2012-12-07.log

--- Log opened Fri Dec 07 00:00:45 2012
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kanzure[09:46] <Jeff2> The Nemaload project, by David Dalrymple, recently updated its website with more information.07:00
kanzurehttps://raw.github.com/gist/4218566/b86c0247c33d07422f69fb2ba116f9096181c232/OpenWorm-Office-12-5-1207:01
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kanzurei didn't know davidad was calling it nemaload07:29
kanzurehttp://nemaload.davidad.org/07:29
archelsoh shit they used the word 'upload'07:30
archelsWhat university are you working at? Or is this a startup?07:31
archelsThis is a privately backed science project, both undertaken and funded for its own sake. It's not a startup (though I collaborate with startups). It's not a university project (though I collaborate with universities, and hold a Research Affiliate appointment at MIT). It's not a new way to do science, because scientists were backed by private patrons centuries ago, but in modern America, it is pretty unusual.07:31
kanzurehaha his dob requirements are a little stupid http://nemaload.davidad.org/jobs07:32
kanzure*job07:32
archelsNemaLoad is backed by the http://thielfoundation.org/07:32
kanzureyeah, he knows thiel.07:32
kanzurenot surprising.07:32
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kirkaHi kanzure07:45
kanzurehello.07:45
kirkaI wanted to ask a few questions about a source of weird bug in NE107:45
kirkaPossible source of course.07:46
kirkaThe bug is described as follows: "When I click over a part or assembly, background goes white and model is clipped by half (!) (everything that's further from viewpoint than some plane is just plain white)". It's also strange that this bug manifests itself only with half of parts07:48
kirkaThese parts are rendered strangely from the beginning: looks like first atom of each subpart is rendered at origin (0,0,0)07:49
kirkaI searched quite a lot across drawing code, but I'm not quite familiar with it07:50
kirkaMaybe it's more obvious to you07:50
kanzurei suggest adding this to https://github.com/kanzure/nanoengineer/issues so that others can see the issue07:50
kanzurethen link to the new issue url and email nanoengineer-dev@googlegroups.com so we can discuss it in public with the other developers07:51
kirkaBut is it okay, since this is windows x64 bug?07:51
kirkaIt doesn't manifest itself on linux07:51
kanzurei don't care07:51
kirkaOkay07:51
kirkabtw, it works very fast on win 64, shaders work too07:53
kirkaIf we want it to be used by wider audience, windows port could be good thing07:54
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kirkakanzure Aren't you tired of NE1? If yes, than I can not to bug you with it anymore.08:00
kirkaI understand that you are quite busy08:00
kanzurei am not tired08:03
kirkaOkay then.08:03
kirkakanzure btw I found class diagram at http://www.nanoengineer-1.com/snapshots/NE1_Documentation/, it's useful08:05
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kanzurekirka: thanks for filing the issue08:25
kanzuredon't forget to email nanoengineer-dev@googlegroups.com with a link to it08:25
kirkaI'm writing it now08:26
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kirkaActually, I think that I should sync my current local repo with my github, so the code were public08:27
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kirkaSo I'm remebering how to use git again, heh08:27
kanzurekirka: you could push it to a different branch08:27
kanzuregit push origin mybranchname:mybranchname (pushes your local branch 'mybranchname' to a branch called 'mybranchname' on github)08:27
kirkaOk, nice idea08:27
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kirka>line: 75(+) 62(-) files: normal=0, non-versioned=5, modified=5943, added=0, deleted=0, conflicted=008:32
kirkaI'm trying to do domethinag about 5943 "modified" files08:32
kirka*something08:33
kirkaThere should be much less08:33
kanzureit should say what was chagned08:33
kanzure"git diff" might help08:33
kirkaYes, it says this08:33
kirkaThat's probably because I cpopied whole local repo from linux to windows08:34
kanzurewell, what are the differences?08:34
kanzurepastebin08:34
kirkaOh, I don't remeber every tiny patch08:34
kirkaI will do something about it by myself, ok.08:35
kirkaWell, I will upload it as it is, then download and check if it works, heh08:44
kirkaThat should do it08:44
kirkaWell, it works like it should. There is new branch Win7x6408:56
kanzurelink?08:56
kirkahttps://github.com/elfion/nanoengineer08:56
kirkaIt's main branch now08:57
kanzurei think you mean https://github.com/elfion/nanoengineer/commits/Win7x6408:57
kanzureit looks like most of the changes are file mode changes08:58
kirkaYes, but you see it thinks that all files were changed, so it's uninformative08:58
