Attitude Adjustment

Dragon Age: Origins - good, but not great

2010-01-25T12:04:00.002-05:00

Dragon Age: Origins is a single player computer role playing game (CRPG) created by Bioware and released in 2009 for PC, PS3 and Xbox 360, with an original fantasy-based setting. Dragon Age: Origins (DA:O) is very true to the Bioware house style established in Neverwinter Nights (2002), Star Wars: Knights of the Old Republic (2003), Jade Empire (2005) and Mass Effect (2008).

If you follow the computer RPG genre you already know this. You will also know that it received glowing reviews from mainstream game review sites such as Gamespot (9.5/10), Gamespy (4.5/5), X-play (5/5) and even generally very favorable mentions from Tycho of Penny Arcade. I was a big fan of NWN, SW: KOTOR, Jade Empire and Mass Effect, so I regret to say that I am somewhat disappointed in DA:O and think that it certainly didn't deserve the ratings it received. It is decent, good even, but not 9/10 great.

The remainder of this review is written under the assumption that the reader has played DA:O, or at least another Bioware game, and is familiar with the tropes of modern CRPGs.

Let me begin by itemizing DA:O strengths.

Characterization: The computer-controlled NPC companions that accompany the player's character are typically a strong feature of Bioware CRPGs, and DA:O is no exception. In addition to improved gameplay means of customising their actions (the so-called "tactics slots"), a few of the companions are simply great characters. Morrigan, Shale (from the free "Stone Prisoner" DLC), and Alastair are very well written and voice-acted. They're fun and interesting. Bioware has produced some great characters in the past (HK-54 from SW: KOTOR in particular), and I'd rank Shale and Morrigan at least as highly as HK-54. They're really one of the bright spots of this game. Contrast Bioware's advanced companion NPC AI (I emphasize the companion part of this, as other NPCs can occasionally be pretty brain-dead at the normal difficultly levels I've played so far), and the relative depth of their characterization, with that of NPC companions in Bethesda's games (Morrowind, Oblivion and Fallout 3), where companions can be more trouble than they're worth. Of course, Bioware's games are written explicitly so that you require the constant use of companion NPCs in order to have a party that includes all the standard skills, whereas Bethesda's philosophy appears to be that you should be able to complete a game solo using any play style in almost in manner you choose.
A non-D&D statistics/skill/magic system. The added power provided by spell combinations (e.g. oil + flame, or freeze/petrify + stonefist) are a nice touch, and fun too.
Distinctly different initial game play depending on chosen race and class (e.g. Dalish Elf, City Elf, Human Noble, Dwarf Commoner, Dwarf Noble, Mage) for the first hours of the game (this is the "Origins" in DA:O), with each origin story integrated into the main story. Great as far as it goes, but it probably doesn't inspire me to replay the game completely because the origins stories only account for a small fraction of total game play.

What is not so good? I'll run through them in order of increasing severity.

The inventory system is absurd. You begin with 60 inventory slots for you entire party, but note that you cannot put anything down you have picked up - you can only sell items (at a vendor) or destroy items (at any time). There is no weight or encumberance system, some items stack and some don't. Realism I think not. One often runs into situations where your inventory is full or nearly full, yet you cannot leave the area to find a vendor, and hence end up not collecting a lot of the loot available on the quest. You can buy backpacks at moderately high cost at vendors that increase you inventory size by 10. Purchasing the DLC pack "Wardens Keep" for $7 does give you a storage chest you can use to put spare items you don't want to sell/destroy in. (Some have speculated that the inventory system was deliberately hobbled in order to encourage people to purchase the DLC.) What adds salt to this wound is that Bioware's preview game, Mass Effect, was criticized in many reviews for similar reasons, namely an unwieldy inventory system with a seemingly arbitrary limits on the number of items.
Enemies suddenly spawning behind you when there is no way they physically could have done so. Time and time again you will have cleared out all enemies from some dungeon, set of rooms, or wide open field, only to have a new set of enemies suddenly appear (often from nowhere) in front and behind you. When there is no physically plausible way they could have got behind you, or sneaked up on you this is both annoying and immersion destroying, DA:O's incorporation of MMO concepts makes enemy crowd control an important part of combat, so this unrealistic and unfair envelopment in enemies is particularly galling.
Both DLC packs I've explored ("The Stone Prisoner", free with game purchase, $15 otherwise, and "Wardens Keep", $7 purchase) offer very little added story content, maybe one hour of game play each. Instead they really provide items, either a new companion character (The Stone Prisoner), or new vendors, items, skills/spells and a functioning item storage chest (Warden's Keep). The integration of the Warden's Keep into the game is particularly grating, and was rightly pilloried at Penny Arcade. Admittedly expansion packs have never been Bioware's strong point, but this focus on virtual consumerism rather than content is both disappointing and disturbing. In comparison the five Fallout 3 DLCs ($10 each, with between 3-10 hours of story content in addition to new items) produced by Bethesda now appear in contrast to be excellent value, when initially they'd seemed rather thin on content.
The side quests offered within the game are particularly weak. Many are MMO-like mindless grinding (get ten mushrooms, make ten healing potions, make ten lyrium potions, recruit three mercenaries, inform three wives of their husbands deaths, get ten corpse galls). Very few quests further develop the world DA:O supposedly takes place in, very few lead to other quests, and most take negligible time to complete (ignoring travel time). Compare this with Bethesda's approach to CRPGs, where side quests are the majority of the game play, and can form well written and developed stories of depth comparable to the main quest (in particular the guild quests in the Elder Schrolls games). In DA:O the companion characters only have minimalistic side quests associated with them, essentially throwing away character development that could have capitalized on Bioware's strength with companion characters. Alastair mentions he has a sister and would like to visit her next time we got to Denerim. Enter Denerim and have a 2 minute conversation with sister. Quest completed. Wynne mentions she feels bad about how she treated a elf apprentice who them ran off to the Dalish. Go to the Dalish. One quick conversion points you to the woods where you meet said elf, with whom you have a one minute conversation. Quest complete. Sten admits his greatest shame is that he lost his sword when his band were ambushed by Darkspawn. Go to place this happened. Get directed to another place. Get directed to another place. Enter building and retrieve sword. Quest complete. Total time, excluding the fast travel screen, maybe five minutes.
Linearity. Bioware's games are structured around small levels with set entry and exit points, separated by loading screens (which can be slowwwww... particularly in DA:O). Individual levels are often rather linear, there being only one or two possible paths from entry to exit, and DA:O is no exception to this. Small puddles of water are impassible obstacles. Woods are turned into a set of of narrow gullies, the rest being impassible terrain. Challenges within levels, in particular with "bosses", seem like they can only be solved in one way: combat employing a balanced group of companions. For example: there is little freedom in design for a rogue to act in character by sneaking about to avoid combat (e.g. unlike Oblivion or Fallout 3). Following the main story line many of the quests involve linear sets of levels: enter and clear out area A, reach exit leading to level B, clear out level B and move onto level C, rinse and repeat. With only one possible path to follow the game feels constrained, and if you have the stomach to replay the game it will replay in exactly the same way once you've got past the first few hours of the Origin story. This linearity is partially a consequence of the technical limitations of Bioware's software, but what was acceptable or understandable in 2003 seems absurdly primitive in 2009. Note that Bethesda had an fully functional 3-D open world sandbox, go anywhere, no loading screen, CRPG game in 2002 (Morrowind), and since then there have been many sandbox games from different publishers. Some technical development by Bioware in the mean time might have been nice (larger levels? less linear level design?). Not all of the blame can be laid on technical limitations, as there are a few places within DA:O that manage to provide entertaining non-linear game play. In particular the nightmare sequence in the Mage's Tower demonstrated how clever writing could provide non-linear game play within the confines of the isolated Bioware small levels system.
Lack of Engagement. DA:O fails to establish a believable world in which the main story quest inspires the player, or has any sense of urgency. It is, to be frank, a little boring. Adding more levels of tunnels full of Darkspawn to be killed, or yet another floor of a tower full of abominations, may make the game take longer to complete than previous Bioware games, but it doesn't make it more exciting. The linear level and quest design fails to make you believe that Ferelden is a real world full of real people and places that require saving: you can't explore Ferelden the way you could explore in Oblivion or Fallout 3. The limitations of Bioware's game engine make Ferelden not a world, but simply a small number of smallish areas accessible via a (not-so) fast travel map. NPCs who are not quest related have little or nothing to say - they don't even move around! More problematic is that the game's story, Ferelden being overrun by an apocalyptic Darkspawn horde coming up from the south, is critically undercut by the actual gameplay. The fast travel map attempts to show this with a dark stain covering the map that grows upward from the south as the game progresses. Great idea, but totally undercut by gameplay, as one can encounter Darkspawn in the north of Ferelden almost at the start of the game when following some of the side quests. Yet quite late in the game one can fast travel through the south of Ferelden, even past towns supposedly overrun by the Darkspawn, with only the chance of a random encounter (not necessarily with Darkspawn either). Once you've criss-crossed this area of the map ten or more times on minor side quests without consequence it becomes hard to believe in the urgency of reality of a Darkspawn invasion. People criticized Bethesda's Oblivion because one could effectively play almost the entire game while ignoring the supposed ongoing demonic invasion via Oblivion gates: the believability of main quest was essentially undercut. DA:O forces you to spend most time on the main quest (as the side quests are MMO-like junk), but with even less sense of urgency or realism than Oblivion's main story quest. But Oblivion felt like a real world: places, people and creatures outside the main quest that could be found and interacted with, and yet that seemed to have a life of their own. In Bioware's Star Wars: Knights of the Old Republic the linear game play was supplemented by the players knowledge that the Star Wars universe was in some sense bigger than just this game, and by a good story that gelled with the game so as to make the Sith threat seem real and immediate. DA:O, in contrast, sabotages the engagement and immersion necessary for a great game.

In combination these problems make Dragon Age: Origins Bioware's weakest game for many years. That is is still better than many other games out there is cold comfort. Maybe Bioware was more invested in developing Mass Effect 2 and their upcoming Star Wars MMO, but that is pure speculation on my part. DA:O's shortcomings (particularly in terms of the weaknesses of the MMO elements they incorporated into the game) certainly make me concerned about the role playing and story quality of the upcoming Star Wars MMO.

(Definitely not) the 100 greatest science fiction or fantasy novels of all time

2010-01-21T10:46:00.008-05:00

Top 10 or top 100 hundred lists are always interesting, and via io9 I came across a new list claiming to be the 100 greatest science fiction or fantasy novels of all time.

Former io9 boffin Alex Carnevale posts his selections for the top 100 science fiction and fantasy books, and it's a pretty compelling list. What do you think? Does he capture the canon? [This Recording]

As Carnevale's list features the cover art for all 100 (a nice touch) it is difficult to reproduce the list, so follow the link above to have a look at it.

How do we assess greatness? Critical response, influence on future writers, commercial success, skill as a writer, or general popularity within the reading community. Top X lists are always good fodder for argument, as subjective choices often replace the harder work of collating and assessing the quantitative criteria I have just mentioned.

Carnevale's list, in my opinion, is a classic example of an utterly subjective and badly flawed list. It might accurately represent his favorite 100 books, or 100 of the books he owns, but its idiosyncrasies, omissions and biases render it useless as an attempt to compile the best 100 speculative fiction books of all time.

What is so wrong with it?

Lets start with the omissions of historical greats. It is supposedly a list of the best science fiction of all time, remember?

There is no Jules Verne (a major influence on the field, and who wrote many great book: Journey to the Center of the Earth; From the Earth to the Moon; 20000 Leagues Under the Sea, etc etc).

How about Arthur Conan Doyle (The Lost World)? Not in the list. Yet Carnevale includes Crighton's "Jurassic Park" in his top 100, which was hardly original and only famous thanks to the special effects of the movie version.

Robert Howard not on the list. You know, the guy who created that obscure and unpopular character Conan the Barbarian.

H.G. Wells at least gets a single mention, for the "War of the Worlds". Certainly a great book, and very influential, but one might also mention "The Invisible Man"; "The Island of Dr Moreau"; "The Shape of Things to Come"; and "The Time Machine".

I might not mind a single mention per author if Carnevale stuck to single mentions per author, but he doesn't. His list is full of multiple Jack Vance, Gene Wolfe, George R.R. Martin and Heinlein mentions, quite a few Haldeman, Stephenson and Crighton books at separate rankings. Yet other good or influential authors, such as Niven or A.C. Clarke get only a single mention. (OK, Clarke was not a good writer in general, but Childhood's End was decent and if we're putting Crighton in because his stuff got turned into movies then 2001: A Space Odyssey counts too).

Speaking of the exercrable Michael Crighton, he gets mentioned for Jurassic Park and Sphere, but not The Andromeda Strain. WTF? Crighton was a terrible writer, despite his commercial success, and his characterizations (especially of scientists) were the crummy 1-dimensional cardboard cut-outs that are typical of bad SciFi (and form a valid if stereotypical criticism of the genre by outsiders). Here is Carnevale's description of Sphere (at position 85):

The slightly better book, Sphere had a really strange Barry Levinson movie. It's basically a sub movie recast as a alien movie recast as a psychological fantasy. I have always found its claustrophobic environment enhancing. Crichton's remaking of adventure novels with science fiction was prescient.

OK, I see he liked it. I think it was one of the worst pieces of dross I've had the misfortune to read: terrible characters with typical Crighton anti-scientist bigotry at full display, terrible plot, total trash.

And don't get me started on discussing why Carnevale thought to include Ayn Rand's "The Fountainhead" at number 49.

Guy Gavriel Kay makes the list twice: once for the Fionavar Tapestry (17th best in Carnevale's list!) and once for Tigana (5th!). I must admit I haven't read Tigana, but that was because I heroically read the entire Fionavar Tapestry trilogy, and it was the worst piece of stale, turgid, boring, badly-written Tolkien emulation I've had the misfortune to suffer through.

Another major problem with Carnevale's list, and strong evidence of its flawed subjectivism is the obscurity of many of the books. I don't claim to have everything ever written in the genre, but it is my favorite book genre, and I've read a lot of it over the last 25+ years. Yet I've never heard of half of the book on this list. In other top 100 or top 50 lists (e.g. this one) I've at least heard of the vast majority of the books, even when I may not have read them all.

Top 100 lists tend to be weighted toward the last few decades, and yet there are glaring omissions from this list of recent authors that are famous, popular and have positive critical reception. There is not a single Iain M. Banks book in the list (seriously, WTF!), not a single William Gibson (Neuromancer is without doubt one of the top 100 speculative fiction books of all time), not a single Greg Bear (Eon, Anvil of Stars, Queen of Angels, Infinity Concerto). Carnevale seems unaware of great or influential fantasy authors such as Keith Roberts (Pavane, admittedly semi-obscure) or David Gemmel (George R.R. Martin's recent fantasy work is refreshing gritty, but Gemmel did inspiring and gritty fantasy decades ago and certainly deserves credit for helping reinvent the field from the cheap Tolkien imitation that plagued it, ala Guy Gavriel Kay and Terry Brooks).

Commenters on Carnevale's highlight other authors worthy of mention: Terry Pratchett, Phillip Jose Farmer among them.

