Added a code snippet to selectively load the NVIDIA IndeX plugin, and…

… fixed an issue in the script to start the Dask-MPI cluster Signed-off-by: Nick Leaf <[email protected]>
NVIDIA · Sep 17, 2020 · 3f83418 · 3f83418
1 parent 074d548
commit 3f83418
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Showing 2 changed files with 64 additions and 55 deletions.
diff --git a/notebooks/Dask-MPI_Volume_Render.ipynb b/notebooks/Dask-MPI_Volume_Render.ipynb
@@ -110,59 +110,68 @@
    "source": [
     "# Define a function for remote execution that will set up the ParaView state\n",
     "def workerState(self, arr):\n",
-    "        import numpy as np\n",
-    "        import vtk\n",
-    "        from vtk.util import numpy_support as vtknp\n",
-    "        \n",
-    "        #Use the undocumented block slicing to get the block for this rank\n",
-    "        wdims = arr.shape[::-1]\n",
-    "        ar = arr.blocks[self.rank].compute()\n",
-    "        dims = ar.shape[::-1]\n",
-    "        print(\"Rank\", self.rank, \"has array with local/global dims\", dims, wdims)\n",
-    "        ar = np.reshape(ar, dims[0]*dims[1]*dims[2])\n",
-    "        \n",
-    "        ext = [0,dims[0]-1, 0,dims[1]-1, max(self.rank*dims[2]-1,0),(self.rank+1)*dims[2]-1]\n",
-    "        wext = [0,wdims[0]-1, 0,wdims[1]-1, 0,wdims[2]-1]\n",
-    "\n",
-    "        vtkimg = vtk.vtkImageData()\n",
-    "        vtkimg.Initialize()\n",
-    "        vtkimg.SetExtent(ext)\n",
-    "        vtkimg.SetSpacing([1,1,1])\n",
-    "        \n",
-    "        #set the extent for the whole dataset\n",
-    "        vi = vtk.vtkInformation()\n",
-    "        vtkimg.CopyInformationToPipeline(vi)\n",
-    "        vi.Set(vtk.vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT(), wext[0],wext[1],wext[2],wext[3],wext[4],wext[5])\n",
-    "        vtkimg.CopyInformationFromPipeline(vi)\n",
-    "\n",
-    "        varnm = 'E' #'E' is entropy for this data\n",
-    "        vtkarr = vtknp.numpy_to_vtk(ar)\n",
-    "        vtkarr.SetName(varnm)\n",
-    "        vtkimg.GetPointData().AddArray(vtkarr)\n",
-    "        vtkimg.GetPointData().SetScalars(vtkarr)\n",
-    "\n",
-    "        self.TP = self.pvs.TrivialProducer()\n",
-    "        self.TP.GetClientSideObject().SetOutput(vtkimg)\n",
-    "        self.TP.UpdatePipeline()\n",
-    "        \n",
-    "        #initializae some renderer settings\n",
-    "        self.renv.ViewSize = [800, 500]\n",
-    "        self.renv.CameraPosition = [650,0,0]\n",
-    "        self.renv.Background = [0.0, 0.0, 0.0]\n",
-    "\n",
-    "        #create a display object for the data, and set it to volume render\n",
-    "        self.TPDisplay = self.pvs.Show(self.TP, self.renv)\n",
-    "        ePWF,eLUT = self.pvs.GetOpacityTransferFunction(varnm), self.pvs.GetColorTransferFunction(varnm)\n",
-    "        eLUT.RGBPoints = [3.0241666020214752e-15, 0.0392156862745098, 1.0, 0.9686274509803922, 0.05988497659564321, 0.0392156862745098, 1.0, 0.9686274509803922, 0.06215288117527962, 0.0, 0.0, 0.0, 0.06337877362966537, 0.0, 0.0, 0.0, 0.06871142238378525, 0.901960784314, 0.0, 0.0, 0.0716535672545433, 0.901960784314, 0.901960784314, 0.0, 0.08403510600328445, 0.9882352941176471, 0.9882352941176471, 0.9882352941176471, 0.11376306414604187, 1.0, 1.0, 1.0]\n",
