If the women don’t find you handsome, they should at least find you handy.” I believe that this description of my father’s hands has shown not only his handiness, but the handsomeness of his character.

Loving and loving

This week marks the fortieth anniversary of the Loving v. Virginia decision, in which Virginia's anti-miscegenation laws were struck down. It seems obvious nowadays that there is no good reason to prohibit members of different "races" from marrying. After all, as we probe into understanding the human genome, we have come to the inescapable conclusion that race is a purely artificial construct.

Also, June is Gay Pride Month. So it seems like the perfect time to talk about marriage equality!

I always end up in a state of awe when I read the insights of the ever-brilliant Terrance of The Republic of T on just about any topic he sets his mind to. His posts on gay marriage are no exception. Of course, the topic is near and dear to his heart, as he is a gay man. But he still has the remarkable ability to remove himself from the equation and examine both the motives of the gay community in desiring marriage equality and the motives of those who oppose legalizing his relationship with his true love, just because they have the same equipment between their legs. (Those are just two of his many amazing posts.)

It's depressing to think that because of their rigid viewpoints, intolerant people are trying to prevent someone from having their loved one at their side when they're on their deathbed, costing taxpayers money by not allowing gays to adopt children out of the costly foster care system or boosting the economy by a cool billion dollars by allowing same-sex marriages, forcing people to, as Terrance so eloquently puts it, "settle for their second-best life,"etc. These people repudiate their own humanity when they deny the existence of true love, just because the lovers in question share similarities in their reproductive system.

I was talking to my younger sister about her future the other day. She will soon graduate with a doctorate in Religious Studies, and she'll be on the job market. I was asking her where she'd like to end up, and I was saddened to realize that if she does what's best for herself, Anne, and any children they might end up having, it won't be anywhere near me.

In Virginia, where she lives, they voted in a new law, prohibiting same-sex marriage from ever even considering being valid in Virginia, even if the marriage is valid elsewhere. My own state is no better, with 80% of the voter turnout showing its ugly, bigoted side by supporting a measure almost as vile as that enacted in Virginia. If it were only our two states complicit in denying people's rights! Alas, it is not. They are but two of the latest casualties to homophobia.

Yes, I am angry. There is no room in this society for bigoted homophobes to ruin the lives of decent people. Tennessee badly needs an influx of creative, dynamic, energetic people to revitalize its economy, pay for needed improvements to its infrastructure, and improve its educational system. But bigoted measures like anti-marriage-equality amendments only repel people the very people we need!

And I'm not just talking about gay people. Until there's a critical mass of diversity, it will be hard to attract anyone who doesn't fit into the white, "Christian" mold. Only the strongest (or perhaps the craziest) misfits will be brave enough to inhabit this state. I am one of them and I'm not going anywhere. This is my home and I have a right to it. And if I wait long enough, I know that rational thought and decency will prevail.

Some insights I have gained from Terrance have given me hope. In particular, he talked about what made the Loving v. Virginia ruling possible. Quoting from this Washington Post article that Terrance cites in his most recent post on the topic,

"Nowadays everyone agrees that bans on interracial marriages are unconstitutional, and even if they weren't, few people would support them. But Loving illustrates something important about the evolution of constitutional law.... At one point, [anti-miscegenation, segregation laws, and discrimination against women] were seen as legitimate reflections of the world, not as invidious attempts to impose inequality. When the court held these practices unconstitutional, it was neither enforcing a rule that had existed since 1868 nor creating a new rule. It was recognizing that social attitudes had shifted, and with them the understanding about what is reasonable and what is invidious."

So maybe we are currently in the depressing middle installment of the gay-marriage saga trilogy. Maybe at this moment, The Empire Strikes Back, but soon, we will mark The Return of the Jedi. Public opinion is shifting towards agreeing that love can bloom in all places, even between two members of the same sex.

Beautifully Said

P.Z. Myers has written one of the most lyrical expressions of non-faith that I have ever seen.

The short summary: We're all humans, afflicted by the human condition. We all face the same universal human experience, and instead of engaging in the escapism and magical thinking of fitting these experiences (square pegs) into the terms of the supernatural (round holes), we should learn to appreciate the human condition for what it is. This does not mean that we must deny our feelings or deprive ourselves of art (created in the past or present); it means that we should appreciate that any meaning in our life is, out of necessity, self-made, and that doesn't make life or the expression of what makes us human any less beautiful.

