--- Log opened Fri Dec 07 00:00:45 2012
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07:00 < kanzure> [09:46] <Jeff2> The Nemaload project, by David Dalrymple, recently updated its website with more information.
07:01 < kanzure> https://raw.github.com/gist/4218566/b86c0247c33d07422f69fb2ba116f9096181c232/OpenWorm-Office-12-5-12
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07:29 < kanzure> i didn't know davidad was calling it nemaload
07:29 < kanzure> http://nemaload.davidad.org/
07:30 < archels> oh shit they used the word 'upload'
07:31 < archels> What university are you working at? Or is this a startup?
07:31 < archels> This 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.
07:32 < kanzure> haha his dob requirements are a little stupid http://nemaload.davidad.org/jobs
07:32 < kanzure> *job
07:32 < archels> NemaLoad is backed by the http://thielfoundation.org/
07:32 < kanzure> yeah, he knows thiel.
07:32 < kanzure> not surprising.
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07:45 < kirka> Hi kanzure
07:45 < kanzure> hello.
07:45 < kirka> I wanted to ask a few questions about a source of weird bug in NE1
07:46 < kirka> Possible source of course.
07:48 < kirka> The 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 parts
07:49 < kirka> These parts are rendered strangely from the beginning: looks like first atom of each subpart is rendered at origin (0,0,0)
07:50 < kirka> I searched quite a lot across drawing code, but I'm not quite familiar with it
07:50 < kirka> Maybe it's more obvious to you
07:50 < kanzure> i suggest adding this to https://github.com/kanzure/nanoengineer/issues so that others can see the issue
07:51 < kanzure> then link to the new issue url and email nanoengineer-dev@googlegroups.com so we can discuss it in public with the other developers
07:51 < kirka> But is it okay, since this is windows x64 bug?
07:51 < kirka> It doesn't manifest itself on linux
07:51 < kanzure> i don't care
07:51 < kirka> Okay
07:53 < kirka> btw, it works very fast on win 64, shaders work too
07:54 < kirka> If we want it to be used by wider audience, windows port could be good thing
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08:00 < kirka> kanzure Aren't you tired of NE1? If yes, than I can not to bug you with it anymore.
08:00 < kirka> I understand that you are quite busy
08:03 < kanzure> i am not tired
08:03 < kirka> Okay then.
08:05 < kirka> kanzure btw I found class diagram at http://www.nanoengineer-1.com/snapshots/NE1_Documentation/, it's useful
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08:25 < kanzure> kirka: thanks for filing the issue
08:25 < kanzure> don't forget to email nanoengineer-dev@googlegroups.com with a link to it
08:26 < kirka> I'm writing it now
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08:27 < kirka> Actually, I think that I should sync my current local repo with my github, so the code were public
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08:27 < kirka> So I'm remebering how to use git again, heh
08:27 < kanzure> kirka: you could push it to a different branch
08:27 < kanzure> git push origin mybranchname:mybranchname (pushes your local branch 'mybranchname' to a branch called 'mybranchname' on github)
08:27 < kirka> Ok, nice idea
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08:32 < kirka> >line: 75(+) 62(-) files: normal=0, non-versioned=5, modified=5943, added=0, deleted=0, conflicted=0
08:32 < kirka> I'm trying to do domethinag about 5943 "modified" files
08:33 < kirka> *something
08:33 < kirka> There should be much less
08:33 < kanzure> it should say what was chagned
08:33 < kanzure> "git diff" might help
08:33 < kirka> Yes, it says this
08:34 < kirka> That's probably because I cpopied whole local repo from linux to windows
08:34 < kanzure> well, what are the differences?
08:34 < kanzure> pastebin
08:34 < kirka> Oh, I don't remeber every tiny patch
08:35 < kirka> I will do something about it by myself, ok.
08:44 < kirka> Well, I will upload it as it is, then download and check if it works, heh
08:44 < kirka> That should do it
08:56 < kirka> Well, it works like it should. There is new branch Win7x64
08:56 < kanzure> link?
08:56 < kirka> https://github.com/elfion/nanoengineer
08:57 < kirka> It's main branch now
08:57 < kanzure> i think you mean https://github.com/elfion/nanoengineer/commits/Win7x64
08:58 < kanzure> it looks like most of the changes are file mode changes
08:58 < kirka> Yes, but you see it thinks that all files were changed, so it's uninformative
08:58 < kanzure> yes, you changed the modes
08:58 < kirka> Ah, that's good
08:58 < kanzure> but why did you do this
08:59 < kirka> That's some OS related things
08:59 < kanzure> jrayhawk: your advice on cleaning this up would be nice
08:59 < kirka> I just copied shole repo as folder from linux to windows
08:59 < kanzure> jrayhawk: any ideas?
