WIP Feature hybrid parallel and SIMD

Common/include/CConfig.hpp

@@ -988,9 +988,11 @@ class CConfig {
   unsigned short Pred_Order;              /*!< \brief Order of the predictor for FSI applications. */
   unsigned short Kind_Interpolation;         /*!< \brief type of interpolation to use for FSI applications. */
   bool ConservativeInterpolation;            /*!< \brief Conservative approach for non matching mesh interpolation. */
+  unsigned short NumNearestNeighbors;        /*!< \brief Number of neighbors used for Nearest Neighbor interpolation. */
   unsigned short Kind_RadialBasisFunction;   /*!< \brief type of radial basis function to use for radial basis FSI. */
   bool RadialBasisFunction_PolynomialOption; /*!< \brief Option of whether to include polynomial terms in Radial Basis Function Interpolation or not. */
-  su2double RadialBasisFunction_Parameter;   /*!< \brief Radial basis function parameter. */
+  su2double RadialBasisFunction_Parameter;   /*!< \brief Radial basis function parameter (radius). */
+  su2double RadialBasisFunction_PruneTol;    /*!< \brief Tolerance to prune the RBF interpolation matrix. */
   bool Prestretch;                           /*!< \brief Read a reference geometry for optimization purposes. */
   string Prestretch_FEMFileName;             /*!< \brief File name for reference geometry. */
   string FEA_FileName;              /*!< \brief File name for element-based properties. */
@@ -3460,27 +3462,27 @@ class CConfig {
   unsigned short GetMarker_All_ZoneInterface(unsigned short val_marker) const { return Marker_All_ZoneInterface[val_marker]; }
 
   /*!
-     * \brief Get the MixingPlane interface information for a marker <i>val_marker</i>.
-     * \param[in] val_marker value of the marker on the grid.
-     * \return 0 if is not part of the MixingPlane Interface and greater than 1 if it is part.
-     */
+   * \brief Get the MixingPlane interface information for a marker <i>val_marker</i>.
+   * \param[in] val_marker value of the marker on the grid.
+   * \return 0 if is not part of the MixingPlane Interface and greater than 1 if it is part.
+   */
   unsigned short GetMarker_All_MixingPlaneInterface(unsigned short val_marker) const { return Marker_All_MixingPlaneInterface[val_marker]; }
 
-    /*!
-     * \brief Get the Turbomachinery information for a marker <i>val_marker</i>.
-     * \param[in] val_marker value of the marker on the grid.
-     * \return 0 if is not part of the Turbomachinery and greater than 1 if it is part.
-     */
+  /*!
+   * \brief Get the Turbomachinery information for a marker <i>val_marker</i>.
+   * \param[in] val_marker value of the marker on the grid.
+   * \return 0 if is not part of the Turbomachinery and greater than 1 if it is part.
+   */
   unsigned short GetMarker_All_Turbomachinery(unsigned short val_marker) const { return Marker_All_Turbomachinery[val_marker]; }
 
-    /*!
-     * \brief Get the Turbomachinery flag information for a marker <i>val_marker</i>.
-     * \param[in] val_marker value of the marker on the grid.
-     * \return 0 if is not part of the Turbomachinery, flag INFLOW or OUTFLOW if it is part.
-     */
+  /*!
+   * \brief Get the Turbomachinery flag information for a marker <i>val_marker</i>.
+   * \param[in] val_marker value of the marker on the grid.
+   * \return 0 if is not part of the Turbomachinery, flag INFLOW or OUTFLOW if it is part.
+   */
   unsigned short GetMarker_All_TurbomachineryFlag(unsigned short val_marker) const { return Marker_All_TurbomachineryFlag[val_marker]; }
 
-    /*!
+  /*!
    * \brief Get the number of FSI interface markers <i>val_marker</i>.
    * \param[in] void.
    * \return Number of markers belonging to the FSI interface.
@@ -8787,6 +8789,16 @@ class CConfig {
    */
   su2double GetRadialBasisFunctionParameter(void) const { return RadialBasisFunction_Parameter; }
 