This is not meant as a comprehensive analysis and critique of Carnevale's list - I don't believe it worthy of more effort - but it should give you an idea of the major shortcomings of this list.

Getting to the beach early... 397 million years early.

2010-01-07T09:36:00.003-05:00

[Update 01/07/10: OK, this result is more exciting than I first appreciated. Matthew Cobb at Why Evolution is True discusses this finding in a much better way than the BBC article did]

The BBC has a nice (accessible) story about a fossil trackway from was a muddy beach dated at 397 million years ago. What is interesting it is that it appears to record the tracks of a four legged creature about 2 metres long, which is slightly older than the famous Tiktaalik fossil (from ~375 million years ago, which is not a direct ancestor of tetrapods) and quite a bit older than the classic early tetrapod Ichthyostega (from ~360 Myr before present).

Some slight re-arrangement of the timeline of when tetrapods arose is not earth-shattering, but it pushes things back a bit, and incremental improvements in knowledge are still nice (to be fair the Nature News & Views article mentioned below thinks this a big deal).

For the genuinely interested:

"Tetrapod trackways from the early Middle Devonian period of Poland", Niedźwiedzki, Nature 463, 40-41 (7 January 2010) (doi:10.1038/463040a; Published online 6 January 2010). et al, 2010,
The Nature News & Views article by Janvier & Clément discussing Niedźwiedzki etal.

The age of the previously identified Devonian tetrapod trackways (short green bars) contrasts with the 397-Myr-old Zachemie tracks identified by Niedźwiedzki and colleagues¹. These newly discovered tracks generate a mismatch between the currently accepted tree of tetrapodomorph fishes (lobe-finned fishes with internal nostrils) and its timing based on the body-fossil record (shown by solid red lines). The temporal mismatch implies the existence of long 'ghost ranges' (dashed red lines) among Devonian tetrapodomorphs. The divergence between elpistostegalian fishes and tetrapods with limbs and digits must have occurred much earlier than previously thought, perhaps during the 10-Myr-long Emsian stage, from which only few tetrapodomorph fishes are recorded. 1, Earliest articulated tetrapod skeletons with limbs and digits (Ichthyostega, Acanthostega)²; 2, earliest isolated tetrapod bones; 3, earliest tetrapodomorph fish (Kenichthys)⁵; 4, possible earlier tetrapodomorph fish⁶.

[Figure and caption from Palaeontology: Muddy tetrapod origins, Philippe Janvier & Gaël Clément, Nature 463, 40-41(7 January 2010), doi:10.1038/463040a]

Newegg versus Tigerdirect

2009-11-28T10:30:00.003-05:00

Is it just me, or do Newegg and Tigerdirect deliberately not stock the same products at the same time?

OpenCL

2009-10-07T10:48:00.002-04:00

Ryan Smith discusses the state of OpenCL support at Anandtech. Surprisingly some of the comments to his post are actually useful too.

Ardipithecus ramidus: 15 or 4,400,000 years late.

2009-10-01T14:11:00.004-04:00

Carl Zimmer (at The Loom) and Matthew Cobb (at Why Evolution is True) have nice short write-ups (with links) on Ardipithecus ramidus, our 4.4 million year old cousin.

Update: John Hawks' weblog has the most detailed runthrough and independent analysis of the Ardipithecus papers I've seen (starting here). If your interested in Ardi, this is the place to go.

Ayn Rand didn't like physics?

2009-09-16T18:40:00.000-04:00

I've been very busy with work and other functional duties, but this is worth a link.

Jonathan Chait has an excellent essay on Ayn Rand and the irrational beliefs of her followers on the political right. There is much worthy of discussion, from her bizarre upbringing and even more outlandish cult-like cliques through to her and modern conservatism's absurdly anti-factual beliefs regarding worth, work and taxation, but I'd love to follow up on this snippet of information:

(she considered the entire field of physics "corrupt")

Maybe the library will get the biographies referred to in the essay, but I doubt I'll have the time to follow up on Rand's physics hatred. After all, some of us have real work to do.

"Unix is the best screwdriver ever built"

2009-08-20T10:00:00.002-04:00

Unix is now 40 years old, if measured from August 1969 when Ken Thompson decided to spend a month while his wife was away by writing the core of what became Unix.

The BBC has a nice article by Mark Ward on Unix's history, ending with a quote

"Unix is the best screwdriver ever built," said Dr Salus.

that echoes the theme of Neal Stephenson's "In the Beginning was the Command Line" that compared Unix to a Hole Hawg drill.

Amazon MP3 downloads from Linux: clamz

2009-08-11T22:22:00.001-04:00

Amazon.com offers quite competitively priced full album DRM-free mp3 downloads. You can purchase and download individual mp3 songs without requiring additional software. But they do require you to install and use their Amazon MP3 Downloader software in order to purchase and download the albums, which are of course better value for money as long as you want most or all of the album.

To their credit they provide their software not only for MS Windows (XP and Vista) and Mac OSX (10.4 and higher), but also for Linux (Debian 4, Ubuntu 8.10, Fedora 9, OpenSUSE 11.0).

Sadly if you're using a version of Linux other than those supported you may have trouble: the Fedora 9 amazonmp3.rpm will not install under Fedora 11 (although vwbusguy provides a work-around for Fedora 10).

Luckily there is another option: a command line tool called clamz (vwbusguy has produced Fedora 11 RPMs of clamz). Attempt to purchase the mp3 album from amazon as normal and once it offers you the chance to open or save the .amz file choose "save to disk" instead. Then run clamz on the .amz file, e.g.

clamz -d ./ AmazonMP3-*.amz

If you don't use the official amazon downloader you do have to jump through some hoops to get the *.amz file that clamz uses:

Select the album you wish to purchase and click the "Buy MP3 album with 1-Click" button.
A page appears asking you to install the Amazon MP3 Downloader application, presenting links to Windows, OSX and Linux versions. At the bottom of this page is a small link saying that if you've already installed the application you need to enable it in your browser and offering a link to do so. Click that link.
You are redirected back to the web page for the album.
Click the "Buy MP3 album with 1-Click"button again.
A new window appears asking if you really want to purchase this album. Click OK.
A dialog window will appear offering options to "Open with" and "Save as". Save the *.amz file its offering you.
Go to the command line and run clamz on the amz file.
Note that you can only run clamz ONCE on any *.amz file.

One thing that is slightly worrying about this is what happens if the download fails? If Amazon thinks you've downloaded the album they wont let you download the files again.

[Updated 10/20/09.]

Coyne reviews Robert Wright's "The Evolution of God"

2009-07-28T18:29:00.001-04:00

Jerry Coyne (author of "Why Evolution is True") has a lengthy review of Robert Wright's latest book "The Evolution of God" (Amazon link).

In short: Wright cherry picks examples in an attempt to demonstrate "moral" progress mediated by historical (supposedly evolutionary) changes in (monotheistic) religions, as his previous books attempted to show progress in biological evolution towards greater complexity (and hence mankind). In short this is a classic religious attempt to ascribe purpose and direction to the Universe.

Nevertheless Coyne's review itself is worth reading.

Gemmel, Quist and Polar Shifts

2009-07-26T18:06:00.002-04:00

Fans of British fantasy novels will no doubt remember David Gemmell as being one of the biggest names in fantasy writing between the mid-1980's and his untimely death from heart disease in 2006.

Gemmell's books were a breath of fresh air in the late 80's, washing away the stale Tolkien-imitation that seemed to dominate the field and replacing it with gritty tales of flawed heros, often hopeless odds, and major characters often dying. Sadly, the more books Gemmel wrote the more formulaic this style became.

One re-occurring theme Gemmell used to tie together the different series of his earlier books was of periodic catastrophes that shifted the Earth's rotation, drowning continents and emptying seas. At the time I read his books I assumed these ideas (absurd, but good fodder for fantasy) were Gemmell's own adaptation of Velikovsky's catastrophism, but most of the Polar Shift concepts used in Gemmell's work appear directly taken from Charles Hapgood's "Maps of the Ancient Sea Kings: Evidence of Advanced Civilization in the Ice Age."

The reason I now know this is John McKay's excellent post on Allan Quist's hilarious attempt to disprove global climate change by claiming that ancient maps show an ice-free Antarctica based on Hapgood's work.

numpy/scipy

2009-07-06T18:17:00.005-04:00

The more I use numpy and scipy the more I like them. Matplotlib has some quirks, but all in all its easy to quickly write something powerful that just works.

Update (09 July 2009): That said, I am surprised at how simplistic the fitting routines (aka optimization, minimization, etc) are in scipy, and the lack of good generalized fitting packages in python. Its all very well if you want to use the routines provided in scipy.optimize and uncertainties in your data aren't a big issue but that's not at all the realm of data I experience daily.

It may be that scipy.optimize's routines can handle data uncertainties properly through some more complicated interface, but all the examples I've seen don't seem to suggest that as they all totally ignore data errors. Nor do they mention even simple fitting concepts like chi squared (I'd survive with chi squared, I don't need log likelihood all the time).

Update (10 July 2009): OK, you can handle data uncertainties using the scipy.optimize routines, you just make sure the function you want to minimize calculates chi squared or log likelihood, and you effectively have chi^2 fitting or Cash statistic fitting. I haven't yet worked out how to calculate the uncertainties on the fit parameters using scipy.optimize -- the most naive way is to use the covariance matrix (not robust, I know).

Space Telescope's stsci_python provides pytools.nmpfit (a numpy version of python mpfit, itself a version of IDL mpfit). This does Levenberg-Marquardt fitting and does provide estimates of the best-fit parameter uncertainties (using the covariance matrix). After giving it a spin I find it works just as well as scipy.optimize, although at the cost of having to install the entire stsci_python package. More interestingly (n)mpfit has a well developed interface for fixing (and unfixing) fit parameters as well as handling limits on the fit parameters. I ended up using this for the HST ACS data analysis routines I'm writing. Still, none of these approach the sophistication of xspec or sherpa. If it weren't for the huge size of these packages I'd try to link to these behemoths (well, sherpa anyway, as it has a python interface), but I'm trying to (a) use more generalized packages, (b) wean myself away from relying on the same software I've used for years and learn something new...

This Cat is Awesome!

2009-07-05T18:13:00.002-04:00

Pet Jungle Cat (NSFW).

[Original "Cat... is Awesome" from Zooillogix]

Fedora 11: Why force beta versions of Firefox and Thunderbird on users?

2009-06-29T17:29:00.002-04:00

Another thing I really dislike about Fedora 11 is the decision to replace the stable versions of Firefox 3 and Thunderbird 2 present in Fedora 10 with beta versions of Firefox 3.5 and Thunderbird 3 in Fedora 11. I'm certainly not the only one who doesn't like it.

This statement (in bold) features prominently in the Thunderbird 3 Beta 2 release notes:

Please do not use Thunderbird 3 Beta 2 in a production environment.

Yet the FESCo went ahead and approved putting the beta in the full release (this is not Rawhide we're talking about).

I haven't had any trouble (yet) with Thunderbird 3b2, but I'm already frustrated after only two days experience with Firefox 3.5 beta 4: page loading will occasionally randomly hang for no obvious reason, in a few cases so badly that I've even been forced to kill -9 the browser. And its only been two days!

Of course, criticism of the decision to put betas in the official distribution generates snarky comments from some people (the full thread is worth reading):

2009/5/11 Stephen Gallagher :
> OK, first off, why in $DEITY's name are we including Firefox 3.5b4 and
> Thunderbird 3.0b2 in Fedora 11?

These were planned features waaaaay back.

http://fedoraproject.org/wiki/Features/Thunderbird_3
http://fedoraproject.org/wiki/Features/Firefox_3.1

I don't recall you raising your objection at the time. Both have had
considerable review by FESCO and others so please don't complain about
this so late in the day.

--
Christopher Brown

There are some people think that being cutting edge is synonymous with including beta beta versions of software in official OS releases (e.g. see the /bin/bash blog's overly glowing preview of Fedora 11 written before its official release), but I am not one of them.

Betas are fine in rawhide versions, but only if there is a real possibility of the full non-beta version being available in time for the full Fedora release, and the ability to revert to a older stable version if the beta is still beta - yet these are the contingency plans presented to and accepted by the Fedora FESCo:

Thunderbird 3:
Contingency Plan
There is no turning back.

Firefox 3.5:
Contingency Plan
There is no turning back.

Ah well, I'm sure its just as bad over in Ubuntu or Gentoo land...

Fedora 10 -> Fedora 11 upgrade problems

2009-06-26T21:03:00.001-04:00

After the last debacle [1, 2] associated with trying a yum upgrade from Fedora 9 to Fedora 10 on my x86_64 Opteron workstation I was sure that this time would be different. I dutifully downloaded and burned a x86_64 installation disk for my Opteron and a i686 for my old home PC.

Neither upgrade worked properly.

I had not run yum update on my home Fedora 10 machine since Fedora 11 was released on June 9 2009. I attempted the DVD upgrade on June 19, left it happily (if slowly) updating the ~1200 packages it wanted to update, only the return to a fatal error message regarding an unhandled exception. On reboot a single Fedora 11 kernel was available which started booting but failed when trying to go to runlevel 5. Reading the Common F11 bugs page indicated that my nvidia AGP card might be the problem, so modifying the kernel boot options as suggested allowed me to boot successfully. A large "yum update" (1.2 GB) was then necessary, but I finally had a working system.

For the Opteron I made sure my Fedora 10 installation was fully updated on the morning of 23rd June, and just before leaving working in the evening I stuck the DVD in the drive, hit the upgrade option when it appeared and left it running overnight. When I returned the upgrade claimed to have completed itself successfully and told me to reboot.

On rebooting grub went straight to a empty command line, without the usual boot menu. Clearly the grub-install that is run every time you update the kernel had not run successfully. As I know /boot is the first partition on my first hard drive I can still find the kernel and boot by doing the following on the grub command line:

root (hd0,0)
kernel /vmlin[hit tab] [select appropriate file] [return]
initrd /initrd[hit tab] [select appropriate file] [return]
boot

I did not use the standard Fedora kernel options "rhgb quiet" as I wanted to watch the services start up to see if there were any problems. Indeed, once the kernel started booting I saw that a variety of services where failing to start, complaining of shared library problems. A classic sign of a incomplete upgrade. Great!

In fact the boot process stalled completely, so I resorted to using the Fedora 11 disk in rescue mode. chrooting into the system once it had booted.

I checked that /boot/grub/grub.conf looked sensible, ran "grub-install /dev/sda" fix the grub problem, and then attempted "yum list updates", only to find that yum wouldn't run as python complained that it could not find the yum module.

"rpm -qa | grep yum" revealed that yum was still a Fedora 10 version, version 3.23. Mounting the Fedora 11 disk (mount -t iso9660 /dev/scd0 /media) revealed that the yum version on the Fedora 11 install disk is 3.22, so clearly the upgrade had failed to update yum because the recently updated Fedora 10 version had a higher version number than the Fedora 11 disk created only a few weeks before! In fact a large number of packages had not been updated to Fedora 11. Luckily rpm had been updated (if rpm was not working I'd have been forced to do a full system restore). Running

rpm -Uvh /media/Packages/yum* --oldpackage

successfully updated yum to the Fedora 11 version, at which point I could run "yum update" and start the process of getting a truly upgrading system underway.

