From cf3f58cf830affa9e0616ace103aa8c213bff481 Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Mon, 25 Nov 2024 14:28:14 +0100
Subject: [PATCH 01/11] add simple kernel

---
 honeycomb-kernels/src/lib.rs                  |  1 +
 honeycomb-kernels/src/shift/mod.rs            |  1 +
 .../src/shift/neighbors_average.rs            | 45 +++++++++++++++++++
 3 files changed, 47 insertions(+)
 create mode 100644 honeycomb-kernels/src/shift/mod.rs
 create mode 100644 honeycomb-kernels/src/shift/neighbors_average.rs

diff --git a/honeycomb-kernels/src/lib.rs b/honeycomb-kernels/src/lib.rs
index ecb0f1b3b..9551f7530 100644
--- a/honeycomb-kernels/src/lib.rs
+++ b/honeycomb-kernels/src/lib.rs
@@ -22,5 +22,6 @@
 // ------ MODULE DECLARATIONS
 
 pub mod grisubal;
+pub mod shift;
 pub mod splits;
 pub mod triangulation;
diff --git a/honeycomb-kernels/src/shift/mod.rs b/honeycomb-kernels/src/shift/mod.rs
new file mode 100644
index 000000000..1b0245ab0
--- /dev/null
+++ b/honeycomb-kernels/src/shift/mod.rs
@@ -0,0 +1 @@
+mod neighbors_average;
diff --git a/honeycomb-kernels/src/shift/neighbors_average.rs b/honeycomb-kernels/src/shift/neighbors_average.rs
new file mode 100644
index 000000000..56724da94
--- /dev/null
+++ b/honeycomb-kernels/src/shift/neighbors_average.rs
@@ -0,0 +1,45 @@
+use honeycomb_core::{
+    cmap::{CMap2, DartIdType, Orbit2, OrbitPolicy, VertexIdType, NULL_DART_ID},
+    prelude::{CoordsFloat, Vertex2},
+    stm::atomically,
+};
+
+pub fn shift<T: CoordsFloat>(cmap: &CMap2<T>) {
+    // fetch all vertices that are not on the boundary of the map
+    let vertices: Vec<VertexIdType> = cmap
+        .fetch_vertices()
+        .identifiers
+        .into_iter()
+        .filter(|v| {
+            !Orbit2::new(&cmap, OrbitPolicy::Vertex, *v as DartIdType)
+                .any(|d| cmap.beta::<2>(d) == NULL_DART_ID)
+        })
+        .collect();
+
+    let neighbors: Vec<Vec<VertexIdType>> = vertices
+        .iter()
+        .map(|v| {
+            Orbit2::new(&cmap, OrbitPolicy::Vertex, *v as DartIdType)
+                .map(|d| cmap.vertex_id(cmap.beta::<2>(d)))
+                .collect()
+        })
+        .collect();
+
+    // main loop
+    vertices
+        .iter()
+        .zip(neighbors.iter())
+        .for_each(|(vid, neigh)| {
+            atomically(|trans| {
+                let mut new_val: Vertex2<T> = Vertex2::default();
+                for v in neigh {
+                    let vertex = cmap.read_vertex(trans, *v)?.unwrap();
+                    new_val.0 += vertex.0;
+                    new_val.1 += vertex.1;
+                }
+                new_val.0 /= T::from(neigh.len()).unwrap();
+                new_val.1 /= T::from(neigh.len()).unwrap();
+                cmap.write_vertex(trans, *vid, new_val)
+            });
+        });
+}

From fdd7912a5bf3e9ca0a4b8b6428efa697e615c91a Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Mon, 25 Nov 2024 16:01:02 +0100
Subject: [PATCH 02/11] bench shift function

---
 benches/Cargo.toml                            |  6 +++
 benches/benches/shift.rs                      | 28 ++++++++++++
 honeycomb-kernels/Cargo.toml                  |  1 +
 honeycomb-kernels/src/shift/mod.rs            |  2 +
 .../src/shift/neighbors_average.rs            | 45 +++++++++++--------
 5 files changed, 64 insertions(+), 18 deletions(-)
 create mode 100644 benches/benches/shift.rs

diff --git a/benches/Cargo.toml b/benches/Cargo.toml
index bb5c80ac6..28b288eb7 100644
--- a/benches/Cargo.toml
+++ b/benches/Cargo.toml
@@ -82,6 +82,12 @@ name = "grisubal-grid-size"
 path = "benches/grisubal/grid_size.rs"
 harness = false
 
+
+[[bench]]
+name = "shift"
+path = "benches/shift.rs"
+harness = false
+
 [[bench]]
 name = "triangulate-quads"
 path = "benches/triangulate/quads.rs"
diff --git a/benches/benches/shift.rs b/benches/benches/shift.rs
new file mode 100644
index 000000000..6e22c8ebc
--- /dev/null
+++ b/benches/benches/shift.rs
@@ -0,0 +1,28 @@
+// ------ IMPORTS
+
+use criterion::{black_box, criterion_group, criterion_main, BenchmarkId, Criterion};
+use honeycomb::{kernels::shift::shift_vertices_to_neigh_avg, prelude::CMap2};
+use honeycomb_benches::FloatType;
+use honeycomb_core::cmap::CMapBuilder;
+
+// ------ CONTENT
+
+pub fn criterion_benchmark(c: &mut Criterion) {
+    let path = "../../../meshing-samples/vtk/2D/many_quads.vtk";
+
+    let mut group = c.benchmark_group("shift");
+
+    let mut map: CMap2<FloatType> = CMapBuilder::from(path).build().unwrap();
+
+    group.bench_function(BenchmarkId::new("to-neighbor-avg", ""), |b| {
+        b.iter(|| {
+            shift_vertices_to_neigh_avg(&map, 200);
+            black_box(&mut map);
+        })
+    });
+
+    group.finish();
+}
+
+criterion_group!(benches, criterion_benchmark);
+criterion_main!(benches);
diff --git a/honeycomb-kernels/Cargo.toml b/honeycomb-kernels/Cargo.toml
index ec6d71f3e..df0075d73 100644
--- a/honeycomb-kernels/Cargo.toml
+++ b/honeycomb-kernels/Cargo.toml
@@ -15,6 +15,7 @@ publish = true
 [dependencies]
 honeycomb-core = { workspace = true, features = ["io", "utils"] }
 num-traits.workspace = true
+rayon = "1.10.0"
 thiserror.workspace = true
 vtkio.workspace = true
 
diff --git a/honeycomb-kernels/src/shift/mod.rs b/honeycomb-kernels/src/shift/mod.rs
index 1b0245ab0..8c52062d7 100644
--- a/honeycomb-kernels/src/shift/mod.rs
+++ b/honeycomb-kernels/src/shift/mod.rs
@@ -1 +1,3 @@
 mod neighbors_average;
+
+pub use neighbors_average::shift as shift_vertices_to_neigh_avg;
diff --git a/honeycomb-kernels/src/shift/neighbors_average.rs b/honeycomb-kernels/src/shift/neighbors_average.rs
index 56724da94..2b17aa345 100644
--- a/honeycomb-kernels/src/shift/neighbors_average.rs
+++ b/honeycomb-kernels/src/shift/neighbors_average.rs
@@ -3,13 +3,14 @@ use honeycomb_core::{
     prelude::{CoordsFloat, Vertex2},
     stm::atomically,
 };
+use rayon::prelude::*;
 
