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Merge pull request #70 from jrenaud90/dev0.6.1
0.6.1 - Improved RS Helper Performance
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‎Benchmarks & Performance/RadialSolver/RadialSolver - General Benchmarks and Performance.ipynb

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‎Benchmarks & Performance/RadialSolver/RadialSolver - Helper Performance.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "b7617924-8ce7-4c34-bb98-1a0ab241c175",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"0.6.1\n"
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]
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}
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],
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"source": [
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"import TidalPy\n",
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"print(TidalPy.version)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "e5431759-b701-4895-8773-dd3c92e4cfd7",
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"from TidalPy.RadialSolver import build_rs_input_homogeneous_layers, build_rs_input_from_data\n",
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"from TidalPy.rheology import Maxwell, Elastic"
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]
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},
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{
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"cell_type": "markdown",
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"id": "f91165e3-cee0-4e6a-810a-35a006b9f521",
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"metadata": {},
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"source": [
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"## `build_rs_input_homogeneous_layers` Performance\n",
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"\n",
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"**v0.6.0:**\n",
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"\n",
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"slices_per_layer = 5; perform_checks=False; num_layers:\n",
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"- 1: 32.2us\n",
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"- 5: 33.4us\n",
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"- 10: 35.8us\n",
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"- 15: 37.7us\n",
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"- 20: 39.5us\n",
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"- 50: 52us\n",
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"- 100: 74us\n",
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"\n",
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"slices_per_layer = 5; perform_checks=True; num_layers:\n",
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"- 1: 32.5us\n",
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"- 5: 34.3us\n",
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"- 10: 35.7us\n",
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"- 15: 38.7us\n",
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"- 20: 40.6us\n",
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"- 50: 54us\n",
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"- 100: 75.3us\n",
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"\n",
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"slices_per_layer = 50; perform_checks=True; num_layers:\n",
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"- 1: 34.9us\n",
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"- 5: 47.8us\n",
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"- 10: 65.4us\n",
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"- 15: 82.0us\n",
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"- 20: 95.0us\n",
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"- 50: 188.0us\n",
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"- 100: 339.0us\n",
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"\n",
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"**v0.6.1:**\n",
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"slices_per_layer = 5; perform_checks=True; num_layers:\n",
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"- 1: 9.39 μs\n",
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"- 5: 10.8 μs\n",
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"- 10: 12.7 μs\n",
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"- 15: 14.6 μs\n",
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"- 20: 16.3 μs\n",
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"- 50: 26.9 μs\n",
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"- 100: 44.4 μs\n",
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"\n",
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"slices_per_layer = 50; perform_checks=True; num_layers:\n",
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"- 1: 11.8 μs\n",
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"- 5: 22.8 μs\n",
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"- 10: 36.5 μs\n",
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"- 15: 50.2 μs\n",
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"- 20: 64.9 μs\n",
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"- 50: 145 μs\n",
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"- 100: 280 μs"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "c14d9a0b-1beb-453d-94cf-4d7aa3cec3c5",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Working on #Layers = 1.\n",
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"9.39 μs ± 54.9 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n",
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"Working on #Layers = 5.\n",
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"10.8 μs ± 227 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n",
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"Working on #Layers = 10.\n",
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"12.7 μs ± 186 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n",
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"Working on #Layers = 15.\n",
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"14.6 μs ± 230 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n",
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"Working on #Layers = 20.\n",
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"16.3 μs ± 184 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n",
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"Working on #Layers = 50.\n",
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"26.9 μs ± 290 ns per loop (mean ± std. dev. of 7 runs, 10,000 loops each)\n",
