--- Day changed Tue Mar 31 2009 00:04 < kanzure> shape optimization with freefem++ - http://www.cmap.polytechnique.fr/~allaire/freefem_en.html 00:14 < fenn> neat stuff 00:15 < gene_> http://www.technologyreview.com/computing/22339/?a=f 00:15 < gene_> check it out 00:16 < gene_> 500,000 of these chips should have around the same number of neurons as a human brain 00:16 < fenn> blah.. i'd much rather that effort go towards an open source reconfigurable FPGA 00:17 < gene_> these people are brain researchers 00:17 < gene_> they aren't interested in such things 00:17 < gene_> but 500,000 is in the range of a production run 00:18 < fenn> it's interesting that it runs 100000x faster than real neurons 00:18 < gene_> wonder if it'd become sentient 00:18 < gene_> damn 00:19 < fenn> needs some i/o at the very least.. and real brains have a lot of hardwired functionality 00:20 < gene_> cameras 00:20 < gene_> the internet 00:20 < gene_> chat rooms 00:21 < katsmeow-afk> i had some hope for the propellor chip, but it remains slow, and no way to tell which cpu is on the io buss at any time 00:21 < katsmeow-afk> so the cpu are forced to share all external resources 00:22 < fenn> propellor looks like an amateur first attempt at getting a chip fabbed 00:23 * katsmeow-afk has a stupid question: why not a state machine with one crosspoint set across them, instead of a box of neurons with the synapse possibilities fixed-in-hardware? 00:24 < katsmeow-afk> so for 50k neurons, you'd have at least 50k^2 possible connections? 00:24 < katsmeow-afk> and that's thinking 2 dimensionally 00:27 < katsmeow-afk> In fact, the current prototype can operate about 100,000 times faster than a real human brain. "We can simulate a day in a second," says Karlheinz. 00:28 < katsmeow-afk> so if they multitask the thing, they can simulate 100k as much hardware with a system as slow as a human 00:28 < fenn> yep 00:29 < fenn> you need on-chip cache though 00:29 < fenn> or else some really fast ram bus 00:29 < katsmeow-afk> lay up some ram literally on top of each neuron, make a cube 00:30 < fenn> i guess 00:30 < fenn> how many layers can they do these days? 00:30 < katsmeow-afk> dunno, but it bet it's not enough 00:31 < kanzure> Markram and IBM were last working on some FPGA or hardwired ICs to simulate neurons 00:31 < kanzure> what are these called again? AISC? fenn? 00:31 < katsmeow-afk> however, if they use a serial data stream, recirculating, and all the ram sync'd, they could keep with the state machine idea and use only one wire to each neuron 00:31 < fenn> ASIC = hardwired IC 00:31 < katsmeow-afk> or 8,, or so 00:31 < fenn> application specific IC 00:32 < fenn> heh. bits in the pipe 00:32 < katsmeow-afk> yeas 00:32 < fenn> propagation delay ring buffer :P 00:32 < katsmeow-afk> yeas 00:32 < fenn> sort of gives a new meaning to volatile memory 00:33 < katsmeow-afk> the neuron either changes the byte, or not, then it's put back in queue, and the next byte is sent in 00:33 < katsmeow-afk> saves a huge buss into the chip, and an addy/data buss all thru it, and the muxes, 3-state buffers, etc 00:37 < fenn> in brain research there are a lot more than 1 byte worth of variables 00:37 < fenn> i'd hate to have to fab a new chip every time you want to add a variable 00:38 < katsmeow-afk> so send in 2 or more 00:38 < katsmeow-afk> well, atm, they have no option either way 00:38 < fenn> ya 00:38 < fenn> see why i'd rather have a reconfigurable FPGA 00:38 < katsmeow-afk> but you get a ton less working density 00:39 < kanzure> Eugen Leitl likes to complain about slow interconnection speeds 00:39 < katsmeow-afk> cost may be even more that way, power use certainly would be 00:39 < kanzure> for massively parallel computing. 00:39 < fenn> the RC constant thing? 00:39 < kanzure> ? 00:39 < katsmeow-afk> i have some 600 128k 15ns ram chips,, to use a mass of them would cost so much more in power and pcb space, it's rediculus 00:39 < fenn> long interconnects have high capacitance which slows down their rise times, introducing delay when communicating across the chip 00:40 < fenn> so some smart kids tried making 'optical interconnects' basically fiber optics from one side of the chip to the other 00:42 < fenn> katsmeow-afk: i dont know how the neuron simulator engine works on the chip, but i really doubt it's analog. so you'd be able to change the evaluation algorithm with an FPGA 00:42 < fenn> um, i forgot where i was going with that 00:42 < kanzure> was it something about IX10 or something? 