kanzureyes, you changed the modes08:58
kirkaAh, that's good08:58
kanzurebut why did you do this08:58
kirkaThat's some OS related things08:59
kanzurejrayhawk: your advice on cleaning this up would be nice08:59
kirkaI just copied shole repo as folder from linux to windows08:59
kanzurejrayhawk: any ideas?08:59
kirka*whole08:59
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kirkaI will try to ensure that all progress is uploaded to github and software works, and when the whole program will be usable, some kind git-guru could help with cleaning the repo.09:04
kanzurekirka: i'll try to clean this up soon.09:04
kirkaMaybe that's too early?09:04
kanzureon windows you have to do a mode change thing with git,09:04
kirkaWhy don't do it when everything works?09:04
kanzuregit config core.filemode false09:05
kanzurebecause windows sucks09:05
kirkaOk09:05
kirka>windows sucks09:06
kirkaI agree, but [video]drivers and heavy CADs work, and that's most important for me.09:06
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kirkakanzure btw Haven't there been eudoxia recently?09:17
kanzurei haven't seen him since 2012-09-2109:17
kirkaOk, I'll get him by email09:18
kirkaHe works on cool LLVM lisp09:18
kanzureif you had used "git clone" you would have not had that filemode problem09:22
kanzurebut by physically copying from linux to windows, git didn't have a chance to configure itself properly09:22
kirkaOk, I will remember it09:22
kanzurekirka: could you do that and then re-commit?09:26
kanzurethis way the commit diff will be more reasonable09:26
kirkaOhh, sorry, I can't. There was large period between, so I forgot which small patches I added. I'm afraid of losing them.09:27
kirkaAdded some docs09:28
kirkaWow, there is activity in nanoengineer-dev09:45
kirkaHmm http://sourceforge.net/projects/moleculardynami/?source=dlp09:50
kirkaI'll try it09:50
kanzureit's just someone's crappy changes.. i wish he would have submitted a diff or something09:52
kanzureinstead of creating a completely new project09:52
kirkaWhat intrigues is v1.1.1 that can work on win 709:52
kanzuresigh09:52
kirkaHeh09:52
kirkaI'll work on linux port too09:53
kirkaActually, I'm interested in parallelizing ND-1 win pthreads09:53
kirka*with09:53
kirkaIf the system is large, splitting pair interactions calculation between threads won't be difficult09:54
kirka*modeled system09:54
kirka>v1.1.109:57
kirkaNope:09:57
kirka>  File "bsddb3\dbshelve.pyc", line 123, in keys09:57
kirkabsddb._db.DBRunRecoveryError: (-30974, 'DB_RUNRECOVERY: Fatal error, run database recovery -- C:\\Users\\Kirka\\Nanorex\\Preferences\\bsddb-shelf: pgin failed for page 1')09:57
kirkaException bsddb._db.DBRunRecoveryError: (-30974, 'DB_RUNRECOVERY: Fatal error, run database recovery -- PANIC: fatal region error detected; run recovery') in09:57
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eudoxiayo kirka10:31
kirkaeudoxia yo10:32
eudoxiai haven't seen you in a while10:33
kirkaYes, I was doing robotics and other stuff10:33
kirkaI'm reading your blog, it's well written10:33
eudoxia<310:33
eudoxiaany progress on nanoengineer?10:33
kirkaYes10:33
kirkaI have (kind of) ported it to windows x6410:34
kirkaBut there are weird bugs10:34
kirkabtw, https://github.com/eudoxia0/Hylas-Lisp looks cool10:34
kirkaI waited for womething like this for years10:34
kirka*something10:34
eudoxiayeah10:36
eudoxiaI should add some docs10:36
kirkaYep10:36
nmz787hi kirka10:37
eudoxiaalso macros aren't implemented yet10:37
kirkanmz787 Hi10:37
kirkaeudoxia I think CL-like macros would be appropriate10:37
eudoxiai don't know much about the differences between scheme and CL macros10:38
kirkaScheme macros are very complex, I honestly haven't mastered them10:38
eudoxiabasically what I have in mind is, have two kinds of macros: 'full' macros, that take all their input as a raw, unprocessed string, and 'safe' macros that have an argument list where some arguments can match any type and others have to be of a specific type10:39
kirkaThat's ok10:39
eudoxiagod i love llvm10:39
kirkaI see, you are linkiking it to SDL10:39
kirkaIt's possible to write a good and fast CAD with this lisp10:40
kirkaAnd simulator10:40
nmz787kirka: you were aksing about my DNA synthesis project... well I'm now thinking of just applying to a Chemistry PhD program to work on it, that way I'll have lots of resources and get a small pay check rather than paying this local lab10:41
kanzurenmz787: but the university will own your work10:41
nmz787kanzure: yeah but it might not happen otherwise10:41
kirkanmz787 That seems reasonable as the project is serious10:41
kanzureit seems completely unreasonable10:41
kirka>will own10:41
eudoxiakirka: the 'fast' part is certainly doable10:41
kirkaIs it true?10:41
kanzurekirka: that's how science works in the US.10:41