-pub fn shift<T: CoordsFloat>(cmap: &CMap2<T>) {
+pub fn shift<T: CoordsFloat>(cmap: &CMap2<T>, n_rounds: usize) {
     // fetch all vertices that are not on the boundary of the map
     let vertices: Vec<VertexIdType> = cmap
         .fetch_vertices()
         .identifiers
-        .into_iter()
+        .into_par_iter()
         .filter(|v| {
             !Orbit2::new(&cmap, OrbitPolicy::Vertex, *v as DartIdType)
                 .any(|d| cmap.beta::<2>(d) == NULL_DART_ID)
@@ -17,7 +18,7 @@ pub fn shift<T: CoordsFloat>(cmap: &CMap2<T>) {
         .collect();
 
     let neighbors: Vec<Vec<VertexIdType>> = vertices
-        .iter()
+        .par_iter()
         .map(|v| {
             Orbit2::new(&cmap, OrbitPolicy::Vertex, *v as DartIdType)
                 .map(|d| cmap.vertex_id(cmap.beta::<2>(d)))
@@ -26,20 +27,28 @@ pub fn shift<T: CoordsFloat>(cmap: &CMap2<T>) {
         .collect();
 
     // main loop
-    vertices
-        .iter()
-        .zip(neighbors.iter())
-        .for_each(|(vid, neigh)| {
-            atomically(|trans| {
-                let mut new_val: Vertex2<T> = Vertex2::default();
-                for v in neigh {
-                    let vertex = cmap.read_vertex(trans, *v)?.unwrap();
-                    new_val.0 += vertex.0;
-                    new_val.1 += vertex.1;
-                }
-                new_val.0 /= T::from(neigh.len()).unwrap();
-                new_val.1 /= T::from(neigh.len()).unwrap();
-                cmap.write_vertex(trans, *vid, new_val)
+    let mut round = 0;
+    loop {
+        vertices
+            .iter()
+            .zip(neighbors.iter())
+            .par_bridge()
+            .for_each(|(vid, neigh)| {
+                atomically(|trans| {
+                    let mut new_val: Vertex2<T> = Vertex2::default();
+                    for v in neigh {
+                        let vertex = cmap.read_vertex(trans, *v)?.unwrap();
+                        new_val.0 += vertex.0;
+                        new_val.1 += vertex.1;
+                    }
+                    new_val.0 /= T::from(neigh.len()).unwrap();
+                    new_val.1 /= T::from(neigh.len()).unwrap();
+                    cmap.write_vertex(trans, *vid, new_val)
+                });
             });
-        });
+        round += 1;
+        if round >= n_rounds {
+            break;
+        }
+    }
 }

From 2c68d07ffe9093a33fb24cdcfc3f6f5a0936da36 Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Tue, 26 Nov 2024 17:26:24 +0100
Subject: [PATCH 03/11] stm experimentation

---
 honeycomb-core/Cargo.toml                        | 3 ++-
 honeycomb-core/src/attributes/collections.rs     | 2 +-
 honeycomb-core/src/attributes/manager.rs         | 2 +-
 honeycomb-core/src/attributes/tests.rs           | 2 +-
 honeycomb-core/src/attributes/traits.rs          | 2 +-
 honeycomb-core/src/cmap/components/betas.rs      | 2 +-
 honeycomb-core/src/cmap/components/unused.rs     | 2 +-
 honeycomb-core/src/cmap/dim2/basic_ops.rs        | 2 +-
 honeycomb-core/src/cmap/dim2/embed.rs            | 2 +-
 honeycomb-core/src/cmap/dim2/links/one.rs        | 2 +-
 honeycomb-core/src/cmap/dim2/links/two.rs        | 2 +-
 honeycomb-core/src/cmap/dim2/sews/one.rs         | 2 +-
 honeycomb-core/src/cmap/dim2/sews/two.rs         | 2 +-
 honeycomb-core/src/cmap/dim2/utils.rs            | 2 +-
 honeycomb-core/src/cmap/error.rs                 | 2 +-
 honeycomb-core/src/lib.rs                        | 2 +-
 honeycomb-kernels/src/shift/neighbors_average.rs | 2 +-
 17 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/honeycomb-core/Cargo.toml b/honeycomb-core/Cargo.toml
index c005a4879..b039c20e6 100644
--- a/honeycomb-core/Cargo.toml
+++ b/honeycomb-core/Cargo.toml
@@ -19,8 +19,9 @@ utils = []
 # deps
 
 [dependencies]
+fast-stm = { git = "https://github.com/imrn99/fast-stm.git", rev = "94a9ff5" }
 downcast-rs.workspace = true
-loom.workspace= true
+loom.workspace = true
 num-traits.workspace = true
 stm.workspace = true
 thiserror.workspace = true
diff --git a/honeycomb-core/src/attributes/collections.rs b/honeycomb-core/src/attributes/collections.rs
index d16d58307..ce2d59cca 100644
--- a/honeycomb-core/src/attributes/collections.rs
+++ b/honeycomb-core/src/attributes/collections.rs
@@ -10,8 +10,8 @@ use crate::{
     cmap::{CMapError, CMapResult},
     prelude::DartIdType,
 };
+use fast_stm::{atomically, StmResult, TVar, Transaction};
 use num_traits::ToPrimitive;
-use stm::{atomically, StmResult, TVar, Transaction};
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/attributes/manager.rs b/honeycomb-core/src/attributes/manager.rs
index 21a70e91a..731aec7c0 100644
--- a/honeycomb-core/src/attributes/manager.rs
+++ b/honeycomb-core/src/attributes/manager.rs
@@ -5,7 +5,7 @@
 
 // ------ IMPORTS
 
-use stm::{StmResult, Transaction};
+use fast_stm::{StmResult, Transaction};
 
 use super::{AttributeBind, AttributeStorage, AttributeUpdate, UnknownAttributeStorage};
 use crate::{
diff --git a/honeycomb-core/src/attributes/tests.rs b/honeycomb-core/src/attributes/tests.rs
index 6ab44fddf..a311f3b3f 100644
--- a/honeycomb-core/src/attributes/tests.rs
+++ b/honeycomb-core/src/attributes/tests.rs
@@ -1,7 +1,7 @@
 // ------ IMPORTS
 
+use fast_stm::{atomically, StmError, Transaction, TransactionControl};
 use loom::sync::Arc;
-use stm::{atomically, StmError, Transaction, TransactionControl};
 
 use super::{
     AttrSparseVec, AttrStorageManager, AttributeBind, AttributeStorage, AttributeUpdate,
diff --git a/honeycomb-core/src/attributes/traits.rs b/honeycomb-core/src/attributes/traits.rs
index ead9ba67d..76b7fca50 100644
--- a/honeycomb-core/src/attributes/traits.rs
+++ b/honeycomb-core/src/attributes/traits.rs
@@ -10,9 +10,9 @@ use crate::{
     prelude::{DartIdType, OrbitPolicy},
 };
 use downcast_rs::{impl_downcast, Downcast};
+use fast_stm::{atomically, StmResult, Transaction};
 use std::any::Any;
 use std::fmt::Debug;
-use stm::{atomically, StmResult, Transaction};
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/cmap/components/betas.rs b/honeycomb-core/src/cmap/components/betas.rs
index e58db9411..d4e4516da 100644
--- a/honeycomb-core/src/cmap/components/betas.rs
+++ b/honeycomb-core/src/cmap/components/betas.rs
@@ -2,7 +2,7 @@
 
 use std::ops::{Index, IndexMut};
 