08:59 < kirka> *whole
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09:04 < kirka> I 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 < kanzure> kirka: i'll try to clean this up soon.
09:04 < kirka> Maybe that's too early?
09:04 < kanzure> on windows you have to do a mode change thing with git,
09:04 < kirka> Why don't do it when everything works?
09:05 < kanzure> git config core.filemode false
09:05 < kanzure> because windows sucks
09:05 < kirka> Ok
09:06 < kirka> >windows sucks
09:06 < kirka> I agree, but [video]drivers and heavy CADs work, and that's most important for me.
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09:17 < kirka> kanzure btw Haven't there been eudoxia recently?
09:17 < kanzure> i haven't seen him since 2012-09-21
09:18 < kirka> Ok, I'll get him by email
09:18 < kirka> He works on cool LLVM lisp
09:22 < kanzure> if you had used "git clone" you would have not had that filemode problem
09:22 < kanzure> but by physically copying from linux to windows, git didn't have a chance to configure itself properly
09:22 < kirka> Ok, I will remember it
09:26 < kanzure> kirka: could you do that and then re-commit?
09:26 < kanzure> this way the commit diff will be more reasonable
09:27 < kirka> Ohh, sorry, I can't. There was large period between, so I forgot which small patches I added. I'm afraid of losing them.
09:28 < kirka> Added some docs
09:45 < kirka> Wow, there is activity in nanoengineer-dev
09:50 < kirka> Hmm http://sourceforge.net/projects/moleculardynami/?source=dlp
09:50 < kirka> I'll try it
09:52 < kanzure> it's just someone's crappy changes.. i wish he would have submitted a diff or something
09:52 < kanzure> instead of creating a completely new project
09:52 < kirka> What intrigues is v1.1.1 that can work on win 7
09:52 < kanzure> sigh
09:52 < kirka> Heh
09:53 < kirka> I'll work on linux port too
09:53 < kirka> Actually, I'm interested in parallelizing ND-1 win pthreads
09:53 < kirka> *with
09:54 < kirka> If the system is large, splitting pair interactions calculation between threads won't be difficult
09:54 < kirka> *modeled system
09:57 < kirka> >v1.1.1
09:57 < kirka> Nope:
09:57 < kirka> >  File "bsddb3\dbshelve.pyc", line 123, in keys
09:57 < kirka> bsddb._db.DBRunRecoveryError: (-30974, 'DB_RUNRECOVERY: Fatal error, run database recovery -- C:\\Users\\Kirka\\Nanorex\\Preferences\\bsddb-shelf: pgin failed for page 1')
09:57 < kirka> Exception bsddb._db.DBRunRecoveryError: (-30974, 'DB_RUNRECOVERY: Fatal error, run database recovery -- PANIC: fatal region error detected; run recovery') in
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10:31 < eudoxia> yo kirka
10:32 < kirka> eudoxia yo
10:33 < eudoxia> i haven't seen you in a while
10:33 < kirka> Yes, I was doing robotics and other stuff
10:33 < kirka> I'm reading your blog, it's well written
10:33 < eudoxia> <3
10:33 < eudoxia> any progress on nanoengineer?
10:33 < kirka> Yes
10:34 < kirka> I have (kind of) ported it to windows x64
10:34 < kirka> But there are weird bugs
10:34 < kirka> btw, https://github.com/eudoxia0/Hylas-Lisp looks cool
10:34 < kirka> I waited for womething like this for years
10:34 < kirka> *something
10:36 < eudoxia> yeah
10:36 < eudoxia> I should add some docs
10:36 < kirka> Yep
10:37 < nmz787> hi kirka
10:37 < eudoxia> also macros aren't implemented yet
10:37 < kirka> nmz787 Hi
10:37 < kirka> eudoxia I think CL-like macros would be appropriate
10:38 < eudoxia> i don't know much about the differences between scheme and CL macros
10:38 < kirka> Scheme macros are very complex, I honestly haven't mastered them
10:39 < eudoxia> basically 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 type
10:39 < kirka> That's ok
10:39 < eudoxia> god i love llvm
10:39 < kirka> I see, you are linkiking it to SDL
10:40 < kirka> It's possible to write a good and fast CAD with this lisp
10:40 < kirka> And simulator
10:41 < nmz787> kirka: 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 lab
10:41 < kanzure> nmz787: but the university will own your work
10:41 < nmz787> kanzure: yeah but it might not happen otherwise
10:41 < kirka> nmz787 That seems reasonable as the project is serious
10:41 < kanzure> it seems completely unreasonable
10:41 < kirka> >will own
10:41 < eudoxia> kirka: the 'fast' part is certainly doable
10:41 < kirka> Is it true?