00:42 < katsmeow-afk> i forgot what it was even pertaining to 00:42 < kanzure> I don't knwo what it's called, but there's an optical interconnect that supercloudcluster advocates like to rant about 00:42 < kanzure> it has an 'X' in the name methinks 00:42 < katsmeow-afk> kanzure, i remember that 00:43 < katsmeow-afk> fenn, i never said cpld or fpga would not work, nor that they were analog 00:43 < katsmeow-afk> i only said a mass of them might cost more than volunteer work at a fab place 00:44 < katsmeow-afk> freeware, cost writeoff, volunteer, price paid in future stock, etc 00:45 < fenn> i bet we will start to see spread spectrum chip-chip interconnects in a few years 00:45 < fenn> instead of optical 00:45 < kanzure> we don't have those yet? 00:45 < katsmeow-afk> have you done the math on them? is one capable of handling 2.4ghz buss 64bits wide? 00:47 < fenn> kanzure: i think they are stuck on just increasing clock speed with a plain squarewave signal 00:51 < kanzure> http://www.maths.bris.ac.uk/~mairw/blog/archive/2006_09_10_archive.html 00:59 < kanzure> anyone have experience with gerris? 01:11 < kanzure> http://gfs.sourceforge.net/wiki/index.php/An_engineer's_pipe_flow 01:30 < fenn> so you didnt know what to tell anythony lamantia? (any non-UT bio stuff in austin) 01:30 < kanzure> I told him a few names 01:30 < kanzure> a few groups, etc. 01:31 < kanzure> just thought I'd forward his message to you and jonathan cline 02:08 < katsmeow-afk> hmm Polycarbonate blocks all UVA and UVB rays 03:28 < gene_> I'm sure there's some non UT bio stuff in austin 03:30 < gene_> I see the come work at biotech company x poster in the halls every now and then 03:33 < kanzure> gene_: did you see this? 03:33 < kanzure> 03:33 < kanzure> http://heybryan.org/bioreactor/membraneless_filtration/2009-03-30_2.png 03:35 < gene_> what the heck is that? 03:35 < kanzure> just a navier strokes problem 03:36 < kanzure> *stokes 03:36 < kanzure> another: http://heybryan.org/bioreactor/membraneless_filtration/2009-03-30.png 03:36 < gene_> something has gone horribly wrong 03:36 < kanzure> well the box is a little small, I'm going to increase it 03:36 < gene_> second one looks much better 03:36 < kanzure> also it's not actually the problem that we want to solve, and the output is all wrong (who wants to look at vectors anyway?) 03:37 < kanzure> ideally a colorful isosurface is what we should be looking at, or something 03:38 < gene_> wait a second are those vectors going through the wall? 03:38 < kanzure> no 03:38 < kanzure> they are just drawn like that :( 03:39 < gene_> umm 03:39 < gene_> it's in a box 03:39 < kanzure> right, it's not on an infinite plane. 03:39 < gene_> yeah 03:40 < gene_> and that's an infinitely thin wall 03:40 < kanzure> anyway, what I've been doing is going back through the literature and grabbing the right equations 03:40 < kanzure> what's wrong with that? 03:40 < kanzure> the walls are just boundaries, they are basically infinitely dense and ignored in the simulation 03:40 < gene_> document what equations you are using 03:40 < kanzure> of course. 03:51 < kanzure> http://science.slashdot.org/article.pl?sid=09/03/30/1218258 03:51 < kanzure> heh, go little turtle, go! 04:02 < gene_> do you know anything about curve fitting? 04:02 < kanzure> functonal induction / regression analysis? 04:02 < kanzure> *functional 04:03 < gene_> least squares method 04:08 < gene_> something like that I guess 04:35 < kanzure> is there any particular way to figure out if a latex-math document is talking about the negative change-in-some-variable, versus the negative gradient vector? 04:37 < kanzure> hm. context I guess. symbols without source code suck. 04:54 < gene_> http://en.wikipedia.org/wiki/Turboencabulator 06:35 < fenn> holy crap it takes 45 minutes to fill up a standard 16GB class 6 SD card 06:42 < willPow3r> sd cards aren't known for their high data transfer rate 06:44 < fenn> yeah as i'm finding out 06:44 < fenn> it might be worth spending 2x for 30MB/s data rate 06:44 < fenn> vs 6MB/s 06:44 < fenn> since i'll probably be all swapon swapoff like karate kid 06:46 < willPow3r> it would cut the time to fill it down to 9 mins theoretically 06:46 < fenn> yeah i'm actually not so concerned about that as much as swap speed 06:49 < willPow3r> hdds have a much higher r/w speed than that 06:49 < willPow3r> so why bother? 