-use stm::{StmError, TVar, Transaction};
+use fast_stm::{StmError, TVar, Transaction};
 
 use crate::cmap::NULL_DART_ID;
 
diff --git a/honeycomb-core/src/cmap/components/unused.rs b/honeycomb-core/src/cmap/components/unused.rs
index 5d85baada..1de378df4 100644
--- a/honeycomb-core/src/cmap/components/unused.rs
+++ b/honeycomb-core/src/cmap/components/unused.rs
@@ -5,7 +5,7 @@ use std::{
     slice::Iter,
 };
 
-use stm::TVar;
+use fast_stm::TVar;
 
 use super::identifiers::DartIdType;
 
diff --git a/honeycomb-core/src/cmap/dim2/basic_ops.rs b/honeycomb-core/src/cmap/dim2/basic_ops.rs
index 889727bf0..c1c996cf6 100644
--- a/honeycomb-core/src/cmap/dim2/basic_ops.rs
+++ b/honeycomb-core/src/cmap/dim2/basic_ops.rs
@@ -17,8 +17,8 @@ use crate::{
     cmap::{EdgeCollection, FaceCollection, VertexCollection},
     geometry::CoordsFloat,
 };
+use fast_stm::{atomically, StmError, Transaction};
 use std::collections::{BTreeSet, VecDeque};
-use stm::{atomically, StmError, Transaction};
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/cmap/dim2/embed.rs b/honeycomb-core/src/cmap/dim2/embed.rs
index 2d0794a35..0ba97a92d 100644
--- a/honeycomb-core/src/cmap/dim2/embed.rs
+++ b/honeycomb-core/src/cmap/dim2/embed.rs
@@ -6,7 +6,7 @@
 
 // ------ IMPORT
 
-use stm::{StmResult, Transaction};
+use fast_stm::{StmResult, Transaction};
 
 use crate::prelude::{AttributeBind, AttributeUpdate, CMap2, Vertex2, VertexIdType};
 use crate::{
diff --git a/honeycomb-core/src/cmap/dim2/links/one.rs b/honeycomb-core/src/cmap/dim2/links/one.rs
index 3c720e976..b1daa1db8 100644
--- a/honeycomb-core/src/cmap/dim2/links/one.rs
+++ b/honeycomb-core/src/cmap/dim2/links/one.rs
@@ -1,6 +1,6 @@
 //! 1D link implementations
 
-use stm::{atomically, StmResult, Transaction};
+use fast_stm::{atomically, StmResult, Transaction};
 
 use crate::{
     cmap::{CMap2, DartIdType},
diff --git a/honeycomb-core/src/cmap/dim2/links/two.rs b/honeycomb-core/src/cmap/dim2/links/two.rs
index 339754985..e9c9b0ef2 100644
--- a/honeycomb-core/src/cmap/dim2/links/two.rs
+++ b/honeycomb-core/src/cmap/dim2/links/two.rs
@@ -1,6 +1,6 @@
 //! 2D link implementations
 
-use stm::{atomically, StmResult, Transaction};
+use fast_stm::{atomically, StmResult, Transaction};
 
 use crate::{
     cmap::{CMap2, DartIdType},
diff --git a/honeycomb-core/src/cmap/dim2/sews/one.rs b/honeycomb-core/src/cmap/dim2/sews/one.rs
index ed9316bea..941a470be 100644
--- a/honeycomb-core/src/cmap/dim2/sews/one.rs
+++ b/honeycomb-core/src/cmap/dim2/sews/one.rs
@@ -1,6 +1,6 @@
 //! 1D sew implementations
 
-use stm::{atomically, StmResult, Transaction};
+use fast_stm::{atomically, StmResult, Transaction};
 
 use crate::{
     attributes::UnknownAttributeStorage,
diff --git a/honeycomb-core/src/cmap/dim2/sews/two.rs b/honeycomb-core/src/cmap/dim2/sews/two.rs
index ceff0c918..2090ae787 100644
--- a/honeycomb-core/src/cmap/dim2/sews/two.rs
+++ b/honeycomb-core/src/cmap/dim2/sews/two.rs
@@ -1,6 +1,6 @@
 //! 2D sew implementations
 
-use stm::{atomically, StmResult, Transaction};
+use fast_stm::{atomically, StmResult, Transaction};
 
 use crate::{
     attributes::{AttributeStorage, UnknownAttributeStorage},
diff --git a/honeycomb-core/src/cmap/dim2/utils.rs b/honeycomb-core/src/cmap/dim2/utils.rs
index adc33354b..61f78ae70 100644
--- a/honeycomb-core/src/cmap/dim2/utils.rs
+++ b/honeycomb-core/src/cmap/dim2/utils.rs
@@ -14,8 +14,8 @@
 use super::CMAP2_BETA;
 use crate::geometry::CoordsFloat;
 use crate::prelude::{CMap2, DartIdType};
+use fast_stm::atomically;
 use std::{fs::File, io::Write};
-use stm::atomically;
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/cmap/error.rs b/honeycomb-core/src/cmap/error.rs
index 3bdcf34c3..b087cd0ca 100644
--- a/honeycomb-core/src/cmap/error.rs
+++ b/honeycomb-core/src/cmap/error.rs
@@ -1,6 +1,6 @@
 //! Main error type
 
-use stm::StmError;
+use fast_stm::StmError;
 
 /// Convenience type alias.
 pub type CMapResult<T> = Result<T, CMapError>;
diff --git a/honeycomb-core/src/lib.rs b/honeycomb-core/src/lib.rs
index ffd3bb5e4..e375a0848 100644
--- a/honeycomb-core/src/lib.rs
+++ b/honeycomb-core/src/lib.rs
@@ -37,7 +37,7 @@ pub mod cmap;
 
 pub mod geometry;
 
-pub use stm; // re-export since we use their items in the API
+pub use fast_stm; // re-export since we use their items in the API
 
 /// commonly used items
 pub mod prelude;
diff --git a/honeycomb-kernels/src/shift/neighbors_average.rs b/honeycomb-kernels/src/shift/neighbors_average.rs
index 2b17aa345..5feefa51d 100644
--- a/honeycomb-kernels/src/shift/neighbors_average.rs
+++ b/honeycomb-kernels/src/shift/neighbors_average.rs
@@ -1,7 +1,7 @@
 use honeycomb_core::{
     cmap::{CMap2, DartIdType, Orbit2, OrbitPolicy, VertexIdType, NULL_DART_ID},
+    fast_stm::atomically,
     prelude::{CoordsFloat, Vertex2},
-    stm::atomically,
 };
 use rayon::prelude::*;
 

