I’m drawn to writing with a clear purpose and logical structure: writing that places the readers’ consumption of the content above all else. When studying a technical subject, I attempt to find the clearest, most concise text(s) available. That is, I look for the book or books that will expose the roots of the area. Further, I find reading more fruitful when the text is designed to lay a foundation for a field using a line of reasoning with a concise argument or set of arguments, as opposed to a purely axiomatic or pedagogical approach.

Typically, such books are shorter than those I use for reference and much longer than a wikipedia article – they are in between. I’ve taken to calling these books “tweeners” (n., pl., pronounced tee-wieners), as in “they are be-tween-ers”. Another possible term was “t’ain’ts” (n., pl., a contracted contraction of it with ain’t), as in “t’ain’t a wikipedia article and t’ain’t a reference book”. While I prefer the equally appropriate term t’ain’t, the unfortunate (inappropriate) slang meaning justifies avoiding this collision of terminology (no link). There are also less severe collisions with “tweener”:

Let it be understood that I am not referring to a tweener, n., (1) a person capable of playing multiple positions in a sport, (2) a person that falls between two age generations, (3) a bowling form, (4) a hobbit between the ages of 20 and 32 or (5) a man that looks like a woman or vice versa.

Currently, I’m reading A.I. Khinchin’s “Mathematical Foundations of Statistical Mechanics”. It’s definitely a tweener! As far as I know, the readers (and writers) of vdov.net are a diverse group. Do you have a tweener? Are you man, woman, man that looks like a woman, woman that looks like a man or hobbit enough to share it?

For awhile now I’ve been doing distributed computing based on two major methods: the METIS graph partitioning method for decomposition and the MPI method for parallelism. Both of these techniques are well established and used extensively in many fields of computational physics, engineering and chemistry. I’ve been doing simulations in a simple mesh for a few months now. This mesh is simply a box with 200 x 200 x 200 cells. I decompose the box into 8 parts, each part to be run on a different processor using MPI as the construct to deal with processor-processor boundaries/communication. It occurred to me that the METIS method does something particularly ridiculous in this case.

If you simply break the box up into 8 pieces, the easiest possible way to do this is just to simply cut through the planes of the box. The faces of the global box do not exist on processor boundaries, as I apply boundary conditions on all these faces. Each cutting plane has 200 x 200 faces, so you don’t need a CS or math degree to know that the number of processor faces in this case would be 120,000. Is this what METIS gives you? No! It gives you 164,033 processor faces. What the hell?

Here’s a little graph of what this looks like (excuse my very quick and dirty xfig’ing). The width of the boundaries is directly related to the number of processor-processor faces between each decomposed domain.

While there is some obvious symmetry here (within a certain level of approximation), this yields far from the cleanest solution. While METIS may be fantastic for complex domains, it doesn’t do well with simple domains with obvious symmetry. Further, each domain should have a maximum of 3 processor-processor boundaries! It’s important to note here that in fact each processor has 3 major processor-processor boundaries (each node has 3 wide connections — this tell us that METIS is in fact roughly trying to get to the optical structure described above). It’s all the little connections that would be removed with some knowledge of the basic full domain structure. I understand and perhaps believe that this could all be due to some convergence criteria in the method which I am unaware of (in my reading of the papers on the subject and the code itself I haven’t found any such parameter), though still, I see no reason why some from-end part of the algorithmic implementation shouldn’t take into consideration the symmetry of the large and subdomain groups.

Cheers.

[UPDATE after the jump] (more…)

There was a time when I sort of believed the standard blogging doctrine “blog often”. I’m not exactly sure what the point of this was, other than to increase the likelihood of something you write being picked up somewhere significant. Or perhaps it was to “keep your blogging skills sharp”, if there are such things to sharpen. Recently though I’ve been subscribing to a huge number of politically influential blogs because I’ve been very engaged in this election cycle. And I have to say, regardless of what side of the isle these people come from, their work is almost exclusively terrible (there are rare exceptions).

I was reminded of a quote from way back in the day when I was first learning BSD (as introduced to me by the first Mac OS X … yes, I was a late bloomer in the grand scheme of things). From Ray & Ray’s Mac OS X Unleashed, reproduced without permission,

Caution [...] Just as some of us are safer not owning super-fast sports cars, some are less a threat to ourselves and others if we don’t have a big box of firecrackers, and some would be better off if we couldn’t buy donuts by the dozen, Unix is just too much for some people. It might be too much power, or too much flexibility, or too much information to remember, but Unix seems specifically designed to create a user who epitomizes the phrase knows just enough to be dangerous.

Each of these examples deals with “excess” in some way shape or form. While I disagree with its application to Unix for obvious reasons, it’s perfect for some of these people. Some of those to which this commentary is directed (not listed) I believe are extremely intelligent and linear in their thinking when writing through other mediums, but good lord, they all just become trivial little assholes who’d rather post off-the-cuff remarks then actually think through anything logically anymore.

Vdov.net has often published prolifically, through just as often we lag in our content production. I will no longer care if in a given month we lag … microblogging belongs at twitter.com.

Cheers.

After dinner at work last night, I met a new postdoc working down the hall from my office. I said hello, attempting to overcome my social awkwardness, and asked what type of research she does in the chemistry department. She replied “I’m an experimentalist. You, ahem, must be a theorist.” Whoa!

How in the spirit of chemistry did she know?! So I asked. She replied “I can just tell.” Baffling! Then I looked down and realized the first corollary and theorem, in my developing theory of how to not behave like a theorist (hereby termed atheorism):

Corollary 1: Chicken noodle soup shrapnel on a shirt is neither necessary nor sufficient to indicate someone is a theorist.

Theorem 1: Chicken noodle soup shrapnel on a male wearing a t-shirt that says “Visionary Women: Challenging assumptions and inspiring change” from 1993 is sufficient but not necessary to indicate the male is a theorist.

It turned out that I had forgotten to bring dining utensils with my dinner to work. Slurping Campbell’s chicken noodle soup seemed like a good idea at dinner time. Forgetfulness is also typical theorist behavior and will be a later theorem, when my sinful theorist nature catches up with me.

Sincerely,
A devoted atheorist

It’s 6:42 am, and polls opened 42 minutes ago here in Indiana. I was 5th in line at my polling place at about 5:51 am, just in time to watch the live news report and be on camera for a few minutes. This was my first primary vote, my first in-person vote in Indiana, and actually my first at-a-machine vote in history (Oregon is all vote-by-mail).

Man did they have issues. As soon as polls opened, each one of their check-in machines crashed at least 10 times. They thought it was due to high activity around the state on whatever servers run the system, but find that sort of hard to believe — it’s not as though everyone was really powering through at 6 am. Though they had tons of issues actually getting people to the polling machines themselves, once I was there, it was surprisingly smooth. Dare I say the voting experience itself was perfectly acceptable. I have no idea what types of machines they were using and my thoughts on electronic voting machines are well known, but absent these more theoretical complaints it couldn’t have gone much better.

This is probably the first election I’ve voted in where there’s some major ambiguity as to who will win (the democratic nomination). Cross your fingers everyone. Cheers.