+  /*!
+   * \brief Get the tolerance used to prune the interpolation matrix (making it sparser).
+   */
+  su2double GetRadialBasisFunctionPruneTol(void) const { return RadialBasisFunction_PruneTol; }
+
+  /*!
+   * \brief Get the number of donor points to use in Nearest Neighbor interpolation.
+   */
+  unsigned short GetNumNearestNeighbors(void) const { return NumNearestNeighbors; }
+
   /*!
    * \brief Get the kind of inlet face interpolation function to use.
    */

Common/include/geometry/CGeometry.hpp

@@ -1621,7 +1621,7 @@ class CGeometry {
    * \param[in] fillLvl - Level of fill of the pattern.
    * \return Reference to the sparse pattern.
    */
-  const CCompressedSparsePatternUL& GetSparsePattern(ConnectivityType type, unsigned long fillLvl);
+  const CCompressedSparsePatternUL& GetSparsePattern(ConnectivityType type, unsigned long fillLvl = 0);
 
   /*!
    * \brief Get the edge to sparse pattern map.
@@ -1630,12 +1630,25 @@ class CGeometry {
    */
   const CEdgeToNonZeroMapUL& GetEdgeToSparsePatternMap(void);
 
+  /*!
+   * \brief Get the transpose of the (main, i.e 0 fill) sparse pattern (e.g. CSR becomes CSC).
+   * \param[in] type - Finite volume or finite element.
+   * \return Reference to the map.
+   */
+  const su2vector<unsigned long>& GetTransposeSparsePatternMap(ConnectivityType type);
+
   /*!
    * \brief Get the edge coloring.
    * \note This method computes the coloring if that has not been done yet.
+   * \param[out] efficiency - optional output of the coloring efficiency.
    * \return Reference to the coloring.
    */
-  const CCompressedSparsePatternUL& GetEdgeColoring(void);
+  const CCompressedSparsePatternUL& GetEdgeColoring(su2double* efficiency = nullptr);
+
+  /*!
+   * \brief Force the natural (sequential) edge coloring.
+   */
+  void SetNaturalEdgeColoring();
 
   /*!
    * \brief Get the group size used in edge coloring.
@@ -1646,9 +1659,15 @@ class CGeometry {
   /*!
    * \brief Get the element coloring.
    * \note This method computes the coloring if that has not been done yet.
+   * \param[out] efficiency - optional output of the coloring efficiency.
    * \return Reference to the coloring.
    */
-  const CCompressedSparsePatternUL& GetElementColoring(void);
+  const CCompressedSparsePatternUL& GetElementColoring(su2double* efficiency = nullptr);
+
+  /*!
+   * \brief Force the natural (sequential) element coloring.
+   */
+  void SetNaturalElementColoring();
 
   /*!
    * \brief Get the group size used in element coloring.