Delicious Baby Food

I spent much of the weekend making homemade baby food for Vinny. On Friday, I made some homemade teething biscuits. It was a bit of a challenge because thanks to my maternal grandfather's wheat allergy, I am trying to minimize Vinny's exposure to wheat for a while longer. So using flour was right out. Instead, I made them with the following recipe, adapted from here:

1 c. dry baby rice cereal
1 c. rolled oats, ground into meal using the coffee grinder
3 T. olive oil
ice cold juice

Whisk together rice cereal and ground oats. Add olive oil one tablespoon at a time, stirring well. Mix in juice, a little at a time, beginning with 1/4 c, until the dough pulls away from the sides of the bowl (like when you make baking powder biscuits). (I used ~ 1/2 c in total.) Roll out dough and cut into desired shapes. Bake on ungreased cookie sheet in preheated 375ºF oven for 10 minutes.

They came out a little soft, actually, so they didn't work too well to begin with. But I think that they will work better now that they have hardened.

Next, I made some peaches for him from some frozen peaches we have. I just steamed them and then ground them up using a baby food grinder that we got as a shower gift. I also poached a chicken breast in plain water and ground it up too. I read on the same website that babies love peaches and chicken together. I laready knew that he liked peaches, so I mixed some chicken and some peaches together in a 2:3 ratio, and he really seemed to like it! That seemed like a good way to moisten the dry chicken.

He's now able to pick up cheerios between his fingers, and put them in his mouth, chew them up, and swallow. Sometimes he gags on them but that is becoming less frequent. And, as often as not, he'll take the cheerio in his hand and move towards his mouth but miss, and the cheerio ends up in his chair or on the floor.

I also fed him some small slices of avocado. He liked them well enough, provided they weren't too big and caused him to gag. But he couldn't pick them up off his tray, because they are too slippery.

I have to admit, making baby food and feeding it to an appreciative audience is quite fulfilling. I'm looking forward to expanding his palette as he grows!

Quality vs. Quantity

I've always been more of a quantity eater. I enjoy the sensation of putting food in my mouth, chewing it up, and swallowing it. The more, the merrier, as far as I'm concerned (although there are certain flavors that I don't care for, such as green peppers, cream cheese, or coconut, which I mostly avoid).

Because of my enjoyment of quantity eating, I learned that the best way for me to lose weight is to eat large but low-calorie meals all day, and then enjoy a large, higher-calorie meal in the evening. For example, I eat a bowl of Dannon Light & Fit strawberry yogurt with rice krispies sprinkled on top for breakfast, along with a glass of water. For lunch I have a can of Campbell's healthy request soup. Then for dinner, I can basically eat whatever I want, within reason, of course. For dinner, we usually have lower-calorie versions of our high-calorie favorites. For example, I love ice cream so we eat ice cream a lot, but we eat Edy's slow-churned or Breyer's fat-free double churned, which have about 1/2-2/3 the calories of regular ice cream per serving.

I used to think that eating was all about shoveling food in your mouth, but becoming more food-aware through Weight Watchers has disabused me of that notion. Now, although I'm still a bit of a novice at it, I try to appreciate the quality of the food I'm eating too.

After I'd been on Weight Watchers for about a year or so, Jeff remarked to me that I was becoming a picky eater. No, I replied. I'm a selective eater, and there's a difference. Before I put something into my mouth, I weigh the options. Is it worth it to eat this piece of food? I have only a certain number of points* to spend today, so this food had better be worth the number of points. I need to enjoy it enough that I don't feel "eater's remorse." I need to have enough quantity of food so as to fill my stomach and stop the hunger pain. Does this food fit into my plan for the day?

Some foods, such as most vegetables, contain no points, so I can shovel them into my mouth mindlessly. Even fruit has one point per cup at most, so I can still enjoy almost as much fruit as I want without thinking. Other foods I know I don't like enough to spend points on them. For example, I never drink fruit juice, because while I do like it, it's just not worth the high number of points to me. Water isn't quite as tasty, but it's points-free. Likewise, I really don't like sandwiches very much, so I almost never eat sandwiches. It has to be a really high-quality, gourmet sandwich before I will be tempted.