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"Working on #Layers = 100.\n",
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"44.4 μs ± 424 ns per loop (mean ± std. dev. of 7 runs, 10,000 loops each)\n"
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]
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}
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],
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"source": [
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"slices_per_layer = 5\n",
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"perform_checks = True\n",
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"\n",
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"for num_layers in (1, 5, 10, 15, 20, 50, 100):\n",
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" planet_radius = 1.0e6\n",
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" forcing_frequency = 1.0e-4\n",
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" density_tuple = tuple([3000.0 for i in range(num_layers)])\n",
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" static_bulk_modulus_tuple = tuple([1.0e10 for i in range(num_layers)])\n",
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" static_shear_modulus_tuple = tuple([1.0e10 for i in range(num_layers)])\n",
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" bulk_viscosity_tuple = tuple([1.0e30 for i in range(num_layers)])\n",
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" shear_viscosity_tuple = tuple([1.0e30 for i in range(num_layers)])\n",
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" layer_type_tuple = tuple(['solid' for i in range(num_layers)])\n",
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" layer_is_static_tuple = tuple([False for i in range(num_layers)])\n",
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" layer_is_incompressible_tuple = tuple([False for i in range(num_layers)])\n",
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" shear_rheology_model_tuple = tuple([Maxwell() for i in range(num_layers)])\n",
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" bulk_rheology_model_tuple = tuple([Elastic() for i in range(num_layers)])\n",
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" thickness_fraction_tuple = tuple([1.0 / num_layers for i in range(num_layers)])\n",
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"\n",
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" inputs = (\n",
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" planet_radius,\n",
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" forcing_frequency,\n",
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" density_tuple,\n",
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" static_bulk_modulus_tuple,\n",
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" static_shear_modulus_tuple,\n",
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" bulk_viscosity_tuple,\n",
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" shear_viscosity_tuple,\n",
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" layer_type_tuple,\n",
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" layer_is_static_tuple,\n",
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" layer_is_incompressible_tuple,\n",
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" shear_rheology_model_tuple,\n",
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" bulk_rheology_model_tuple\n",
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" )\n",
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"\n",
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" # Make sure it works once\n",
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" print(f\"Working on #Layers = {num_layers}.\")\n",
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" output = build_rs_input_homogeneous_layers(*inputs, thickness_fraction_tuple=thickness_fraction_tuple, slice_per_layer=slices_per_layer, perform_checks=perform_checks)\n",
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"\n",
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" %timeit build_rs_input_homogeneous_layers(*inputs, thickness_fraction_tuple=thickness_fraction_tuple, slice_per_layer=slices_per_layer, perform_checks=perform_checks)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "a3e7dcc4-da35-43c2-a6cb-f3aec3a62cf7",
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"metadata": {},
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"source": [
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"## `build_rs_input_from_data` Performance\n",
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"**v0.6.0:**\n",
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"slices_per_layer = 5; perform_checks=True; num_layers:\n",
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"- 1: 145us\n",
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"- 5: 586us\n",
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"- 10: 1.15ms\n",
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"- 15: 1.7ms\n",
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"- 20: 2.29ms\n",
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"- 50: 5.89ms\n",
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"- 100: 12ms\n",
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"\n",
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"slices_per_layer = 50; perform_checks=True; num_layers:\n",
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"- 1: 153 μs\n",
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"- 5: 658 μs\n",
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"- 10: 1.28 ms\n",
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"- 15: 1.92 ms\n",
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"- 20: 2.51 ms\n",
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"- 50: 6.58 ms\n",
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"- 100: 13.8 ms\n",
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"\n",
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"**v0.6.1:**\n",
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"slices_per_layer = 5; perform_checks=True; num_layers:\n",
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"- 1: 14.6 μs \n",
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"- 5: 18.7 μs\n",
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"- 10: 22.1 μs\n",
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"- 15: 26.1 μs\n",
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"- 20: 28.7 μs\n",
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"- 50: 51.3 μs\n",
