freenode/#clasp - IRC Chatlog
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12:36:30
drmeister
scymtym: I just discovered that the SMARTS spec is a bit broader than we originally thought.
12:38:23
drmeister
They mean Carbon<single-bond>Nitrogen, Carbon<single-bond>Nitrogen, Carbon<double-bond>Nitrogen, Carbon<any-bond>Nitrogen
12:38:35
catchme
-> task in '' failed with exit status -9 (run with -v to display more information)"
12:39:57
drmeister
But there's also things like C-;@N which means Carbon<single-bond weak-and ring-bond>Nitrogen
12:42:26
drmeister
catchme: we don't have a binary for ubuntu at the moment. We build binaries for debian, which might work but our ability to build binaries is hindered at the moment by a broken 'dev' branch and a buildbot that is tied to 'dev'.
12:44:06
drmeister
I'm adding support to our cheminformatics code to recognize these and then i'm going to dive into the parser and add support therre.
12:45:47
drmeister
Ha - well, we merged a bunch of compiler changes that build clasp and cando fine but choke on something in babel. That prevents the cando chemistry code from building.
12:46:21
drmeister
Bike is working on incorporating better source tracking because the error is very cryptic - something about the lexical 'e' not being defined.
12:46:57
scymtym
drmeister: i will try to have a look later. can you put the spec reference into the GitHub issue tracker?
12:48:51
drmeister
scymtym: If you don't have time - don't worry about it - I don't want to keep hounding you with requests. I mention it because I know you are invested in it. It was a surprise to me when i discovered it yesterday because it adds so much complexity where I didn't think there was any.
12:51:33
drmeister
stassats: We have some deadlines coming up - so I'll upgrade to llvm7 once they are past (April 23rd or so).
12:52:33
drmeister
eight shmate - I don't want to get ahead of package manager releases or we have to go back to externals-clasp.
12:54:22
drmeister
The jump from 6 to 7 is going to be wrenching because Lang Hames completely rebuilt the ORC JIT API.
12:55:57
drmeister
They added an API for concurrent bitcode and object file incorporation into the JIT. I might be able to ditch calling out to the 'ld' linker for routine operation.
12:58:44
drmeister
selwyn: No - that's something else. Clasp has C++ source-to-source translation capabilities built into it. We are going to use them to clean up the internal API's and function/class/method names.
13:04:35
selwyn
i made some changes to magicl https://github.com/selwynsimsek/magicl . loading it takes up all of my 100gb swap file and it hangs indefinitely. will carry on working on it today..
13:05:58
drmeister
That sounds pathological - the "Ironclad" quicklisp system expands a lot of macros but they don't blow up that bad.
13:06:59
selwyn
i suspect the problem is with lapack-cffi.lisp, which contains 100,000 lines (!) of generated cffi bindings
13:08:43
selwyn
my current (only) idea is to simply split it up into different files and hope for the best
13:22:31
drmeister
Make sure it's reproducible - and turn off compile-file-parallel if you don't have the fix I just pushed to the 'work' branch.
13:30:07
drmeister
scymtym: I posted this issue - it took a little work to get the smarts strings to survive markup.
13:31:09
drmeister
No problem. I think it's going to be fairly straightforward to copy/edit/paste the logical code for atoms to bonds.
13:33:29
Bike
the last reasonable call is to eclector.prase-result:make-expression-result, which does have a recursive local function, but i can read a cyclic structure fine
13:41:09
scymtym
is eclector.*prase*-result:make-expression-result a typo or is that really in the backtrace?
14:43:04
drmeister
The presentation the DOD is giving right now has a big Microsoft Windows error dialog box covering the middle of every slide.
14:43:58
drmeister
A sigh of relief just went up when one of the tech support people managed after 5 min to drag the dialog box out of the presentation.
14:44:59
drmeister
This was in a presentation about basic research to allow warfighters to work in radioactive environments. Good grief.
14:50:46
drmeister
The presenters have a lot of plans, very little money and the audience is full of about 200 anxious academics. It's a powder keg.
15:18:30
drmeister
Paraphrased from the current slide: "There does not yet exist a predictive model of human society".
15:19:49
drmeister
We have transitioned from nuclear physics and materials to something to do with social networking. I don't follow what they are getting at - but phrases like "Social behavior modeling", "infrastructure response" are being tossed out.
15:23:32
drmeister
This is another good book in that vein: https://www.amazon.com/Country-Blind-Michael-Flynn/dp/152260586X
15:27:29
drmeister
They mentioned Puerto Rico and the slow recovery from the hurricanes last year as a model of how infrastructure changes with a disaster. Everything they said about it assumes a rational adminstration that wants to improve things and protect people. It's good to know that at least the "Deep State" cares about people.
15:28:39
Bike
if they're using phrases like "predictive model of human society" with any amount of seriousness they're making a whole lot of assumptions like that
15:32:09
drmeister
They want more involvement from graduate students, undergraduates and high school students in defense from WMD research.
15:38:15
drmeister
These folks are serious and thoughtful. The administrations that run things... not so much.
15:39:57
drmeister
Good lord - "Nuclear Fireball Plasma Chemistry" and "High temperature properties of organophosphorus species".
15:41:56
drmeister
ACTION goes back to soothing himself by writing code to recognize logical combinations of chemical bonds.
15:43:56
drmeister
The SMARTS "specification" specifies a test for a "ring bond" '@' - but they don't specify how large of a ring. How annoying is that.
17:45:08
Bike
i think it could be rewritten iteratively, guess i'll do that for at least my purposes
22:20:07
drmeister
Got it. I'm still an hour out from Philadelphia. Somehow I got off my normal path and ended up in more rural Rhode Island and Delaware.
22:23:46
drmeister
I'm doing "dream time" in Delaware. I'm at a Krispy Kreme watching an amazing cloud burst come down.
22:25:18
drmeister
For some reason people really like to take selfies with donuts rolling down the conveyor belt behind them.
22:26:28
drmeister
I've changed every lexical 'e' in the clasp source file to something more recognizable and i'm building 'dev' on an AWS instance.