eudoxiabut I'm not linking to SDL10:42
eudoxia-ldl is for the dynamic loading of libraries10:42
nmz787yes the Uni will own it, my name will still be on it10:42
kirkaeudoxias I mean example with SDL10:42
eudoxiawhat was the filename again?10:42
kanzurenmz787: what do you need so that you don't go back to school?10:42
kirkanmz787 So, it won't be possible to license it under some OSS (OSHW?) license?10:43
eudoxiakirka: i know i have an example with SDL but I thought it was in the docs folder that isn't up yet10:43
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kirkakanzure Seems my uni is quite relaxed about IP questions, I haven't heard about it "owning" researcher's works.10:46
nmz787kanzure: umm, cash flow would be a good one, since the lab wants $20/hr and I could see myself easily spending 5-15 hrs a week10:46
nmz787kirka: as far as I can tell, keeping this device (if it works) an industry secret would be the best thing for making $10:47
nmz787anything else requires $$$ for lawyers10:48
kirkanmz787 Well, it's your right.10:48
kirkaeudoxia You use LLVM's type system (machine types and vectors)?10:49
nmz787or maybe keeping it closed, make some $ on DNA sales, then get noticed enough to be approached about a buyout, approached with some legal suit if they think I'm certainly stepping on some bigshot corp's IP10:49
kirkaAh, and structures10:49
kirkanmz787 I see, you could violate a lot of patents with your device.10:49
nmz787or make some $ then once my school is payed off and I have some $ for getting married and for lawyers, then look into OSHW for real10:50
kanzureyour debt really constraints your options10:50
nmz787I'm not sure about 'a lot10:50
nmz787'10:50
kanzure*constrains10:50
nmz787but even one is enough to get sued and shutdown10:50
kanzureif you go around worrying about every patent under the sun, you will never do anything10:51
nmz787kanzure: I don't see it that way really, I just haven't any good means of making income that can be channeled into what could turn out to be an expensive hobby10:51
nmz787but if I do it under a PhD program, if the device fails, I still get a PhD nametag10:51
nmz787and that nametag is what get's a lot of the investors all hot10:52
kanzurenot completely. it's one thing that helps you get noticed by investors but it's not obligatory.10:52
kanzurebesides, you probably don't want investors anyway. it really complicates things.10:52
kanzureespecially when you have no prototype.10:52
kirkanmz787 strategy benefits him (PhD degree is useful), isn't that good?10:54
nmz787I think so10:54
nmz787there are a lot more toys at the university10:54
nmz787a lot more ppl willing to collaborate since you're an alum10:55
nmz787if I'm working on campus in a lab, I'll physically be close to other's with lots of knowledge for the probulation10:55
kirkaPersonal gain should be of first priority, isn't it?10:55
nmz787well i def want to gain, but I want to eventually spread the wealth/love10:56
kanzurei don't think you want to collaborate with assholes who only collaborate with you because you're an alum.10:57
kanzurethat doesn't make sense.10:57
kanzurekirka: well, if he wants to go off and make his own proprietary project that's a new direction that wasn't really talked about before.10:57
nmz787i just figure if i'm going to spend money on this project, a PhD program means I don't have to spend $..... if it works I'll still get a piece of the pie, if it doesn't I still get a PhD10:57
nmz787if I'm doing this DIY, I get no PhD if it fail10:58
kanzurebut you already have all of that other debt. is this one of those sunken costs fallacies?10:58
nmz787not sure what you mean by that10:58
nmz787if I get into PhD I will get paid by the Uni10:59
nmz787and my debts are put on pause10:59
nmz787but I'll actually be able to pay them off with the Uni's pay check10:59
kirkakanzure But this way the probability of success is higher. And nmz787's device could hit the market sometime. If it'll make DNA synthesis cheaper, then everybody wins.10:59
nmz787and my primary job won't be flipping burgers or some dumb lab tech job or programming stuff that isn't related to science11:00
kanzurekirka: i completely disagree that it increases his probability of success.11:00
nmz787kanzure: i disagree with that11:00
kanzureyou disagree that i disagree? how the fuck would you know better than me whether or not i disagree or agree?11:00
kanzurewtf is going on here11:00
nmz787heh11:00
nmz787i disagree that it won't affect the project's success11:01
kanzuremaking it a university project changes the project and it's something different.11:01
kanzureso, open source hardware microfluidic dna synthesizer success probabiltiy is set to zero11:01
nmz787nah, the DNA synthesizer is just a solution for a problem that I need to find11:02
