Merge pull request #391 from ankith26/ankith26-gsoc

[GSoC 2024] Binding PyElastica with Elastica++

.github/workflows/elasticapp.yml

@@ -0,0 +1,37 @@
+name: elasticapp (Elastica++ based backend) tests
+
+# trigger run only on changes to the backend folder.
+on:
+  push:
+    paths:
+      - backend/**
+  pull_request:
+    paths:
+      - backend/**
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"] #, "3.12"]
+        os: [ubuntu-latest] # , macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4.2.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install PyElastica
+        run: pip install . -v
+
+      - name: Install elasticapp backend
+        run: pip install ./backend -v
+
+      - name: Run elasticapp tests
+        run: |
+          python -m pip install pytest
+          pytest backend/tests

.gitignore

@@ -236,3 +236,6 @@ outcmaes/*
 
 # csv files
 *.csv
+
+# ./backend dependencies
+deps

backend/.clang-format

@@ -0,0 +1,17 @@
+---
+# We'll use defaults from the Google style.
+# See http://clang.llvm.org/docs/ClangFormat.html for help.
+Language: Cpp
+BasedOnStyle: Google
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+PointerAlignment: Left
+DerivePointerAlignment: false
+FixNamespaceComments: true
+IncludeCategories:
+  - Regex: "^<.*"
+    Priority: 1
+  - Regex: ".*"
+    Priority: 2
+NamespaceIndentation: All
+SortIncludes: false

backend/.gitignore

@@ -9,3 +9,13 @@ install_manifest.txt
 compile_commands.json
 CTestTestfile.cmake
 _deps
+
+subprojects/packagecache
+
+subprojects/blaze
+subprojects/blaze_tensor
+subprojects/brigand
+subprojects/cxxopts-3.1.1
+subprojects/sleef
+subprojects/tbb
+subprojects/yaml-cpp

backend/README.md

@@ -0,0 +1,44 @@
+# Elasticapp backend for PyElastica
+
+This file serves as the documentation for the `elasticapp` backend.
+
+## Installation
+
+In the root of the PyElastica source tree, run the following command
+
+```
+pip install ./backend
+```
+
+> Make sure you install the package from _PyElastica source tree_.
+
+This command will take care of installation of all build-time dependencies, compilation of C++ source files and install the a python package called `elasticapp`.
+
+## Testing
+
+Make sure you have `pytest` installed. In the root of the PyElastica source tree, run the following command
+
+```
+pytest backend/tests
+```
+
+## Benchmarking
+
+Standalone scripts for benchmarking purposes are available in `backend/benchmarking` folder.
+
+### Benchmarking `matmul`
+
+For benchmarking various `matmul` implementations, run
+
+```
+python3 backend/benchmarking/matmul.py
+```
+
+## Contributed By
+
+- Tejaswin Parthasarathy (Teja)
+- [Seung Hyun Kim](https://github.com/skim0119)
+- Ankith Pai
+- [Yashraj Bhosale](https://github.com/bhosale2)
+- Arman Tekinalp
+- Songyuan Cui

backend/benchmarking/batchcross.py

@@ -0,0 +1,50 @@
+from elasticapp._linalg_numpy import batch_cross
+from elasticapp._linalg import batch_cross as batch_cross_final
+from elasticapp._PyArrays import Matrix
+from elastica._linalg import _batch_cross
+import numpy
+import time
+
+# warm up jit for fair comparison
+random_1 = numpy.random.random((3, 1))
+random_2 = numpy.random.random((3, 1))
+out1 = _batch_cross(random_1, random_2)
+
+
+def benchmark_batchsize(funcs: list, batches: list[int], num_iterations: int = 1000):
+    ret: dict = {}
+    for batch_size in batches:
+        random_a = numpy.random.random((3, batch_size))
+        random_b = numpy.random.random((3, batch_size))
+
+        ret[batch_size] = {}
+        for func_name, func, func_wrap in funcs:
+            random_a_w = func_wrap(random_a) if func_wrap else random_a
+            random_b_w = func_wrap(random_b) if func_wrap else random_b
+
+            start = time.perf_counter()
+            for _ in range(num_iterations):
+                func(random_a_w, random_b_w)
+
+            ret[batch_size][func_name] = (time.perf_counter() - start) / num_iterations
+
+    return ret
+
+
+results = benchmark_batchsize(
+    [
+        ("pyelastica", _batch_cross, None),
+        ("elasticapp_blaze_copy", batch_cross, None),
+        ("elasticapp_blaze_final", batch_cross_final, Matrix),
+    ],
+    [2**i for i in range(14)],
+)
+for size, data in results.items():
+    pyelastica = data["pyelastica"]
+    elasticapp_blaze_copy = data["elasticapp_blaze_copy"]
+    elasticapp_blaze_final = data["elasticapp_blaze_final"]
+    print(f"{size = }")
+    print(f"{pyelastica = }")
+    print(f"{elasticapp_blaze_copy = }, ratio: {elasticapp_blaze_copy / pyelastica}")
+    print(f"{elasticapp_blaze_final = }, ratio: {elasticapp_blaze_final / pyelastica}")
+    print()