With hindsight my mistake was updating my Fedora 10 system after Fedora 11 had been released. When doing yum upgrades it is a good idea to have your system as closely matching the new version of Fedora as possible, but this appears not to be the case for a DVD-based upgrade.

I'm still surprised that the DVD-based Fedora upgrade doesn't think to correct for version mismatches - you'd think it'd be logical for any f11 package to automatically obsolete a f10 package, even if the version numbers of the f10 package are higher. Or the upgrade could simple run rpm with the "--oldpackage" command line option.

Overall I have little satisfaction with the upgrading process under recent versions of Fedora. Web-based yum upgrades used to work very well, at least between versions ~6 and 8, but with Fedora 9 -> 10 and now with Fedora 10 -> 11 neither web-based or disk based upgrades has worked without significant problems.

Admittedly I've also experienced occasional severe problems with upgrades between different versions of Ubuntu when I was experimenting with it, so this is not a problem unique to Fedora.

The alternative - moving to a long-lifespan distribution such as RHEL or a free clone of it like Scientific Linux - simply replaces upgrade problems with equally severe out-of-date software problems (a friend who relies of the department's sysadmins to maintain his Scientific Linux distribution has had terrible problems with being stuck with old buggy versions of important software that require major version changes to fix, which the standard updates in RHEL/SL don't often do).

The only pro-active solution I can see is to become more involved with testing process on Fedora, and to have a dedicated test machine that I can easily revert to its original state when upgrade tests fail badly.

Missing printers with Firefox 3 and linux.

2009-06-26T18:01:00.001-04:00

The Problem: All printing options except "Print to File" have disappeared from the print dialog box in Firefox 3 under Linux. Yet inspection of the print configuration options in about:config reveals no obvious changes and furthermore values related to the expected printers are present.

Crude Fix: Add the following line in /etc/gtk-2.0/gtkrc

gtk-print-backends = "lpr,file"

This will give access to very minimals command line interface to lpr, which means you must know the printer names and options you wish to invoke. Another fine example of of newer Linux software sacrificing core functionality for superficial improvements in other areas.

[From my "Random Unix and Linux tips and tricks" page]

Wolverine Returns!

2009-06-19T17:57:00.000-04:00

Interesting NYT article by Cornelia Dean: "After 90 Years, the Wolverine (Just One) Returns to Colorado."

[Wolverine image from the National Geographic website]

Who knew that echidnas were so interesting?

2009-06-12T09:58:00.007-04:00

The NYT has a nice article by Natalie Angier on the long-beaked echidna, Zaglossus bartoni.

You may be forgiven for considering one of the three remaining groups of egg-laying mammals as "primitive", yet they're anything but.

They lay eggs but feed the babies ("puggles") with an iron-enriched pinkish milk that emerges from chest glands rather than teats.
They have multiple sex chromosomes, not just the X and Y chromosomes found in placental mammals.
They have a bird/reptile-like cloaca through which excretion, sex and egg-laying is performed...
...and male echidnas extrude their four-headed penis through this cloacal opening.
They have long lifespans of up to 45 years in the wild.

Sadly these fascinating and poorly-understood animals are endangered.

More long-beaked echidna information can be found at animalinfo.org. (I'm note sure why the Latin name of the species seems to be different on the Animal Info website.)

Leon Kass

2009-06-04T18:02:00.000-04:00

If the name Leon Kass means anything to you, and you can master your repugnance, then read these articles:

Tough Love for the Humanities, by Serena Golden, 2009, Inside Higher Ed (News).

Kass Backwards, by Scott McLemee, 2009, Inside Higher Ed (Views).

Which amusing prompts various right-leaning crotchety academics to come out complaining how nasty, left-wing, and authoritarian academia is, and also to demonstrate how little they understand when they claim people have not understood Kass's "Wisdom Of Repugnance".

Reason as Our Guide, Elizabeth Blackburn & Janet Rowley, 2004, PLoS Biology 2(4): e116. doi:10.1371/journal.pbio.0020116.

Clarifying The President's Council's Clarification of the Obama Stem Cell Policy, Insoo Hyun, Bioethics Forum (thehastingscenter.org), 2009.

Calling C++ from Fortran 90

2009-06-03T14:49:00.002-04:00

Calling Fortran 90 from C++: not too terribly difficult although character strings are a pain.

Calling C++ from Fortran 90: Rather more complicated if you're not going to use pre-written interface-generating software. Best summary of the information you'll need I've found so far is this conference proceeding by Wang et al (2005), see also their ppt presentation.

Yang Wang, Raghurama Reddy, Roberto Gomez, Junwoo Lim, Sergiu Sanielevici, Jaideep Ray, James Sutherland5and Jackie Chen, 2005, "A General Approach to Creating Fortran Interface for C++ Application Libraries", in Current Trends in High Performance Computing and Its Applications, (Springer Berlin Heidelberg), 145-154, DOI 10.1007/3-540-27912-1_14

Tortured analogy

2009-05-06T08:54:00.001-04:00

Embattled Conservatives Look To Star Wars For Guidance [io9.com].

Items of note

2009-04-30T18:42:00.000-04:00

I've been busy starting up a new research project that I intend to present results from at the end of May, so I haven't had time to blog much, but here are a variety of small things that attracted my attention.

I was pleasantly surprised to find that the awesome doxygen source code documentation tool is now even more awesome: starting from version 1.5.5 it can now be used with Fortran! WRITE(6,'(A)') 'Praise the Parser!'

Speaking of programming: Intelligent Design Sort - it never gets old - praise the Sorter!

Pascal Boyer admits he has a problem: he is really interested in crackpots. Admittedly crackpots are a fascinating, if understudied, from a sociological point, but Boyer attempts to remedy this with his analysis of the group. He reproduces the well-known finding that a large fraction of crackpots have engineering backgrounds, but he does make some valid points (that appear obvious in hindsight, as all good analyses should), in particular: "the crackpot alternative is, almost universally, less mathematically challenging than the standard account" and "The crackpot theory is based on textbooks" with no exposure or understanding of actual research literature.

While we're on the subject of cranks, I must admit that I view most flavors of libertarianism with scorn, so I have a soft spot for those uncivil bloggers who ridicule it: Gavin M. over at Sadly, No! dissects Glenn Reynolds's libertarian conservatism and finds feudalism.

Still on the subject of cranks, PFAW dissect Orson Scott Card's absurdist bigotry using the scalpel of sarcasm.
http://www.rightwingwatch.org/content/does-national-organization-marriage-want-overthrow-government
I still do not understand why people think "Ender's Game" was great.

Finally dispensing with the crank theme, and moving onto more serious stuff (although with a Speculative Fiction flavor), I could not agree more with the following argument (hat tip io9):

"But the one—the most absolutely key, the rock star green technology—that I champion over all others is birth control: vasectomies, IUDs, the pill, condoms. I don't care which kind you or your family prefers or finds most appropriate, I love them all. Any technology that reduces the absolute number of consumers (and particularly Americans and Europeans who consume the most) now that's a TECHNOLOGY!" — Pump Six And Other Stories author Paolo Bacigalupi, interviewed at EcoGeek.org.

If you, like me, had not previously heard of this Stanley Fish guy the NYT has added to their Opinion section, this (rather old) Slate article "The Indefensible Stanley Fish" by Judith Shulevitz will provide you with some useful background information. (Note clever segue from Speculative Fiction to tedious postmodernist analysis of Fiction.)

Finally some science! Evidence of forethought in Chimpanzees: Ed Yong at Not Exactly Rocket Science nicely summarizes the story of Santino the Chimp's premeditated ammunition collection for later attacks on Zoo visitors.

NPR

2009-04-05T13:41:00.002-04:00

This article at Daily Kos sums up many of the reasons why I haven't bothered listening to NPR since 2004 - their excessive reliance on talking heads from (mainly right wing) Think Tanks, and their credulous acceptance of whatever the pundits say.

Game AI

2009-03-31T19:41:00.004-04:00

The guys at Penny Arcade were referring to Wanted: Weapons of Fate when they created this comic, but it sadly applies to most game AIs.

My favourite example of this (and I don't mean that in a sarcastic way) are the mercenaries in Far Cry 2 who camp out by the gas (petrol) stations. One shot at a pump, and Oh the humanity!

Fedora upgrade problems solved?

2009-03-31T10:13:00.003-04:00

Just to follow up from last week's post on my problems upgrading my x86_64 workstation to Fedora 10, I think I now have everything fully functional once again.

The booting/grub problems were definitely related to grub's attempted probing for a floppy drive (/var/log/messages will show kernel I/O errors associated with fd0), even though I've never had a floppy drive in the system and it had never caused a problem before. It appears this is not an uncommon problem, see e.g. here and here, but its not obvious why I'd only experience this now with Fedora 9 an 10.

The command line workaround (install grub to the MBR using the grub shell with "grub --no-floppy," setup (hd0,0), etc, instead of using grub-install) is not ideal as it appears that any kernel update (e.g. when updating the system after a DVD upgrade) will run grub-install itself and fall foul of the problem.

In the end I had to switch off floppy support completely in the BIOS (even though no floppy drive or any associated cabels were present in my system) to solve this problem.

Upgrading from Fedora 8 -> Fedora 9, and then Fedora 9 -> Fedora 10 using the x86_64 DVD install/upgrade disks ultimately worked, in a fashion, but displayed some annoying features that reminded me why I switched to the yum upgrade method before.

The problem is that after "upgrading" and rebooting I found many packages (indeed, the majority) had not been updated to Fedora 9. I presume the reason is that a fully up-to-date Federa 8 system has packages that are more recent, with higher version numbers, than the original Fedora 9 DVD distribution, and that the DVD upgrade process then does not replace the fc8 packages with the fc9 packages.

I had to run "yum update" at least twice (why twice? I don't know why it didn't pick up all the packages that needed updating the first time) before the older Fedora 8 packages were replaced with normal fc9 packages. Even with a fast internet connection updating > 1000 packages takes a full day or so. I then had the same problem with Fedora 9 -> Fedora 10, where the situation was so bad that after the basic DVD upgrade firefox and konqueror simply didn't work at all. Then yet another day waiting for "yum update" to complete.

I did discover some useful yum tips here, in particular how to force yum-fastestmirror to retest the mirror speeds without doing "yum clean all." (Important if you've just spent several hours downloading hundreds of packages, but they haven't yet been installed before the transaction check found a problem, and you need to download more but the once-fast mirror you were downloading from is now incredibly slow.)

The update process was exacerbated by some odd changes the DVD upgrade made to my networking setup that basically messed up /etc/resolv.conf and my DNS configuration. It took me a while to work out that the "Error: Cannot find a valid baseurl for repo: fedora" was basically a DNS/dhclient problem. I don't remember DVD upgrades messing with network settings before, so I'm not sure how or why this happened.

To add insult to injury my rsync backup scripts then no longer worked because the newly installed Gvfs (specificaly ~/.gvfs) breaks rsync. The work-around is to add .gvfs to the rsync excludefile, but what a pain!

All in all a very tiring upgrade process, and all the more annoying because the exact same upgrades for i386/i686 work fine on my other machines. I presume part of the problem, in particular with the DVD upgrade, was leaving the upgrade so late after Fedora 9 and Fedora 10 had come out, so I may upgrade the x86_64 workstation to Fedora 11 relatively soon after it comes out. But on the other hand I don't like to upgrade to a new Fedora version before some of the kinks in the new version are worked out...

Fedora upgrade problems

2009-03-27T10:55:00.002-04:00

I've been having a lot of trouble with my main workstation this week, brought on by an attempted yum upgrade from Fedora 8 x86_64 to Fedora 10 x86_64, but probably complicated by hardware problems associated with the floppy drive (or lack of it, to be more precise) that then messed up (and continue to mess up) the grub bootloader.

I had to do a full system restore yesterday from my incremental rsync backups (which worked wonderfully), but I'm still struggling with the system and was forced to do a rpm database rebuild this morning. The DVD-based Fedora 9 upgrade I set running last night, although supposedly successful, in truth failed thanks to grub-install's (which seems to be run whenever you install a new kernel) insistence on probing for a floppy drive even when there isn't one present and even when the device.map correctly excludes fd0 (note that recent versions of grub-install do not have or honor a --no-floppy command line option, despite what people on the Internet seem to think). Attempts to run grub-install from the command line simply hang, and /var/log/messages starts showing kernel I/O errors associated with fd0 (which I'm pretty sure I dont have!).

The messed up Fedora 9 install also seem to have messed up rpm, as on booting I found that even simple rpm queries would hang and /var/lib/rpm/ had the classic __db* files.

Still, looking on the bright side it has been a good test of my linux sysadmin knowledge.

My rsync backup method (based on Mike Rubel's incremental rsync backup with hard links method described here, see also Kevin Korb's page on rsync backups) works well and restore's easily. Note that the method's Rubel and Korb describe don't quite work on my system as rsync can't handle the number of files of my system in one go - I basically run the method by script separately on each of /boot /bin /etc /home /var etc etc).

I still remember how to use the grub command line to find files and boot, even if grub.conf is totally messed up, and I've learnt (the hard way) that grub-install can't quite be trusted and that its better to use the grub shell to install grub to the MBR (Remember to use "grub --no-floppy" to prevent probing for a floppy, even if you dont have on).

The annoying rpm stale locks and corrupted rpm database thing can be fixed ... "rpm -vv -rebuilddb" worked, thankfully.

I'm still surprised that the basic yum upgrade failed, as I've done yum upgrades from Fedora 8 directly to Fedora 10 successfully before, although only with i686 systems and not an x86_64 system. Based on the error messages I experienced it seems that /usr/lib64/libc.so.6 is the problem child in the jump from Fedora 8 to Fedora 10. I really should have done Fedora 8 -> Fedora 9 -> Fedora 10, or burnt myself an upgrade DVD and done a DVD-based upgrade.

That the DVD upgrade from my recovered Fedora 8 system to Fedora 9 also failed (because of the grub/fd0 problem) does suggest that a classic DVD upgrade, and not doing a yum upgrade would not have prevented me from experiencing problems (although it might have saved me a full days work). However I do find it hard to believe two separate problems, one software and one hardware related, would appear simultaneously.

I'm still waiting for the Fedora 9 yum update to finish before I shutdown and go poking inside the machine to see if I can find out what is causing my floppy drive problems. Without solving that issue there is no point attempting to upgrade to Fedora 10...

Anyway, time will tell whether I can get the system safely upgraded to Fedora 10.

Dyson

2009-03-26T18:45:00.001-04:00

The NYT magazine covers Freeman Dyson in a multi-page article by Nicholas Dawidoff: "The Civil Heretic." Sadly the elderly Dyson is now more famous for his current climate change contrarianism than his more interesting earlier work, or even the fun but speculative stuff like Dyson Spheres or Project Orion.

This prompted Andrew Revkin to produce a somewhat more nuanced discussion of Dyson on his Dot Earth blog: "Some Inconvenient Thinkers", although it annoyingly stops short of actually discussing why Dyson is wrong, and instead pretty falls into modern journalism's classic statement of false objectivity: "He might be right, he might be wrong. What do you think?"

