From 7d3899eda099b6d3aa170208f51ccf88eeaa48b7 Mon Sep 17 00:00:00 2001 From: KevinCawley <72036796+KevinCawley@users.noreply.github.com> Date: Mon, 12 Jul 2021 08:39:29 -0500 Subject: [PATCH] Create profiling documentation directory (#1691) * Create profiling directory * Update to notebook, [build docs] * [build docs] --- docs/development/index.rst | 2 +- .../cpu_threads_dict_128_threads_1_node.csv | 3840 +++++++++++++++++ docs/development/profiling/index.rst | 10 + .../{ => profiling}/profiling_example.ipynb | 11 +- docs/development/profiling/tardis_example.yml | 1 + .../{images => profiling}/tardis_prof.png | Bin .../profiling/tardis_profiling_threads.ipynb | 368 ++ .../threads_dict_128_threads_1_node.csv | 3840 +++++++++++++++++ docs/development/tardis_example.yml | 1 - 9 files changed, 8066 insertions(+), 7 deletions(-) create mode 100644 docs/development/profiling/cpu_threads_dict_128_threads_1_node.csv create mode 100644 docs/development/profiling/index.rst rename docs/development/{ => profiling}/profiling_example.ipynb (98%) create mode 120000 docs/development/profiling/tardis_example.yml rename docs/development/{images => profiling}/tardis_prof.png (100%) create mode 100644 docs/development/profiling/tardis_profiling_threads.ipynb create mode 100644 docs/development/profiling/threads_dict_128_threads_1_node.csv delete mode 120000 docs/development/tardis_example.yml diff --git a/docs/development/index.rst b/docs/development/index.rst index d8a65c31b9b..3d0fe9ab0b0 100644 --- a/docs/development/index.rst +++ b/docs/development/index.rst @@ -31,4 +31,4 @@ the core team (active maintainers) of TARDIS. update_refdata matterbridge debug_numba - profiling_example + profiling/index diff --git a/docs/development/profiling/cpu_threads_dict_128_threads_1_node.csv b/docs/development/profiling/cpu_threads_dict_128_threads_1_node.csv new file mode 100644 index 00000000000..60eac8f6afb --- /dev/null +++ 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1413.312024116516 +128, 22, 1452.2413532733917 +128, 23, 1478.6487591266632 +128, 24, 1550.2475006580353 +128, 25, 1430.3216829299927 +128, 26, 1396.086347103119 +128, 27, 1330.2720942497253 +128, 28, 1368.9243438243866 +128, 29, 1443.3298432826996 +128, 30, 1403.636640071869 diff --git a/docs/development/profiling/index.rst b/docs/development/profiling/index.rst new file mode 100644 index 00000000000..100b0c5e481 --- /dev/null +++ b/docs/development/profiling/index.rst @@ -0,0 +1,10 @@ +===================== +Profiling Information +===================== + + +.. toctree:: + :maxdepth: 2 + + profiling_example + tardis_profiling_threads \ No newline at end of file diff --git a/docs/development/profiling_example.ipynb b/docs/development/profiling/profiling_example.ipynb similarity index 98% rename from docs/development/profiling_example.ipynb rename to docs/development/profiling/profiling_example.ipynb index a82246a16af..3398c10269a 100644 --- a/docs/development/profiling_example.ipynb +++ b/docs/development/profiling/profiling_example.ipynb @@ -71,11 +71,12 @@ ] }, { - "source": [ - "![](images/tardis_prof.png)" - ], "cell_type": "markdown", - "metadata": {} + "id": "65b28478", + "metadata": {}, + "source": [ + "![](tardis_prof.png)" + ] } ], "metadata": { @@ -100,4 +101,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/docs/development/profiling/tardis_example.yml b/docs/development/profiling/tardis_example.yml new file mode 120000 index 00000000000..665fe53411f --- /dev/null +++ b/docs/development/profiling/tardis_example.yml @@ -0,0 +1 @@ +../../tardis_example.yml \ No newline at end of file diff --git a/docs/development/images/tardis_prof.png