Llm/mem mgmt #117

GeorgeR227 · 2023-04-24T18:06:07Z

Introduces numerous improvements to the simulation code in Decapodes.

Greatly reduces memory usage from calling DEC functions and seems to work well with contract operators

Do not run Brusselator on an earth-sized mesh!

Strange error occuring in Simulations Test

commit 9fc12f8 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 12:08:24 2023 -0400 fix missing compat entries commit 7533c9f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:48:23 2023 -0400 add more contributors commit 71a015f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:39:05 2023 -0400 fix github action versionf for julia-actions commit 1790e48 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Mar 7 15:28:59 2023 -0500 Import compile from Catlab.Programs (#104) commit e7ffee9 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Wed Feb 22 00:53:43 2023 -0500 Fix old tests and add compatibility specs (#103) * Explicitly give initial primal orientations * Fix MvNormal deprecation * Set some compatibilities commit 69d63b5 Author: GeorgeR227 <78235421+GeorgeR227@users.noreply.github.com> Date: Tue Feb 21 17:46:08 2023 -0500 Gr/parsing overhaul (#95) * Basic literal support * Added Lit data term * Fix composed op2s and add test * Replaced Var for term in \circ decomp * Quick patch for arbitrary multiplication support. * Fixed Tvar's unable to parse on rhs * Added inferred spaces for variables * Do not infer literals as states * Check types are in recognized set * Fixed strange TVar behavior * Fix cache invalidation error and add tests * Add new parsing features tests * Updated visualization for support new parsing. Also cleaned up the parsing code. * Support Literals in simulations * Do not namespace Literals, and do not vcat Nothing * Move CombinatorialSpaces using * Remove erroneous for loop --------- Co-authored-by: Luke Morris <lukelukemorrismorris@gmail.com> Co-authored-by: Luke Morris <70283489+lukem12345@users.noreply.github.com> commit ead3181 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Sat Feb 18 13:07:37 2023 -0500 Add Brusselator Example * Add Brusselator, type, and function resolve * Generate and run first phase of simulation * Change alpha and add gif * Perform second stage of simulation * Showcase using F as a time-varying parameter * Keep compatibility with old CombinatorialSpaces * Demonstrate brusselator on sphere * Clean and change gif frames * Add GLMakie back commit 4027d3e Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Fri Feb 3 16:47:44 2023 -0500 Check if name attribute is nothing (#96)

Still need to handle dual forms and add specific constant/parameter typing

Also added AdvDiff and Brusselator simulations to test new compilation

Also moved out type inference rules relating to parameters.

commit 34ea660 Author: AlgebraicJulia Bot <129184742+algebraicjuliabot@users.noreply.github.com> Date: Mon Apr 24 10:39:01 2023 -0400 Set version to 0.2.0 commit f80c513 Author: Micah Halter <micah@mehalter.com> Date: Fri Apr 21 09:49:04 2023 -0400 Remove architecture specific integer types commit 3b3ab55 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Apr 10 14:55:55 2023 -0400 Remove NamedDecapode constructor and compiler commit d2d5cfb Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Apr 10 14:44:44 2023 -0400 Use @decapode macro commit 28d6eb5 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 27 10:36:20 2023 -0400 Move to organization level github actions commit b3c2476 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Mar 20 14:38:08 2023 -0400 Remove Decapodes_v0.1 files commit a40d7a1 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Apr 18 14:46:50 2023 -0400 Do not convert edge labels that are already Strings (#115) commit 9fc12f8 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 12:08:24 2023 -0400 fix missing compat entries commit 7533c9f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:48:23 2023 -0400 add more contributors commit 71a015f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:39:05 2023 -0400 fix github action versionf for julia-actions commit 1790e48 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Mar 7 15:28:59 2023 -0500 Import compile from Catlab.Programs (#104) commit e7ffee9 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Wed Feb 22 00:53:43 2023 -0500 Fix old tests and add compatibility specs (#103) * Explicitly give initial primal orientations * Fix MvNormal deprecation * Set some compatibilities commit 69d63b5 Author: GeorgeR227 <78235421+GeorgeR227@users.noreply.github.com> Date: Tue Feb 21 17:46:08 2023 -0500 Gr/parsing overhaul (#95) * Basic literal support * Added Lit data term * Fix composed op2s and add test * Replaced Var for term in \circ decomp * Quick patch for arbitrary multiplication support. * Fixed Tvar's unable to parse on rhs * Added inferred spaces for variables * Do not infer literals as states * Check types are in recognized set * Fixed strange TVar behavior * Fix cache invalidation error and add tests * Add new parsing features tests * Updated visualization for support new parsing. Also cleaned up the parsing code. * Support Literals in simulations * Do not namespace Literals, and do not vcat Nothing * Move CombinatorialSpaces using * Remove erroneous for loop --------- Co-authored-by: Luke Morris <lukelukemorrismorris@gmail.com> Co-authored-by: Luke Morris <70283489+lukem12345@users.noreply.github.com> commit ead3181 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Sat Feb 18 13:07:37 2023 -0500 Add Brusselator Example * Add Brusselator, type, and function resolve * Generate and run first phase of simulation * Change alpha and add gif * Perform second stage of simulation * Showcase using F as a time-varying parameter * Keep compatibility with old CombinatorialSpaces * Demonstrate brusselator on sphere * Clean and change gif frames * Add GLMakie back commit 4027d3e Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Fri Feb 3 16:47:44 2023 -0500 Check if name attribute is nothing (#96)