Climate Progress (who really seem to dislike Revkin despite the fact he's generally does a decent job of covering science and climate change - he's certainly infinitely better than Tierney) then produced a rather uncivil blog article pointing out how Dyson has been far from civil when discussing actual qualified climate scientists. Although uncivil, it at least has some discussion of why Dyson's beliefs are simply absurd, and links to Only In It For The Gold's calmer explanation of Dyson's mistakes.

Ultimately I think Dyson's contrarianism is not as harmful as many of the other climate change contrarians, largely because Dyson's rejection of climate change are not driven by political or economic biases, but rather a mistaken belief in his scientific ability. Its somewhat sad to see once great scientists go off the deep end when they get old. Some, like Fred Hoyle, go off the deep end even before they get old.

Non-Tweetle Beetle Battle

2009-03-26T10:35:00.003-04:00

Nicholas Wade at the NYT has a nice article about the often extravagant results of sexual selection, which as accompanied by a beautiful slide show of beetle horns. Worth a look!

Why am I reading the NYT science section during work hours? Because I have to do something educational while I wait for my full system restore on my workstation to complete (recovering from a tragically failed upgrade to Fedora 10 x86_64 from Fedora 8).

Cephalopods, Old and New

2009-03-19T18:01:00.000-04:00

PZ Myers at Pharyngula discusses some spectacularly preserved 95 million year old fossil octupuses from Lebanon. Although superficially similar to modern octopuses in external appearance (8 tentacles and all that stuff) the structure of the their gladius (the remnant of the molluscan shell) is intermediate between older cephalopods and modern octopuses.

Ed Yong at Not Exactly Rocket Science discusses what the stomach contents of Sperm Whales can tell us about large deep-sea squid (including Giant Squid) and octupuses. ¹³C to ¹²C isotope ratios in the undigested squid/octopus beaks tell you about the depth at which the animals live, while ¹⁵N to ¹⁴N ratios tell you its position on the food chain.

[Image of scientists examining whale stomach contents from a whale that stranded itself come from Karen Evans's web page.]

Why subsidizing Solar power makes sense

2009-03-17T08:14:00.003-04:00

George Musser defends himself against claims that he is a "freeloader" for installing state-subsidized Solar panels on his home over at SciAm.

I wonder if the reader who accused him of being a freeloader also calls farmers, or the coal and oil industry, freeloaders as they are also very heavily subsidized by the taxpayer?

Sustainability

2009-03-10T08:15:00.003-04:00

SciAm has a short but interesting article by Michael Lemonick on the "Top 10 Myths about Sustainability":

Myth 1: Nobody knows what sustainability really means.
Myth 2: Sustainability is all about the environment.
Myth 3: “Sustainable” is a synonym for “green.”
Myth 4: It’s all about recycling.
Myth 5: Sustainability is too expensive.
Myth 6: Sustainability means lowering our standard of living.
Myth 7: Consumer choices and grassroots activism, not government intervention, offer the fastest, most efficient routes to sustainability.
Myth 8: New technology is always the answer.
Myth 9: Sustainability is ultimately a population problem.
Myth 10: Once you understand the concept, living sustainably is a breeze to figure out.

[Trash image from: http://farm1.static.flickr.com/129/319298351_724779cb39_b.jpg]

Please go Galt.

2009-03-07T12:50:00.003-05:00

Hilzoy at Obsidian Wings urges conservatives to do what they've started threatening to do: go Galt. I wish they would.

Hilzoy expresses (mock) puzzlement that none of them seem to have acted on the beliefs they're so eager insist are correct, rational and "objective". Its pretty obvious why they only threaten to go Galt, but never do so.

If they all did go Galt society would continue as well if not better than before, so the glorious social experiment would only serve to demolish the sophomoric fantasy they use to justify their greed and lack of compassion.

OSX Leopard: What is the /home directory for?

2009-03-06T21:41:00.002-05:00

What is the /home directory in OSX 10.5 for? It appears to be:

Empty.
Created or last modified when the machine last booted up, with user.group of root.wheel (this differs from /Users which is root.admin).
Impossible to copy to, even as root. You just get "Input/output error".

I was trying to change the default user home directory location on my Macbook from /Users/<username> to /home/<username>, so as match Linux and simply rsyncing between my linux boxes and the macbook, using one of the following methods described on macosxhints (1 , 2 ). (They were not trying to use /home but move the home directories to a separate volume.)

I can't find any mention of "/home" and OSX anywhere on the web, and leaving off the / just gives articles talking about /Users/. BSD seems to use /home (just like a sensible *nix), so I doubt its a BSD versus Linux thing.

Macports?

2009-03-06T15:46:00.001-05:00

I see scipy is available under Macports. Doubt is setting in. Maybe I shouldn't have gone with fink.

I wish I had a transparent skull...

2009-02-24T10:46:00.003-05:00

...just like the barreleyes fish (Macropinna microstoma).

Not sure what I'd do with such an arrangement, but it'd still be pretty cool.

Full reference: Robison BH, Reisenbichler KR (2008) Macropinna microstoma and the Paradox of Its Tubular Eyes. Copeia 2008(4):780-784.

Unprecedented investment opportunity!

2009-02-20T09:33:00.002-05:00

I met with my financial advisor yesterday for the first time in about three months. He looked tired, as he'd probably been dealing every client asking him the same question I did: "Tell me why I shouldn't take all my investments out and hide it in my mattress before it loses another 35% of its value..."

He did a reasonable job of explaining that the current value of the shares is not what is important if you're planning on using the money for retirement in 25 years, that buying cheap and continuing to buy cheap should in the long run pay off as those shares regain their value at some point in the future. That getting out now and then trying to get back in when things appear to get better would also directly translate into a significant loss, worse than staying in and not messing with them.

All well and good. "Think of it as an unprecendented investment opportunity." he said. "When are you ever going to be able to buy shares this cheaply?" I certainly appreciated the valiant attempt at optimism, even if I didn't quite feel it myself.

"The market is going to come back, eventually... The only way it won't increase beyond its former levels is if you think the World's already achieved maximum productivity and maximum growth." A decent enough point, although I immediately thought "Oh oh. Peak Oil. Global Climate Change."

So how long is it going to take? The wall of his conference room had a log-linear graph of the return on $1 invested in 1920 in various different ways, stock market, federal bonds, bank savings account (maybe). The Great Depression was visible as an order of magnitude drop in value that took about a decade to recover to its former value (and that only really associated with the economic growth associated with the US's waging of WWII). Paul Krugman had an editorial yesterday (2/19/09) that again argues that demand will ultimately drive recovery, but not before 2011 and maybe in 5 to 10 years.

Rational reasons to believe it will ultimately get better eventually are perhaps all we ask for now.

pdffonts, updmap, epstopdf and ps2pdf

2009-02-20T09:05:00.003-05:00

The occasion of the U.S. National Academy of Sciences "Astro2010" Decadal Survey of Astronomy and Astrophysics has forced me to (re)confront the issue of font embedding in PDF documents produced with LaTeX.

The last time I did this was about five years ago for various NASA ROSES proposals (ATP, the now defunct LTSA, etc) and it was something of a messy process. Which font package to use, what dvips command line options to use to make the postscript file, and then what ps2pdf command line options to use, etc etc.

Nowadays its much easier to produce high quality PDFs from latex source, thanks to pdflatex, and I'd assumed all fonts ended up being embedded properly automatically now. But in writing my Astro2010 White Paper I ended up discovering the very useful pdffonts tool, which in turn informed me that all my fonts where not being embedded. In the process of solving that I got to learn about updmap (not actually the source of the problem, as its correctly set up in Fedora 8 and 10) before realizing the problem was with my figures.

I still produce and include EPS figures, relying on the latex epstopdf package to automatically convert the figures to PDF for pdflatex. Turns out epstopdf (the command line tool used by the epstopdf latex package) does not correctly embed the fonts when coverting the EPS files, so thats where the problem was. The command line ps2pdf tool does embed the fonts, but only when you use the -dPDFX command line option (-dEmbedAllFonts does not work!).

Anyway, all this is now documented on my Unix tips and tricks site.

Things fall apart (latex2html, tth, webalizer)

2009-02-03T23:01:00.001-05:00

Things fall apart; the centre cannot hold;
Mere anarchy is loosed upon the world,

Yeats -- The Second Coming

Much too busy to spend much time posting except on this (now cold) coffee break, but this line from Yeats summarizes my current feelings about software.

I have recently had sudden need to covert a LaTeX document to HTML, only to discover that the old standard latex2html hasn't been maintained or updated for many years. It used to work well... but my current pdflatex-friendly documents cause latex2html to fail spectacularly. It seems to reserve special hate for \newcommand (which I now use a lot in place of the older \def). Even removing all the \newcommands results in half of the equations being totally mangled.

A desperate search for a equation-friendly replacement did yield a fully acceptable solution either. The best of the bunch seems to be TtH, but even that doesn't handle my document's fairely pedestrian equations properly, nor does it handle images properly given that I'm using the epstopdf package. Argh!

After hours of pulling my hair out over the weekend I decided to forget about HTML completely and just post a link to a PDF. In the process of doing that I discovered that my Apache was not playing nice with webalizer anymore (I want to easily see who accesses the document, you see), despite the configs supposedly allowing me to view the webalizer output. It used to work... Sigh. No time to hunt down and fix the problem either.

XFCE4 impresses, Amarok 2 fails.

2009-01-28T16:34:00.000-05:00

Still in the process of switching to XFCE4 as the window manager of every Linux machine I own (six machines, counting both work and personal machines), but I'm getting the process of customizing it quickly to my liking down to an art. The more I use it the more I like it, or the more I can make it look and act like KDE 3.5 (only seemingly more responsive).

I also worked out how to get ssh-add to start when the XFCE desktop comes up, slightly different from autostarting processes on KDE.

I only just realized Amarok has changed as well, as we now have Amarok 2 on Fedora 10. As with other KDE4 rewrites of well established KDE tools this is sadly another great step backwards in terms of functionality, despite the standard claims of "significant improvements". Not only has the iTunes-like playlist interface totally disappeared but the customization options are severly restricted compared to the old KDE 3.5 Amarok (just go to Settings -> Configure Amarok and take a look at the barren emptiness). You can right-click to add KDE4's totally awesome Plasmoids, but none of the ones available on Fedora 10's version of Amarok 2 add back the basic playlist/tracklist functionality we've lost.

I do not appear to be the only naysayer either. Add to that the fact that it can't resume playback if you pause playing, and you can appreciate why I'm less than impressed. I may have to switch music players completely.

I hate acting like the Grinch, continually criticizing KDE4 and its developer's ernest belief that their hard effort was producing an improved product. Yet too much of KDE4 has basic functionality missing (despite the fact that they clearly had the time to add new and unnecessary eye-candy) for me to continue with it.

I may have said this before, but I'll say it again. I can understand the motivation for a complete rewrite of some code when the existing code becomes too difficult to extend or add to. There are strong pragmatic reasons to embark upon such a project. But with KDE4, as with Gnome 2 years ago, you end up getting the impression that the developers were more interesting in add fancy new things (Plasmoids) than in recapturing the basic functionality of the older versions. If your new application can't recapture the core of the old application then it'd be better to call it something completely different, rather than adverstise it as "a new and improved" version of the old application.

Its a year since KDE 4 came out, and while KDE 4.1 fixed some of the most annoyingly trivial oversights (like a clock panel application that couldn't shown seconds), many other things I consider to be important (more important than eye candy) still haven't been fixed. I presume they've been redefined as features or expected behavior now.

I get the (possibly mistaken) impression that many of its developers lack a certain attention to detail, or a view of the big picture. Did they sit down before starting to write new code and consider what is essential functionality, what parts of our existing application work best, which part are used most, for example? The KDE4 page on wikipedia makes everything sound semi professional (although with a worrying emphasis on style, icons, multimedia API, desktop effects etc), but something must have gone wrong to end up with a product that radicalizes long term KDE fans (e.g. see here, here or even here).

Of course, KDE4 does have fans too (I suspect they don't use it the same way I do). Ryan Paul at Ars Technica defends KDE4 here. I am not at all convinced by his arguments, and tend to agree with Steven Vaughan-Nichols criticisms:

My real problems with KDE 4.1 is far more fundamental. The developers believe that they have a better way of handling the desktop. For them, I’m sure they do. For users, this user anyway, the new desktop fails at a desktop’s main job: enabling the user to get their work done as easily as possible.

[...]

I could go on, but I’m not going to bother. KDE 4.1 is full of visual improvements that dont’ improve anything. You can see KDE 4’s Plasma interface for yourself. Maybe it will work for you. It certainly doesn’t work for me.

KDE 4 developers, lead by Aaron Seigo, wanted to make a radical change to the desktop. They have. However, in so doing, I don’t think that they have made that classic engineering mistake of making something that’s great for them, but not for users.

Seigo assures me that he can explain what KDE developers are doing to me. I’m sure he sincerely believes that. Unfortunately, in so doing, he’s making my point for me. Desktops shouldn’t need explanations They should just let you do your work. KDE 4.1 gets in the way of my doing work.

Is it because I’m an old foggie? Maybe.

I'm not the only one who has no love for KDE 4. As Linus 'Mr. Linux' Torvalds recently said, "I used to be a KDE user. I thought KDE 4.0 was such a disaster I switched to GNOME. I hate the fact that my right button doesn't do what I want it to do. But the whole 'break everything' model is painful for users and they can choose to use something else."

This last paragraph is from another Vaughan-Nichols article, this time on KDE4.2.

Anyway, enough on KDE. Until the XFCE4 folks do something similar (I'm sure it'll happen eventually) KDE is dead to me. Long live XFCE!

Tomshardware has a Macbook / OSX review from a long time Windows user. All pretty standard stuff given that worldview, but it does inspire me to formalize my impressions of Apples OS from the perspective of a long term *nix power user. Just need to find the time.

i810 problems on Fedora 10

2009-01-25T19:31:00.003-05:00

I just got back from a relaxing holiday on Grand Cayman, only to waste time fiddling around with the Intel i810 driver problems on Fedora 10.

A rough and ready work-around is to remove your xorg.conf completely and let Xorg automatically detect the settings to use... X has certainly come a long way in the last 10 years, especially since the Xorg/XFree86 split. The only problem with this is that it ends up using the "intel" driver instead of the "i810" driver, and i810 used to be both faster and allow the cloned screen operation I used to use for giving presentations...

Far Cry 2 mini-review

2009-01-15T19:35:00.001-05:00

Far Cry 2 is the best FPS game of 2008, IMHO. Enjoying it a lot. It is a slightly slow and very repetitive sand-box of a game (running in guns blazing is not a good idea in Far Cry 2), and requires patience, so the ADHD crowd won't be able to understand it.

Technically its amazing. It has the best simulation of fire I've seen in any game, and the destructable aspects of the environment are also handled incredibly well (I've spent a fair bit of time shooting individual fronds off palm-like trees, and even more time watching fire spread through the grass, bush and trees).

Graphically quite impressive, although I suspect the graphics on the Xbox 360 are inferior to those on a high-end PC. The wide range of environments: lush jungle, savanna/veld, and semi-desert, are all rendered beautifully. The mixed grass/bush veld-like environments really captured my memories of South African veld incredibly well, even down to the shape and placement of rocks and streams. The South African and British accents and phrases of a lot of the mercs were also a nice touch. Eh my china?