10:41 < kanzure> kirka: that's how science works in the US.
10:42 < eudoxia> but I'm not linking to SDL
10:42 < eudoxia> -ldl is for the dynamic loading of libraries
10:42 < nmz787> yes the Uni will own it, my name will still be on it
10:42 < kirka> eudoxias I mean example with SDL
10:42 < eudoxia> what was the filename again?
10:42 < kanzure> nmz787: what do you need so that you don't go back to school?
10:43 < kirka> nmz787 So, it won't be possible to license it under some OSS (OSHW?) license?
10:43 < eudoxia> kirka: i know i have an example with SDL but I thought it was in the docs folder that isn't up yet
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10:46 < kirka> kanzure Seems my uni is quite relaxed about IP questions, I haven't heard about it "owning" researcher's works.
10:46 < nmz787> kanzure: 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 week
10:47 < nmz787> kirka: as far as I can tell, keeping this device (if it works) an industry secret would be the best thing for making $
10:48 < nmz787> anything else requires $$$ for lawyers
10:48 < kirka> nmz787 Well, it's your right.
10:49 < kirka> eudoxia You use LLVM's type system (machine types and vectors)?
10:49 < nmz787> or 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 IP
10:49 < kirka> Ah, and structures
10:49 < kirka> nmz787 I see, you could violate a lot of patents with your device.
10:50 < nmz787> or make some $ then once my school is payed off and I have some $ for getting married and for lawyers, then look into OSHW for real
10:50 < kanzure> your debt really constraints your options
10:50 < nmz787> I'm not sure about 'a lot
10:50 < nmz787> '
10:50 < kanzure> *constrains
10:50 < nmz787> but even one is enough to get sued and shutdown
10:51 < kanzure> if you go around worrying about every patent under the sun, you will never do anything
10:51 < nmz787> kanzure: 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 hobby
10:51 < nmz787> but if I do it under a PhD program, if the device fails, I still get a PhD nametag
10:52 < nmz787> and that nametag is what get's a lot of the investors all hot
10:52 < kanzure> not completely. it's one thing that helps you get noticed by investors but it's not obligatory.
10:52 < kanzure> besides, you probably don't want investors anyway. it really complicates things.
10:52 < kanzure> especially when you have no prototype.
10:54 < kirka> nmz787 strategy benefits him (PhD degree is useful), isn't that good?
10:54 < nmz787> I think so
10:54 < nmz787> there are a lot more toys at the university
10:55 < nmz787> a lot more ppl willing to collaborate since you're an alum
10:55 < nmz787> if I'm working on campus in a lab, I'll physically be close to other's with lots of knowledge for the probulation
10:55 < kirka> Personal gain should be of first priority, isn't it?
10:56 < nmz787> well i def want to gain, but I want to eventually spread the wealth/love
10:57 < kanzure> i don't think you want to collaborate with assholes who only collaborate with you because you're an alum.
10:57 < kanzure> that doesn't make sense.
10:57 < kanzure> kirka: 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 < nmz787> i 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 PhD
10:58 < nmz787> if I'm doing this DIY, I get no PhD if it fail
10:58 < kanzure> but you already have all of that other debt. is this one of those sunken costs fallacies?
10:58 < nmz787> not sure what you mean by that
10:59 < nmz787> if I get into PhD I will get paid by the Uni
10:59 < nmz787> and my debts are put on pause
10:59 < nmz787> but I'll actually be able to pay them off with the Uni's pay check
10:59 < kirka> kanzure 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.
11:00 < nmz787> and my primary job won't be flipping burgers or some dumb lab tech job or programming stuff that isn't related to science
11:00 < kanzure> kirka: i completely disagree that it increases his probability of success.
11:00 < nmz787> kanzure: i disagree with that
11:00 < kanzure> you disagree that i disagree? how the fuck would you know better than me whether or not i disagree or agree?
11:00 < kanzure> wtf is going on here
11:00 < nmz787> heh
11:01 < nmz787> i disagree that it won't affect the project's success
11:01 < kanzure> making it a university project changes the project and it's something different.