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"- 100: 85.5 μs\n",
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"\n",
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"slices_per_layer = 50; perform_checks=True; num_layers:\n",
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"- 1: 20.3 μs\n",
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"- 5: 49.8 μs\n",
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"- 10: 71.5 μs\n",
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"- 15: 101 μs\n",
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"- 20: 129 μs\n",
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"- 50: 302 μs\n",
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"- 100: 595 μs"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d4ab3cfc-301a-4d96-b135-c3acd41206bc",
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"metadata": {
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"scrolled": true
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Working on #Layers = 1.\n",
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"20.3 μs ± 196 ns per loop (mean ± std. dev. of 7 runs, 10,000 loops each)\n",
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"Working on #Layers = 5.\n",
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"49.8 μs ± 7.7 μs per loop (mean ± std. dev. of 7 runs, 10,000 loops each)\n",
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"Working on #Layers = 10.\n",
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"76.5 μs ± 3.07 μs per loop (mean ± std. dev. of 7 runs, 10,000 loops each)\n",
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"Working on #Layers = 15.\n"
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]
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}
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],
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"source": [
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"slices_per_layer = 50\n",
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"perform_checks = False\n",
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"warnings = False\n",
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"\n",
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"for num_layers in (1, 5, 10, 15, 20, 50, 100):\n",
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" planet_radius = 1.0e6\n",
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" forcing_frequency = 1.0e-4\n",
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" layer_thickness = planet_radius / num_layers\n",
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" dr = layer_thickness / slices_per_layer\n",
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"\n",
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" # The dr addition below ensures there is a small error in the radius array that the helper has to fix\n",
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" radius_array = np.concatenate([np.linspace(layer_thickness * i + 0.1 * dr, layer_thickness * (i + 1), slices_per_layer) for i in range(num_layers)])\n",
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" density_array = np.linspace(10_000.0, 4_000.0, radius_array.size)\n",
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" static_bulk_modulus_array = np.linspace(1000.0e9, 250.0e9, radius_array.size)\n",
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" static_shear_modulus_array = np.linspace(250.0e9, 50.0e9, radius_array.size)\n",
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" bulk_viscosity_array = np.logspace(30, 26, radius_array.size)\n",
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" shear_viscosity_array = np.logspace(30, 18, radius_array.size)\n",
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" \n",
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" layer_upper_radius_tuple = tuple([(i+1) * layer_thickness for i in range(num_layers)])\n",
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" layer_type_tuple = tuple(['solid' for i in range(num_layers)])\n",
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" layer_is_static_tuple = tuple([False for i in range(num_layers)])\n",
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" layer_is_incompressible_tuple = tuple([False for i in range(num_layers)])\n",
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" shear_rheology_model_tuple = tuple([Maxwell() for i in range(num_layers)])\n",
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" bulk_rheology_model_tuple = tuple([Elastic() for i in range(num_layers)])\n",
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" thickness_fraction_tuple = tuple([1.0 / num_layers for i in range(num_layers)])\n",
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"\n",
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" inputs = (\n",
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" forcing_frequency,\n",
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" radius_array,\n",
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" density_array,\n",
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" static_bulk_modulus_array,\n",
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" static_shear_modulus_array,\n",
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" bulk_viscosity_array,\n",
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" shear_viscosity_array,\n",
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" layer_upper_radius_tuple,\n",
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" layer_type_tuple,\n",
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" layer_is_static_tuple,\n",
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" layer_is_incompressible_tuple,\n",
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" shear_rheology_model_tuple,\n",
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" bulk_rheology_model_tuple\n",
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" )\n",
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"\n",
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" # Make sure it works once\n",
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" print(f\"Working on #Layers = {num_layers}.\")\n",
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" output = build_rs_input_from_data(*inputs, perform_checks=perform_checks, warnings=warnings)\n",
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"\n",
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" %timeit build_rs_input_from_data(*inputs, perform_checks=perform_checks, warnings=warnings)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.11"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎CHANGES.md

