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14:46:15
drmeister
Then Cando loads the dynamics coordinates using netcdf/static-vectors and renders a movie using cl-nglview.
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.
14:55:33
drmeister
7435 molecules in that simulation (one benzene, one protein and the rest are water)
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!
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".
20:46:38
drmeister
Found this: https://github.com/clasp-developers/clasp/wiki/How-to-load-staple-server-in-clasp
21:19:17
drmeister
I got an error: CL-FAD::GETENV is not supported on your implementation . - no one mentioned this - is this new?
21:29:10
Shinmera
drmeister: generating docs for Clasp doesn't require the server btw. https://plaster.tymoon.eu/view/1180#1180
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
21:48:42
Colleen
Special variable *catch-errors-p* https://edicl.github.io/hunchentoot/#*catch-errors-p*
21:54:59
drmeister
I've been coding as fast as I can to get static-vectors and netcdf working so that I can setup AMBER jobs and then visualize the molecular dynamics trajectories with a movie.
21:56:25
drmeister
I don't have a lot of time but I thought I could quickly get staple-server up so I can show a documentation server.
21:57:12
Shinmera
note that staple-server currently only knows how to document ASDF systems. systems-less stuff like an implementation is something I'll have to think about how to integrate
22:03:29
drmeister
Other than the compiler being slow for large systems - I'm pretty pleased with how things are going.
22:04:38
drmeister
I like getting all this stuff for free - meaning I didn't have to write everything.
22:05:30
drmeister
Common Lisp code seems to merge together well. I don't know quite how to describe it.
22:06:45
drmeister
It's like the cl-netcdf stuff - the original project was bare bones and developed for a different use case than what I needed. I was able to get it to do what I wanted with like 2 days of work.
22:07:45
drmeister
Then I extended static-vectors for clasp and then I put the two together - and they "just worked" with the cl-nglview dynamics visualizer.
22:42:03
Shinmera
I think staple server compiles the documentation on-demand, so the first load of a system might take a while
22:43:44
Colleen
drmeister: Function staple-server:cache-system https://shinmera.github.io/staple/staple-server/#FUNCTION%20STAPLE-SERVER%3ACACHE-SYSTEM
22:45:13
Shinmera
but you can generate the html pages manually with plain staple. https://plaster.tymoon.eu/view/1180
22:47:39
drmeister
The staple-markdown page has a lot of prose and a header - I'd like to customize the home page sort of like the staple-markdown page