backend/benchmarking/inv_rotate.py

@@ -0,0 +1,46 @@
+from elasticapp._rotations import inv_rotate, inv_rotate_scalar
+from elasticapp._PyArrays import Tensor
+from elastica._rotations import _inv_rotate
+import numpy
+import time
+
+# warm up jit for fair comparison
+random_1 = numpy.random.random((3, 3, 1))
+out1 = _inv_rotate(random_1)
+
+
+def benchmark_batchsize(funcs: list, batches: list[int], num_iterations: int = 1000):
+    ret: dict = {}
+    for batch_size in batches:
+        random_a = numpy.random.random((3, 3, batch_size))
+
+        ret[batch_size] = {}
+        for func_name, func, func_wrap in funcs:
+            random_a_w = func_wrap(random_a) if func_wrap else random_a
+
+            start = time.perf_counter()
+            for _ in range(num_iterations):
+                func(random_a_w)
+
+            ret[batch_size][func_name] = (time.perf_counter() - start) / num_iterations
+
+    return ret
+
+
+results = benchmark_batchsize(
+    [
+        ("pyelastica", _inv_rotate, None),
+        ("elasticapp_simd", inv_rotate, Tensor),
+        ("elasticapp_scalar", inv_rotate_scalar, Tensor),
+    ],
+    [2**i for i in range(14)],
+)
+for size, data in results.items():
+    pyelastica = data["pyelastica"]
+    elasticapp_simd = data["elasticapp_simd"]
+    elasticapp_scalar = data["elasticapp_scalar"]
+    print(f"{size = }")
+    print(f"{pyelastica = }")
+    print(f"{elasticapp_simd = }, ratio: {elasticapp_simd / pyelastica}")
+    print(f"{elasticapp_scalar = }, ratio: {elasticapp_scalar / pyelastica}")
+    print()

backend/benchmarking/matmul.py

@@ -0,0 +1,62 @@
+from elasticapp._linalg_numpy import (
+    batch_matmul_naive,
+    batch_matmul_blaze,
+    batch_matmul,
+)
+from elasticapp._linalg import batch_matmul as batch_matmul_final
+from elasticapp._PyArrays import Tensor
+from elastica._linalg import _batch_matmul
+import numpy
+import time
+
+# warm up jit for fair comparison
+random_1 = numpy.random.random((3, 3, 1))
+random_2 = numpy.random.random((3, 3, 1))
+out1 = _batch_matmul(random_1, random_2)
+
+
+def benchmark_batchsize(funcs: list, batches: list[int], num_iterations: int = 1000):
+    ret: dict = {}
+    for batch_size in batches:
+        random_a = numpy.random.random((3, 3, batch_size))
+        random_b = numpy.random.random((3, 3, batch_size))
+
+        ret[batch_size] = {}
+        for func_name, func, func_wrap in funcs:
+            random_a_w = func_wrap(random_a) if func_wrap else random_a
+            random_b_w = func_wrap(random_b) if func_wrap else random_b
+
+            start = time.perf_counter()
+            for _ in range(num_iterations):
+                func(random_a_w, random_b_w)
+
+            ret[batch_size][func_name] = (
+                time.perf_counter() - start
+            ) / num_iterations
+
+    return ret
+
+
+results = benchmark_batchsize(
+    [
+        ("pyelastica", _batch_matmul, None),
+        ("elasticapp_naive", batch_matmul_naive, None),
+        ("elasticapp_blaze", batch_matmul_blaze, None),
+        ("elasticapp_blaze_copy", batch_matmul, None),
+        ("elasticapp_blaze_final", batch_matmul_final, Tensor),
+    ],
+    [2**i for i in range(14)],
+)
+for size, data in results.items():
+    pyelastica = data["pyelastica"]
+    elasticapp_naive = data["elasticapp_naive"]
+    elasticapp_blaze = data["elasticapp_blaze"]
+    elasticapp_blaze_copy = data["elasticapp_blaze_copy"]
+    elasticapp_blaze_final = data["elasticapp_blaze_final"]
+    print(f"{size = }")
+    print(f"{pyelastica = }")
+    print(f"{elasticapp_naive = }, ratio: {elasticapp_naive / pyelastica}")
+    print(f"{elasticapp_blaze = }, ratio: {elasticapp_blaze / pyelastica}")
+    print(f"{elasticapp_blaze_copy = }, ratio: {elasticapp_blaze_copy / pyelastica}")
+    print(f"{elasticapp_blaze_final = }, ratio: {elasticapp_blaze_final / pyelastica}")
+    print()