From 61c4404779df9aeb2f80f4bea2110bb2fde1cac6 Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Wed, 27 Nov 2024 09:01:41 +0100
Subject: [PATCH 04/11] add binary for perf

---
 benches/Cargo.toml        |  5 +++++
 benches/src/shift.rs      | 24 ++++++++++++++++++++++++
 honeycomb-core/Cargo.toml |  2 +-
 3 files changed, 30 insertions(+), 1 deletion(-)
 create mode 100644 benches/src/shift.rs

diff --git a/benches/Cargo.toml b/benches/Cargo.toml
index 28b288eb7..de2d62ef5 100644
--- a/benches/Cargo.toml
+++ b/benches/Cargo.toml
@@ -34,6 +34,11 @@ path = "src/builder.rs"
 name = "grisubal"
 path = "src/grisubal.rs"
 
+[[bin]]
+name = "shift"
+path = "src/shift.rs"
+
+
 # benches
 
 ## Core benchmarks
diff --git a/benches/src/shift.rs b/benches/src/shift.rs
new file mode 100644
index 000000000..1141a4070
--- /dev/null
+++ b/benches/src/shift.rs
@@ -0,0 +1,24 @@
+use honeycomb::{
+    kernels::shift::shift_vertices_to_neigh_avg,
+    prelude::{CMap2, CMapBuilder},
+};
+
+fn main() {
+    // ./binary ~/path/to/file.vtk n_rounds
+    let args: Vec<String> = std::env::args().collect();
+    let path = if let Some(path) = args.get(1) {
+        path.clone()
+    } else {
+        "examples/quads.vtk".to_string()
+    };
+    let n_rounds = args
+        .get(2)
+        .and_then(|s| s.parse::<usize>().ok())
+        .unwrap_or(100);
+
+    let map: CMap2<f64> = CMapBuilder::default().vtk_file(path).build().unwrap();
+
+    shift_vertices_to_neigh_avg(&map, n_rounds);
+
+    std::hint::black_box(map);
+}
diff --git a/honeycomb-core/Cargo.toml b/honeycomb-core/Cargo.toml
index b039c20e6..162165c26 100644
--- a/honeycomb-core/Cargo.toml
+++ b/honeycomb-core/Cargo.toml
@@ -19,7 +19,7 @@ utils = []
 # deps
 
 [dependencies]
-fast-stm = { git = "https://github.com/imrn99/fast-stm.git", rev = "94a9ff5" }
+fast-stm = { git = "https://github.com/imrn99/fast-stm.git", rev = "9179010" }
 downcast-rs.workspace = true
 loom.workspace = true
 num-traits.workspace = true

From 4f7ce38db5fe258fac659320d1b2b3b263d9a17f Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Wed, 27 Nov 2024 10:47:37 +0100
Subject: [PATCH 05/11] add oncollide

---
 benches/Cargo.toml              |  4 ++
 benches/src/shift.rs            | 62 ++++++++++++++++++++----
 benches/src/shift_noncollide.rs | 84 +++++++++++++++++++++++++++++++++
 3 files changed, 140 insertions(+), 10 deletions(-)
 create mode 100644 benches/src/shift_noncollide.rs

diff --git a/benches/Cargo.toml b/benches/Cargo.toml
index de2d62ef5..87c5567d6 100644
--- a/benches/Cargo.toml
+++ b/benches/Cargo.toml
@@ -17,6 +17,7 @@ _single_precision = []
 [dependencies]
 cfg-if.workspace = true
 honeycomb.workspace = true
+rayon = "1.10.0"
 
 [dev-dependencies]
 honeycomb-core = { workspace = true, features = ["utils"] }
@@ -38,6 +39,9 @@ path = "src/grisubal.rs"
 name = "shift"
 path = "src/shift.rs"
 
+[[bin]]
+name = "shift-nc"
+path = "src/shift_noncollide.rs"
 
 # benches
 
diff --git a/benches/src/shift.rs b/benches/src/shift.rs
index 1141a4070..a88fca622 100644
--- a/benches/src/shift.rs
+++ b/benches/src/shift.rs
@@ -1,24 +1,66 @@
-use honeycomb::{
-    kernels::shift::shift_vertices_to_neigh_avg,
-    prelude::{CMap2, CMapBuilder},
+use rayon::prelude::*;
+
+use honeycomb::core::fast_stm::atomically;
+use honeycomb::prelude::{
+    CMap2, CMapBuilder, DartIdType, Orbit2, OrbitPolicy, Vertex2, VertexIdType, NULL_DART_ID,
 };
 
 fn main() {
     // ./binary ~/path/to/file.vtk n_rounds
     let args: Vec<String> = std::env::args().collect();
-    let path = if let Some(path) = args.get(1) {
-        path.clone()
-    } else {
-        "examples/quads.vtk".to_string()
-    };
+    let n_squares = args
+        .get(1)
+        .and_then(|s| s.parse::<usize>().ok())
+        .unwrap_or(256);
     let n_rounds = args
         .get(2)
         .and_then(|s| s.parse::<usize>().ok())
         .unwrap_or(100);
 
-    let map: CMap2<f64> = CMapBuilder::default().vtk_file(path).build().unwrap();
+    let map: CMap2<f64> = CMapBuilder::unit_grid(n_squares).build().unwrap();
+
+    // fetch all vertices that are not on the boundary of the map
+    let tmp: Vec<(VertexIdType, Vec<VertexIdType>)> = map
+        .fetch_vertices()
+        .identifiers
+        .into_iter()
+        .filter_map(|v| {
+            if Orbit2::new(&map, OrbitPolicy::Vertex, v as DartIdType)
+                .any(|d| map.beta::<2>(d) == NULL_DART_ID)
+            {
+                None
+            } else {
+                Some((
+                    v,
+                    Orbit2::new(&map, OrbitPolicy::Vertex, v as DartIdType)
+                        .map(|d| map.vertex_id(map.beta::<2>(d)))
+                        .collect(),
+                ))
+            }
+        })
+        .collect();
+    // main loop
+    let mut round = 0;
+    loop {
+        tmp.par_iter().for_each(|(vid, neigh)| {
+            atomically(|trans| {
+                let mut new_val = Vertex2::default();
+                for v in neigh {
+                    let vertex = map.read_vertex(trans, *v)?.unwrap();
+                    new_val.0 += vertex.0;
+                    new_val.1 += vertex.1;
+                }
+                new_val.0 /= neigh.len() as f64;
+                new_val.1 /= neigh.len() as f64;
+                map.write_vertex(trans, *vid, new_val)
+            });
+        });
 