It's the really delicious but really calorie-intensive stuff that I have to make decisions about. I know that for some reason, I cannot stop eating peanut M&M's once I start, so I have banned them from the house. I'll eat just about anything that's sweet, but as long as it's not peanut M&M's, I'm able to control myself.

They say that three bites of a food is enough to satisfy any craving. I think that's true, but sometimes it's hard to synchronize. Sometimes you're in the middle of eating something when you realize, you know what, I've had enough. It's hard to stop eating at that point, especially if you feel a compulsion to clean your plate, as I do. But I have had more success at stopping myself as I've become more food-aware.

I'm a professional cheapskate, so I balk at buying expensive foods. I'm a loyal purchaser of the store brands, because it's cheaper and I was taught that you're getting the same thing for a cheaper price because they don't have to pay for advertising, fancy labels, sweepstakes, etc. The thing is, I apply that logic only to foods, because I always buy brand-name laundry detergent, toilet bowl cleaner, toothpaste, etc. And in the case of those products, there really is a difference. Is my assumption that you're getting the same food product true?

So I decided, as an experiment, to see if there was a difference between cheaper and more expensive foods of the same type, and if so, whether it was worth it. For example, if you get the Campbells' Cream of Mushroom soup, it is creamier than the store brand, but we decided that it wasn't creamier enough for the price. Next I think I'd like to try brand name frozen vegetables vs. store brand frozen vegetables, and see if there is a difference.

Another related question is whether using supposedly higher-quality (and therefore more expensive) ingredients makes something taste significantly better. I made a cake using cake flour and butter rather than all-purpose flour and margarine. The cake was much fluffier and lighter, and a lot better. Since I don't bake cakes very often, and when I do, it's for a special occasion and I'd like it to be the best cake possible, I think that the extra cost of using cake flour and butter is worth it.

*Weight Watchers shorthand for mapping calories, fiber, and fat content of food to a single number.

Make Your Own Climate Model

Do you think you might have the solution to global warming? You will soon be able to test your hypothesis using state-of-the-art climate models on the web. The climate modeling tool was announced on Wednesday at the annual TeraGrid users' meeting in Madison, Wisconsin this past Wednesday. It uses the Community Climate System Model (CCSM) running on the TeraGrid (on an IBM DataStar at the San Diego Supercomputing Center) to compute, and a Condor pool (a set of heterogeneous, distributed computers from which compute time is borrowed) at Purdue for post-processing.

This is not the first, but to me it is by far the coolest looking web portal for scientific applications. GridChem is a big web portal for computational chemistry applications, and there's also a portal for neutron science, but I'm not sure of the name or status of it.

Anyhow, for more information, here's Purdue's press release.

My Colorful Life

I was inspired by a meme that my fearless sister Laura had done, writing seven things about yourself with a certain theme. So I decided to do a variation on that meme and write about seven colors in my life.

Red: I used to have the most beautiful ground-cover roses in the front yard when we lived in Illinois, and they were a deep red. I miss those roses. Red is also the color of my favorite fruit, cherries!

Yellow: When I was growing up, each person in our family was assigned a color for our coat hook, cup, toothbrush, etc. My color was yellow. Despite that fact, I still like the color yellow, and if I'm shopping and I see a bright yellow shirt I will probably buy it, if I like the style. Also, yellow is the color of my favorite flower, the sunflower. I picked a sunflower border for our dining room, which was installed by Dad and Marvis shortly after Vinny was born.

Green: I grew up in Central Kentucky, which was green and hilly. Then I lived in Illinois for seven years, which was green but flat. I spent a summer in Albuquerque, which is hilly but not green, and that helped me to realize that if I have to choose between green and hilly, I'd pick green. Luckily I now live in a place that is both. Actually, now that I'm used to the mountains, Central Kentucky seems really flat.

Blue: I grew up in Kentucky, so I'm a Wildcats fan (Go Big Blue!). I just can't get into the orange of my new state, unfortunately. Volunteer orange is a particularly hideous shade, in my opinion.

Gray: We lived in England for a year when I was 13 years old. I went to the Highworth School for Girls that school year, and we had to wear a uniform. It was particularly hideous: a gray skirt, a sky blue blouse, a mustard colored tie, and a gray v-neck pullover, with gray socks and brown or black shoes. I positively detested having to wear a uniform, and especially wearing such a hideously ugly uniform. I promised myself that after that school year was over, I would never wear gray again. So I haven't!