kanzureand commercially-encumbered university microfluidic dna synthesizer is somewhere above zero11:02
kanzurethe problem is dna synthesis11:02
kirkaWell, in robotics there are OSHW uni projects.11:02
nmz787why does the NIH or military need 1000bp sequences11:02
kanzurethat's not hard to find.11:02
kanzurethey don't need 1000 bp sequences, they need genomes, but they are too poor to buy them.11:02
nmz787that is how this turns from a DIY project to a funded PhD thesis11:02
kanzurewhy would you want a funded phd thesis -_-11:02
kanzurediy isn't a bad thing11:03
kirkaIt's good11:03
kanzurekirka: you should check the policies of those universities. more often than not, they are using non-open-source licenses and still claiming it's open source.11:03
nmz787I want to be paid to do science11:03
kanzuresometimes the legal departments get it right11:03
kanzurebut most often it's through the office of technology commercialization11:03
kanzurefor instance, aquinas bioscience was parading around at open science summit recently claiming they were gpl compatible or something. but their office of technology commercialization was busy signing a patent deal with a company.11:04
kanzurewith some exclusion terms.11:04
kirkaThis thing is GPL http://www.icub.org/11:05
kirkaBut it's EU11:05
kanzurei'm not claiming that open source work from a university is impossible. sometimes it happens. i was working in a university lab that worked on some open source software, for example.11:05
kirkaSeems that in biotech there is a lot of recent patents, so it's more complex than robotics11:06
kirka*complex to release something under BSD or GPL11:07
kirkabtw eudoxia Have run NE1 by yourself? On which platforms?11:07
nmz787kanzure: jrayhawk has told me that PSU is pretty relaxed, and that pretty much anyone with self-motivation that walks in there will excel... So I think this is an overall good plan11:11
kanzurenmz787: if it's still important to you, then you should check with their legal department before applying for their phd program.11:11
kanzureif you're completely uninterested in open source, i don't know what to tell you except that people telling you that open source can't make money are telling you lies.11:12
nmz787i'll def check out their legal dept11:13
nmz787re: OSHW though, I just foresee that taking a lot of $11:13
ThomasEgihehe.. and to prove it. have a look at redhat business numbers.11:13
nmz787I know provisional patents are $200, but the actual patent is like $10000 if you do all the filing yourself11:14
nmz787so if the thing got patented, then it'd be a lot easier to make it OSHW11:14
nmz787because I think at that point it would be public anyway11:15
kanzureand why do you think the university would pay that $10,000 for you, for them to see no upside?11:18
kanzurei don't understand.11:18
kirkakanzure PR?11:18
nmz787for them it would be more, because they are paying someone to do the filing11:18
kanzurekirka: unlikely11:18
nmz787well companies do spin off of uni work11:18
kanzureusually by selling patent rights11:19
kirkakanzure Every uni wants to have cutting edge research, especially is such area as biotech. 10k$ doesn't look like much for this purpose11:19
kanzureand then the owners of the company get sued by investors for not taking advantage of patents and blah blah blah..11:19
nmz787right, so it'd be their IP that I had exclusive license to or something and they'd receive X% of the companies profit or something11:19
kanzurekirka: in biotech, they patent everything because they are required to by US federal law11:19
nmz787but I think that's OK for my first idea11:20
kanzureok, an exclusive license isn't open source -_-11:20
kanzureusually they make it an exclusive, non-transferable license11:20
nmz787that is all tweakable in the fine print though11:21
kanzureshow me evidence of that.11:21
nmz787yes I want exclusivity to the rights for some time, yes I would be fine with DIYbio ppls making them theirselves, no I don't want cloners11:21
kanzurei want the idea to work more than anybody, but why would you be more successful at forcing a university to make patentable research open source than everyone else who has tried?11:21
nmz787seems like that's a 1 line exemption for DIY use11:22
kanzureok, that's not open source11:22
kanzureopen source is not a DIY exemption11:22
nmz787i dont care if it has the open-source logo on it11:22
kanzureopen source refers to business11:22
nmz787ahh11:22
nmz787ok11:22
kanzureyou know what, i give up11:22
* kanzure goes away11:22
nmz787kirka: anyway that's what's going through my head11:23
nmz787the last thing i did before flying back east and driving the car out west was reading up a lot on the DNA synthesis chemistry11:23
nmz787but there are things that being down the hall from a few chemists would make easier11:24