The game's story does a good job of showing the moral vacuity of warring groups, the mercenaries and arms dealers that serve them, and the mixed complicity and indifference of the wider world. Ostensibly you are a mercenary yourself tasked (by whom?) to kill the mysterious Jackal, an arms dealer involved in providing the weapons for any number of conflicts around the world. Obvious evil bad guy eh? But the game manages to rise above such a simplistic one dimensional caricature.

Thats not to say its without flaws. The worst is that is easy to sick of all the damn roadblocks staffed by endlessly respawning mercenaries, especially when quests seem to deliberately send you the exact opposite side of the country as you're in when you get the job to bump some one off.

Far Cry 2 has little to do with the original semi-scifi Far Cry, apart from also being a sand-box like FPS set in a tropical environment that avoid traditional linear FPS game play. Its not even made by Crytek, but instead by Ubisoft Montreal (who did also-excellent Assassin's Creed, I believe). I really liked the original Far Cry, but have to say I think Far Cry 2 is a better game.

[Update 01/28/09. I've just finished Far Cry 2. Can't say I'm particularly pleased with the way it ended, as the various characters actions seemed unrealistic given their prior actions and stated motivations. But weak endings are hardly unusual for games. Still, overall a great game from my perspective, and I'm looking forward to replaying it in the future.]

Consider the Snowclone

2009-01-15T18:24:00.000-05:00

Language Log discusses snowclones, which I hadn't previously realized "Consider the X" were examples of, but with hindsight it makes perfect sense.

Here is wikipedia's definition of snowclone.

A snowclone is a type of cliché and phrasal template originally defined as "a multi-use, customizable, instantly recognizable, time-worn, quoted or misquoted phrase or sentence that can be used in an entirely open array of different jokey variants by lazy journalists and writers."

I must admit that the first time I heard the term snowclone was in reference to lolcats.

Least favorite weather condition: freezing rain

2009-01-07T09:16:00.003-05:00

My least favorite form of weather: freezing rain. Least favorite thing to do during or after episodes of freezing rain: the rush hour commute to or from work.

Attenborough interview

2008-12-31T13:54:00.003-05:00

Ed Yong has an interesting interview with Sir David Attenborough, which worth a read if you enjoy his nature documentaries (and what discerning mind doesn't?).

The version of the Planet Earth documentary series available through Netflix here in the US differs from the version aired here by the Discovery Channel in 2007. The Netflix version has Attenborough narrating, and although the lines are probably identical to those said by Sigourney Weaver in the Discovery Channel version, the Attenborough version seems much serious and informative to me.

Nevertheless, on rewatching it I still consider Planet Earth to inferior to Attenborough's "Life" series of documentaries, or the Blue Planet series made by the people who later did Planet Earth. Planet Earth, despite some great footage, never seems to me to have the same level of focus or information content of these other series. The rapid changes in shots and scenes in Planet Earth make it seem like it was put together by someone with an attention deficit disorder, or that it was aimed at an audience whose attention span is measured in tens of seconds. But perhaps their is a niche for a wildlife documentary aimed at non-documentary watchers?

Anyway, Attenborough never ceases to amaze me. At the release of this years "Life in Cold Blood" series he was 82 years old and was still jaunting around the world into all sorts of inhostipatable environments. This year he is behind one of the BBC's Darwin "The Genius of Evolution" season (marking the 200th anniversary of the birth of Charles Darwin).

More Mac installing...

2008-12-29T18:55:00.004-05:00

Spent some of the day setting up the new work Macbook. Firefox 3 instead of Safari. iTerm as an alternative to the Terminal. More importantly. I installed Xcode 3.1.2 from the Apple Developer Connection, gfortran direct from GNU itself, fink 0.9.0 from http://www.finkproject.org/, and then a whole bunch of fink packages installed tetex using FinkCommander.

For now I've decided against installing MacTex, despite it being a more up-to-date Texlive-based tex/latex distrbution than fink's tetex.

It looks like getting scipy installed will take some work (or at least more work than installing it on Fedora, "yum -y install scipy python-matplotlib ipython"), as its not available by default in fink.

Anyway, the most important set of software installation is now over with compilers on the system and access to installable unix tools through fink, so I should be able to continue at a more relaxed pace while starting to do actual work (at the very least, paper writing) on the laptop.

Progress on setting the Mac up properly...

2008-12-28T19:22:00.002-05:00

Enabled a root account:

In versions prior to 10.5 this could be done with NetInfo (part of the Apps/Utilities folder). Now this is done graphically using Directory Manager (not System Preferences/Accounts, as you might have assumed). Selected Edit->Enable Root User and enter a password.

Set up the locate database for the the locate command:

Become root or use sudo to execute the following command:
/usr/libexec/locate.updatedb

Ignore the warning about this being a security risk. Control over which directories to scan should be set in /etc/locate_rc, although Apple does not provide one by default. TODO: By default the locate database is only updated once a week. This should be changed to once a day. See the /etc/periodic/weekly directory.

Setting a fixed machine name:

The main ComputerName can be set/reset in System Preferences/Sharing. However this is not the same as the node name as you'd see executing "uname -n". As far I can determine the best way to set the machine name(s) is to use "scutil --set" to set the ComputerName, LocalHostName and HostName.

scutil --set ComputerName azathoth
scutil --set LocalHostName azathoth
scutil --set HostName azathoth

These changes are retained between successive boots of the machine.

Making Terminal and X11 appear by default in the dock:

Start either app the normal way from Finder. Their icon will appear in the dock. Right-click on their icon (if you have set up right click, otherwise control-click on the icon) and select "Keep in Dock" and/or "Open at Login".

Switch off xterm beeping:

Failure!

xset b off doesn't seem to work by default as /usr/X11/bin is not in the default path. Doing /usr/X11/bin/xset b off does work within the invoking xterm, but so far I have failed in preventing beeps on an automatic and system-wide basis.

Trying to create a user-specific .xinitrc, even one that invokes quartz-wm, does not work for me. In most cases X doesn't even start successfully, and if it does then the xterm it starts still invokes the bell. I am beginning to suspect that I may have to set it to use visual bell. Copying the system xinitrc from/usr/X11/lib/X11/xinitrc and modifying that doesn't seem to work either.

Focus Follows Mouse:

It appears to be impossible to get full focus follows mouse behaviour under OSX, which is incredibly backwards. However a very limited form of it is possible just for Terminal windows (and possibly xterms) by executing the following in a Terminal:

defaults write com.apple.Terminal FocusFollowsMouse -string yes

This works (after a small delay) in giving limited FFM in just the Terminal.

For xterms the following is claimed to work:

defaults write com.apple.x11 wm_ffm true

But this does not appear to work on my Macbook, with or without a -bool between the wm_ffm and the true. As I don't really intend to use a vanilla xterm for real work anyway I'm hoping this (and the copy/paste difficulties between X11 and OSX) limitation won't end up driving me crazy.

OS X, Fedora 10, KDE 4.1.2, XFCE

2008-12-26T15:57:00.004-05:00

Still playing around with the new Macbook and OS X 10.5.6, getting used to the odd Mac key and the associated keyboard shortcuts.

Overall I'm quite impressed at the speed and slickness of the basic OS, as much as I try to avoid being impressed with eye-candy. The lack of "focus follows mouse" is a major pain, and copy/paste seems broken or tricky between X11 and non-X11 apps. The Terminal program is OK, less fancy than I was expecting based on word-of-mouth, although nicer than the lowest-common-denominator of the basic X11 xterm.

I was going to say the OS X Terminal is less capable than the KDE Konsole, but then I was rudely reminded last week that the KDE4 Konsole is less capable, and less configurable, than the KDE3 Konsole. Currently I'd say the OS X Terminal and KDE4's Konsole appear pretty comparable in capability and available configuration options at present.

I've complained before about KDE4 on Fedora 9, but had noted some progress and had hoped the version Fedora 10 shipped with would be further improved. Last week I upgraded my work back-up machine to Fedora 10, largely as a test, and experienced many of the same problems...

The Konsole no longer has a login shell "--ls" command line option. Transparency is still not available. Add an application laucher to the Plasma-based panel and dare to change the "Icon Settings" and its icon will be replaced with a question mark. Worse still, the changes you've made to the panel launcher have been propagated back to the main KDE menu, so don't make a mistake! As for trying to move icons around on the panel... it didn't appear to be possible at all (no right click, "Move" option anymore) and its seems other are as confused by this as I am, although here is the non-intuitive way to do it.

And its slowwwww. The price we pay for KDE trying to implement desktop graphical effects similar to OSX, I suppose.

Any, sick of the fuss, I ditched KDE4 on the Fedora 10 machine and switched to XFCE, and managed to quickly configure my desktop into looking something like KDE3.5 with nicely transparent terminals in less time that it took me to get the KDE4 Konsole to use a login shell.

One step forward and one step backwards, I suppose... Ah well.

Bérubé reviews Sokal's "BEYOND THE HOAX: Science, Philosophy and Culture"

2008-12-20T09:06:00.003-05:00

Michael Bérubé has an interesting review, dare we say critique, at the American Scientist of Alan Sokal's latest book "BEYOND THE HOAX: Science, Philosophy and Culture" (Amazon.com link)

Here is a snippet of the review to whet your appetite:

When some people hear the term Western science, they think first of Hiroshima, Agent Orange and the Union Carbide plant in Bhopal—and not, say, of the discovery of neutrino oscillation. This mordant skepticism about the benefits of Western science is then underlined by a dogmatic conviction that the Enlightenment was little more than a stalking horse for imperialism. As for why postmodern intellectuals would champion “local knowledges” and the “heterogeneity of language games” against the universalist aspirations of the Enlightenment, my sense is that when academic leftists in the humanities speak glowingly about “local knowledges,” they’re thinking of all the warm and fuzzy feelings we lefties have about “the local”—from our local independent bookstore to our local independent food co-op. These are good things by every measure (local and universal), but they seem to have obscured the fact that many of the world’s “local knowledges” are parochial, reactionary and/or theocratic. Likewise, the defense of the “heterogeneity of language games” has proceeded as if it is the moral equivalent of a defense of species diversity—when, in fact, it is morally neutral, agnostic with regard to the question of whether the language games of charlatans or fascists should be preserved alongside the language games of the indigenous peoples of the Americas.

However, while there is much that is good about Sokal's book, it is not all good. Bérubé does a good job of explaining to lay-people like me where Sokal (and Sam Harris, before him) has gone wrong.

[Update 12/26/08: Hopefully have corrected the weird font problems.]

New Macbook! (and Fallout 3)

2008-12-19T18:23:00.000-05:00

My new work laptop arrived yesterday - a 13" 2.4 GHz Macbook. This is my first Mac ever, something of an experiment for me, so lets hope it goes well. So far I'm quite pleased with it, especially now that I've worked out how to right click using the touch pad and found how to add a terminal to the dock.

My old Lenovo Thinkpad X60, dual boot Fedora 8 and Windows XP, was (and still is) a good software development machine but was imperfect at its primary role of conference/travel laptop. On Windows the separate Lenovo and Windows wifi managers would often conflict with one another, although it worked once you'd found and killed one or the other. I'd bought the thing based on the fact that people at ThinkWiki had the wireless hardware working under Linux, but for whatever reason it would only work intermittently and often would disconnect from a wireless network it had managed to connect to. It even did this when I swapped the Intel a/b/g wireless internal card for an Atheros-based one that was supposed to work even better under linux. I spent a lot of time getting into old-school kernel patching and micro-code nonsense, before giving up trying to make wireless work robustly under linux. This was a pain at conferences, where wired ethernet connections are rarely provided.

And I never got sound working under Linux - a failure that rankles me considering I managed to hack sound into working on linux on every laptop I've ever had until the Thinkpad came along two years ago.

I'd originally chosen a dual-boot Windows/Linux combo (as opposed to pure Linux, which is what I did on previous laptops) because conferences had stopped letting you hook your own laptop up to the projector to give your presentation (which used to work fine under linux with OpenOffice for me and still does for departmental Seminars, apart from one memorable incident at a conference in the Canary Islands...).

Now all conferences have adopted a policy of transferring all talks to one of two-conference computers, usually one Windows and one Mac. This initially lead to font problems with talks saved in powerpoint format from OpenOffice Impress, although installing and using Microsoft web fonts under linux solves that problem. I added Windows to the Thinkpad X60 so I can load the ppt in powerpoint to check it. All good so far. This is almost foolproof, except when conference organizers put your powerpoint talk from a XP machine onto a Mac running powerpoint (or vice versa), at which point all hell breaks loose. This has happened to me only a few times, but it happens to some poor soul at every conference I go to.

So, sick of powerpoint's inability to work properly on both XP and Mac, and having to reboot out of a working environment (linux) to get into XP to check the presentation, I have decided to do all future talks in Keynote. Hence the Mac. And once I've unixified the Mac I should be able to do some decent work on the thing at the same time, no rebooting required. Wish me luck.

PS: Fallout 3 did not disappoint. An awesome game, with only minor flaws of an overly-low level cap and a rather abrupt termination to the main quest.

Unix Semaphores - A finite resource!

2008-12-12T18:56:00.000-05:00

One of the things about unix-like operating systems is that you never learn them all - there is always something more that you didn't know about that some other unix-user will tell you about that you'd never heard of but is cool and/or useful nonetheless.

I've been using *nixes pretty much full time since 1994, and sys-adminning my own Linux boxes since 1996, and yet yesterday I learned something completely new.I was messing around stress-testing some Message Passing parallel code using MPICH on a shared memory system (couldn't be bother to mess around with going across the network and set up ssh keys for a simple test, OK), only to discover after some weird errors, that the ch_shmem system of MPICH relies on System V-style inter process communication, which in terms uses semaphores, of which each user is only allocated a small number (32 arrays or something silly). Interestingly, nothing else on my system appears to be using semaphores or message arrays.

If MPI crashes while running it fails to clean up the semaphore(s), and if you do this too many times you end up not being able to run anything that relies on semaphores, which causes much confusion if you didn't know about this stuff. Hence you need to run ipcs -s to see your semaphores (hopefully none, if your MPI program has finished running), and ipcrm -s to delete any improperly terminated semaphores. I'd never heard of these commands before, but they solved my problems.

dd, python, google charts and amazon cloud computing

2008-12-02T18:04:00.001-05:00

The latest RedHat magazine has a neat little article mixing dd, python, the Google Charts API and virtual machines with Amazon's version of cloud computing - the aim is a pretty pedestrian rough benchmark of disk I/O, but as a mix of computing metaphors (classic *nix command line, modern interpreted language, Web 2.0, virtualization) it is noteworthy.

The National Resources Defense Council's flawed game console study

2008-12-02T18:00:00.000-05:00

The SciAm blog from November 28th uncritically highlights a claim by the National Resources Defense Council that

video game systems are huge energy wasters, mostly because people (read: kids) tend to leave them on even when they're not using them.

[...]

Sony PlayStation 3 (which uses 150 Watts of energy) and Microsoft Xbox 360 (which uses 119 Watts) are the biggest offenders, while the Nintendo Wii draws less than 20 Watts, according to the NRDC report. The PlayStation 3 and Xbox 360 each if left on all the time [emphasis mine], consume more than 1,000 kilowatt-hours each year—equal to the annual energy use of two new refrigerators. The PlayStation 3, which can also be used as a high-definition video player, uses five times the power of a stand-alone Sony Blu-ray player to show the same movie.