b/docs/development/profiling/tardis_prof.png similarity index 100% rename from docs/development/images/tardis_prof.png rename to docs/development/profiling/tardis_prof.png diff --git a/docs/development/profiling/tardis_profiling_threads.ipynb b/docs/development/profiling/tardis_profiling_threads.ipynb new file mode 100644 index 00000000000..b0dd15af057 --- /dev/null +++ b/docs/development/profiling/tardis_profiling_threads.ipynb @@ -0,0 +1,368 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "61f49e0f", + "metadata": {}, + "source": [ + "# Profiling the effect of input parameters on TARDIS runtime #" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2c26cee6", + "metadata": {}, + "outputs": [], + "source": [ + "import tardis\n", + "from tardis import run_tardis\n", + "\n", + "from tardis.io.config_reader import Configuration\n", + "from tardis.io.atom_data.base import AtomData\n", + "from tardis.simulation import Simulation\n", + "from tardis import run_tardis\n", + "from tardis.io.atom_data.util import download_atom_data\n", + "download_atom_data('kurucz_cd23_chianti_H_He')\n", + "\n", + "import time\n", + "import numpy as np\n", + "from astropy import units as u\n", + "import csv\n", + "import statistics\n", + "import matplotlib.pyplot as plt" + ] + }, + { + "cell_type": "markdown", + "id": "dac6305a", + "metadata": {}, + "source": [ + "### Functions for building the dictionaries and interacting with files ###" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a806b64e", + "metadata": {}, + "outputs": [], + "source": [ + "def build_dictionary(fp):\n", + " \"\"\"\n", + " Uses the fp generated from open_file to return a dictionary. Then closes\n", + " the file at the end of execution.\n", + "\n", + " 'testing_param' : dict\n", + " 'iteration' : time\n", + " \n", + " Parameters\n", + " ----------\n", + " fp : file\n", + " \n", + " Returns\n", + " -------\n", + " data_dict : dictionary\n", + " \"\"\"\n", + " \n", + " data_dict = {}\n", + " reader = csv.reader(fp)\n", + " for line in reader:\n", + " testing_param = int(line[0])\n", + " \n", + " iteration = int(line[1])\n", + " \n", + " time_of_run = float(line[2])\n", + " \n", + " if testing_param not in data_dict:\n", + " data_dict[testing_param] = {}\n", + " if iteration not in data_dict[testing_param]:\n", + " data_dict[testing_param][iteration] = time_of_run\n", + " fp.close()\n", + " return data_dict \n", + "\n", + "def add_to_dictionary(data_dict, info):\n", + " \"\"\"\n", + " Adds the data to the dictionary\n", + " \n", + " Parameters\n", + " ----------\n", + " data_dict : dictionary\n", + " info : list\n", + " It is set up as [testing_param, iteration, run_time]\n", + " \"\"\"\n", + " \n", + " testing_param = info[0]\n", + " iteration = info[1]\n", + " time_of_run = info[2]\n", + " if testing_param not in data_dict:\n", + " data_dict[testing_param] = {}\n", + " data_dict[testing_param][iteration] = time_of_run\n", + "\n", + "\n", + "def check_existance(data_dict, info):\n", + " \"\"\"\n", + " Checks to see if a data poitn already exists in data_dict.\n", + " Returns true if it exists, false if it does not.