Bug fixes PolyhedralGrid #513

rbe051 · 2021-02-02T08:42:35Z

It was suggested that #512 should be split in two parts; one for the polyhedral grid bugfixes and one for the vertical equilibrium grid. This pull request contains the bugfixes to the polyhedral grid.

The main two fixes in this pull request is to
1, make the PolyhedralGrid work for embedded lower dimensional grids
2, assign a geometry type to all codimensions (~ line 1600)

In 1d faces and nodes have the same codimension. We assume that the unstructured grid has a one to one mapping between the faces and the nodes

This commit contains two bugfixes: - The geometry type was only set to codim 0 and 1. - To make the PolyhedralGrid work for lower dimensional grids embedded in a higher dimensional domain (e.g., 2d grid in 3d domain), the UnstructuredGrid dimension must equal the domain dimension. Then all coordinates are expressed in global coordinates.

rbe051 · 2021-02-02T08:49:29Z

opm/grid/polyhedralgrid/grid.hh

+        return grid_.face_nodepos[ index+1 ] - grid_.face_nodepos[ index ];
+      if (codim==dim)
+         return 1;
+      return 0;


This change is necessary to make PolyhedralGrid work for 1D grids (then dim = 1, and two cases in the switch are equal). In this case faces and nodes have the same co-dimension. With the current change we always return the face properties for codim=1. If the grid dimension is 1, should we rather return the node properties? I'm not sure if it matters as there is (always?) a one-to-one mapping between faces and nodes in 1D.

blattms · 2021-02-02T13:41:48Z

One question:
If we are using a 1D grid, of what size will the C-arrayface_nodepos of UnstructuredGrid be?

blattms · 2021-02-02T13:58:41Z

Should have figured that out before posting the question. It is the number of faces as each face is a node.

blattms · 2021-02-02T13:58:55Z

jenkins build this please

blattms

Thanks for the contribution and the additional check.

You might want to check with valgrind and investigate, though. For this branch it complains
about missmatched frees when running test_polyhedralgrid.cpp. Here is the additional output when comparing to master:

0
0
Lifetime / consistency check for entities, codim 2
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 1
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 0
WARNING! Requested check of first 32 entities, but grid view only contains 1 entities
Intersection Lifetime / consistency check
WARNING! Requested check of intersections for first 32 elements, but grid view only contains 1 elements
Lifetime / consistency check for entities, codim 2
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 1
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 0
WARNING! Requested check of first 32 entities, but grid view only contains 1 entities
Intersection Lifetime / consistency check
WARNING! Requested check of intersections for first 32 elements, but grid view only contains 1 elements
==120816== Mismatched free() / delete / delete []
==120816==    at 0x4836F9E: operator delete(void*, unsigned long) (vg_replace_malloc.c:585)
==120816==    by 0x7DFCD2: main (test_polyhedralgrid.cpp:379)
==120816==  Address 0x5fb70050 is 0 bytes inside a block of size 144 alloc'd
==120816==    at 0x4835753: malloc (vg_replace_malloc.c:299)
==120816==    by 0x96E8AE: create_grid_empty (UnstructuredGrid.c:64)
==120816==    by 0x96EA26: allocate_grid (UnstructuredGrid.c:97)
==120816==    by 0x96EE5B: allocate_grid_from_file (UnstructuredGrid.c:216)
==120816==    by 0x96F84E: read_grid (UnstructuredGrid.c:538)
==120816==    by 0x7DFBF2: main (test_polyhedralgrid.cpp:368)
==120816== 
0
0
Lifetime / consistency check for entities, codim 1
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 0
WARNING! Requested check of first 32 entities, but grid view only contains 2 entities
Intersection Lifetime / consistency check
WARNING! Requested check of intersections for first 32 elements, but grid view only contains 2 elements
Lifetime / consistency check for entities, codim 1
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 0
WARNING! Requested check of first 32 entities, but grid view only contains 2 entities
Intersection Lifetime / consistency check
WARNING! Requested check of intersections for first 32 elements, but grid view only contains 2 elements
==120816== Mismatched free() / delete / delete []
==120816==    at 0x4836F9E: operator delete(void*, unsigned long) (vg_replace_malloc.c:585)
==120816==    by 0x7E013E: main (test_polyhedralgrid.cpp:415)
==120816==  Address 0x5fb78670 is 0 bytes inside a block of size 144 alloc'd
==120816==    at 0x4835753: malloc (vg_replace_malloc.c:299)
==120816==    by 0x96E8AE: create_grid_empty (UnstructuredGrid.c:64)
==120816==    by 0x96EA26: allocate_grid (UnstructuredGrid.c:97)
==120816==    by 0x96EE5B: allocate_grid_from_file (UnstructuredGrid.c:216)
==120816==    by 0x96F84E: read_grid (UnstructuredGrid.c:538)
==120816==    by 0x7E0067: main (test_polyhedralgrid.cpp:404)
==120816== 
0
0
Lifetime / consistency check for entities, codim 1
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 0
WARNING! Requested check of first 32 entities, but grid view only contains 2 entities
Intersection Lifetime / consistency check
WARNING! Requested check of intersections for first 32 elements, but grid view only contains 2 elements
Lifetime / consistency check for entities, codim 1
WARNING! Requested check of first 32 entities, but grid view only contains 3 entities
Lifetime / consistency check for entities, codim 0
WARNING! Requested check of first 32 entities, but grid view only contains 2 entities
Intersection Lifetime / consistency check
WARNING! Requested check of intersections for first 32 elements, but grid view only contains 2 elements
==120816== Mismatched free() / delete / delete []
==120816==    at 0x4836F9E: operator delete(void*, unsigned long) (vg_replace_malloc.c:585)
==120816==    by 0x7E0598: main (test_polyhedralgrid.cpp:451)
==120816==  Address 0x5fb80190 is 0 bytes inside a block of size 144 alloc'd
==120816==    at 0x4835753: malloc (vg_replace_malloc.c:299)
==120816==    by 0x96E8AE: create_grid_empty (UnstructuredGrid.c:64)
==120816==    by 0x96EA26: allocate_grid (UnstructuredGrid.c:97)
==120816==    by 0x96EE5B: allocate_grid_from_file (UnstructuredGrid.c:216)
==120816==    by 0x96F84E: read_grid (UnstructuredGrid.c:538)
==120816==    by 0x7E04C1: main (test_polyhedralgrid.cpp:440)
==120816== 
==120816== 
==120816== HEAP SUMMARY:
==120816==     in use at exit: 23,172 bytes in 126 blocks
==120816==   total heap usage: 466,764 allocs, 466,638 frees, 20,392,434 bytes allocated
==120816== 
==120816== LEAK SUMMARY:
==120816==    definitely lost: 1,217 bytes in 43 blocks
==120816==    indirectly lost: 0 bytes in 0 blocks
==120816==      possibly lost: 10,912 bytes in 31 blocks
==120816==    still reachable: 11,043 bytes in 52 blocks
==120816==         suppressed: 0 bytes in 0 blocks
==120816== Rerun with --leak-check=full to see details of leaked memory
==120816== 
==120816== For counts of detected and suppressed errors, rerun with: -v
==120816== ERROR SUMMARY: 3 errors from 3 contexts (suppressed: 0 from 0)