There are a number of things about this report (PDF), or at least the popular reporting of it, that I consider flawed.

As we've discussed twice before now [1, 2], the energy used to produce an electronic device is a non-negligible fraction of its total lifetime energy usage (the study I linked to before claims that production of a personal computer [which game consoles effectively are] accounts for ~80% of the total energy usage over its entire lifetime). Focusing solely on energy efficiency in use is a flawed metric to assess the net cost to the climate.
The report chooses to highlight the energy cost associated with leaving the devices on all the time, with no power saving options selected. This is a maximum cost, but is it at all a realistic scenario? Their figure 1 shows that, according to their own calculations, the net energy use by users who switch their consoles off after use is typically ~10% of leaving it on all the time. Any Xbox 360 user knows that heat associated with use can lead to the Red Ring of Death - I certainly don't leave my Xbox on when I'm not using it. Their summary and the news reports all focus on the worst case scenario, without mentioning the equally plausible or more plausible scenario. Of course, one can't make a big fuss about game consoles being bad for the environment under the conscientious user scenario, can we?
Any technologically savvy computer user knows that there is a difference between peak energy usage and idle energy usage. The report quotes power uses when active and idle in Table 3 (e.g. an average of 119 W for an Xbox 360 when active, 118 W when Idle). Unfortunately they redefine "Idle" when gaming to mean a game is running, but the user is not touching the controller - this is simply not realistic. Even if we assume people leave their consoles on all the time they certainly don't have games loaded and paused 24/7 365 days a year - I certainly don't. Any Xbox 360 user also is aware of the annoying whine associated with a spinning disk, which no one would put up with 24/7. Yet the NRDC study deliberately rejects manufacturers Idle power usage numbers (i.e. no disk inserted, no game running, what I consider to be a realistic scenario and akin to standard personal computer Idle power ratings) and states on p26 that "Some video game console manufacturers define Idle mode as a state during which there is no game disc inserted in the console. We believe that users are more likely to leave game discs in their consoles when they are left in Idle mode (a user who takes the time to eject the game disc would more likely just power down the console completely rather than leave it running) and have defined this mode accordingly."
They did not themselves assess usage patterns - in Chapter 5 they quote a Nielsen Group study that finds that "on average, users who account for close to 75 percent of all playing time have their consoles on for an average of 5 hours and 45 minutes per day." This implies that the per console there is 7 hours 40 minutes play time per day. The NRDC study has footnote (p26) associated with the previous quote questioning the Nielsen numbers: "Nielsen’s statistics can be difficult to interpret because the time in Active mode reflects an average across only the days when the console was turned on, rather than a true daily average reflecting use across the entire time metered. It is likely, however, that many heavy users often have the console on every day. For all of these reasons, we built upon the information available and the following assumptions to complete the energy analysis. ... Many users are assumed to leave their video game consoles on when they are finished with a game, even when they go to sleep at night." [emphasis mine]. On p27 they absurdly claim that a Lawrence Berkely National Laboratory study of 60% of their computers being on overnight and over weekends somehow justifies their assumptions about game consoles. This is idiotic - a national laboratory where many computers are workstations that effectively have to be on 24/7 has nothing to do with home entertainment usage by children and young adults. My work machines are on 24/7 365, as they need to be, for example either they're running programs or I need access to the disks from home. My Xbox 360 is only on when I'm using it. Hidden in Endote 1 (p28) is the nugget of information that "Due to the absence of any studies, we based our calculations on the assumption that 50 percent of users leave their device on when they are finished playing a game or watching a movie."
Items 2 and 3 raise very serious concerns in my mind about how the NRDC assessed (a) the fraction of users who leave their consoles on all the time, and (b) the net energy usage. It is obvious that if either of these aspects of the study is flawed then its conclusions are totally untrustworthy. In fact, both aspects are deeply flawed.

Item 4 suggests that the NRDC did not use the Nielsen numbers (I must say I'd consider the Nielsen numbers to be suspiciously high, personally) at all, but simply assumed that 50% of all users leave their consoles on all the time. Note the phrasing of the quote in Item 4: first they assume that "heavy users" leave their consoles on all the time. Then they move from that to assuming all users leave their consoles on. As far as I can tell they did not measure actual power usage. Rather they took their (inaccurately high) "Idle" power numbers and multiplied up by the hours in a year and the number of consoles, and then multiplied by their made-up 50% figure. Assumption after assumption, and all unwarranted.

In summary I think its pretty clear that this study is fundamentally flawed. All assumptions appear to have been made to in order to achieve the result they want, and evidence to the contrary (realistic Idle power ratings using, estimated usage times from Nielsen) has been rejected without justification. The Endnote mentioned above is telling: although this is supposedly a study of the energy cost associated with console use they have no data of actual console usage, and rather than actually trying to find out they simply assume 50% of all consoles are left on all the time. If you're going to do a study why not actually try to find out as accurately as you can the numbers you need? Never mind the issue of the end-to-end energy usage (of personal computers, at least) being dominated by manufacture, not actual use.

I'd suspect that who ever wrote this "study" (deliberate use of sarcastic quotation marks) does not own a game console of their own, and has no training in hypothesis testing or scientific quantitative analysis. The lack of analytical skill or scientific rigor in this study astounds me.

This report reflects very badly on the NRDC and the Ecos consulting group who performed it. This feeds into the "computer games are bad and are making our children bad" narrative our sensationalist media loves to feed to us. Environmental groups should not resort to bogus studies in order to make the case for conserving - doing so weakens the cause and gives ammunition to the denialists and polluters. It also pisses off your potential allies, who don't want to associate with bumblers.

Furthermore, it ignores the big picture. Even if we accepted this flawed study, how significant is this energy waste compared to TVs, lights or other electronics being left on, or cars being idled in the morning to warm up? A decent study would place the numbers in context. This study would never pass any form of peer review - its terrible. I'm also annoyed at SciAm adopting the parroting-the-press-release school of journalism.

Finally the focus on consoles is blatantly a PR gimmick from the NRDC, timed for the holidays so they can get some media attention while picking on a group (gamers) that it is socially acceptable to pick on.

Energy conservation and reducing resource waste is not about consoles, it has to extend to all areas of life. Water, electricity, gas, food stuffs. If you haven't taught your child to turn off the light when he leaves the room then why expect him to turn off the TV, computer, or game console. Its about personal responsibility.
Without that a million studies, flawed or accurate, won't make an iota of a difference.

Electronic waste and Apple

2008-12-01T18:52:00.000-05:00

Just when I'm thinking about replacing(*) my old work laptop (a Lenovo X60) for one of the new Apple Macbooks, Greenpeace trashes Apple for its inaccurate claims regarding how green its laptops are (Daily Tech article, Greenpeace report on Apple [PDF]).

As I've noted before there is much more to being green than just energy efficiency, so in this respect Apple's claims about being green are disingenuous at the very least.

However, if you take time to look at the Greenpeace ratings and their change over time its clear that of the main laptop manufactures are all pretty in the same general area - the electronics manufacturers scoring more highly tend to be more related to consumer electronics and cell-phones. And the real bad guys are Microsoft and Nintendo.

(*) Supplementing is perhaps a more accurate description, rather than replacing. The X60 is still a great ultraportable laptop that I do a lot of real work on, but for conferences and travel I'm hoping a Mac may be more practical.

No posting for a while, thanks to Fallout 3

2008-11-25T18:27:00.000-05:00

I won't have much time for blogging for a while, as currently exploring the Capitol Wasteland is consuming
what spare time I have. After a slightly slow start Fallout 3 is rapidly becoming an engrossing experience, despite the annoyance of horizontal colors bands below the HUD that may signal problems with my Xbox 360's graphics processor.

Electronic waste

2008-11-21T07:45:00.000-05:00

Scientific American online has a short article on e-waste - junked electronics such as old computers, televisions, iPods , and so on, which contain a variety of toxic heavy metals.

An investigation by the U.S. Government Accountability Office (GAO) earlier this year found that the EPA had "no plans and no timetable for developing the basic components of an enforcement strategy" to ensure proper disposal of harmful e-waste, which includes recycling components and safely handling and disposing of toxic materials, including lead, mercury and cadmium, despite having launched new e-waste guidelines in 2007 called "Responsible Recycling," or R2.

But the EPA's standard does nothing to prevent e-waste export or keep it out of landfills, nor does it offer any tracking of toxic components to ensure proper disposal. As it stands, the U.S. produces three million metric tons of the estimated 50 million metric tons of electronics garbage produced worldwide annually, according to EPA.

Often recycled e-waste is exported illegally (in ways that circumvent what rules exist) from the US to China or other developing world countries, where their citizens and children suffer from the resulting pollution.

Another interesting factoid from the article is that process of making a computer from the raw materials consumes about 4 times more energy than the computer itself will ever use.

At the same time, it takes 1.8 tons (1,630 kilograms) of raw materials and roughly 529 pounds (240 kilograms) of coal or other fossil fuels to manufacture every personal computer—81 percent of the energy an average unit will use in its lifetime, according to a study from United Nations University in Tokyo. By extending product life, such energy expenditure—as well as recycling issues—could be restrained.

Recycling old electronics in this country as a private individual is difficult - RadioShack and BestBuy will accept and safely dispose of (?) old batteries, including laptop batteries. Dell and Apple supposedly have programs to take back old electronics from you, but I'm not sure if they'll take anything or only their own products when you buy something new from them. Other than those examples I have yet to find a place that accepts broken computer electronics for recycling without charging you.

Review: Eschalon Book I

2008-11-17T21:11:00.005-05:00

Eschalon Book 1 is a deliberately old-school computer role playing game produced by the indy studio Basilisk games, and available for Windows, Mac OS X and Linux. By old-school I mean turn-based, isometric, fixed camera, with strong textual elements, think of an intermediate between Legend of Zelda and Neverwinter Nights. If you liked those games, then for $19.95 Eschalon Book I might be worth your consideration.

Online reviews of the game can be found at the following sites:
http://www.shamusyoung.com/twentysidedtale/?p=1485
http://jayisgames.com/archives/2008/06/eschalon_book_1.php
http://www.2404.org/reviews/2881/Eschalon:-Book-I-Review
http://www.scorpia.com/?p=812

Overall, I quite enjoyed the game myself, although the first few hours were tough on the Ranger character I generated, as I soon ran out of arrows and the money needed to buy arrows. The strong element of random encounters in the game, while familiar from the pen and paper RPGs I used to play as a teenager, also made life difficult as I'd camp to try to heal wounds only to have camping lead to a random encounter that would cause me more wounds, and exhaust my meagre stock of healing potions and arrows. Reading the reviews shows that others also thought that the random encounters and early game money scarcity needed better play balancing.

Ultimately I got a bit tired of the grind - at one point I had to fight opponents with my fists as I'd broken my only dagger trying to open a sealed barrel (note to self: I should have RTFM before beginning playing, as it tells you to use cleaving or bludgeoning weapons on barrels and chests) and didn't feel like restarting with a swordsman or a magic user.

For the Linux version Basilisk had fixed the game exploits found in the Windows version, so I took matters into my own hands and used a hex editor on the same game file to give myself 45000 gold. After that, able to buy whatever I wanted, and all the arrows I needed, the game was actually a lot more fun.

I was finally able to take the time to notice the excellent audio(*) sound effect work (owls hooting as you walk through the woods, for example), and the prettiness of the level design given the limitations of the isometric engine.

I've previously mentioned I was giving Indy games a try, given my recent dissatisfaction with recent big-budget big-game studio games that given only a few hours game play for $60. Fully playing through Eschalon Book 1 took me about 25 hours (a little longer than the 20 hours some of its reviews mentioned, but for reasons I mentioned above), so at approximately $1 per hour its pretty cheap entertainment. While you won't get as much for that $20 as if bought a big-studio like NWN a few years after it came out, there is something to be said for supporting Indy game studios that do a decent job. Think of it as buying Organic food - maybe its better for the environment.

(*) One annoyance I experienced was occasional interference-like audio buzzing, but I'm not sure if this was intrinsic to the game or really a pulseaudio problem in Fedora 9.

The problem with the world today is... education

2008-11-17T17:30:00.001-05:00

So sayeth the wise and (not learned) Right Reverend Patrick O'Donoghue, Bishop of Lancaster (thats in England, for you safely uneducated folks out there). From the Telegraph on November 16th:

Bishop O'Donoghue, who has recently published a report on how to renew Catholicism in Britain, argued that mass education has led to "sickness in the Church and wider society".

"What we have witnessed in Western societies since the end of the Second World War is the development of mass education on a scale unprecedented in human history - resulting in economic growth, scientific and technological advances, and the cultural and social enrichment of billions of people's lives," he said.

"However, every human endeavor has a dark side, due to original sin and concupiscence. In the case of education, we can see its distortion through the widespread dissemination of radical scepticism, positivism, utilitarianism and relativism.

"Taken together, these intellectual trends have resulted in a fragmented society that marginalizes God, with many people mistakenly thinking they can live happy and productive lives without him."

I suppose the Bishop feels that the marginalization of a mythical figure is too high a price to pay for the "cultural and social enrichment of billions of people's lives."

The Catholic Church clearly deserves more deep thinkers like Bishop O'Donoghue. With more men like him I'm sure the Church can make itself even more obviously irrelevant to society.

[Image: Jan Luyken. Burning. Engraving. XVII.]

Corn monoculture.

2008-11-14T18:16:00.000-05:00

I'm glad I avoid fast food:

Americans spend >100 billion dollars on restaurant fast food each
year; fast food meals comprise a disproportionate amount of both
meat and calories within the U.S. diet. We used carbon and
nitrogen stable isotopes to infer the source of feed to meat
animals, the source of fat within fries, and the extent of fertilization
and confinement inherent to production. We sampled food
from McDonald’s, Burger King, and Wendy’s chains, purchasing
>480 servings of hamburgers, chicken sandwiches and fries within
geographically distributed U.S. cities: Los Angeles, San Francisco,
Denver, Detroit, Boston, and Baltimore. From the entire sample set
of beef and chicken, only 12 servings of beef had delta 13C < -21‰; for
these animals only was a food source other than corn possible. We
observed remarkably invariant values of delta 15N in both beef and
chicken, reflecting uniform confinement and exposure to heavily
fertilized feed for all animals. The delta 13C value of fries differed
significantly among restaurants indicating that the chains used
different protocols for deep-frying: Wendy’s clearly used only corn
oil, whereas McDonald’s and Burger King favored other vegetable
oils; this differed from ingredient reports. Our results highlighted
the overwhelming importance of corn agriculture within virtually
every aspect of fast food manufacture.

Hope Jahren and Rebecca A. Kraft, Carbon and nitrogen stable isotopes in fast food: Signatures of corn and confinement, PNAS 2008, November 10, 2008, doi: 10.1073/pnas.0809870105has more.

Effect Measure provides an interesting analysis of this work.