-    "        eLUT.ColorSpace = 'RGB'\n",
-    "        ePWF.Points = [3.0241666020214752e-15, 0.0, 0.5, 0.0, 0.032547514885663986, 0.0, 0.5, 0.0, 0.03309916704893112, 0.3529411852359772, 0.5, 0.0, 0.03346693515777588, 0.0, 0.5, 0.0, 0.06215288117527962, 0.0, 0.5, 0.0, 0.06779199838638306, 0.05882352963089943, 0.8863638639450073, 0.0, 0.07698621600866318, 0.11029411852359772, 0.5, 0.0, 0.08078648895025253, 0.04411764815449715, 0.5, 0.0, 0.08244144916534424, 0.4852941334247589, 0.5, 0.0, 0.08378992974758148, 0.0, 0.5, 0.0, 0.08746761322713148, 0.0, 0.5, 0.0, 0.09617146849632263, 0.0, 0.5, 0.0, 0.10965631902217865, 0.4117647111415863, 0.5, 0.0, 0.11376306414604187, 1.0, 0.5, 0.0]\n",
-    "\n",
-    "        # trace defaults for the display properties.\n",
+    "    import numpy as np\n",
+    "    import vtk\n",
+    "    from vtk.util import numpy_support as vtknp\n",
+    "\n",
+    "    useIndex = True\n",
+    "\n",
+    "    if useIndex:\n",
+    "        self.pvs.LoadPlugin('/usr/local/paraview/lib/paraview-5.8/plugins/pvNVIDIAIndeX/pvNVIDIAIndeX.so', remote=False, ns=globals())\n",
+    "\n",
+    "    #Use the undocumented block slicing to get the block for this rank\n",
+    "    wdims = arr.shape[::-1]\n",
+    "    ar = arr.blocks[self.rank].compute()\n",
+    "    dims = ar.shape[::-1]\n",
+    "    print(\"Rank\", self.rank, \"has array with local/global dims\", dims, wdims)\n",
+    "    ar = np.reshape(ar, dims[0]*dims[1]*dims[2])\n",
+    "\n",
+    "    ext = [0,dims[0]-1, 0,dims[1]-1, max(self.rank*dims[2]-1,0),(self.rank+1)*dims[2]-1]\n",
+    "    wext = [0,wdims[0]-1, 0,wdims[1]-1, 0,wdims[2]-1]\n",
+    "\n",
+    "    vtkimg = vtk.vtkImageData()\n",
+    "    vtkimg.Initialize()\n",
+    "    vtkimg.SetExtent(ext)\n",
+    "    vtkimg.SetSpacing([1,1,1])\n",
+    "\n",
+    "    #set the extent for the whole dataset\n",
+    "    vi = vtk.vtkInformation()\n",
+    "    vtkimg.CopyInformationToPipeline(vi)\n",
+    "    vi.Set(vtk.vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT(), wext[0],wext[1],wext[2],wext[3],wext[4],wext[5])\n",
+    "    vtkimg.CopyInformationFromPipeline(vi)\n",
+    "\n",
+    "    varnm = 'E' #'E' is entropy for this data\n",
+    "    vtkarr = vtknp.numpy_to_vtk(ar)\n",
+    "    vtkarr.SetName(varnm)\n",
+    "    vtkimg.GetPointData().AddArray(vtkarr)\n",
+    "    vtkimg.GetPointData().SetScalars(vtkarr)\n",
+    "\n",
+    "    self.TP = self.pvs.TrivialProducer()\n",
+    "    self.TP.GetClientSideObject().SetOutput(vtkimg)\n",
+    "    self.TP.UpdatePipeline()\n",
+    "\n",
+    "    #initializae some renderer settings\n",
+    "    self.renv.ViewSize = [800, 500]\n",
+    "    self.renv.CameraPosition = [650,0,0]\n",
+    "    self.renv.Background = [0.0, 0.0, 0.0]\n",
+    "\n",
+    "    #create a display object for the data, and set it to volume render\n",
+    "    self.TPDisplay = self.pvs.Show(self.TP, self.renv)\n",
+    "    ePWF,eLUT = self.pvs.GetOpacityTransferFunction(varnm), self.pvs.GetColorTransferFunction(varnm)\n",