-    shift_vertices_to_neigh_avg(&map, n_rounds);
+        round += 1;
+        if round >= n_rounds {
+            break;
+        }
+    }
 
     std::hint::black_box(map);
 }
diff --git a/benches/src/shift_noncollide.rs b/benches/src/shift_noncollide.rs
new file mode 100644
index 000000000..efd266f8f
--- /dev/null
+++ b/benches/src/shift_noncollide.rs
@@ -0,0 +1,84 @@
+use rayon::prelude::*;
+
+use honeycomb::core::fast_stm::atomically;
+use honeycomb::prelude::{
+    CMap2, CMapBuilder, DartIdType, Orbit2, OrbitPolicy, Vertex2, VertexIdType, NULL_DART_ID,
+};
+
+fn main() {
+    // ./binary ~/path/to/file.vtk n_rounds
+    let args: Vec<String> = std::env::args().collect();
+    let n_squares = args
+        .get(1)
+        .and_then(|s| s.parse::<usize>().ok())
+        .unwrap_or(256);
+    let n_rounds = args
+        .get(2)
+        .and_then(|s| s.parse::<usize>().ok())
+        .unwrap_or(100);
+
+    let map: CMap2<f64> = CMapBuilder::unit_grid(n_squares).build().unwrap();
+
+    // fetch all vertices that are not on the boundary of the map
+    let tmp = map
+        .fetch_vertices()
+        .identifiers
+        .into_iter()
+        .filter_map(|v| {
+            if Orbit2::new(&map, OrbitPolicy::Vertex, v as DartIdType)
+                .any(|d| map.beta::<2>(d) == NULL_DART_ID)
+            {
+                None
+            } else {
+                Some((
+                    v,
+                    Orbit2::new(&map, OrbitPolicy::Vertex, v as DartIdType)
+                        .map(|d| map.vertex_id(map.beta::<2>(d)))
+                        .collect(),
+                ))
+            }
+        });
+
+    #[allow(clippy::type_complexity)]
+    let (first_batch, second_batch): (
+        Vec<(VertexIdType, Vec<VertexIdType>)>,
+        Vec<(VertexIdType, Vec<VertexIdType>)>,
+    ) = tmp.partition(|(v, _)| ((v - 1) / 4) % 2 == 0); // this yields 2 ind. batches, just trust me
+
+    // main loop
+    let mut round = 0;
+    loop {
+        first_batch.par_iter().for_each(|(vid, neigh)| {
+            atomically(|trans| {
+                let mut new_val = Vertex2::default();
+                for v in neigh {
+                    let vertex = map.read_vertex(trans, *v)?.unwrap();
+                    new_val.0 += vertex.0;
+                    new_val.1 += vertex.1;
+                }
+                new_val.0 /= neigh.len() as f64;
+                new_val.1 /= neigh.len() as f64;
+                map.write_vertex(trans, *vid, new_val)
+            });
+        });
+        second_batch.par_iter().for_each(|(vid, neigh)| {
+            atomically(|trans| {
+                let mut new_val = Vertex2::default();
+                for v in neigh {
+                    let vertex = map.read_vertex(trans, *v)?.unwrap();
+                    new_val.0 += vertex.0;
+                    new_val.1 += vertex.1;
+                }
+                new_val.0 /= neigh.len() as f64;
+                new_val.1 /= neigh.len() as f64;
+                map.write_vertex(trans, *vid, new_val)
+            });
+        });
+        round += 1;
+        if round >= n_rounds {
+            break;
+        }
+    }
+
+    std::hint::black_box(map);
+}

From b88000f2c99c47d82fb776f40398a2cd1f7aba7b Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Wed, 27 Nov 2024 11:17:23 +0100
Subject: [PATCH 06/11] revert to regular stm

---
 benches/src/shift.rs                             | 2 +-
 benches/src/shift_noncollide.rs                  | 2 +-
 honeycomb-core/Cargo.toml                        | 3 +--
 honeycomb-core/src/attributes/collections.rs     | 2 +-
 honeycomb-core/src/attributes/manager.rs         | 2 +-
 honeycomb-core/src/attributes/tests.rs           | 2 +-
 honeycomb-core/src/attributes/traits.rs          | 2 +-
 honeycomb-core/src/cmap/components/betas.rs      | 2 +-
 honeycomb-core/src/cmap/components/unused.rs     | 2 +-
 honeycomb-core/src/cmap/dim2/basic_ops.rs        | 2 +-
 honeycomb-core/src/cmap/dim2/embed.rs            | 2 +-
 honeycomb-core/src/cmap/dim2/links/one.rs        | 2 +-
 honeycomb-core/src/cmap/dim2/links/two.rs        | 2 +-
 honeycomb-core/src/cmap/dim2/sews/one.rs         | 2 +-
 honeycomb-core/src/cmap/dim2/sews/two.rs         | 2 +-
 honeycomb-core/src/cmap/dim2/utils.rs            | 2 +-
 honeycomb-core/src/cmap/error.rs                 | 2 +-
 honeycomb-core/src/lib.rs                        | 2 +-
 honeycomb-kernels/src/shift/neighbors_average.rs | 2 +-
 19 files changed, 19 insertions(+), 20 deletions(-)

diff --git a/benches/src/shift.rs b/benches/src/shift.rs
index a88fca622..d4b29884a 100644
--- a/benches/src/shift.rs
+++ b/benches/src/shift.rs
@@ -1,6 +1,6 @@
 use rayon::prelude::*;
 
-use honeycomb::core::fast_stm::atomically;
+use honeycomb::core::stm::atomically;
 use honeycomb::prelude::{
     CMap2, CMapBuilder, DartIdType, Orbit2, OrbitPolicy, Vertex2, VertexIdType, NULL_DART_ID,
 };
diff --git a/benches/src/shift_noncollide.rs b/benches/src/shift_noncollide.rs
index efd266f8f..86d367392 100644
--- a/benches/src/shift_noncollide.rs
+++ b/benches/src/shift_noncollide.rs
@@ -1,6 +1,6 @@
 use rayon::prelude::*;
 
-use honeycomb::core::fast_stm::atomically;
+use honeycomb::core::stm::atomically;
 use honeycomb::prelude::{
     CMap2, CMapBuilder, DartIdType, Orbit2, OrbitPolicy, Vertex2, VertexIdType, NULL_DART_ID,
 };
diff --git a/honeycomb-core/Cargo.toml b/honeycomb-core/Cargo.toml
index 162165c26..c005a4879 100644
--- a/honeycomb-core/Cargo.toml
+++ b/honeycomb-core/Cargo.toml
@@ -19,9 +19,8 @@ utils = []
 # deps
 
 [dependencies]
-fast-stm = { git = "https://github.com/imrn99/fast-stm.git", rev = "9179010" }
 downcast-rs.workspace = true
-loom.workspace = true
+loom.workspace= true
 num-traits.workspace = true
 stm.workspace = true
 thiserror.workspace = true
diff --git a/honeycomb-core/src/attributes/collections.rs b/honeycomb-core/src/attributes/collections.rs
index ce2d59cca..d16d58307 100644
--- a/honeycomb-core/src/attributes/collections.rs
+++ b/honeycomb-core/src/attributes/collections.rs
@@ -10,8 +10,8 @@ use crate::{
     cmap::{CMapError, CMapResult},
     prelude::DartIdType,
 };
-use fast_stm::{atomically, StmResult, TVar, Transaction};
 use num_traits::ToPrimitive;
+use stm::{atomically, StmResult, TVar, Transaction};
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/attributes/manager.rs b/honeycomb-core/src/attributes/manager.rs
index 731aec7c0..21a70e91a 100644
--- a/honeycomb-core/src/attributes/manager.rs
+++ b/honeycomb-core/src/attributes/manager.rs
@@ -5,7 +5,7 @@
 