\n", + " \n", + " Parameters\n", + " ----------\n", + " data_dict : dictionary\n", + " info : list\n", + " [testing_param, iteration]\n", + " \n", + " Returns\n", + " -------\n", + " Boolean\n", + " \"\"\"\n", + " \n", + " testing_param = info[0]\n", + " iteration = info[1]\n", + " #Checks if it thread already exists\n", + " if testing_param not in data_dict:\n", + " return False\n", + " #If it does\n", + " elif (testing_param in data_dict):\n", + " #Does the iteration exist yet\n", + " if iteration not in data_dict[testing_param]:\n", + " return False\n", + " return True" + ] + }, + { + "cell_type": "markdown", + "id": "92662ad4", + "metadata": {}, + "source": [ + "## Timing of a specific parameter in TARDIS ##" + ] + }, + { + "cell_type": "markdown", + "id": "a55336ba", + "metadata": {}, + "source": [ + "### Number of Threads ###" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "411e12a2", + "metadata": {}, + "outputs": [], + "source": [ + "def generate_data(thread_count, \n", + " iteration_count, \n", + " thread_dictionary, \n", + " cpu_timing_dictionary, \n", + " tardis_file, \n", + " thread_file, \n", + " cpu_file,):\n", + " \"\"\"\n", + " This function generates data for running a tardis file on different numbers of threads different times.\n", + " It writes the data to two dictionaries and their respecitve files.\n", + " \n", + " This function can be modified to write to as many or as few dictionaries and files as necessary.\n", + " In order to test different parameters, the index into the tardis_config must be adjusted. This must be done \n", + " manually in order to select the correct testing parameter.\n", + " \n", + " Parameters\n", + " ----------\n", + " thread_count : int\n", + " Max number of threads to be tested\n", + " iteration_count : int\n", + " Amount of testing on each thread\n", + " thread_dictionary : dict\n", + " cpu_timing_dictionary : dict\n", + " tardis_file : str\n", + " TARDIS config file\n", + " thread_file : str\n", + " .csv file name\n", + " cpu_file : str\n", + " .csv file name\n", + " \"\"\"\n", + "\n", + " tardis_config = Configuration.from_yaml(tardis_file)\n", + "\n", + " for threads in range(1, thread_count+1):\n", + " for i in range(1, iteration_count+1):\n", + " #Continue if this data point already exists. If it exists in one it exists in both\n", + " if check_existance(thread_dictionary, [threads, i]):\n", + " continue\n", + "\n", + " print(threads, \" : \", i)\n", + " tardis_config[\"montecarlo\"][\"nthreads\"] = threads\n", + "\n", + " sim = Simulation.from_config(tardis_config)\n", + " start = time.monotonic()\n", + " sim.run()\n", + " end = time.monotonic()\n", + " run_time = end-start\n", + " \n", + " add_to_dictionary(thread_dictionary, [threads, i, run_time])\n", + " add_to_dictionary(cpu_timing_dictionary, [threads, i, (run_time * threads)])\n", + "\n", + " with open(thread_file, \"a\") as data_file:\n", + " data_file.write(\"{}, {}, {}\\n\".format(threads, i, run_time))\n", + " with open(cpu_file, \"a\") as data_file:\n", + " data_file.write(\"{}, {}, {}\\n\".format(threads, i, run_time * threads))\n", + " \n", + " print(\"Completed\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d6966653", + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "TARDIS_FILE = 'tardis_example.yml'\n", + "STORAGE_FILE = 'threads_dict_128_threads_1_node.csv'\n", + "CPU_STORAGE_FILE = 'cpu_threads_dict_128_threads_1_node.csv'\n", + "\n", + "#Compile the numba functions\n", + "run_tardis(TARDIS_FILE)\n", + "\n", + "#Opens file and builds the dictionary\n", + "with open(STORAGE_FILE, \"r\") as threads_fp:\n", + " threads_dict = build_dictionary(threads_fp)\n", + "\n", + "with open(CPU_STORAGE_FILE, \"r\") as cpu_fp:\n", + " cpu_threads_dict = build_dictionary(cpu_fp)\n", + "\n", + "#Creates list of main data\n", + "threads_numbers = [i for i in range(1, 129, 1)]\n", + "cpu_threads_numbers = [i for i in range(1, 129, 1)]\n", + "\n", + "generate_data(128, 30, threads_dict, cpu_threads_dict, TARDIS_FILE, STORAGE_FILE, CPU_STORAGE_FILE)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7056ee6e", + "metadata": {}, + "outputs": [], + "source": [ + "def