Rainbow: I bought a lot of work-related books with some fellowship money one year. They were all related to the work that I do, but they were on a wide variety of subjects, so I didn't quite know how best to order them on my shelf. So instead of ordering them by subject, I settled for ordering them by color. That made it easy because I tend to remember the books more by appearance than by title. Here is a picture of me from a long time ago at my office in grad school with my rainbow books in the background.

Crime and Context

What would you do if your co-worker confided in you that last night, her son had screamed in her face, scratched his sharp nails across her cheek, and kicked her in the stomach?

Well, if your co-worker was somebody like me, with an eight-month old baby, you would probably not be alarmed. If, on the other hand, her son was eighteen, you might feel a little concerned. You'd want to know more about the situation. Does her son have mental health issues? Was this attack unprecedented and unwarranted? Or did the son lash out after his mom physically attacked him first?

What a difference context makes! By itself, the act of screaming, scratching, and kicking is not a crime. (If it were, all babies would be in jail!) When it's combined with malicious intent, it's definitely a criminal act. But when it's performed under duress or under the influence of mental illness, the circumstances of the act may exonerate the perpetrator.

The idea of context is central to our legal system. That's why we have different classes of crimes for the act of killing someone. At the end of the day, the victim is still dead, but an accidental death is charged as manslaughter and carries a light sentence, while a pre-meditated execution nets the perpetrator a murder conviction and a place on death row.

In 1969, the United States Congress passed 18 USC 245 (b)(2), which made it a federal crime to target someone for their race, color, religion, or national origin, and recent pending legislation seeks to expand the existing law to cover crimes targeting someone due to gender, sexual orientation, gender identity, or disability.

The problem with crimes targeting members of a particular group is that the repercussions spread widely to include anyone who is a member of that group or even looks like they could be a member of that group. If I kill my husband, it probably won't have much of an impact on society at large, because it's just a domestic dispute. It will hurt my family, and his family, and our friends and neighbors, but it won't make husbands cower in fear at the thought of going out. If, on the other hand, I set up a sniper rifle, look for men with something glinting on their left ring finger, and shoot, and people begin to make the link between these dead men and the fact that they were targeted precisely because they are husbands, then I have just changed the dynamics of the community. Men will start to remove their rings before they go out, assuming they brave the outdoors at all. And my goal of intimidation has been met.

And that's precisely why hate crimes belong in a class of their own. They cause members of a particular group of people to feel like being themselves is hazardous to their own health. In certain cases, such as being targeted for skin color, there's really nothing that they can do about it. The men in the example above might disguise their married state by hiding their rings, but I might still be able to tell that they're married by their behavior. But the thing is, even unmarried men wouldn't be safe. The only thing required for me to target a man is that I think he's married. I might mistakenly kill a man who's not married, just because he's wearing his class ring on his left ring finger, or he's wearing a metal finger brace, or he kisses his sister (whom I mistake for his wife) on the cheek before leaving for work. So my reign of terror would extend to more than just my original target group. Now it's all men who might appear to be married who are afraid to be themselves.

I used the phrase "reign of terror" on purpose, because hate crimes are really just terrorism. They're used to intimidate groups of people into behaving in a certain way. My purely hypothetical rampage against married men would cause men to start behaving in the way that I want them to. I have the power and they don't.

When my rampage against married men finally ends and I'm being tried in front of a jury of my peers, the hate crimes legislation will come into play. Assuming that it hasn't been vetoed, that is, the legislation will now cover crimes motivated by gender, and the rampage was definitely motivated by my purely hypothetical dislike of men. After all, the law covers crimes against any group, even white, Christian men targeted for being white, Christian men. There's no kind of special privilege being afforded to minorities by hate crimes legislation, unless you count "being able to walk around and be yourself without fear of danger or death" as a special privilege. In that case, then everyone is entitled to special privilege.


For more information, I recommend reading this page from religioustolerance.org; in addition, Greta Christina had a good entry about hate crimes legislation a few weeks ago, and I also liked this explanation by Pandagon.

Adventures in Kentucky

We went to Kentucky for an extended weekend from Saturday to Monday. The main purpose of the trip was to celebrate Jeff's parents' 40th wedding anniversary, but we also found some time to spend with my dad and Marvis.

