Contiguous storage of CPoint(s) #966

pcarruscag · 2020-04-30T22:21:30Z

Proposed Changes

Along the lines of #753 and #959

If this causes someone lots of conflicts when merging, or you have a lot of new code using the old CPoint (that will not compile anymore) it may be helpful to run this python script (refactor_cpoint.txt) before or after respectively, it was used for 80% of the refactoring done here.

PR Checklist

I am submitting my contribution to the develop branch.
My contribution generates no new compiler warnings (try with the '-Wall -Wextra -Wno-unused-parameter -Wno-empty-body' compiler flags).
My contribution is commented and consistent with SU2 style.
I have added a test case that demonstrates my contribution, if necessary.
I have updated appropriate documentation (Tutorials, Docs Page, config_template.cpp) , if necessary.

Common/src/geometry/CGeometry.cpp

…nup others

pcarruscag · 2020-05-02T10:27:00Z

Common/include/geometry/CGeometry.hpp

-  CPoint** node;                         /*!< \brief Node vector (dual grid information). */
+  CPoint* nodes;                         /*!< \brief Node vector (dual grid information). */


Usual change no 1

pcarruscag · 2020-05-02T10:27:16Z

Common/include/geometry/CPhysicalGeometry.hpp

-      node[iPoint]->SetWall_Distance(val);
+      nodes->SetWall_Distance(iPoint, val);


Usual change no 2.

pcarruscag · 2020-05-02T10:28:43Z

Common/include/geometry/dual_grid/CPoint.hpp

+  CCompressedSparsePatternUL Point;       /*!< \brief Points surrounding the central node of the control volume. */
+  CCompressedSparsePatternL Edge;         /*!< \brief Edges that set up a control volume (same sparse structure as Point). */
+  CCompressedSparsePatternL Elem;         /*!< \brief Elements that set up a control volume around a node. */


Significant change no 1a: Adjacency information is stored in compressed format (instead of vector of vectors).

pcarruscag · 2020-05-02T10:32:07Z

Common/src/geometry/CPhysicalGeometry.cpp

-      node[jPoint] = new CPoint(Local_Coords[iPoint*nDim+0],
-                                Local_Coords[iPoint*nDim+1],
-                                Local_Coords[iPoint*nDim+2],
-                                Local_to_Global_Point[jPoint], config);
+    nodes->SetCoord(jPoint, &Local_Coords[iPoint*nDim]);
+    nodes->SetGlobalIndex(jPoint, Local_to_Global_Point[jPoint]);


Significant change 2: After allocating the nodes we set data into each instead of instantiating a CPoint object per node.

pcarruscag · 2020-05-02T10:35:30Z

Common/src/geometry/CPhysicalGeometry.cpp

-  for (iPoint = 0; iPoint < nPoint; iPoint++)
-    node[iPoint]->SetnNeighbor(node[iPoint]->GetnPoint());
+  SU2_OMP_MASTER
+  nodes->SetPoints(points);


Significant change 1b: We set the adjacency for all points in one call, the input is a temporary vector<vector> or similar which the function SetPoints compresses, this is only done in 3 places.

pcarruscag · 2020-05-02T10:44:28Z

SU2_CFD/src/solvers/CSolver.cpp

+  /// TODO: No comms needed for this gradient? The Rmatrix should be allocated somewhere.

-  /*--- Deallocate memory ---*/
-  for (iVar = 0; iVar < nDim; iVar++)
-    delete [] Cvector[iVar];
-  delete [] Cvector;
+  const auto& gridVel = geometry->nodes->GetGridVel();
+  auto& gridVelGrad = geometry->nodes->GetGridVel_Grad();
+  auto rmatrix = CVectorOfMatrix(nPoint,nDim,nDim);

+  computeGradientsLeastSquares(nullptr, GRID_VELOCITY, PERIODIC_NONE, *geometry, *config,
+                               true, gridVel, 0, nDim, gridVelGrad, rmatrix);


Usual change 4: Grid velocity gradients are no longer duplicated.

pcarruscag · 2020-05-02T10:48:51Z

Common/src/geometry_structure_fem_part.cpp

-              su2double Coord_3D[3];
-              point_line >> Coord_3D[0]; point_line >> Coord_3D[1]; point_line >> Coord_3D[2];
-              node[ii] = new CPoint(Coord_3D[0], Coord_3D[1], Coord_3D[2], i, config);
-              ii++;
-              break;
-            }
-          }
+          su2double Coord[3] = {0.0};
+          point_line >> Coord[0];
+          point_line >> Coord[1];
+          if (nDim==3) point_line >> Coord[2];
+          nodes->SetCoord(ii, Coord);
+          nodes->SetGlobalIndex(ii, i);


@vdweide do the DG regressions cover all the types of mesh formats? I think the changes in this PR only affect the DG solver during mesh reading.

pcarruscag · 2020-05-02T10:50:06Z

Common/src/grid_adaptation_structure.cpp

@@ -42,211 +42,211 @@ CGridAdaptation::CGridAdaptation(CGeometry *geometry, CConfig *config) {
  size = SU2_MPI::GetSize();
  rank = SU2_MPI::GetRank();

-	unsigned long iPoint;


40% of the changes are in this file, I had to replace tabs because of Codefactor

pcarruscag · 2020-05-02T10:51:53Z

Common/src/grid_movement_structure.cpp

-  
+


Another 20% of the changes are here were I accidentally stripped the spaces...