06:50 < fenn> because i'll be strapping it to my leg 06:50 < willPow3r> good reason. i figured you were using it in a standard computing environment 06:51 < fenn> also thinking about getting multiple cards and doing RAID over USB :P 06:52 < fenn> but i need one "main" card for the SD slot anyway 06:53 < fenn> the adapters are $2 and a 4GB card is like $5 so why not 06:53 < willPow3r> what are you doing with it anyway 06:54 < fenn> i just need to find a small low-power USB2.0 hub 06:54 < fenn> this is going to be my borg attachment versino 1.0 06:54 < fenn> "memory glasses" 06:54 < fenn> i guess i should draw something up in inkscape 07:08 < willPow3r> for augmented reality applications? 07:08 < fenn> yes 07:08 < fenn> and general not-tied-to-a-computer-ness 07:09 < fenn> except i am, literally - that's the irony of it 07:13 < willPow3r> it seems ironic but it really isn't 07:13 < fenn> dealextreme has some weird stuff - Name Badge SD Card, Visor Eyeglasses Clip (type R for RACING), LED Light Illuminated Ear Pick 07:14 < willPow3r> you're just getting rid of the ball-and-chain power cord 07:14 < willPow3r> type R 07:14 < fenn> http://www.dealextreme.com/details.dx/sku.6833 07:15 < fenn> it looks like a mutated USB key 07:15 < willPow3r> it only got 3 stars out of 5 07:16 < fenn> well i can't figure out all these different lithium battery formats, so i'll just stick with AA NiMH 07:51 < fenn> is there a name for this type of buckle/clip? http://www.amazon.com/Op-Tech-Connector-Uni-Loop-Customize/dp/B0010HA6A6/ref=pd_sim_p_3_img/192-9126761-4820535 07:51 < fenn> and the typical black nylon ribbon strap that it goes with 07:55 * fenn checks mcmaster-carr 08:08 < fenn> aha they are called webbing side-release or quick-release buckles 08:09 < fenn> and i can even get it in kevlar if needed :D 08:09 < fenn> not like the connector would survive that kind of treatment anyway 08:11 < fenn> funny that the strap is so much stronger than the beefiest fitting 08:17 < willPow3r> at least that way you know where the breaking point will be given enough stress to the system 08:26 < fenn> apparently also called "fastex" buckles 09:14 < fenn> hmm. today's lesson: make sure all the files are chowned to your username before uploading/extracting the .tar file 09:15 < fenn> that is obnoxious 09:17 < fenn> the wiki script makes new pages owned by www-data, and i just did chmod g-w somehow so i can't edit them 09:17 < willPow3r> on flaminggay? 09:17 < fenn> yeah 09:17 < fenn> much obliged if you could chown fenn /var/www/fennetic.net/ -R 09:18 < willPow3r> k done 09:20 < fenn> ah. the bastard creates them as g-r 09:20 < fenn> er, g-w 09:21 < willPow3r> you want 2750 on the permissions? 09:21 < willPow3r> they're set to 2770 now 09:21 < willPow3r> so apache can write if you need to use a cms for anything 09:22 < fenn> oh is that an apache setting? 09:22 < willPow3r> apache runs under the www-data group 09:22 < fenn> i want to be able to modify any files that are group www-data 09:23 < willPow3r> if you use the # groups command you can see the groups that you are in 09:23 < willPow3r> you should be in www-data as well 09:23 < fenn> i am 09:24 < fenn> i just made a new page in the wiki, and it created /var/www/fennetic.net/machines/wiki/6D6F72657374756666.txt 09:24 < fenn> see the problem? 09:25 < willPow3r> it created it as www-data:www-data 09:25 < fenn> and -rw-r--r-- 09:25 < willPow3r> yeah, i see it 09:25 < fenn> which means i can't write to it 09:26 < willPow3r> the stickybit isn't set for the directory. just a sec 09:27 < fenn> i dont think that matters 09:30 < willPow3r> try making a wiki page now 09:31 < fenn> same thing 09:33 < fenn> don't worry about it - i am dumping pukiwiki before long and i'll bug you then 09:33 < willPow3r> heh k 09:33 < fenn> or not.. i can just move the dir to a dark corner 09:33 < willPow3r> still something i need to know how to fix 09:33 < fenn> i am afraid it's some kind of php file creation mode setting 09:34 < willPow3r> could be 09:37 < willPow3r> its the umask setting in apache2.conf. i'll change it in a sec 09:43 < willPow3r> its set, see if it works now 09:44 < fenn> yes that worked 09:45 < willPow3r> excellent 09:46 < fenn> while you're at it.. the .htaccess files aren't doing anything 09:46 < fenn> (allowoverride all) 09:48 < willPow3r> done 09:50 < fenn> cool thanks 11:59 < ybit> kanzure, didn't you form an open manufacturing ieee online group? 