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Saturday, 26th of November 2022, 22:59:07 UTC
3:37:15
consolers
so i hit the llvm orc bits. if i use gentoo it'll be 210MB and over 6 hours of compilation with OOM problems, i could download a release amd64 tarball thats just half a gig
3:37:47
consolers
gentoo is already dropping packages because they dont compile with clang 16
3:38:30
consolers
maybe shelf life for 14 is not going be long. i alrady had 7,10,11,13 locally
3:41:36
drmeister
Bike: Are you online?
3:41:41
drmeister
Did you make it back yet?
3:43:40
drmeister
I got the parser working and I can generate all the training molecules and their focus monomer contexts.
3:43:53
drmeister
https://www.irccloud.com/pastebin/oChqvRRu/
4:17:42
drmeister
First training molecule...
4:17:44
drmeister
https://usercontent.irccloud-cdn.com/file/Ysqoldea/image.png
4:17:55
drmeister
It takes 1.5 seconds
4:19:40
drmeister
So with 223 trainers assuming we need to generate 500 conformations for each trainer and it takes 1.5 seconds per conformation ...
4:20:57
drmeister
47 hours to generate all the conformations with just two functional groups.
4:23:15
drmeister
Each additional functional group is 18 minutes.
4:26:27
drmeister
The little ones are super fast
4:26:28
drmeister
https://usercontent.irccloud-cdn.com/file/Qdq0KmLy/image.png
4:27:36
Bike
what takes the calculations so long?
4:28:22
drmeister
It does a non-linear optimization from essentially random coordinates.
4:28:41
drmeister
It first optimizes the geometry where the atoms are bonded together but they repel each other.
4:28:52
drmeister
Then it dials down the repulsive force to zero.
4:29:44
drmeister
It uses three non-linear optimizers (1) steepest descent (2) conjugate gradients (3) truncated Newton
4:29:59
drmeister
It switches between them as the solution gets closer and closer to optimal.
4:30:07
drmeister
Lots of complicated math.
4:31:05
drmeister
I think I've nailed it. Now I just need to glue a bunch of the code together.
5:27:09
consolers
i almost remember what a functional group is
5:27:16
consolers
well i did have a degree in chemistry in some other century
5:48:06
drmeister
Hello consolers - you were/are a chemist?
5:49:21
drmeister
Are you having trouble with clasp and llvm14?
5:50:02
drmeister
I started to build with llvm15 - but I haven't finalized it yet.
10:23:17
consolers
turns out there isnt an amd64 binary download for linux, but i think i've donwloaded one before probably for clang8
10:26:30
consolers
12:39PM to 16:00 PM for compiling multilib llvm alone -j8 -l4 without OOM on 8GB ram. that wasn't so bad.
10:38:22
consolers
maybe i can do better with clasp at some libraries where i've failed to make any progress with claw-cxx
10:38:59
consolers
but if the problem is a lack of knowledge on my part of how the stuff works...
10:39:59
consolers
also i hope llvm-14 will last a year without something requiring me to install a later version
10:54:45
consolers
but looks like clang might bring the oom on me
Sunday, 27th of November 2022, 10:59:07 UTC