We made it to Lexington on Saturday afternoon, and had a late lunch with Dad and Marvis, who had graciously agreed to take Vinny overnight so that Jeff and I could enjoy some time alone together. We spent the afternoon walking around the campus of the University of Kentucky, and reminiscing about our time there as students. It was a lot of fun to see the old sites as well as to marvel at all the new buildings, landscaping, and renovations.

Then we went out to dinner together and we had a good time talking and just spending time together. We spent the night in a hotel and it was great to be able to sleep without worrying about being awakened. Dad and Marvis said that Vinny was his usual cheerful self the whole time we were away.

On Sunday afternoon, we headed on over to Rhonda's house to celebrate the anniversary. All the kids, their spouses, and their kids were there. I brought a cake that I had made before we left, and Jeff made a salad for the dinner. In addition, we had really delicious steak, baked potatoes, and bread. Jeff gave his dad a picture of his dad and Vinny that he had drawn, and we gave Jeff's mom a keychain digital photo frame filled with pictures of Vinny. We also gave them a card from my dad and his wife. It was a lot of fun to see everybody and get together. We'll definitely have to do it again sometime.

We spent Monday with Dad and Marvis. Marvis is a teacher and the school year is out, and Dad took a day off from work, as did I. We celebrated Father's Day a little early, and gave Dad a joint present from us and Laura, a bocce game. He had become enamored of the game which is called pétanque in France, while he was living there, but hadn't ever picked up a game of his own. Unfortunately, it was raining on and off yesterday, so we didn't get a chance to try it out.

We left Lexington at about 5:30 or 6, and at the time Vinny was asleep, but he woke up when we stopped for gas. I turned around to comfort him, became dizzy, and got a migraine. I took some of my new migraine medicine, but unfortunately it did not help at all. In fact, I still have a headache now, 24 hours later. Vinny cried for most of the way home. We stopped and fed him, but he still cried, until he eventually fell asleep. That did not help my headache any. When we got home, we fed him and I took him to bed.

Existence, Uniqueness, and Continuous Dependence on the Data

I was inspired to contribute to the Carnival of the Postdocs by Sciencewoman's theme. The theme is uniqueness, and the word immediately triggered what has become an automatic reflex for me: reciting the definition of a well-posed problem. A well-posed problem has a solution that

1. Exists,
2. Is unique, and
3. Depends continuously on the data (meaning that a small perturbation in the input results in a small perturbation in the output).

A problem is ill-posed if its solution fails to meet one or more of those criteria. A problem with a non-existent solution is boring, so it's usually problems that don't meet the second and/or third criterion that people study.

One of the major themes of my dissertation was ill-posed problems. But it could just as easily be a theme of life, not just for me, but for everybody. Do our lives depend continuously on the data, or do small perturbations result in big changes?

They say that the beating of a butterfly's wing can lead to a hurricane, and likewise, the smallest things in our lives can make a big difference. I often think of one very pivotal moment in my life, a moment that at the time seemed so mundane, a moment that wasn't really even my life's moment, but that drastically changed the trajectory of my professional life.

It was a weekday afternoon, the same as any other. Jeff was at work, taking calls about the cable modem service, and solving people's problems over the phone. He helped a man who worked at the supercomputing center on campus, and the man thanked him profusely. They got to chatting a little bit, and the customer asked Jeff about himself, and Jeff told him that his wife was a grad student in computer science at the university. The man told Jeff about an opening for a Research Assistant position at the center, and told him to encourage his wife to apply.

I applied for that job, and I got it. I didn't realize it at the time, but it was the best job I've ever had. It opened so many doors for me! The experience I acquired by doing that job made it possible for me to lose my fear of parallel computing, enabling me to apply for and use supercomputing resources for my dissertation. Ultimately, it led me to the place I am right now. If I'd never heard of that job, I wouldn't be nearly as employable as I am today. If it weren't for that job, I wouldn't have had four interviews and two job offers straight out of grad school. If it weren't for that job, I might feel less optimistic about my future at this lab, where the focus is on leadership computing. So I'm really glad that my husband just happened to be working that afternoon and took that call. Who knows where I'd be, otherwise?

I tend to think that I would have just gone in a different direction, and things would have worked out well anyhow. But this little perturbation really influenced the outcome. Life is an ill-posed problem.

What pivotal event(s) changed your life?

postdoc carnival