11:59 < ybit> ah, there it is 11:59 < ybit> manufacturing automation 13:06 < kanzure> you're going to run out of ip addresses 14:05 < kanzure> does anyone know what Smari was talking about when he mentioned "permaculture"? 14:06 < kanzure> I looked it over on wikipedia the other day and found that it started off like a reasonably good idea- taking responsibility for building human life support infrastructure- 14:06 < kanzure> but then it turned into this terrible anti-tech campaign/movement thingy by the third or fourth sentence of the Wikipedia article 19:58 -!- any32072065 is now known as katsmeow-afk 20:04 < kanzure__> I have a terrible idea 20:06 < kanzure__> compute the center of mass of the density distribution resulting from the flow through a channel of some arbitrary geometry 20:07 < kanzure__> compare the location of that center of mass to a target location (x,y) where you would prefer the density to end up at 20:08 < kanzure__> then use some sort of design algorithm (SA, GA, A*, BFS, DFS, ..) to 'design' (and then consequently evaluate) various geometries, and test them for that flow 20:08 < kanzure__> in particular I am thinking of test cases where an arbitrary channel geometry is specified but with one side as a straight line- so only one side is 'arbitrary' 20:09 < kanzure__> there are a few particular cases that I can imagine: (1) the line is defined as a sequence of different characteristics: rounded edges, jagged edges, etc., which are really just the perimeters of 2D shapes strung together; (2) specific cases where there are only a handful of variables to manipulate 20:09 < kanzure__> in case #2, it would be something like "vary the increaese in channel diameter by some function blah" 20:09 < kanzure__> or some other multivariable optimization problem. 20:10 < kanzure__> it was interesting that in my multivariable calculus class lecture today we were going over a density function for laminar objects and double integrals. haven't had such a ridiculously relevant lecture in a while now. 20:11 < kanzure__> woah wtf http://en.wikipedia.org/wiki/Mind_uploading flagged for deletion 20:16 < kanzure__> http://heybryan.org/books/papers/Cheap%20third-generation%20sequencing%20-%20nanopores%20-%20cyclodextrin%20-%20hemolysin%20-%202009.pdf 20:17 < kanzure__> Cheap third-generation sequencing via alpha-hemolysin nanopores and cyclodextrin. 20:18 < kanzure__> "an exonuclease digests single-stranded DNA, and as single bases fall into the pore, they transiently interact with the cyclodextrin and block an electric current that runs through the pore- the current amplitude is then easily converted into a known nucleotide" 20:19 < kanzure__> how sure are they that the nucleotide will fall into the pore? 20:19 < kanzure__> oh 20:19 < kanzure__> turns out they are struggling with that particular problem. 20:31 < kanzure__> oh 20:31 < kanzure__> so if you're able to discriminate between nucleotides based off of current, 20:31 < kanzure__> shouldn't the same be true for discriminating between two strands of DNA? 20:32 < kanzure__> you take a measurement of the current flow before the exonuclease chops off a nucleotide, and then a measurement after it chops off a nucleotide, and then you compare the two and if you have the ability to discriminate between individual nucleotides to begin with, then surely you have the same level of accuracy even with a much larger molecule? 20:33 < kanzure__> and the difference is then what's missing. --- Log closed Tue Mar 31 22:11:04 2009 --- Log opened Tue Mar 31 22:13:24 2009 22:13 -!- Irssi: #hplusroadmap: Total of 15 nicks [0 ops, 0 halfops, 0 voices, 15 normal] 22:14 -!- Irssi: Join to #hplusroadmap was synced in 92 secs 23:31 < kanzure> lesson learned: never ever call apt-get -t unstable r-base