Common/src/geometry/dual_grid/CPoint.cpp

pcarruscag · 2020-05-03T15:57:30Z

Common/src/geometry/dual_grid/CPoint.cpp

+CPoint::CPoint(unsigned long npoint, unsigned long ndim) : nDim(ndim) {



Significant change 3: There is a "minimal constructor" that only allocates the fields needed to read the mesh file (when geometry_aux is built).

pcarruscag · 2020-05-09T20:34:51Z

Can we get this going folks?

pr-triage bot added the PR: draft label Apr 30, 2020

pcarruscag added 8 commits May 1, 2020 09:33

re-write CPoint for contiguous storage

31000a6

first auto pass

b9b609c

second auto pass

e5419ba

Common compiles (with todos)

fc6e88d

address the TODO's

b413e0d

SU2_CFD compiles

80551a2

cgns fixes

87c5ba9

cleanup (still not going to work)

0cbc58e

pcarruscag force-pushed the contiguous_cpoint branch from 9f4d95b to 0cbc58e Compare May 1, 2020 13:49

pcarruscag commented May 1, 2020

View reviewed changes

Common/src/geometry/CGeometry.cpp Outdated Show resolved Hide resolved

pcarruscag added 2 commits May 1, 2020 17:01

fix the segfaults (hopefully)

fb4224c

Merge branch 'contiguous_cedge' into contiguous_cpoint

ab64512

pcarruscag changed the title ~~Contiguous storage of CPoint(s) [WIP]~~ Contiguous storage of CPoint(s) May 1, 2020

pcarruscag marked this pull request as ready for review May 1, 2020 16:28

pr-triage bot added PR: unreviewed and removed PR: draft labels May 1, 2020

pcarruscag added changelog:chore enhancement labels May 1, 2020

pcarruscag added 3 commits May 1, 2020 18:15

fix for DG problems

31e9148

make some methods of CPoint operate on entire set

047d1f2

Merge remote-tracking branch 'upstream/develop' into contiguous_cpoint

7bf5e2e

pcarruscag mentioned this pull request May 1, 2020

Failure to Restart on Large Meshes with Time-Averaged Data #949

Closed

pcarruscag added 6 commits May 1, 2020 22:20

contiguous storage of adjacency info in CPoint

fd6fe1a

fix and cleanup

4a629c5

sort Point adjacency, cleanup GriVelGrad methods

9338faf

add some hybrid parallel to easy geometry preprocessing methods, clea…

6830c09

…nup others

make code factor happy

d74f0f8

revert sorting of points

394dbd2

pcarruscag commented May 2, 2020

View reviewed changes

pcarruscag mentioned this pull request May 2, 2020

Hybrid OpenMP-MPI implementation Strategy + Vectorization (SIMD) #789

Closed

fine tune what structures of CPoint are allocated for different uses

eccac75

pcarruscag commented May 3, 2020

View reviewed changes

pcarruscag added 6 commits May 3, 2020 19:08

Merge branch 'multigrid_tweaks' into cpoint_and_mg

41b36c9

Merge branch 'multigrid_tweaks' into cpoint_and_mg

133098d

Merge branch 'multigrid_tweaks' into cpoint_and_mg

7b53c2f

Merge branch 'multigrid_tweaks' into cpoint_and_mg

6182c97

Merge branch 'multigrid_tweaks' into cpoint_and_mg

dc63f1e

Merge remote-tracking branch 'upstream/develop' into contiguous_cpoint

2577b07

pcarruscag mentioned this pull request May 9, 2020

Hybrid parallel boundary conditions for turbulence and compressible flow solvers #975

Merged

3 tasks

pcarruscag and others added 7 commits May 12, 2020 20:38

experiment on adjacency sorting

5e509c8

fix compilation

26ffc6f

fix for MSH

016b482

give up on the sorted point idea, cleanup RCM ordering

c1da478

try to put the residuals back... more cleanup...

9d5caec

Merge branch 'develop' into contiguous_cpoint

165ffa8

use stable_sort trying to avoid one residual change

5418396

talbring approved these changes May 13, 2020

View reviewed changes

pr-triage bot added PR: reviewed-approved and removed PR: unreviewed labels May 13, 2020

talbring merged commit a81b0ac into develop May 13, 2020

talbring deleted the contiguous_cpoint branch May 13, 2020 14:11

pr-triage bot added PR: merged and removed PR: reviewed-approved labels May 13, 2020

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Contiguous storage of CPoint(s) #966

Contiguous storage of CPoint(s) #966

pcarruscag commented Apr 30, 2020 •

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pcarruscag May 3, 2020 •

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pcarruscag commented May 9, 2020

		CPoint** node; /!< \brief Node vector (dual grid information). /
		CPoint* nodes; /!< \brief Node vector (dual grid information). /

		node[iPoint]->SetWall_Distance(val);
		nodes->SetWall_Distance(iPoint, val);

		CPoint::CPoint(unsigned long npoint, unsigned long ndim) : nDim(ndim) {

Contiguous storage of CPoint(s) #966

Contiguous storage of CPoint(s) #966

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pcarruscag commented Apr 30, 2020 • edited Loading

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