nmz787like what are the general properties of dichloromethane and nitromethane, how do they differ/similar11:24
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kirka>chris_99 Isn't it that chris?! http://crnano.org/11:56
kanzureno, that's chris phoenix.11:57
jrayhawkkirka/kanzure: msysgit and cygwin git are smart enough to set core.filemode=false and core.ignorecase=true when cloning12:00
kanzurehe didn't clone, he used fucking "cp" :(12:00
jrayhawkthe decision to *copy* a repository over was unwise, but actually using git on windows is not typically a big deal.12:00
kanzureand he doesn't want to clean up his mess, so i have to do it12:01
kanzurei guess filter-branch is my best option?12:01
jrayhawkOr diffing out his changes and repatching yourself.12:01
kirkaI thpught about diffing12:02
kanzurejrayhawk: ok thanks.12:02
kirkaFor me, it's more important to get NE1 running right now12:02
kirkabtw, One guy tests it on linux right now12:02
jrayhawkYeah, the pedanticism about history on a project that already has problems attracting contributors seems a little wird.12:02
kanzurejrayhawk: well terrible commits aren't going to attract better contributors12:03
kanzurekirka: it's been working fine on linux for months now12:04
kanzurejust use the chroot or my non-gui branch.12:04
kirka>non-gui12:04
kanzurei said or12:04
kirkaWell, he has ubuntu and "kirka-updates" branch works for him12:04
jrayhawkoh, cool12:04
kirkaWith gui, model loading and modifying12:04
kirkaGL works fine12:04
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kirkaI didn't repaired DNA or protein functions yet12:06
kirkaStiff covalent structures are simpler and more interesting for me now12:06
kanzurejrayhawk: come on, you can't seriously think NE1_ubuntu_update_log.txt is a good idea12:06
kanzurejrayhawk: https://github.com/elfion/nanoengineer/commit/5618d63cf2734746b43126dc605cf397e7a2a385.diff12:07
kirkaHehe12:07
kirkaDon't include it12:07
kirkaIf you don't need it12:07
kanzureit is included12:07
kanzurewtf are you talkinga bout12:07
kirkaOk ok12:07
kirkaSo, that GL bug is windows only12:09
kirkaAnd it depends on Part12:09
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jrayhawkSuboptimal is not the same as bad.12:11
kanzureremote: 2012/12/07 12:16:18 socat[26764] E connect(3, AF=1 "/home/gnusha/.irssi/socket", 28): Connection refused12:16
kanzureoh i imagine this might be because the socket changed12:17
kanzureand then it wasn't created again?12:17
jrayhawkthat's odd12:19
kanzureif i was to try to fix this, it's in the post-receive hook somewhere?12:19
jrayhawkYeah.12:20
kanzureor, rather, some dtach socket thing.12:20
kanzurehrm.12:20
jrayhawkThe socket is a special irssi plugin.12:20
jrayhawkI should probably redo that whole infrastructure.12:24
kirkajrayhawk Are you interested in NE1?12:24
jrayhawkI think it's neat, but have no particular intention of developing it or using it.12:25
kirkaI understand12:26
kirkaI'm actually interested in using it12:26
jrayhawkanyway, re: connection refused: I probably won't have time to look at that today, but I am interested in improving it.12:26
kanzurejrayhawk: thanks for letting me know, but i didn't actually expect you to care on this one. it's a bryan/joe race to see who experiences the most boredom first to bother to go do it.12:30
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kirkaTime to sleep, bye.15:09
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@kanzureis there a screensaver like hackertyper.net?18:07
@kanzurei might have to just make this i guess.18:07
@kanzurei don't want to have to give it input. i figure scrolling screens of coding might be fun to have in my peripheral vision.18:07
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@fennfind / *.c | xargs cat18:13
@fennthere are enough terrible screensavers already, why not18:14
@kanzurebah cat isn't the right effect18:18
@kanzuremore like compromised_cat18:18
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abetuskevening all20:02
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@kanzurebleep22:51
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abetuskhey kanzure23:24
* kanzure sleeps23:25
abetuskI am unable to23:25
@kanzurei don't understand that guy who forked nanoengineer onto sourceforge23:28
@kanzurelike who the fuck chooses sourceforge these days23:28
@kanzurehttps://groups.google.com/group/nanoengineer-dev/t/fa0b8b80513eeda023:29
@kanzurehttps://groups.google.com/group/nanoengineer-dev/t/e0e7fcb291e984f223:29
abetuskdid you see the floating water droplets?23:31
@kanzurekanzure is busy sleeping, you have activated the automated irc bot23:33
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--- Log closed Sat Dec 08 00:00:29 2012

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