 // ------ IMPORTS
 
-use fast_stm::{StmResult, Transaction};
+use stm::{StmResult, Transaction};
 
 use super::{AttributeBind, AttributeStorage, AttributeUpdate, UnknownAttributeStorage};
 use crate::{
diff --git a/honeycomb-core/src/attributes/tests.rs b/honeycomb-core/src/attributes/tests.rs
index a311f3b3f..6ab44fddf 100644
--- a/honeycomb-core/src/attributes/tests.rs
+++ b/honeycomb-core/src/attributes/tests.rs
@@ -1,7 +1,7 @@
 // ------ IMPORTS
 
-use fast_stm::{atomically, StmError, Transaction, TransactionControl};
 use loom::sync::Arc;
+use stm::{atomically, StmError, Transaction, TransactionControl};
 
 use super::{
     AttrSparseVec, AttrStorageManager, AttributeBind, AttributeStorage, AttributeUpdate,
diff --git a/honeycomb-core/src/attributes/traits.rs b/honeycomb-core/src/attributes/traits.rs
index 76b7fca50..ead9ba67d 100644
--- a/honeycomb-core/src/attributes/traits.rs
+++ b/honeycomb-core/src/attributes/traits.rs
@@ -10,9 +10,9 @@ use crate::{
     prelude::{DartIdType, OrbitPolicy},
 };
 use downcast_rs::{impl_downcast, Downcast};
-use fast_stm::{atomically, StmResult, Transaction};
 use std::any::Any;
 use std::fmt::Debug;
+use stm::{atomically, StmResult, Transaction};
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/cmap/components/betas.rs b/honeycomb-core/src/cmap/components/betas.rs
index d4e4516da..e58db9411 100644
--- a/honeycomb-core/src/cmap/components/betas.rs
+++ b/honeycomb-core/src/cmap/components/betas.rs
@@ -2,7 +2,7 @@
 
 use std::ops::{Index, IndexMut};
 
-use fast_stm::{StmError, TVar, Transaction};
+use stm::{StmError, TVar, Transaction};
 
 use crate::cmap::NULL_DART_ID;
 
diff --git a/honeycomb-core/src/cmap/components/unused.rs b/honeycomb-core/src/cmap/components/unused.rs
index 1de378df4..5d85baada 100644
--- a/honeycomb-core/src/cmap/components/unused.rs
+++ b/honeycomb-core/src/cmap/components/unused.rs
@@ -5,7 +5,7 @@ use std::{
     slice::Iter,
 };
 
-use fast_stm::TVar;
+use stm::TVar;
 
 use super::identifiers::DartIdType;
 
diff --git a/honeycomb-core/src/cmap/dim2/basic_ops.rs b/honeycomb-core/src/cmap/dim2/basic_ops.rs
index c1c996cf6..889727bf0 100644
--- a/honeycomb-core/src/cmap/dim2/basic_ops.rs
+++ b/honeycomb-core/src/cmap/dim2/basic_ops.rs
@@ -17,8 +17,8 @@ use crate::{
     cmap::{EdgeCollection, FaceCollection, VertexCollection},
     geometry::CoordsFloat,
 };
-use fast_stm::{atomically, StmError, Transaction};
 use std::collections::{BTreeSet, VecDeque};
+use stm::{atomically, StmError, Transaction};
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/cmap/dim2/embed.rs b/honeycomb-core/src/cmap/dim2/embed.rs
index 0ba97a92d..2d0794a35 100644
--- a/honeycomb-core/src/cmap/dim2/embed.rs
+++ b/honeycomb-core/src/cmap/dim2/embed.rs
@@ -6,7 +6,7 @@
 
 // ------ IMPORT
 
-use fast_stm::{StmResult, Transaction};
+use stm::{StmResult, Transaction};
 
 use crate::prelude::{AttributeBind, AttributeUpdate, CMap2, Vertex2, VertexIdType};
 use crate::{
diff --git a/honeycomb-core/src/cmap/dim2/links/one.rs b/honeycomb-core/src/cmap/dim2/links/one.rs
index b1daa1db8..3c720e976 100644
--- a/honeycomb-core/src/cmap/dim2/links/one.rs
+++ b/honeycomb-core/src/cmap/dim2/links/one.rs
@@ -1,6 +1,6 @@
 //! 1D link implementations
 
-use fast_stm::{atomically, StmResult, Transaction};
+use stm::{atomically, StmResult, Transaction};
 
 use crate::{
     cmap::{CMap2, DartIdType},
diff --git a/honeycomb-core/src/cmap/dim2/links/two.rs b/honeycomb-core/src/cmap/dim2/links/two.rs
index e9c9b0ef2..339754985 100644
--- a/honeycomb-core/src/cmap/dim2/links/two.rs
+++ b/honeycomb-core/src/cmap/dim2/links/two.rs
@@ -1,6 +1,6 @@
 //! 2D link implementations
 
-use fast_stm::{atomically, StmResult, Transaction};
+use stm::{atomically, StmResult, Transaction};
 
 use crate::{
     cmap::{CMap2, DartIdType},
diff --git a/honeycomb-core/src/cmap/dim2/sews/one.rs b/honeycomb-core/src/cmap/dim2/sews/one.rs
index 941a470be..ed9316bea 100644
--- a/honeycomb-core/src/cmap/dim2/sews/one.rs
+++ b/honeycomb-core/src/cmap/dim2/sews/one.rs
@@ -1,6 +1,6 @@
 //! 1D sew implementations
 
-use fast_stm::{atomically, StmResult, Transaction};
+use stm::{atomically, StmResult, Transaction};
 
 use crate::{
     attributes::UnknownAttributeStorage,
diff --git a/honeycomb-core/src/cmap/dim2/sews/two.rs b/honeycomb-core/src/cmap/dim2/sews/two.rs
index 2090ae787..ceff0c918 100644
--- a/honeycomb-core/src/cmap/dim2/sews/two.rs
+++ b/honeycomb-core/src/cmap/dim2/sews/two.rs
@@ -1,6 +1,6 @@
 //! 2D sew implementations
 
-use fast_stm::{atomically, StmResult, Transaction};
+use stm::{atomically, StmResult, Transaction};
 
 use crate::{
     attributes::{AttributeStorage, UnknownAttributeStorage},
diff --git a/honeycomb-core/src/cmap/dim2/utils.rs b/honeycomb-core/src/cmap/dim2/utils.rs
index 61f78ae70..adc33354b 100644
--- a/honeycomb-core/src/cmap/dim2/utils.rs
+++ b/honeycomb-core/src/cmap/dim2/utils.rs
@@ -14,8 +14,8 @@
 use super::CMAP2_BETA;
 use crate::geometry::CoordsFloat;
 use crate::prelude::{CMap2, DartIdType};
-use fast_stm::atomically;
 use std::{fs::File, io::Write};
+use stm::atomically;
 
 // ------ CONTENT
 
diff --git a/honeycomb-core/src/cmap/error.rs b/honeycomb-core/src/cmap/error.rs
index b087cd0ca..3bdcf34c3 100644
--- a/honeycomb-core/src/cmap/error.rs
+++ b/honeycomb-core/src/cmap/error.rs
@@ -1,6 +1,6 @@
 //! Main error type
 