Common/include/geometry/dual_grid/CVertex.hpp

@@ -37,26 +37,25 @@
  */
 class CVertex : public CDualGrid {
 protected:
-  unsigned long *Nodes; /*!< \brief Vector to store the global nodes of an element. */
-  su2double *Normal;      /*!< \brief Normal coordinates of the element and its center of gravity. */
-  su2double Aux_Var;      /*!< \brief Auxiliar variable defined only on the surface. */
-  su2double CartCoord[3];   /*!< \brief Vertex cartesians coordinates. */
-  su2double VarCoord[3];    /*!< \brief Used for storing the coordinate variation due to a surface modification. */
-  su2double *VarRot;   /*!< \brief Used for storing the rotation variation due to a surface modification. */
-  long PeriodicPoint[5];      /*!< \brief Store the periodic point of a boundary (iProcessor, iPoint) */
-  bool ActDisk_Perimeter;     /*!< \brief Identify nodes at the perimeter of the actuator disk */
-  short Rotation_Type;      /*!< \brief Type of rotation associated with the vertex (MPI and periodic) */
+  unsigned long Nodes[1];        /*!< \brief Vector to store the global nodes of an element. */
+  su2double Normal[3];           /*!< \brief Normal coordinates of the element and its center of gravity. */
+  su2double Aux_Var;             /*!< \brief Auxiliar variable defined only on the surface. */
+  su2double CartCoord[3];        /*!< \brief Vertex cartesians coordinates. */
+  su2double VarCoord[3];         /*!< \brief Used for storing the coordinate variation due to a surface modification. */
+  su2double *VarRot;             /*!< \brief Used for storing the rotation variation due to a surface modification. */
+  long PeriodicPoint[5];         /*!< \brief Store the periodic point of a boundary (iProcessor, iPoint) */
+  bool ActDisk_Perimeter;        /*!< \brief Identify nodes at the perimeter of the actuator disk */
+  short Rotation_Type;           /*!< \brief Type of rotation associated with the vertex (MPI and periodic) */
   unsigned long Normal_Neighbor; /*!< \brief Index of the closest neighbor. */
-  unsigned long *Donor_Points; /*!< \brief indices of donor points for interpolation across zones */
-  unsigned long *Donor_Proc; /*!< \brief indices of donor processor for interpolation across zones in parallel */
-  unsigned long Donor_Elem;   /*!< \brief Store the donor element for interpolation across zones/ */
-  unsigned short Donor_Face;  /*!<\brief Store the donor face (w/in donor element) for interpolation across zones */
-  su2double Basis_Function[3]; /*!< \brief Basis function values for interpolation across zones. */
-  su2double *Donor_Coeff; /*!\brief Store a list of coefficients corresponding to the donor points. */
-  unsigned short nDonor_Points; /*!\brief Number of points in Donor_Points; at least there will be one donor point (if the mesh is matching)*/
+  unsigned long *Donor_Points;   /*!< \brief indices of donor points for interpolation across zones */
+  unsigned long *Donor_Proc;     /*!< \brief indices of donor processor for interpolation across zones in parallel */
+  unsigned long Donor_Elem;      /*!< \brief Store the donor element for interpolation across zones/ */
+  unsigned short Donor_Face;     /*!< \brief Store the donor face (w/in donor element) for interpolation across zones */
+  su2double Basis_Function[3];   /*!< \brief Basis function values for interpolation across zones. */
+  su2double *Donor_Coeff;        /*!< \brief Store a list of coefficients corresponding to the donor points. */
+  unsigned short nDonor_Points;  /*!< \brief Number of points in Donor_Coeff. */
 
 public:
-
   /*!
    * \brief Constructor of the class.
    * \param[in] val_point - Node of the vertex.
@@ -358,17 +357,6 @@ class CVertex : public CDualGrid {
    */
   inline unsigned long GetNormal_Neighbor(void) const { return Normal_Neighbor; }
 
-  /*!
-   * \brief Increment the number of donor points by 1.
-   */
-  inline void IncrementnDonor(void) {nDonor_Points++;}
-
-  /*!
-   * \brief Set the value of nDonor_Points
-   * \param[in] nDonor - the number of donor points
-   */
-  inline void SetnDonorPoints(unsigned short nDonor) {nDonor_Points = nDonor;}
-
   /*!
    * \brief Return the value of nDonor_Points
    * \return nDonor - the number of donor points
@@ -419,9 +407,9 @@ class CVertex : public CDualGrid {
 
   /*!
    * \brief Allocate memory based on how many donor points need to be stored.
-   * Uses nDonor_Points
+   * \param[in] nDonor - the number of donor points
    */
-  void Allocate_DonorInfo(void);
+  void Allocate_DonorInfo(unsigned short nDonor);
 
   /*!
    * \brief Get the rotation variation