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# TidalPy Major Change Log
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### Version 0.6.1 (2025-01-11)
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#### Benchmarks and Performance
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* Added performance benchmark for `TidalPy.RadialSolver.helpers`.
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#### Fixes
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* Fixed memory leak that was occurring in the EOS Solver (therefore also RadialSolver) due to CyRK's CySolverSolution not being dereferenced (this is a problem with CyRK, but hack applied to TidalPy until a fix can be made to CyRK).
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#### Performance
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* Improved `TidalPy.RadialSolver.helpers.build_rs_input_from_data` performance by factor of 10x to 150x depending on layer structure.
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* Improved `TidalPy.RadialSolver.helpers.build_rs_input_homogeneous_layers` performance by factor of 15% to 3.5x depending on layer structure.
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* Improved `TidalPy.RadialSolver.radial_solver` performance by around 10% depending on layer structure.
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## Version 0.6.0 (2025-01-07)
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#### Removed
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* Removed support for the older non-cythonized `TidalPy.radial_solver` module in favor of `TidalPy.RadialSolver`

‎Demos/prem_data.csv

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5951000,3748.95,9236.31,4990.83,93380286530,1.95314E+11,1.00E+24
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5961000,3736.35,9185.11,4961.66,91981725679,1.9258E+11,1.00E+24
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5971000,3543.26,8905.24,4769.9,80616060219,1.73504E+11,1.00E+24
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5971000,3723.75,9133.92,4932.49,90596817738,1.89871E+11,1.00E+24
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5981000,3537.29,8886,4762.9,80244189155,1.72316E+11,1.00E+24
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5991000,3531.32,8866.77,4755.9,79873460911,1.71133E+11,1.00E+24
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6001000,3525.35,8847.53,4748.9,79503873733,1.69955E+11,1.00E+24

‎Documentation/RadialSolver/3 - Radial Solver Helpers.md

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The helper functions described here are designed to give users an easy interface to provide data that is then translated into the inputs required by the `radial_solver` function.
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These functions are not designed to be particularly efficient. So it is recommended to use them until you get comfortable with the kind of inputs `radial_solver` requires.
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At that point it would be more efficient to make the inputs correctly from the beginning and forego using these functions.
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At that point it would be more efficient to make the inputs correctly from the beginning and forego using these functions.
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That being said, benchmarking shows that they only add about a 2% -- 10% overhead depending on the layer structure.
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[^1]: If a crash does occur, please report it on TidalPy's GitHub issues page. Please include the exact inputs used.
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‎README.md

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---
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<a href="https://github.com/jrenaud90/TidalPy/releases"><img src="https://img.shields.io/badge/TidalPy-0.6.0 Alpha-orange" alt="TidalPy Version 0.6.0 Alpha" /></a>
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<a href="https://github.com/jrenaud90/TidalPy/releases"><img src="https://img.shields.io/badge/TidalPy-0.6.1 Alpha-orange" alt="TidalPy Version 0.6.1 Alpha" /></a>
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**Tidal Dynamics and Thermal-Orbital Evolution Software Suite Implemented in Cython and Python**
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‎Tests/Test_RadialSolver/test_a_helpers.py

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for layer_i in range(num_layers):
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if layer_i == 0:
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radius_array_new[0] == 0.0
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assert radius_array_new[0] == 0.0
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elif layer_i == (num_layers - 1):
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# One copy of upper radius at planet surface
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np.sum(radius_array_new == layer_upper_radius_tuple[layer_i]) == 1
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assert np.sum(radius_array_new == layer_upper_radius_tuple[layer_i]) == 1
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else:
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# Two copies of radius at interfaces
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np.sum(radius_array_new == layer_upper_radius_tuple[layer_i]) == 2
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assert np.sum(radius_array_new == layer_upper_radius_tuple[layer_i]) == 2
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# Check that other properties match expectations
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first_index = np.argwhere(radius_array_new == layer_upper_radius_tuple[layer_i])[0]
@@ -332,7 +332,10 @@ def test_build_rs_input_from_data(num_layers, num_slices, r0):
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assert radius_array_new[first_index + 1] == layer_upper_radius_tuple[layer_i]
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# Assert that physical properties are the same at this and below
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assert density_array_new[first_index] == density_array_new[first_index - 1]
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try:
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assert density_array_new[first_index] == density_array_new[first_index - 1]
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except:
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import pdb; pdb.set_trace()
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assert complex_bulk_array_new[first_index] == complex_bulk_array_new[first_index - 1]
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assert complex_shear_array_new[first_index] == complex_shear_array_new[first_index - 1]
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assert density_array_new[first_index] == density_array_new[first_index - 1]

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