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0:57:13
drmeister
Prior to this I'm getting a lot of: GC Warning: Repeated allocation of very large block (appr. size 2101248):
0:57:30
Bike
i messed with make instances obsolete a little, and i realized today i did it wrong, but it shouldn't be a huge issue
0:58:08
drmeister
I'm wondering (1) is this a bug that is just now showing up (2) is it due to the GC getting stressed out and something going wrong?
0:59:18
drmeister
What do you think? It's while compiling traitlets - that's very, very late in the build.
0:59:35
Bike
i think i messed up make instances obsolete so that it's called while the slot is unbound
1:01:27
Bike
https://github.com/clasp-developers/clasp/blob/master/src/lisp/kernel/clos/change.lsp#L189 it's in the :after
1:10:46
Bike
that's not even the right definition of make instances obsolete, i left it in by mistake
1:14:00
drmeister
Well, I can get cando up and running - the Boehm GC seems to complain more often as well. But things are running.
1:14:28
drmeister
I'm feeling pretty good about the demo on Thursday - I'm just going to be very careful what I let into the 'demo' branch.
1:16:20
drmeister
I'm working on aspects of the demo - if you fix this tomorrow - I'll incorporate it.
1:17:53
drmeister
I'm working on the PDB reader right now and adding a _Type slot to Molecule_O and Residue_O. I should have just added one to the base class Matter_O. Everything has a type - but the types are different depending on if it's a Molecule_O or a Residue_O. It's more of a 'classification' than a 'type' really.
1:18:51
drmeister
Molecules can be (member 'protein 'ligand 'solvent 'ion) - but that only applies to proteins - what if it's a DNA structure - then 'protein doesn't make sense.
2:22:11
drmeister
Now that I've got a bug report in for the 'ld' crash in the 'cst' branch I'll switch to LTO_OPTION='obj' and continue working on that problem you (Bike) pointed out.
8:30:08
kpoeck
@Bike, when you have time - if there is time before the demo - could you have a look at issue 454?
8:31:11
kpoeck
Definining shared-initialize on a struct throws an error about allocate-instance not being defined for structure-class
11:34:20
scymtym
drmeister: the SMILES/SMARTS material you provided doesn't seem too complicated. so far, the main difficulties seem to be handling the separation into SMILES and SMARTS intelligently and managing the apparently numerous variants and extensions
11:46:13
drmeister
scymtym: Agreed - but that would be gravy - I don't implement SMILES at the moment. SMARTS is the really important capability.
11:48:10
drmeister
Bike: Now that other people are working on the ld crashing issue I rebuilt cst with your partial inlining turned on and reproduced the STORE issue.
11:50:30
drmeister
Shiho and Bike: I found some PDF's on the Shrodinger web site that describe their user interface for setting up these FEP calculations.
11:51:39
drmeister
It's the typical pointy-clicky-menu-dialog GUI that drives me nuts. I think we can do a much better job with the Jupyter Notebook interface.
11:52:09
drmeister
I figure if they publish it on their web site then it is fair game for us to look at it.
12:02:11
scymtym
drmeister: i see. a basic parser for SMARTS shouldn't be too much work, then. i mean, i seem to have most(?) of it, from playing around while learning how the languages work
12:07:43
drmeister
Yeah - the tricky part is turning it into the model. I have a yacc/bison parser that does it. I posted a link and I can repost it if you like.
12:09:33
scymtym
my thinking at the moment is having the parser and maybe generic language support in a separate system and having a suitable builder in cando. does that make sense?
12:13:18
drmeister
I have to prepare for teaching. I’ll be more available to talk after a couple of hours.
12:14:58
drmeister
But since ideally we want one parser and two model generators - yeah I think it makes a lot of sense to have the parser in its own system.