Every day I drive past on the Burger Kings the authors sampled from in Baltimore. Always wondered who ate there. Now I know. ;)

teTex -> TeXlive transition on Fedora 9

2008-11-13T18:28:00.000-05:00

Practically every document I have written professionally since 1994 uses LaTeX, either old vanilla latex (tex -> dvi -> ps) or pdflatex (tex -> pdf), often with non-standard cls files (aastex.cls, mn2e.cls).

Ever since I noticed that Fedora 9 was replacing teTeX with TeXlive I've been dreading the transition, and have kept all my work machines on Fedora 8 rather than transition to Fedora 9. (The KDE4 transition also gave me additional reason to wait until the bugs are fixed.)

I finally got time yesterday to back-up all my papers from work to my home Fedora 9 test machine, and just for fun tried running the TeXlive versions of latex and pdflatex on some of my papers and proposals... and they all worked first time, no messing about or reinstalling of the astro cls files required.

My old cls files that were installed in the /usr/share/texmf tree had not been messed with, and the ls-R file had been automatically updated to include them.

I'm pleasantly surprised, given the prevalence of problems a "texlive tetex" google search reveals. Good job Fedora team!

Family Values

2008-11-13T18:25:00.000-05:00

Why those elitist coastal liberals are all about true family values.

Funny

2008-11-12T11:27:00.002-05:00

Funny pre-election predictions.

I'm quite pleased with myself: predicted Obama getting 367 EVs, whereas the current total is 365 EVs.

90 years since the end of World War I

2008-11-11T11:00:00.000-05:00

On the 11th hour of the 11th day of the 11th month of 1918 the Armistice between the Allies and the Central Powers came into effect and the Great War, the "war to end all wars," was over. Only a few veterans of WWI now remain to mark the commemoration ceremonies.

My grandfather on my mother's side served in WWI with the South African troops, and took part in the battle of Passchendaele (aka the Third Battle of Ypres). There he was captured by the Germans and spent the rest of the war in a prison camp, but was certainly better off than the 140000 Allied troops who died in that battle alone.

Volcano and eruption slideshow

2008-11-07T18:10:00.000-05:00

Related to the Lusi mud volcano post from a few days ago, SciAm has a nice slide show of images related to volcanic eruptions.

Michael Crichton has died.

2008-11-05T18:21:00.000-05:00

Michael Crichton has died at age 66, after a struggle with cancer. I loathed his writing, but I commiserate with his family over this sad news.

Okteta

2008-11-04T20:57:00.000-05:00

Having previously complained about KDE4 on Fedora 9, it is only fair that I also mention something I like about it.

KDE 4.1 comes with Okteta, a gui-based Hex editor, and its pretty easy to use even for someone like me who has no experience with editing raw binary files (*). It turned out to be very useful when I need to alter some Eschalon Book 1 save game files (more on this in a later post).

Still, GUIs are only so useful, and I had to use the command line "cmp" utility to identify the bytes that differed between two different save game files before I could actually do anything useful with Okteta. Another cool command line tool I discovered for the first time: "xxd." Long live the all-powerful command line!

(*) No experience with messing around in binary of unknown format. Binary files with known formats are easy to deal with, you just write a program to process them.)

Do big studio computer games have less bang for buck these days?

2008-11-04T18:22:00.002-05:00

Maybe I'm becoming old and jaded, but recently big budget games (PC or console) have been a bit of a disappointment to me.... $60 for <10 hours play time in a First Person Shooter (with maybe 2-3 times more the play time in an CRPG), and frustrating game-play seems the norm these days. I'd even have to buy a new PC to play some of the latest and greatest PC-only titles, as my trusty old Pentium 4 requires the obsolete AGP graphics. With less free time and spare cash (who could have thought that the rampant ideologically-driven deregulation of the financial markets might cause problems!) than I used to have its seems more important to find something decent to play...

After recent disappointments with NWN2 (and its expansion Mask of the Betrayer), Oblivion: Shivering Isles (Oblivion was good, but not as fun as Morrowind) and Star Wars: The Force Unleashed, and giving more money that I can really afford to the Democrats I've been looking for something where the emphasis is on fun and game-play, rather than graphics and movie-quality cut-scene work.

The original title of this post was going to be "Are big studio computer games less fun these days?" But what is fun? Certainly modern computer games, in particular those mentioned above, are graphically outstanding compared to games of even five years ago, let alone 10 or 15 years ago. Yet I remember getting a lot of enjoyment out of such graphically-primitive games such as Legend of Zelda, Civ 2, and X-Com: Terror from the Deep (probably my favorite games of all time). Basically the ingredients and mechanics of game play of different genres of computer games really haven't changed significantly over the same time, and its game play that counts for a lot in terms of enjoyment.

As I also spent vast amount of time playing those games - not only did they take a long time to master and play through, but they kept my attention for the ~100 hours I put into them. If a game is going to be shorter, then I expect to pay less for it. Or to put it another way (combining both fun and value) bang-for-buck is an element in my relative enjoyment of something.

That is not to say pure economics (or buyer's remorse) is the sole determinant of fun (remember, game play counts), but I think it also a crucial part of the recipe. For example, a typical Hollywood big-budget movie (e.g. the latest Indiana Jones movie) might be more fun when rented through Netflix for a net cost of a few bucks, than if you went to the theatre and paid $9 + gas and parking to see it.

Personally, as far as games are concerned I think the paying less than or approximately equal to $1 per hour of first-time game play is great value (e.g. KOTOR, Morrowind, Oblivion), ~a few $ per hour decent (e.g. Far Cry, Half Life 2, Assassin's Creed), and more than $5 per hour (e.g. SW: TFU, Halo 3 single player) poor value for money.

So if my hypothesis is right, what types of games should be fun if I'm not liking the games produced by the current big game studios?

If game play is roughly the same, and graphics really aren't super important, and bang-for-buck is a factor, then games by small independent developers should be fun. They may be short, or lack graphical or play testing finesse, but they should be enjoyable. (The alternative is simply to purchase the big studio games about a year after they first came out, at which their reduction in price makes up for their imperfections.)

So instead of the big games studios, I'm going to give independent developers a chance. In particular developers who support multiple operating systems (I keep a Windows machine to play games on, but if I could play games on other OSs I would happily avoid the use of Windows).

Playgreenhouse.com is perhaps best known as the distributor of Penny Arcade's "On the Rain-Slick Precipice of Darkness", but it now has a few other games available, all for prices of $20 or less. To put my money where my mouth is I've purchased the old-school isometric CRPG Eschalon Book 1 (linux version) for the princely sum of $19.95.

I've spent about 10 hours playing so far, but will hold off on the full review for a while. In the mean time here are some reviews of the game (with screen-shots in some cases) of Eschalon Book 1, should you be interested in wasting a few minutes reading time:
http://www.shamusyoung.com/twentysidedtale/?p=1485
http://jayisgames.com/archives/2008/06/eschalon_book_1.php
http://www.2404.org/reviews/2881/Eschalon:-Book-I-Review
http://www.scorpia.com/?p=812

Oil drilling most likely cause of Indonesian mud volcano

2008-11-04T07:19:00.002-05:00

The BBC reports that the majority of the scientists attending the American Association of Petroleum Geologists' meeting in Cape Town, South Africa, believe that a bore hole drilled by an oil company was most likely responsible for the creation of a mud volcano (Lusi) on the island of Java in 2006.

Since then the mud volcano has continued to spew mud, displacing tens of thousands of people, destroyed four villages and 25 factories, and is indirectly responsible for the death of 13 people. It may continue to erupt for decades.

The drilling company involved denies any responsibility, blaming instead a magnitude 6.3 earthquake 280km away.

You can read more about the Lusi volcano at Highly Allochthonous, with an update here.

I was tempted to title this post "Drill, Baby, Drill!" but encouraging stupidity is never wise.

[Image of Lusi mud volcano, credit: Durham University, found on this UC Berkeley press release regarding the Lusi volcano.]

[update 11/06/08: Highly Allochthonous was at the AAPG meeting and has a nice run down of the earthquake vs drilling talks at the Lusi debate.]

Spore: Unintelligent Design

2008-11-03T19:19:00.001-05:00

One of the things that surprised me when reading the initial reviews of Spore (e.g. the gamespot Spore review) was how short the early cell-based, oceanic and land creature phases of the game were said to be. Indeed, the reviews found these early stages, despite their shortness, to be "not very interesting and [to wear] out its welcome quickly."

When the game was first announced several years ago it was exactly those early stages that seemed most interesting and most unique - the later two Civilization-like and Master of Orion-like phases sounded much more traditional and less unique. OK, I realize that as a scientist my interests may not be quite in tune with Joe Sixpack, but I'm pretty sure that you can make an interesting and informative game out of those cellular, oceanic and animal stages. After all, people bought and played Railroad Tycoon.

It now appears that the early stages were indeed going to be far more unique and innovative (cellular automata are indeed cool), but that some of the developers got cold feet and forced the rest to stick to more traditional gameplay. Read the story of the dumbing down of Spore at Pharyngula.

[Update 11/04/08: Carl Zimmer has quick piece up at The Loom on perceived scientific problems with Spore. This is not to say all games must adhere to strict scientific accuracy, merely that adopting features of reality might make for a more interesting and varied game. After all, almost every game these day uses the Havok engine to do some simple physics. At the very least realism aids immersion.]

Core i7 reviews beginning to appear.

2008-11-03T18:26:00.000-05:00

Engadget summarizes the Intel Core i7 benchmarks and system reviews that are starting to appear.

I can't wait till they appear on Newegg.

Still Alive

2008-11-01T13:17:00.002-04:00

I'm still alive (Wisdom Teeth almost healed, thank you for asking). I haven't forgotten about the follow-up to the first part of my analysis of why Halo 3 wasn't as much fun (for me) as the original Halo: Combat Evolved, but have been too busy to finish editing the post (blogger really lacks a nice way of doing HTML tables).

Everything tastes like cloves

2008-10-22T21:22:00.000-04:00

My coffee tastes like cloves, as does the banana bread and my strawberry yogurt I had for lunch. The icecream I had last night tastes like cloves, as did the Tilapia and boiled vegetables. I swill my mouth out with water, but that only makes the clove taste even more intense. I even smell like cloves (so I am told).

Currently I am recovering from having all my wisdom teeth removed on the 10th of this month. After developing dry socket over the weekend (worst pain ever, thank-you very much, and that is despite me taking heavy-duty prescription painkillers) my oral surgeon has packed the sockets where my impacted wisdom teeth once were with gauze soaked in Oil of Cloves.

Oil of Cloves is obtained from the clove plant, Syzygium aromaticum, in fact from pretty much any part of the clove plant. The only active ingredient is eugenol, and it and Oil of Cloves have some pretty weird and wonderful uses. It is basically the clove-like smell associated with going to the dentists, as it is a natural topical anaesthetic (hence it being stuffed in the gaping holes where my teeth once were). It is also present, at smaller concentrations, in Cinnamon, Nutmeg and Bay Leaves. But its also toxic when ingested in large amounts (lethal dose for humans is 3.7g/kg) and is used to euthanize fish, in addition to being used to polish and clean Samurai swords.

And it tastes horrible. Really quite nasty. Try spending every waking moment for several days tasting it - if it weren't for the fact that its saving me from indescribable agony I wouldn't put up with it. But as Molecule of the Day notes, eugenol is not that dissimilar in chemical structure from vanillin, and vanilla is one of my favorite flavors. Artificial vanilla flavoring used to be synthesized using eugenol as a starting point, although now different methods (in the 60's the predominant one was based on Canadian wood-pulp) are used (at least, thats what wikipedia claims).

To think I would never have known all this had it not been for those damn impacted wisdom teeth!

[Image of eugenol structure taken from the Molecule of the Day eugenol entry]

Who contributes most to the Linux kernel?

2008-10-22T18:59:00.002-04:00

The latest Redhat magazine has an interesting aside on who contributes most to the Linux kernel. According to Greg Kroah-Hartman's (*) analysis, and as measured in raw number of patches the general community comes in first, with Redhat coming in second. Canonical, the commercial sponsor of the now popular Ubuntu (a spiffy modification of Debian) comes in 79th.

The overall largest contributions to Linux code come from individuals who have no apparent affiliation with any company, as Kroah-Hartman surmised by looking at their e-mail addresses. Red Hat came in second overall, with 11,846 patches.

By comparison, Canonical, the company behind Ubuntu Linux, is the 79th most active contributor, with 100 patches. Kroah-Hartman said that such behavior on the part of Canonical will be detrimental to the company and the Ubuntu distribution over time [emphasis mine].

“Then there are the distros that base themselves off of other distros, like Ubuntu and [Lance Davis’] CentOS. These distros have yet another layer between them and the original developers. Patches rarely, if ever, flow backwards into an upstream distro, and the developers are very unlikely to push their changes into the upstream packages as they don’t feel the need or don’t realize the issues involved as they rely on the upstream distro so tightly,” said Kroah-Hartman.

This is interesting, and not just as food for a meaningless distro-war. While I personally prefer Fedora to Ubuntu or Gentoo, I can recognize that as a distribution Ubuntu is pretty slick and well structured, and has done a lot to combat the myth that Linux is unfriendly and difficult. Ubuntu has been the most popular distribution according to distrowatch for several years. But somehow the heavy work on Ubuntu has not not flowed back into the kernel, at least as measured in patches. Why?

If forced to speculate without any evidence to support it I'd guess that much of the work on Ubuntu has been in terms of user-interface and applications, and not at the deeper level of the Linux kernel. Yet Redhat clearly feels the need to work very heavily at the kernel level. So this guess doesn't satisfactorily answer the question.

If anyone has a better hypothesis or insight, please let me know.

(*) Greg Kroah-Hartman works for Novell's SUSE labs division.

Mini-review: Star Wars: The Force Unleashed

2008-10-22T18:58:00.000-04:00

My overly-long post criticizing Halo 3 now seems a little out of proportion. I finally got Star Wars: The Force Unleashed (Xbox 360 version) to cheer me up while I recovered from having my wisdom teeth out. Boy, that is really a game with fundamental problems.

I was aware of the less-than-ecstatic reviews by X-play and gamespot (following their rather over-hyped pre-launch coverage), but sometimes things that bug other people don't really end up being something that bothers you (e.g. I liked the repetitiveness of Assassin's Creed, because that stuff was fun for me and I liked doing it again and again).

Given my generation I have a soft spot for Star Wars and even Star Wars games, and ST: TFU is great... in parts. Visually, even story-wise it varies between good and great.

But every now and again I ended up spending two hours trying to jump over the same damn chasm, or gap between two bridges, in an endless loop of button-mashing frustration.

Dodgy auto-aim, check. The only enemy any near me is a purge trooper right in front of me, except the auto-aim has my force lightning zapping off at some crate at 90 degrees angle to where I'm looking. Try to throw something with the force, and half the time it wont go where you want.

Boss battles where the bosses are immune to half of your force powers - thats just nasty - but add in the suddenly fixed camera and quick-time events spoil what should be epic cinematic moments. I don't remember any of the awesome moves Starkiller is supposed to have performed killing the Bull Rancor or defeating Vader, because all my attention was focussed on the bottom of the screen looking for the next X, B, A, Y to appear.

And don't even talk to me about that stupid bit trying to pull the star destroyer out of the sky. Which also looked totally different to the preview trailer they produced a year or so ago. Yes, lets create a situation completely different to the rest of the game control-wise and not explain any of it at all. Another hour or so of frustrated load, struggle, die, load... etc before I gave up and searched the web on what to do.

