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Wednesday, 20th of February 2019, 9:52:27 UTC
14:33:44
drmeister
Kevslinger: Are you online?
14:33:52
drmeister
I know Temple is closed (storm)
14:34:20
drmeister
I am able to generate molecular dynamics runs from cando and I can animate them.
14:34:27
drmeister
I'm trying to figure out how to hide the water.
14:41:42
drmeister
https://www.dropbox.com/s/xlm6ay0ox7lqdwf/dynamics.mov?dl=0
14:45:03
drmeister
https://www.irccloud.com/pastebin/lmcSv97E/
14:45:22
drmeister
This does the following to a protein in a box of waters:
14:45:41
drmeister
minimize it -> heat -> pressurize -> run dynamics (simulate the motion)
14:46:15
drmeister
Then Cando loads the dynamics coordinates using netcdf/static-vectors and renders a movie using cl-nglview.
14:46:32
drmeister
I just need to hide the #$*@!*%! waters and we could see the protein
14:49:51
drmeister
Oh - and the amber:generate-all-code generates a makefile and scripts that cracauer's distributor distributes to GPU accelerated AWS instances.
14:50:30
drmeister
We can programmatically generate a job that would run thousands of molecular dynamics runs in parallel.
14:51:02
drmeister
We have gone exascale.
14:53:53
selwyn
how many molecules are simulated in a single typical run?
14:55:33
drmeister
7435 molecules in that simulation (one benzene, one protein and the rest are water)
14:55:51
drmeister
(chem:content-size *agg*) -> 7435
14:56:15
drmeister
(chem:number-of-atoms *agg*) -> 24916
15:18:51
drmeister
Yeah - I think it's going to be big
15:38:22
drmeister
Found it - they've been changing the Javascript out from under us!
15:38:52
drmeister
I thought we had pinned the Javascript code we were using for this but clearly not
15:39:28
drmeister
In the Javascript code the RPC call "clearRepresentations" has been changed to "removeAllRepresentations". Once I updated the Common Lisp code it worked fine! ARGH!
15:39:31
drmeister
https://usercontent.irccloud-cdn.com/file/yBUpaF3n/image.png
15:46:24
drmeister
https://www.dropbox.com/s/nqgkjkyoaq4idpi/dynamics2.mov?dl=0
17:54:58
Kevslinger
drmeister: Hi. I'm online now (but not in lab)
17:55:37
drmeister
Hi Kevslinger - I found the problem.
17:56:09
drmeister
Somewhere in the build system we are pulling nglview Javascript from the internet.
17:56:34
Kevslinger
Yeah that's kinda what I was thinking, but I wasn't able to figure out where exactly it was happening
17:56:49
drmeister
I found that the Javascript RPC function "clearRepresentations" was renamed to "removeAllRepresentations".
20:45:13
drmeister
Do we still have the problem running staple/plump wrt the type error
20:46:10
drmeister
I thought kpoeck had a workaround
20:46:38
drmeister
Found this: https://github.com/clasp-developers/clasp/wiki/How-to-load-staple-server-in-clasp
20:54:20
Shinmera
it's a workaround, but I won't put it upstream
20:54:34
Shinmera
and you'll have plenty other code that'll subtly or not so subtly break
21:05:10
drmeister
I started discussing the possible remedies in the issue
21:05:55
drmeister
https://github.com/clasp-developers/clasp/issues/698
21:06:14
drmeister
I may need to generate a new class for every specialized array type.
21:19:17
drmeister
I got an error: CL-FAD::GETENV is not supported on your implementation . - no one mentioned this - is this new?
21:22:04
selwyn
(cl-fad::getenv "HOME") -> "/home/selwyn"
21:25:49
drmeister
Hmm, I have a local-projects clone of cl-fad - I'll get rid of it.
21:26:29
selwyn
Ah - it seems that I do too...
21:27:32
selwyn
I am using clasp-developers/cl-fad
21:29:10
Shinmera
drmeister: generating docs for Clasp doesn't require the server btw. https://plaster.tymoon.eu/view/1180#1180
21:30:46
drmeister
Yeah - why do we have cl-fad?
21:31:02
Shinmera
probably pulled in by hunchentoot
21:31:11
Shinmera
for my snippet you only need to load staple
21:35:13
drmeister
Does staple server run on some port?
21:35:34
Shinmera
once it's running it'll tell you
21:36:07
drmeister
Can/Does it use a fixed port? I'll want to expose that port from docker.
21:38:49
Shinmera
Colleen: tell drmeister look up staple-server start
21:38:49
Colleen
drmeister: Function staple-server:start https://shinmera.github.io/staple/staple-server/#FUNCTION%20STAPLE-SERVER%3ASTART
21:45:39
Shinmera
If staple docs are published online somewhere, it also only takes a single line of code for me to add lookup into Colleen so you can reference it like the clhs
21:46:07
drmeister
Is there something I need to run to build initial documentation?
21:46:36
drmeister
I (ql:quickload :staple-server) and then (staple-server:start :port 4006)
21:46:47
drmeister
https://usercontent.irccloud-cdn.com/file/GwNQ8fM1/image.png
21:47:10
Shinmera
well, then there's more problems that need workarounds :)
21:48:32
Shinmera
try setting hunchentoot:*catch-errors-p* to NIL
21:48:42
Shinmera
Colleen: look up hunchentoot *catch-errors-p*
21:48:42
Colleen
Special variable *catch-errors-p* https://edicl.github.io/hunchentoot/#*catch-errors-p*
21:49:07
drmeister
This is what I get starting up
21:49:09
drmeister
https://www.irccloud.com/pastebin/jKc2L7ju/
21:49:34
drmeister
Sorry - quickloading it
21:50:11
drmeister
https://www.irccloud.com/pastebin/Km6kVZ7r/
21:50:27
Shinmera
those warnings mean nothing.
21:50:48
Shinmera
do what I said, and reload the page
21:52:18
drmeister
NIL doesn't do anything
Wednesday, 20th of February 2019, 21:52:27 UTC