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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example 5.2: Molli XT Benchmark\n",
    "\n",
    "## Hardware Specification for Rerun\n",
    "\n",
    "Desktop workstation with 2x (AMD EPYC 7702 64-Core) with total of 128 physical and 256 logical cores, 1024 GB DDR4 with Ubuntu 22.04 LTS operating system."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import molli as ml\n",
    "import molli_xt\n",
    "from scipy.spatial.distance import cdist\n",
    "import numpy as np\n",
    "import timeit\n",
    "\n",
    "arr1 = np.random.rand(100, 30, 3).astype(\"f4\")\n",
    "test_arrs = {\n",
    "    size: np.random.rand(size, 3).astype(\"f4\") for size in (10, 100, 1000, 10000, 20000)\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Distance (Euclidean) calculation with scipy.cdist:\n",
      "size=10: t_sp/t_ml=9.535875 molli=0.001277 scipy=0.012177\n",
      "size=100: t_sp/t_ml=3.079132 molli=0.006536 scipy=0.020125\n",
      "size=1000: t_sp/t_ml=4.997022 molli=0.065151 scipy=0.325563\n",
      "size=10000: t_sp/t_ml=2.504050 molli=0.744849 scipy=1.865138\n",
      "size=20000: t_sp/t_ml=1.908507 molli=1.464665 scipy=2.795323\n"
     ]
    }
   ],
   "source": [
    "# Comparison for euclidean distance\n",
    "print(\"Distance (Euclidean) calculation with scipy.cdist:\")\n",
    "for size, arr2 in test_arrs.items():\n",
    "    times_scipy = timeit.Timer(\n",
    "        \"\"\"[cdist(x, arr2, \"sqeuclidean\") for x in arr1]\"\"\",\n",
    "        globals=globals(),\n",
    "    ).repeat(5, 10)\n",
    "\n",
    "    times_molli = timeit.Timer(\n",
    "        \"\"\"molli_xt.cdist32f_eu2(arr1, arr2)\"\"\",\n",
    "        globals=globals(),\n",
    "    ).repeat(5, 10)\n",
    "\n",
    "    t_sp = min(times_scipy)\n",
    "    t_ml = min(times_molli)\n",
    "\n",
    "    print(f\"{size=}: {t_sp/t_ml=:3f} molli={t_ml:4f} scipy={t_sp:4f}\")\n"
   ]
  }
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