11:01 < kanzure> so, open source hardware microfluidic dna synthesizer success probabiltiy is set to zero
11:02 < nmz787> nah, the DNA synthesizer is just a solution for a problem that I need to find
11:02 < kanzure> and commercially-encumbered university microfluidic dna synthesizer is somewhere above zero
11:02 < kanzure> the problem is dna synthesis
11:02 < kirka> Well, in robotics there are OSHW uni projects.
11:02 < nmz787> why does the NIH or military need 1000bp sequences
11:02 < kanzure> that's not hard to find.
11:02 < kanzure> they don't need 1000 bp sequences, they need genomes, but they are too poor to buy them.
11:02 < nmz787> that is how this turns from a DIY project to a funded PhD thesis
11:02 < kanzure> why would you want a funded phd thesis -_-
11:03 < kanzure> diy isn't a bad thing
11:03 < kirka> It's good
11:03 < kanzure> kirka: 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 < nmz787> I want to be paid to do science
11:03 < kanzure> sometimes the legal departments get it right
11:03 < kanzure> but most often it's through the office of technology commercialization
11:04 < kanzure> for 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 < kanzure> with some exclusion terms.
11:05 < kirka> This thing is GPL http://www.icub.org/
11:05 < kirka> But it's EU
11:05 < kanzure> i'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.
11:06 < kirka> Seems that in biotech there is a lot of recent patents, so it's more complex than robotics
11:07 < kirka> *complex to release something under BSD or GPL
11:07 < kirka> btw eudoxia Have run NE1 by yourself? On which platforms?
11:11 < nmz787> kanzure: 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 plan
11:11 < kanzure> nmz787: if it's still important to you, then you should check with their legal department before applying for their phd program.
11:12 < kanzure> if 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.
11:13 < nmz787> i'll def check out their legal dept
11:13 < nmz787> re: OSHW though, I just foresee that taking a lot of $
11:13 < ThomasEgi> hehe.. and to prove it. have a look at redhat business numbers.
11:14 < nmz787> I know provisional patents are $200, but the actual patent is like $10000 if you do all the filing yourself
11:14 < nmz787> so if the thing got patented, then it'd be a lot easier to make it OSHW
11:15 < nmz787> because I think at that point it would be public anyway
11:18 < kanzure> and why do you think the university would pay that $10,000 for you, for them to see no upside?
11:18 < kanzure> i don't understand.
11:18 < kirka> kanzure PR?
11:18 < nmz787> for them it would be more, because they are paying someone to do the filing
11:18 < kanzure> kirka: unlikely
11:18 < nmz787> well companies do spin off of uni work
11:19 < kanzure> usually by selling patent rights
11:19 < kirka> kanzure Every uni wants to have cutting edge research, especially is such area as biotech. 10k$ doesn't look like much for this purpose
11:19 < kanzure> and then the owners of the company get sued by investors for not taking advantage of patents and blah blah blah..
11:19 < nmz787> right, so it'd be their IP that I had exclusive license to or something and they'd receive X% of the companies profit or something
11:19 < kanzure> kirka: in biotech, they patent everything because they are required to by US federal law
11:20 < nmz787> but I think that's OK for my first idea
11:20 < kanzure> ok, an exclusive license isn't open source -_-
11:20 < kanzure> usually they make it an exclusive, non-transferable license
11:21 < nmz787> that is all tweakable in the fine print though
11:21 < kanzure> show me evidence of that.
11:21 < nmz787> yes 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 cloners
11:21 < kanzure> i 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?
11:22 < nmz787> seems like that's a 1 line exemption for DIY use
11:22 < kanzure> ok, that's not open source
11:22 < kanzure> open source is not a DIY exemption
11:22 < nmz787> i dont care if it has the open-source logo on it
11:22 < kanzure> open source refers to business
11:22 < nmz787> ahh
11:22 < nmz787> ok
11:22 < kanzure> you know what, i give up
11:22  * kanzure goes away
11:23 < nmz787> kirka: anyway that's what's going through my head
11:23 < nmz787> the last thing i did before flying back east and driving the car out west was reading up a lot on the DNA synthesis chemistry
11:24 < nmz787> but there are things that being down the hall from a few chemists would make easier
11:24 < nmz787> like what are the general properties of dichloromethane and nitromethane, how do they differ/similar
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11:56 < kirka> >chris_99 Isn't it that chris?! http://crnano.org/
11:57 < kanzure> no, that's chris phoenix.
12:00 < jrayhawk> kirka/kanzure: msysgit and cygwin git are smart enough to set core.filemode=false and core.ignorecase=true when cloning
12:00 < kanzure> he didn't clone, he used fucking "cp" :(
12:00 < jrayhawk> the decision to *copy* a repository over was unwise, but actually using git on windows is not typically a big deal.