create_stat_dictionaries(main_dict):\n", + " \"\"\"\n", + " This builds two dictionaries, one that holds the mean of the data and the other that holds the stdev\n", + " \n", + " Parameters\n", + " ----------\n", + " main_dict : dict\n", + " Data dictionary, format of\n", + " testing_param : dictionary\n", + " iteration : time\n", + " \n", + " Returns\n", + " -------\n", + " main_dict_mean : dict\n", + " main_dict_stdev : dict\n", + " \"\"\"\n", + "\n", + " main_dict_list = {}\n", + " for thread, iteration_dict in main_dict.items():\n", + " main_dict_list[thread] = [v for (k, v) in iteration_dict.items()]\n", + "\n", + " main_dict_mean = {}\n", + " main_dict_stdev = {}\n", + " for thread, timing_list in main_dict_list.items():\n", + " main_dict_mean[thread] = statistics.mean(timing_list)\n", + " main_dict_stdev[thread] = statistics.stdev(timing_list)\n", + "\n", + " return main_dict_mean, main_dict_stdev\n", + "\n", + "threads_dict_mean, threads_dict_stdev = create_stat_dictionaries(threads_dict)\n", + "cpu_threads_dict_mean, cpu_threads_dict_stdev = create_stat_dictionaries(cpu_threads_dict)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ae1e8624", + "metadata": { + "scrolled": false + }, + "outputs": [], + "source": [ + "def graph_data(testing_params, mean_dict, stdev_dict, x_axis_title, y_axis_title, graph_title, text_labels=False):\n", + " \"\"\"\n", + " Uses pyplot to graph the data given the mean and standard deviation of data.\n", + " \n", + " Parameters\n", + " ----------\n", + " testing_params : list\n", + " This is a list of the testing parameters, which is used for the axis construction.\n", + " mean_dict : dict\n", + " stdev_dict : dict\n", + " x_axis_title : str\n", + " y_axis_title : str\n", + " graph_title : str\n", + " text_labels : bool\n", + " This is a boolean parameter for if the testing parameters are text. If they are text, then\n", + " it will set each tick mark on the x-axis to be a label in testing_params.\n", + " \"\"\"\n", + " \n", + " lists = sorted(mean_dict.items())\n", + " lists_stdev = sorted(stdev_dict.items())\n", + " x, y = zip(*lists)\n", + " x_stdev, y_stdev = zip(*lists_stdev)\n", + "\n", + " fig = plt.figure(figsize=(20,10))\n", + " ax = fig.add_subplot(1,1,1)\n", + " ax.set_xlabel(x_axis_title)\n", + " ax.set_ylabel(y_axis_title)\n", + " ax.set_title(graph_title)\n", + " ax.grid(True)\n", + " \n", + " if text_labels:\n", + " xtick_spacer = np.arange(0, len(testing_params), 1)\n", + " xticks = testing_params\n", + " ax.set_xticks(xtick_spacer)\n", + " ax.set_xticklabels(xticks, rotation='horizontal', fontsize=18)\n", + " elif not text_labels:\n", + " #If there are a lot of ticks, it will reduce for visibility.\n", + " interval = testing_params[1] - testing_params[0]\n", + " if len(testing_params) > 80:\n", + " xticks = np.arange(testing_params[0], testing_params[-1]+interval, interval*2)\n", + " else:\n", + " xticks = np.arange(testing_params[0], testing_params[-1]+interval, interval)\n", + " ax.set_xticks(xticks)\n", + " \n", + " ax.plot(x, y, color='tab:blue', label=\"{} vs {}\".format(x_axis_title, y_axis_title))\n", + " plt.errorbar(x, y, yerr=y_stdev, label='stdev')\n", + " leg = plt.legend(loc='best', ncol=1, mode='expanded', fancybox=False)\n", + " leg.get_frame().set_alpha(0.5)\n", + "\n", + "graph_data(threads_numbers, threads_dict_mean, threads_dict_stdev, \"threads\", \"time (sec)\", \"threads vs time\")\n", + "graph_data(cpu_threads_numbers, cpu_threads_dict_mean, cpu_threads_dict_stdev, \"threads\", \"time (sec)\", \"threads vs cpu time\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": 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