-use fast_stm::StmError;
+use stm::StmError;
 
 /// Convenience type alias.
 pub type CMapResult<T> = Result<T, CMapError>;
diff --git a/honeycomb-core/src/lib.rs b/honeycomb-core/src/lib.rs
index e375a0848..ffd3bb5e4 100644
--- a/honeycomb-core/src/lib.rs
+++ b/honeycomb-core/src/lib.rs
@@ -37,7 +37,7 @@ pub mod cmap;
 
 pub mod geometry;
 
-pub use fast_stm; // re-export since we use their items in the API
+pub use stm; // re-export since we use their items in the API
 
 /// commonly used items
 pub mod prelude;
diff --git a/honeycomb-kernels/src/shift/neighbors_average.rs b/honeycomb-kernels/src/shift/neighbors_average.rs
index 5feefa51d..2b17aa345 100644
--- a/honeycomb-kernels/src/shift/neighbors_average.rs
+++ b/honeycomb-kernels/src/shift/neighbors_average.rs
@@ -1,7 +1,7 @@
 use honeycomb_core::{
     cmap::{CMap2, DartIdType, Orbit2, OrbitPolicy, VertexIdType, NULL_DART_ID},
-    fast_stm::atomically,
     prelude::{CoordsFloat, Vertex2},
+    stm::atomically,
 };
 use rayon::prelude::*;
 

From 78b824d09fa4341e28bb9146d2cd63b6e4cf533c Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Wed, 27 Nov 2024 13:16:38 +0100
Subject: [PATCH 07/11] remove the kernel function & criterion bench

---
 benches/Cargo.toml                            |  7 +--
 benches/benches/shift.rs                      | 28 ----------
 honeycomb-kernels/src/lib.rs                  |  1 -
 honeycomb-kernels/src/shift/mod.rs            |  3 --
 .../src/shift/neighbors_average.rs            | 54 -------------------
 5 files changed, 1 insertion(+), 92 deletions(-)
 delete mode 100644 benches/benches/shift.rs
 delete mode 100644 honeycomb-kernels/src/shift/mod.rs
 delete mode 100644 honeycomb-kernels/src/shift/neighbors_average.rs

diff --git a/benches/Cargo.toml b/benches/Cargo.toml
index 87c5567d6..d7fdbf64b 100644
--- a/benches/Cargo.toml
+++ b/benches/Cargo.toml
@@ -91,13 +91,8 @@ name = "grisubal-grid-size"
 path = "benches/grisubal/grid_size.rs"
 harness = false
 
-
-[[bench]]
-name = "shift"
-path = "benches/shift.rs"
-harness = false
-
 [[bench]]
 name = "triangulate-quads"
 path = "benches/triangulate/quads.rs"
 harness = false
+
diff --git a/benches/benches/shift.rs b/benches/benches/shift.rs
deleted file mode 100644
index 6e22c8ebc..000000000
--- a/benches/benches/shift.rs
+++ /dev/null
@@ -1,28 +0,0 @@
-// ------ IMPORTS
-
-use criterion::{black_box, criterion_group, criterion_main, BenchmarkId, Criterion};
-use honeycomb::{kernels::shift::shift_vertices_to_neigh_avg, prelude::CMap2};
-use honeycomb_benches::FloatType;
-use honeycomb_core::cmap::CMapBuilder;
-
-// ------ CONTENT
-
-pub fn criterion_benchmark(c: &mut Criterion) {
-    let path = "../../../meshing-samples/vtk/2D/many_quads.vtk";
-
-    let mut group = c.benchmark_group("shift");
-
-    let mut map: CMap2<FloatType> = CMapBuilder::from(path).build().unwrap();
-
-    group.bench_function(BenchmarkId::new("to-neighbor-avg", ""), |b| {
-        b.iter(|| {
-            shift_vertices_to_neigh_avg(&map, 200);
-            black_box(&mut map);
-        })
-    });
-
-    group.finish();
-}
-
-criterion_group!(benches, criterion_benchmark);
-criterion_main!(benches);
diff --git a/honeycomb-kernels/src/lib.rs b/honeycomb-kernels/src/lib.rs
index 9551f7530..ecb0f1b3b 100644
--- a/honeycomb-kernels/src/lib.rs
+++ b/honeycomb-kernels/src/lib.rs
@@ -22,6 +22,5 @@
 // ------ MODULE DECLARATIONS
 
 pub mod grisubal;
-pub mod shift;
 pub mod splits;
 pub mod triangulation;
diff --git a/honeycomb-kernels/src/shift/mod.rs b/honeycomb-kernels/src/shift/mod.rs
deleted file mode 100644
index 8c52062d7..000000000
--- a/honeycomb-kernels/src/shift/mod.rs
+++ /dev/null
@@ -1,3 +0,0 @@
-mod neighbors_average;
-
-pub use neighbors_average::shift as shift_vertices_to_neigh_avg;
diff --git a/honeycomb-kernels/src/shift/neighbors_average.rs b/honeycomb-kernels/src/shift/neighbors_average.rs
deleted file mode 100644
index 2b17aa345..000000000
--- a/honeycomb-kernels/src/shift/neighbors_average.rs
+++ /dev/null
@@ -1,54 +0,0 @@
-use honeycomb_core::{
-    cmap::{CMap2, DartIdType, Orbit2, OrbitPolicy, VertexIdType, NULL_DART_ID},
-    prelude::{CoordsFloat, Vertex2},
-    stm::atomically,
-};
-use rayon::prelude::*;
-
-pub fn shift<T: CoordsFloat>(cmap: &CMap2<T>, n_rounds: usize) {
-    // fetch all vertices that are not on the boundary of the map
-    let vertices: Vec<VertexIdType> = cmap
-        .fetch_vertices()
-        .identifiers
-        .into_par_iter()
-        .filter(|v| {
-            !Orbit2::new(&cmap, OrbitPolicy::Vertex, *v as DartIdType)
-                .any(|d| cmap.beta::<2>(d) == NULL_DART_ID)
-        })
-        .collect();
-
-    let neighbors: Vec<Vec<VertexIdType>> = vertices
-        .par_iter()
-        .map(|v| {
-            Orbit2::new(&cmap, OrbitPolicy::Vertex, *v as DartIdType)
-                .map(|d| cmap.vertex_id(cmap.beta::<2>(d)))
-                .collect()
-        })
-        .collect();
-
-    // main loop
-    let mut round = 0;
-    loop {
-        vertices
-            .iter()
-            .zip(neighbors.iter())
-            .par_bridge()
-            .for_each(|(vid, neigh)| {
-                atomically(|trans| {
-                    let mut new_val: Vertex2<T> = Vertex2::default();
-                    for v in neigh {
-                        let vertex = cmap.read_vertex(trans, *v)?.unwrap();
-                        new_val.0 += vertex.0;
-                        new_val.1 += vertex.1;
-                    }
-                    new_val.0 /= T::from(neigh.len()).unwrap();
-                    new_val.1 /= T::from(neigh.len()).unwrap();
-                    cmap.write_vertex(trans, *vid, new_val)
-                });
-            });
-        round += 1;
-        if round >= n_rounds {
-            break;
-        }
-    }
-}