12:01 < kanzure> and he doesn't want to clean up his mess, so i have to do it
12:01 < kanzure> i guess filter-branch is my best option?
12:01 < jrayhawk> Or diffing out his changes and repatching yourself.
12:02 < kirka> I thpught about diffing
12:02 < kanzure> jrayhawk: ok thanks.
12:02 < kirka> For me, it's more important to get NE1 running right now
12:02 < kirka> btw, One guy tests it on linux right now
12:02 < jrayhawk> Yeah, the pedanticism about history on a project that already has problems attracting contributors seems a little wird.
12:03 < kanzure> jrayhawk: well terrible commits aren't going to attract better contributors
12:04 < kanzure> kirka: it's been working fine on linux for months now
12:04 < kanzure> just use the chroot or my non-gui branch.
12:04 < kirka> >non-gui
12:04 < kanzure> i said or
12:04 < kirka> Well, he has ubuntu and "kirka-updates" branch works for him
12:04 < jrayhawk> oh, cool
12:04 < kirka> With gui, model loading and modifying
12:04 < kirka> GL works fine
12:06 -!- Netsplit *.net <-> *.split quits: audy
12:06 -!- Netsplit *.net <-> *.split quits: Sanky
12:06 < kirka> I didn't repaired DNA or protein functions yet
12:06 < kirka> Stiff covalent structures are simpler and more interesting for me now
12:06 < kanzure> jrayhawk: come on, you can't seriously think NE1_ubuntu_update_log.txt is a good idea
12:07 < kanzure> jrayhawk: https://github.com/elfion/nanoengineer/commit/5618d63cf2734746b43126dc605cf397e7a2a385.diff
12:07 < kirka> Hehe
12:07 < kirka> Don't include it
12:07 < kirka> If you don't need it
12:07 < kanzure> it is included
12:07 < kanzure> wtf are you talkinga bout
12:07 < kirka> Ok ok
12:09 < kirka> So, that GL bug is windows only
12:09 < kirka> And it depends on Part
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12:11 < jrayhawk> Suboptimal is not the same as bad.
12:16 < kanzure> remote: 2012/12/07 12:16:18 socat[26764] E connect(3, AF=1 "/home/gnusha/.irssi/socket", 28): Connection refused
12:17 < kanzure> oh i imagine this might be because the socket changed
12:17 < kanzure> and then it wasn't created again?
12:19 < jrayhawk> that's odd
12:19 < kanzure> if i was to try to fix this, it's in the post-receive hook somewhere?
12:20 < jrayhawk> Yeah.
12:20 < kanzure> or, rather, some dtach socket thing.
12:20 < kanzure> hrm.
12:20 < jrayhawk> The socket is a special irssi plugin.
12:24 < jrayhawk> I should probably redo that whole infrastructure.
12:24 < kirka> jrayhawk Are you interested in NE1?
12:25 < jrayhawk> I think it's neat, but have no particular intention of developing it or using it.
12:26 < kirka> I understand
12:26 < kirka> I'm actually interested in using it
12:26 < jrayhawk> anyway, re: connection refused: I probably won't have time to look at that today, but I am interested in improving it.
12:30 < kanzure> jrayhawk: 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.
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15:09 < kirka> Time to sleep, bye.
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18:07 <@kanzure> is there a screensaver like hackertyper.net?
18:07 <@kanzure> i might have to just make this i guess.
18:07 <@kanzure> i don't want to have to give it input. i figure scrolling screens of coding might be fun to have in my peripheral vision.
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18:13 <@fenn> find / *.c | xargs cat
18:14 <@fenn> there are enough terrible screensavers already, why not
18:18 <@kanzure> bah cat isn't the right effect
18:18 <@kanzure> more like compromised_cat
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20:02 < abetusk> evening all
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22:51 <@kanzure> bleep
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23:24 < abetusk> hey kanzure
23:25  * kanzure sleeps
23:25 < abetusk> I am unable to
23:28 <@kanzure> i don't understand that guy who forked nanoengineer onto sourceforge
23:28 <@kanzure> like who the fuck chooses sourceforge these days
23:29 <@kanzure> https://groups.google.com/group/nanoengineer-dev/t/fa0b8b80513eeda0
23:29 <@kanzure> https://groups.google.com/group/nanoengineer-dev/t/e0e7fcb291e984f2
23:31 < abetusk> did you see the floating water droplets?
23:33 <@kanzure> kanzure is busy sleeping, you have activated the automated irc bot
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--- Log closed Sat Dec 08 00:00:29 2012