048-Grosch-3.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"https://gitlab.version.fz-juelich.de/grosch1/pvlink_demo_for_jupytercon/-/raw/JupyterCon2020/img/logo.png\"\n",
    "     style=\"float:right; width:25%; height:25%; margin-top:25px;\">\n",
    "\n",
    "# Jupyter for interactive in-situ visualization with ParaView/Catalyst\n",
    "\n",
    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.version.fz-juelich.de%2Fgrosch1%2Fpvlink_demo_for_jupytercon/JupyterCon2020)  \n",
    "Try out the *pvlink* extension and the example notebooks in binder."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Large dataset with a parallel `pvserver`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Start a parallel ParaView server on the command line, for example via `$ mpirun -np <numberOfProc> ./pvserver`.\n",
    "\n",
    "In this example, 64 compute nodes were used for a dataset of approximatly 1.2TB.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ipywidgets as widgets\n",
    "import os\n",
    "import pvlink\n",
    "\n",
    "from paraview.simple import *"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup pvlink renderer\n",
    "We are using *jupyter server proxy* to access our ParaViewWeb server since it is running on the HPC system."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "renderer = pvlink.RemoteRenderer(\n",
    "    baseURL='jupyter-jsc.fz-juelich.de'+os.environ['JUPYTERHUB_SERVICE_PREFIX'], \n",
    "    disableExternalPort=True, useJupyterServerProxyHttps=True,\n",
    "    pvserverHost=\"localhost\", pvserverPort=11111,\n",
    "    timeout=\"0\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup paraview pipeline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Setup RenderView"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "renderView = CreateView('RenderView', 'view')\n",
    "pvlink.utility.SetRecommendedRenderSettings(renderView)\n",
    "\n",
    "renderView.Background = [0, 0, 0]\n",
    "renderView.OrientationAxesVisibility = 0\n",
    "renderView.ShowAnnotation = 1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Read .xmf file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "box2xmf = XDMFReader(FileNames=['./visu/box2c.xmf'])\n",
    "box2xmf.GridStatus = ['Structured Grid']\n",
    "box2xmf.UpdatePipeline()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# box2xmfDisplay = Show(box2xmf, renderView)\n",
    "# box2xmfDisplay.SetRepresentationType('Volume')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Hide(box2xmf, renderView)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Apply filters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "contour = Contour(Input=box2xmf)\n",
    "contour.Isosurfaces = [0.3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "contourDisplay = Show(contour, renderView, 'GeometryRepresentation')\n",
    "contourDisplay.SetRepresentationType('Surface')\n",
    "contourDisplay.RescaleTransferFunctionToDataRange(True, False)\n",
    "contourDisplay.SetScalarBarVisibility(renderView, True);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "ColorBy(contourDisplay, ('POINTS', 'PS'))\n",
    "psLUT = GetColorTransferFunction('PS')\n",
    "psLUT.ApplyPreset('Blue Orange (divergent)', True);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Reset camera and focal point and display renderer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "pvlink.utility.ResetCamera(renderView, renderer)\n",
    "renderer.update_render()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9b848c6e88764ef3b4ee04b406a3e7a1",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Box(children=(RemoteRenderer(authKey='1da0ea24ad20daada608fc5de87325fb709b07fb8816cb7e', sessionURL='wss://jup…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "renderContainer = widgets.Box(children=[renderer], layout={'height': '800px'})\n",
    "display(renderContainer)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Print memory usage information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataInfo = box2xmf.GetDataInformation()\n",
    "\n",
    "memory_size = dataInfo.DataInformation.GetMemorySize()\n",
    "number_points = dataInfo.DataInformation.GetNumberOfPoints()\n",
    "number_cells = dataInfo.DataInformation.GetNumberOfCells()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "from paraview import benchmark\n",
    "memuse = benchmark.logbase.get_memuse()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of points:\t 77976270099\n",
      "Number of cells:\t 77629109375\n",
      "Memory size:\t\t 1218379428\n"
     ]
    }
   ],
   "source": [
    "print(\"Number of points:\\t\", number_points)\n",
    "print(\"Number of cells:\\t\", number_cells)\n",
    "print(\"Memory size:\\t\\t\", memory_size)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CL[0] 252244 / 52058712\n",
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     ]
    }
   ],
   "source": [
    "for use in memuse:\n",
    "    print(use)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Disconnect()"
   ]
  }
 ],
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   "display_name": "PyParaView-5.8",
   "language": "python",
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