codecov · 2023-04-28T18:18:55Z

Codecov Report

Patch coverage: 90.80% and project coverage change: +1.19 🎉

Comparison is base (34ea660) 87.14% compared to head (0b6f284) 88.34%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #117      +/-   ##
==========================================
+ Coverage   87.14%   88.34%   +1.19%     
==========================================
  Files           9        9              
  Lines         770      995     +225     
==========================================
+ Hits          671      879     +208     
- Misses         99      116      +17

Impacted Files	Coverage Δ
src/Decapodes.jl	`100.00% <ø> (ø)`
src/visualization.jl	`66.66% <ø> (ø)`
src/simulation.jl	`91.07% <87.55%> (-2.48%)`	⬇️
src/decapodeacset.jl	`96.44% <98.85%> (+3.11%)`	⬆️
src/rewrite.jl	`88.09% <100.00%> (-0.37%)`	⬇️

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src/simulation.jl

src/simulation_old.jl

src/simulation.jl

examples/Testing Range/AdvDiff.jl

examples/Testing Range/Brusselator.jl

Deleted unnecessary files and cleaned up default_dec_generate

src/simulation.jl

As per request

This shift allows us to infer types for variables that were originally parameters or constants before being set to infer by the compiler.

lukem12345 · 2023-05-02T21:34:34Z

Closes #109 and closes #92.

lukem12345 and others added 30 commits February 2, 2023 15:52

Contract operators

43b475c

Generate functions with composed ops

fedc238

Start chains from results of summations

888a9d6

Define unpacked operators

c954758

Added DEC matrix precomputation

36aaf53

Greatly reduces memory usage from calling DEC functions and seems to work well with contract operators

Rough implementation of prealloc wedge product.

cb65bd2

Improved decapodes wedge_product

a06a850

Added support for more DEC operators

2a2ddd8

Run Brusselator on Icosphere6

4c9f966

Rearranged memory testing files

d08531b

Quick fix for Brusselator mem test

6cd6074

Do not run Brusselator on an earth-sized mesh!

Prevented duplicate ops from being defined in compile_env

b5ddc2e

Strange error occuring in Simulations Test

Fixed Multiscalearrays and Simulation tests

3728415

Add scaffolding for recursive node deletion

225f0dd

Remove pasted line

167aa8e

Use stack for recursive var deletion

d2ced72

Testing for memory optimizations

9c8af2d

Updated testing brusselator

600f8ab

Remove unnecessary broadcast assignment

c124a3f

Run Brusselator on GPU

87410d1

Cast to CPU for plotting

8a4b5e4

Use views in GPU

34a78b5

Fix parent check in sums and add tests

6005be3

Cleaned up testing Brusselator

a31ea69

Started work on compiler optimizations

4709635

Added optimizations for Op2 and Summations

9acf396

Support using mul! for op1 DEC calls

e624241

Added optimizing compiler

8f679a5

Still need to handle dual forms and add specific constant/parameter typing

Added support for DualForms in optimizations

7bf3e9a

GeorgeR227 added 5 commits April 6, 2023 16:20

Cleaned up the type inference system

945e9dd

Integrated optimizing compiler into Decapodes

30dcd5e

Also added AdvDiff and Brusselator simulations to test new compilation

Run optimizations on pressure-driven flow

4c3a645

Also moved out type inference rules relating to parameters.

Patched some errors caused by merging

4079da7

GeorgeR227 marked this pull request as ready for review April 28, 2023 17:43

Merge branch 'main' into llm/mem_mgmt

d337e8c

lukem12345 reviewed Apr 28, 2023

View reviewed changes

Cleaned up some code

cc8430b

Deleted unnecessary files and cleaned up default_dec_generate

lukem12345 reviewed Apr 28, 2023

View reviewed changes

src/simulation.jl Outdated Show resolved Hide resolved

GeorgeR227 and others added 3 commits April 28, 2023 15:54

Removed return

781c76c

As per request

Shifted type inference ahead

93bcaba

This shift allows us to infer types for variables that were originally parameters or constants before being set to infer by the compiler.

Removing debugging packages from Project.toml

0b6f284

lukem12345 approved these changes May 2, 2023

View reviewed changes

lukem12345 merged commit d094503 into main May 2, 2023

This was referenced May 2, 2023

Memory Efficiency of compile #92

Closed

Check types at compile-time, not parse-time #109

Closed

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Llm/mem mgmt #117

Llm/mem mgmt #117

GeorgeR227 commented Apr 24, 2023

codecov bot commented Apr 28, 2023 •

edited

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lukem12345 commented May 2, 2023

Llm/mem mgmt #117

Llm/mem mgmt #117

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GeorgeR227 commented Apr 24, 2023

codecov bot commented Apr 28, 2023 • edited Loading

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lukem12345 commented May 2, 2023

codecov bot commented Apr 28, 2023 •

edited

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