+    "    eLUT.RGBPoints = [3.0241666020214752e-15, 0.0392156862745098, 1.0, 0.9686274509803922, 0.05988497659564321, 0.0392156862745098, 1.0, 0.9686274509803922, 0.06215288117527962, 0.0, 0.0, 0.0, 0.06337877362966537, 0.0, 0.0, 0.0, 0.06871142238378525, 0.901960784314, 0.0, 0.0, 0.0716535672545433, 0.901960784314, 0.901960784314, 0.0, 0.08403510600328445, 0.9882352941176471, 0.9882352941176471, 0.9882352941176471, 0.11376306414604187, 1.0, 1.0, 1.0]\n",
+    "    eLUT.ColorSpace = 'RGB'\n",
+    "    ePWF.Points = [3.0241666020214752e-15, 0.0, 0.5, 0.0, 0.032547514885663986, 0.0, 0.5, 0.0, 0.03309916704893112, 0.3529411852359772, 0.5, 0.0, 0.03346693515777588, 0.0, 0.5, 0.0, 0.06215288117527962, 0.0, 0.5, 0.0, 0.06779199838638306, 0.05882352963089943, 0.8863638639450073, 0.0, 0.07698621600866318, 0.11029411852359772, 0.5, 0.0, 0.08078648895025253, 0.04411764815449715, 0.5, 0.0, 0.08244144916534424, 0.4852941334247589, 0.5, 0.0, 0.08378992974758148, 0.0, 0.5, 0.0, 0.08746761322713148, 0.0, 0.5, 0.0, 0.09617146849632263, 0.0, 0.5, 0.0, 0.10965631902217865, 0.4117647111415863, 0.5, 0.0, 0.11376306414604187, 1.0, 0.5, 0.0]\n",
+    "\n",
+    "    # trace defaults for the display properties.\n",
+    "    if useIndex:\n",
+    "        self.TPDisplay.Representation = 'NVIDIA IndeX'\n",
+    "    else:\n",
     "        self.TPDisplay.Representation = 'Volume'\n",
-    "        self.TPDisplay.ColorArrayName = ['POINTS', varnm]\n",
-    "        self.TPDisplay.LookupTable = self.pvs.GetColorTransferFunction(varnm)\n",
-    "        self.TPDisplay.OpacityArray = ['POINTS', varnm]\n",
-    "        self.TPDisplay.ScalarOpacityFunction = self.pvs.GetOpacityTransferFunction(varnm)\n",
+    "\n",
+    "    self.TPDisplay.ColorArrayName = ['POINTS', varnm]\n",
+    "    self.TPDisplay.LookupTable = self.pvs.GetColorTransferFunction(varnm)\n",
+    "    self.TPDisplay.OpacityArray = ['POINTS', varnm]\n",
+    "    self.TPDisplay.ScalarOpacityFunction = self.pvs.GetOpacityTransferFunction(varnm)\n",
     "\n",
     "\n",
     "# Submit the setup function for execution on Dask workers\n",
@@ -204,7 +213,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,

diff --git a/scripts/runCluster.sh b/scripts/runCluster.sh
@@ -11,7 +11,7 @@ fi
 mkdir -p dask-worker-space
 
 CLEAN_CMD='rm -rf /tmp/scheduler.json *.lock dask-worker-space/*' #cleans up leftover lock files from last run
-SCHED_CMD='mpiexec -n 1 dask-mpi --scheduler-file /tmp/scheduler.json --no-nanny --local-directory dask-worker-space' #executes one scheduler process
-WORK_CMD="mpiexec -n $N dask-mpi --scheduler-file /tmp/scheduler.json --no-nanny --local-directory dask-worker-space --no-scheduler" #executes $N workers, connects them to scheduler
+SCHED_CMD='mpiexec --allow-run-as-root -n 1 dask-mpi --scheduler-file /tmp/scheduler.json --no-nanny --local-directory dask-worker-space' #executes one scheduler process
+WORK_CMD="mpiexec --allow-run-as-root -n $N dask-mpi --scheduler-file /tmp/scheduler.json --no-nanny --local-directory dask-worker-space --no-scheduler" #executes $N workers, connects them to scheduler
 
 $CLEAN_CMD ; $SCHED_CMD & $WORK_CMD ; fg