Anyway, it did have enjoyable moments, but the flaws were real and significant. I can't imagine that play testers didn't point out the problem areas that broke the flow and immersion of what would otherwise have been a pretty spectacular (if short) game.

What now for Star Wars fans? Bioware has finally announced what was long suspected: A Star Wars MMORPG set in the time of the Old Republic. I love Bioware's RPGs, but an MMO? It appears Bioware has accepted that almost everyone will want to be either Jedi or Sith, but I wonder how well balanced this will work out to be in practice.

[ST: TFU image from the gamespot review of the game.]

Replay: Halo 3

2008-10-18T09:24:00.000-04:00

Why am I only replaying the Halo 3 campaign for only the second time now, almost a year after it came out? That is the question I'm asking myself. I can't remember how many times I replayed the original Xbox Halo campaign, but the number is probably near or over 10. I've replayed the (not quite as satisfying but still fun) Halo 2 campaign at least four or five times.

It is not that I'm spending significant amounts of time on the multi-player... yes, Halo/2/3 multi-player is certainly nicer than Counter Strike and with the right people playing (i.e. not teenagers) its engrossing fun for a while, but multi-player isn't my favorite game play style.

I've been a big Halo fan from the get-go. I got the original Xbox to play Halo. I bought the PC version of Halo and upgraded my PC in order to be able to play it. I got Halo 2 the day it came out, and thought it was a way more enjoyable game than the similarly-timed Half-Life 2. I bought the Xbox 360 specifically to be able to play Halo 3. So I'm kind of bugged that I find I'm not playing Halo 3 all the time. I played it when it came out and enjoyed it, deliberately ignoring the critics. But playing through the first three levels for the second time last night left me... empty. There is something in the original that isn't quite there in the Halo 3, but what is it?

From a superficial standpoint Halo 3 should beat the pants off of Halo. Graphics technology from 2007 compared to 2001-era graphics, in a machine with vastly more CPU and GPU power. Improved AI. Wider and cooler array of weapons and vehicles. And the same company is at the helm, this isn't just a quick retread by a different company working on a time-limit (you know I mean you Obsidian!). All of these things matter - and in their little way they do add to the fun. But the problems lies elsewhere, and is to big and too general to be papered over by superficial gimmicks like detachable mini-guns.

Its not that Halo 3 is bad game, or not fun, its just that some part of the gestalt is not quite right, not as good as the original Halo.

Let us go through the list of things I've considered and see if they stand up under scrutiny.

Rushed and over-specified storyline, with
Spotty and inconsistent voice acting.
Play balance is off kilter for single player.
Linear game-play and levels that lack the expansiveness and freedom of Halo.

Lets consider 1 and 2 today, and return to items 3 and 4 in a later post.

Voice Acting: Early in the game, Cortana's frequent apparitional interruptions of the Master Chief are both annoying and curiously flat emotionally. Lord Hood's various statements (voiced by Ron Perlman) are pretty flat and lifeless even when they are meant to be rousing calls to arms. Later in the game, e.g. when the Master Chief is rescuing Cortana from High Charity, Cortana's voice is over-dramatic. Is this the writing (some of the lines are pretty sophomoric), or the deliberate direction given to the voice actors?

Although this is annoying and somewhat immersion-breaking it doesn't really bring down the game play. There is some truly horrific voice acting in games (e.g. Bloodrayne 2) that are still fun.

Story line: The story line is a real weakness in Halo 3.

In the original (Halo: Combat Evolved) there was no back story, and the story and game-universe unfolded as we played: A beleaguered human race under attack by a federation of alien religious fanatics who could not be talked or reasoned with, a fleeing human ship finding, exploring and destroying a mysterious alien artifact: Halo. What the story didn't reveal itself was left up to the mind of the player to fill in. By not saying too much the writers of Halo made their imaginary universe seem more real.

By the time Halo 3 comes out the Halo franchise has been stuffed full of pulp novels and comic books. There is now an elaborate back story whose level of internal self-consistency and quality is decidedly non-uniform (too many cooks spoil the broth). The enemies (both Covenant and the Flood), now fleshed out by all the genre merchandising, speak better English and are much chattier. Rather than the implacable alien foes of Halo: CE we now have enemies who appear merely misunderstood, petulant, or had bad childhoods, or something. The Elites don't bat an eye at co-operating with the Humans, nor express a moment's regret at abandoning the only religion they've supposedly had for thousands of years? Its just not believable. Its cheesy.

As with Halo 2 the game tries to tell too much in one game. Halo 3 has the Master Chief returning to earth, dealing with the Prophet's invasion of Africa, activation of the portal to the true Ark, attack of the flood, visiting the Ark, invading and destroying High Charity, activation and destruction of the replacement Halo ring. It is way too rushed.

Now I understand the dramatic impact of driving the story fast: get to Truth before he activates the rings and wipes out all life in the galaxy. No time to dawdle around exploring one thing at a time. But that could have been accomplished better in a single environment, be it Earth or the second Halo (had they been sensible about not rushing things in Halo 2 either). Halo was cool because you got to explore, at your own pace, all the different environments afforded by a ringworld, and they were often wide open and non-linear (I'll discuss level design some more in the next post on Halo 3). One had variety within a unifying theme.

But the writers of Halo 2 and Halo 3 seem to have run out of imagination regarding the rings - instead we have Earth, the Ark, etc etc. Multiple epic image that are never well fleshed out before being abandoned for the next new thing. Coupled with the rushed pace of the story line, all we end up with is a blur of images (most of them painted on sky boxes) as we move the Master Chief along the fixed linear line imposed by the story from Earth to the Ark to High Charity to the new Halo...

So the quality of the story line is inferior in Halo 3 compared to Halo: CE. Is this enough to damn the game? After all, when you start to get picky there are few games who's story lines stand up to close inspection. Half-Life, Half-life 2 and its subsequent episodes are all entertaining, but are hardly masterpieces of writing or paragons of internal consistency. When I next post on Halo 3 I'll discuss what I think of play balance and level design in Halo 3 with respect to Halo.

Linux Journal covers number crunching with GPUs and scientific python

2008-10-17T21:35:00.000-04:00

From a number cruncher's perspective the November 2008 issue of Linux Journal is actually quite interesting. In addition to an article on the petaflop Roadrunner supercomputer at LANL, there are two articles on number crunching with GPUs (one by Robert Farber, the other by Michael Wolfe) and one article on numpy/scipy by Joey Bernard.

Farber's article is really an advert for NVIDIA's CUDA, and unfortunately doesn't actually show any examples of doing something (this is something of a trend in LJ, as it seems to drift away from showing you how to actually code things and toward merely describing point-and-click mega-code-projects). Wolfe's article shows snippets of matrix multiplication using both CUDA and Brook, but is really more of a discussion about how to write a compiler that would automatically parallelize for GPGPU work.

Joey Bernard's article on numpy does try to scratch the surface with simple worked examples, including the use of matplotlib for plotting (or "ipython -pylab").

For a moment after reading his article I was terrified that I'd totally messed up using numpy in my python projects, as Bernard states that array multiplication in numpy (e.g. a3=a1*a2) is handled as a matrix multiplication!

However, its pretty easy to verify that unless you specifically created matrix objects (which his example did not do), then a1*a2 is an element-wise array multiplication.

To do matrix-like multiplication on numpy array objects you need to specifically do something like "a4=numpy.dot(a1,a2)" or "a5=numpy.mat(a1)*numpy.mat(a2)."

Anyway, I hope this issue is a sign that Linux Journal may get back to publishing more "hands-on" articles on general programming topics interspersed between all the Web 2.0 and database articles.

Less than impressed with KDE4

2008-10-08T19:42:00.001-04:00

My first Linux window manager experience was with fvwm - a step up from twm but hardly fancy and barely, just barely, functional. I forget the names of the window managers we used on the Decs and Suns used back in the mid-90's, but they weren't particularly fancy either. Since then I've used fvwm2, early versions of Enlightenment, Gnome (version 1), KDE2 and KDE3.

And over the years there has generally been progress, and progress by definition is good. Progress until now, that is.

I switched to KDE after experiencing major dissatisfaction with Gnome 2, and now that KDE4 is out I'm contemplating switching window managers again. Only it can't be the latest version of Gnome, as I have that on a spare laptop and don't like that either.

My first experience of KDE4 was on Kubuntu 8.04, an upgrade from 7.10 on an old Dell Latitude C400. That didn't last long enough for me to get a taste of KDE4, as the machine started freezing for no obvious reason after relatively short uptimes. A wipe and fresh install of Fedora 8 with KDE3.5 and the laptop worked fine once again. Was it Ubuntu, or KDE4?

Upgrading my home desktop to Fedora 9 (with KDE4.0) was the first real experience I had with KDE 4 and I was not impressed. Yes - I've read the blogs that discuss the fundamental reasons for chucking out vast amounts of the KDE3 code and rewriting things like the panel from scratch. Maintainable, extensible code is good.

But when the panel clock widget can't even handle displaying seconds you begin to think of KDE4 as a major step backwards. For an application as simple as a clock the KDE4 folks failed to provide the same functionality as KDE3. How the hell did this happen?

As for adding a terminal launcher to the panel - what happened to "Add Application Launcher?" I can add a widget - there seem to be an large number of widgets, most of which are thoroughly useless - but I don't want a widget. It took at least 30 minutes of messing around to work out that items in the launch menu (Kickoff its called, replacing Kmenu), when right clicked on, give an option to add to the panel. But you can't click on the panel itself and add an application launcher from there, even though its (a) the way KDE2 and KDE3 worked and hence the way KDE users expect, and (b) the old was more intuitive.

Oh, and don't edit the launcher's setting because the terminal icon will disappear and be replaced with a question mark. Progress, I tell you.

And transparent Konsoles (terminals) - we used to have those. Except now we can't have that. Sure, we can make the whole window transparent, including the writing, but that makes the writing hard to read.

As for the new panel (Plasma), well, hum, I totally agree that the power to add widgets to the desktop as well as the panel really makes up for the major lack on control over the panel appearance and lack of old panel (kicker features). That's what Linux is all about. Eye candy. No one really uses it because it is (or used to be) more functional, that is just a lie we tell the Windoze fanboyz.

Yes, I'm being sarcastic.

Its enough to make you suspect that major parts of KDE4 were written by 13-year olds whose Ritalin or interest ran out before they'd finished coding even the most basic of applications.

Now I'm a patient kind of guy. KDE4 and Fedora 9 came out ages ago and I refrained from complaining because I expected these "bugs" to be ironed out. "Yes, all very unfortunate to roll out a product clearly not ready for prime time, and that is functionally inferior to its predecessor, but I'm sure it'll get better" I thought in my typical latte-sipping, elitist, East Coast liberal mode of thinking...

So I waited. And lo and behold, the clock widget now does seconds. Hallelujah Brother! Can I get an Amen? Except the damn Konsole launcher in the panel is now failing, and takes a minute or two to tell me "KDEInit: can not launch /usr/bin/konsole". Acting on a hunch I remove the --enable-transparency option and it works again... for now.

So KDE4 remains on probation as far as I'm concerned. I have a lot of experience invested in KDE, which I am loath to lose by switching to Enlightenment or XFCE, but I'm warning you KDE: Mess me around some more and it is over.

Anathem. You either get it or you don't.

2008-10-06T11:51:00.000-04:00

If you know what this figure is, then I think you might like Neal Stephenson's Anathem. If you don't know what this is, or worse, know but don't think its cool, then you're not going to understand Anathem. Sadly PZ Myers is in the "I don't get it" camp.

The figure is of course Euclid's famous but overly complicated geometrical proof of the Pythagorean Theorem (the image from the Wolfram web page on this subject, which is worth reading).

Forget the later half of Anathem - its just an extended action scene - the real meat is in the first half and if you're not hooked by the dialectical discourse between Theors by half way through then you're not going to get it.

Anathem is a exploration of math, physics, and metaphysics, OK? Square root of two demonstrated by cutting cakes. Many-worlds interpretation of quantum mechanics. Platonic forms. Etc.

If you don't know much math, physics or metaphysics, you might not be able of appreciating it. The same way Cryptonomicon is best appreciated by people with *nix experience (and OSX doesn't count, apple dweebs!), Anathem is best appreciated by people similar to the Theors it describes.

Misology: You learn something new every day

2008-10-03T21:08:00.000-04:00

Actually if you are a misologist you probably don't learn something new every day because you fear or hate reason, logic and knowledge. Not a good character trait in someone who has to run a country, but some people insisted on voting for the folksy ones.

I don't think I'd heard the term before today, but now I'm going to use it all the time.

Berube is back.

2008-09-30T21:28:00.000-04:00

The Lord High Professor of Dangeral Studies has returned in time to lead us out of the economic meltdown. Thats right, Michael Berube has resumed blogging.

And if your name needs characters that aren't pure ASCII its just tough OK? Suck it up.

Wiki vs Google Groups/Sites

2008-09-27T12:40:00.000-04:00

For work reasons I've been looking at wikis, as for our international collaboration will need an electronic way of outlining what we're doing, discussing it, and uploading files/images and other such info (and we're not allowed to spend money on flying furriners over here). Oh, and it has to be private and secure...

I must say I hadn't realized how horribly messy and complicated wikis are to set up, or how many non-obvious capabilities and requirements you have with the various wiki options available.

I quickly decided that I didn't want a relational database at the back end, which narrowed the field nicely, before settling on what I hoped to be a relatively simple set of wiki software: the python-powered MoinMoin. Flat file back end and powered by python - it sounded ideal to me.

Five hours later I had a full test site up, but I can't say it was as easy as I'd have liked. Nor was the security and authorization stuff at all transparent (try reading this), in fact I had no idea of whether the test site was secure or not. And wiki syntax is terrible (non intuitive!). I'm amazed wikipedia works at all.

Luckily I then discovered Google Sites ("Create websites and secure group wikis") which I must say I'm very impressed with so far. Simple Google account password protection, revision history and alerts, semi-WYSIWYG editor, comments and attachments. Maybe not industrial strength but much simpler and easier to use. Maybe we'll end up using Google Groups instead, but still much much easier than setting up a localized CMS. Good job Google!

Game Piracy is not the reason your sales are bad

2008-09-26T21:31:00.000-04:00

Wise words from a Stardock developer, who manage to have massive sales despite not putting copy protection on their games. Yes, game piracy (a) exists (I suppose, never felt the need myself), and (b) is bad, but thats not the reason why Crysis did so poorly, despite the BS some people talk.

Maybe I should run the full Dreadlords campaign on Gal Civ II while waiting for Fallout 3 to come out?

Anathem's ending?

2008-09-24T09:10:00.000-04:00

I finished reading Anathem last night.

For the first 400 pages I thought this was the most intellectually interesting and stimulating book that Neal Stephenson has written to date, although I wonder whether someone not in the physical or mathematical sciences would find it so interesting. As a venue for a discussion on metaphysics its brilliantly written.

The ending? I'm a little confused by the last 100 pages, in particular the last 20 or so pages. Stephenson's endings to his book have always been the weakest part of his writing, so in perspective this is better than most of his endings. Maybe I'll have to read it again...