From ea97cdd591e6dcbc106fa6bf0e3141ad15b2dbe8 Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Wed, 27 Nov 2024 13:28:38 +0100
Subject: [PATCH 08/11] move rayon dep to workspace

---
 Cargo.toml         | 1 +
 benches/Cargo.toml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/Cargo.toml b/Cargo.toml
index ea659005a..87e6d3c95 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -36,6 +36,7 @@ honeycomb-render = { version = "0.6.0", path = "./honeycomb-render" }
 
 # common
 cfg-if = "1"
+rayon = "1.10.0"
 rustversion = "1.0.18"
 thiserror = "2.0.3"
 
diff --git a/benches/Cargo.toml b/benches/Cargo.toml
index d7fdbf64b..146e80776 100644
--- a/benches/Cargo.toml
+++ b/benches/Cargo.toml
@@ -17,7 +17,7 @@ _single_precision = []
 [dependencies]
 cfg-if.workspace = true
 honeycomb.workspace = true
-rayon = "1.10.0"
+rayon.workspace = true
 
 [dev-dependencies]
 honeycomb-core = { workspace = true, features = ["utils"] }

From ab9ae8d7105e65d34e02990924d52cede442728f Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Wed, 27 Nov 2024 13:37:03 +0100
Subject: [PATCH 09/11] fix comment

---
 benches/src/shift.rs            | 2 +-
 benches/src/shift_noncollide.rs | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/benches/src/shift.rs b/benches/src/shift.rs
index d4b29884a..8586d9c7f 100644
--- a/benches/src/shift.rs
+++ b/benches/src/shift.rs
@@ -6,7 +6,7 @@ use honeycomb::prelude::{
 };
 
 fn main() {
-    // ./binary ~/path/to/file.vtk n_rounds
+    // ./binary grid_size n_rounds
     let args: Vec<String> = std::env::args().collect();
     let n_squares = args
         .get(1)
diff --git a/benches/src/shift_noncollide.rs b/benches/src/shift_noncollide.rs
index 86d367392..0e064ef69 100644
--- a/benches/src/shift_noncollide.rs
+++ b/benches/src/shift_noncollide.rs
@@ -6,7 +6,7 @@ use honeycomb::prelude::{
 };
 
 fn main() {
-    // ./binary ~/path/to/file.vtk n_rounds
+    // ./binary grid_size n_rounds
     let args: Vec<String> = std::env::args().collect();
     let n_squares = args
         .get(1)

From fed3027b02b4dc0e41e017ed395474226752d724 Mon Sep 17 00:00:00 2001
From: imrn99 <95699343+imrn99@users.noreply.github.com>
Date: Wed, 27 Nov 2024 13:54:36 +0100
Subject: [PATCH 10/11] rename binary file

---
 benches/Cargo.toml                                        | 2 +-
 benches/src/{shift_noncollide.rs => shift_no_conflict.rs} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename benches/src/{shift_noncollide.rs => shift_no_conflict.rs} (100%)

diff --git a/benches/Cargo.toml b/benches/Cargo.toml
index 146e80776..9854204a0 100644
--- a/benches/Cargo.toml
+++ b/benches/Cargo.toml
@@ -41,7 +41,7 @@ path = "src/shift.rs"
 
 [[bin]]
 name = "shift-nc"
-path = "src/shift_noncollide.rs"
+path = "src/shift_no_conflict.rs"
 
 # benches
 
diff --git a/benches/src/shift_noncollide.rs b/benches/src/shift_no_conflict.rs
similarity index 100%
rename from benches/src/shift_noncollide.rs
rename to benches/src/shift_no_conflict.rs

From cb24350632b66e2dca516c01809a994f7e2107d5 Mon Sep 17 00:00:00 2001
From: imrn99 <github@imrn.fr>
Date: Tue, 3 Dec 2024 14:31:55 +0100
Subject: [PATCH 11/11] add desxcriptions

---
 benches/src/shift.rs             | 29 ++++++++++++++++++++++++++++
 benches/src/shift_no_conflict.rs | 33 ++++++++++++++++++++++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/benches/src/shift.rs b/benches/src/shift.rs
index 8586d9c7f..0045d515f 100644
--- a/benches/src/shift.rs
+++ b/benches/src/shift.rs
@@ -1,3 +1,32 @@
+//! Simple vertex relaxation routine.
+//!
+//! # Usage
+//!
+//! ```
+//! cargo build --release --bin=shift
+//! ./target/release/shift <GRID_SIZE> <N_ROUNDS>
+//! ```
+//!
+//! With:
+//! - `GRID_SIZE` the dimension of the generated (square) grid along one axis
+//! - `N_ROUNDS` the number of iterations of the relaxa6tion algorithm
+//!
+//! # Description
+//!
+//! ## Routine
+//!
+//! The algorithm fetches all vertices that are not on the border of the map, fetch all identifiers of each
+//! respective vertices' neighbors. Then, for all vertices:
+//!
+//! - compute the average between neighbors
+//1 - overwrite current vertex value with computed average
+//!
+//! ## Benchmark
+//!
+//! This binary is meant to be use to evaluate scalability of geometry-only kernels. It is parallelized using
+//! rayon, and the number of thread used for execution can be controlled using `taskset`. By controlling this,
+//! and the grid size, we can evaluate both strong and weak scaling characteristics.
+
 use rayon::prelude::*;
 
 use honeycomb::core::stm::atomically;
diff --git a/benches/src/shift_no_conflict.rs b/benches/src/shift_no_conflict.rs
index 0e064ef69..4bff8bb87 100644
--- a/benches/src/shift_no_conflict.rs
+++ b/benches/src/shift_no_conflict.rs
@@ -1,3 +1,36 @@
+//! Simple vertex relaxation routine.
+//!
+//! # Usage
+//!
+//! ```
+//! cargo build --release --bin=shift
+//! ./target/release/shift <GRID_SIZE> <N_ROUNDS>
+//! ```
+//!
+//! With:
+//! - `GRID_SIZE` the dimension of the generated (square) grid along one axis
+//! - `N_ROUNDS` the number of iterations of the relaxa6tion algorithm
+//!
+//! # Description
+//!
+//! ## Routine
+//!
+//! The algorithm fetches all vertices that are not on the border of the map, fetch all identifiers of each
+//! respective vertices' neighbors. The set of vertices is then split into independent subset, to create
+//! groups with no RW access conflicts. Then, for all vertices of each set:
+//!
+//! - compute the average between neighbors
+//1 - overwrite current vertex value with computed average
+//!
+//! ## Benchmark
+//!
+//! This binary is meant to be use to evaluate scalability of geometry-only kernels. It is parallelized using
+//! rayon, and the number of thread used for execution can be controlled using `taskset`. By controlling this,
+//! and the grid size, we can evaluate both strong and weak scaling characteristics.
+//!
+//! Using this, along with the regular `shift` binary highlights the cost of access conflict and transaction
+//! cancellations.
+
 use rayon::prelude::*;
 
 use honeycomb::core::stm::atomically;