blattms · 2021-02-02T10:37:09Z

opm/grid/polyhedralgrid/grid.hh

+            if( hasSimplex ){
+              tmp = Dune::GeometryTypes::simplex(dim - codim);
+              geomTypes_[ codim ].push_back( tmp );
+              }
+            else if ( hasCube ){
+              tmp = Dune::GeometryTypes::cube(dim - codim);
+            geomTypes_[ codim ].push_back( tmp );}
+            else if (hasPolyhedron){
+              tmp = Dune::GeometryTypes::none(dim - codim);
+            geomTypes_[ codim ].push_back( tmp );}


Nitpick: Formatting is messed up (not enough indentation and } on the same line) which makes this hard to read.

Test embedded grids in higher dimensional domains

rbe051 · 2021-02-02T16:54:35Z

Thanks for the review.

I have updated the formatting and tried to fixe the memory leaks. Valgrind is still complaining about possible memory leaks, however, I get the same results when testing on master.

==183467== 
==183467== HEAP SUMMARY:
==183467==     in use at exit: 7,584 bytes in 15 blocks
==183467==   total heap usage: 433,796 allocs, 433,781 frees, 15,130,718 bytes allocated
==183467== 
==183467== LEAK SUMMARY:
==183467==    definitely lost: 0 bytes in 0 blocks
==183467==    indirectly lost: 0 bytes in 0 blocks
==183467==      possibly lost: 3,344 bytes in 11 blocks
==183467==    still reachable: 4,240 bytes in 4 blocks
==183467==         suppressed: 0 bytes in 0 blocks
==183467== Rerun with --leak-check=full to see details of leaked memory
==183467== 
==183467== For lists of detected and suppressed errors, rerun with: -s
==183467== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

blattms

thanks for the changes. The double frees are gone and I think this got to go in (if jenkins agrees).

blattms · 2021-02-02T19:50:48Z

jenkins build this please

rube051 added 3 commits February 1, 2021 12:07

[Feature][PolyhedralGrid] Make polyhedral grid work in 1d

a172f54

In 1d faces and nodes have the same codimension. We assume that the unstructured grid has a one to one mapping between the faces and the nodes

Give PolyhedralgridIntersection an empty constructor

e27e001

rbe051 commented Feb 2, 2021

View reviewed changes

blattms requested changes Feb 2, 2021

View reviewed changes

rube051 added 2 commits February 2, 2021 17:19

Added grid tests to PolyhedralGrid

129dcb0

Test embedded grids in higher dimensional domains

Fixed formating in polyhedralgrid/grid.hh

52bb4b8

rbe051 force-pushed the bug_fixes_polyhedral_grid branch from 1b16a4f to 52bb4b8 Compare February 2, 2021 16:37

blattms approved these changes Feb 2, 2021

View reviewed changes

blattms merged commit 750a7ed into OPM:master Feb 3, 2021

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Bug fixes PolyhedralGrid #513

Bug fixes PolyhedralGrid #513

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Bug fixes PolyhedralGrid #513

Bug fixes PolyhedralGrid #513

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