feat: Implement EDFM loading from VTK (serial only) #3082

ouassimkh · 2024-04-16T15:04:51Z

No description provided.

ouassimkh · 2024-10-21T15:24:30Z

Implement serial loading (fails on MPI) and tested it on a 2.5D EDFM case. Below is an input example containing 2 fracture elements:

fracture_ids_points: represent all the fracture patch point ids including shared points (no duplicates).
fracture_to_paren_matrix_cell_mapping: maps each edfm fracture element to matrix element.
permeability : fracture elements permeability (loaded but not used yet, we continue to use constant fracture props provided with CompressibleSolidParallelPlatesPermeability)
aperture: is fracture aperture
tangential_width_vectors, tangential_length_vectors and normal_vectors are the 3 principal vectors of a fracture patch plan.
connectivity: each patch is represented by a 4 points (quad).

<?xml version="1.0"?>
<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
  <UnstructuredGrid>
    <Piece NumberOfPoints="6" NumberOfCells="2">
      <PointData>
        <DataArray type="Int32" Name="fracture_ids_points" NumberOfComponents="1" format="ascii">
         0
         1
         2
         3
         4
         5
        </DataArray>
      </PointData>
      <CellData>
        <DataArray type="Int32" Name="fracture_to_parent_matrix_cell_mapping" NumberOfComponents="2" format="ascii">
         0 4
         1 13
        </DataArray>
        <DataArray type="Float32" Name="permeability" NumberOfComponents="1" format="ascii" RangeMin="0.1" RangeMax="0.1">
          0.1
          0.1
        </DataArray>
        <DataArray type="Float32" Name="aperture" NumberOfComponents="1" format="ascii" RangeMin="0.0001" RangeMax="0.0001">
          0.0001
          0.0001
        </DataArray>
        <DataArray type="Float32" Name="tangential_width_vectors" NumberOfComponents="3" format="ascii">
          0 0 1
          0 0 1
        </DataArray>
        <DataArray type="Float32" Name="tangential_length_vectors" NumberOfComponents="3" format="ascii">
          0 1 0
          0 1 0
        </DataArray>
        <DataArray type="Float32" Name="normal_vectors" NumberOfComponents="3" format="ascii">
          1 0 0
          1 0 0
        </DataArray>
      </CellData>
      <Points>
        <DataArray type="Float32" Name="Points" NumberOfComponents="3" format="ascii" RangeMin="0" RangeMax="1">
          0.5 0.3333 0
          0.5 0.6666 0
          0.5 0.3333 0.5
          0.5 0.6666 0.5
          0.5 0.3333 1
          0.5 0.6666 1
          <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
            <Value index="0">
              0
            </Value>
            <Value index="1">
              1
            </Value>
          </InformationKey>
        </DataArray>
      </Points>
      <Cells>
        <DataArray type="Int64" Name="connectivity" format="ascii" RangeMin="0" RangeMax="5">
        1 0 2 3
        3 2 4 5
        </DataArray>
        <DataArray type="Int64" Name="offsets" format="ascii" RangeMin="4" RangeMax="8">
          4
          8
        </DataArray>
        <DataArray type="UInt8" Name="types" format="ascii" RangeMin="9" RangeMax="9">
          9
          9
        </DataArray>
      </Cells>
    </Piece>
  </UnstructuredGrid>
</VTKFile>

paveltomin · 2024-12-02T19:02:30Z

@CusiniM and @rrsettgast please have a look

paveltomin · 2024-12-09T23:47:44Z

src/coreComponents/mainInterface/ProblemManager.cpp

-      meshBody.deregisterCellBlockManager();
+      // Cell block manager is needed for EDFM loading from VTK
+      // Can't be deregistred here
+      //meshBody.deregisterCellBlockManager();


TODO restore that

paveltomin · 2024-12-12T16:40:58Z

@CusiniM, @castelletto1, @corbett5, @jhuang2601, @rrsettgast, @untereiner, and/or @wrtobin please have a look

rrsettgast · 2024-12-12T21:20:55Z

@paveltomin @ouassimkh Please remember to post a copy of the error message you get in parallel. Thanks!

paveltomin · 2024-12-12T21:25:33Z

@rrsettgast @CusiniM parallel run crash

Num ranks: 2
GEOS version: 1.1.0 (Feature/ouassim/edfm_loader_new, sha1: cec6ed26f)
  - c++ compiler: gcc 11.4.0
  - MPI version: Open MPI v4.1.2, package: Debian OpenMPI, ident: 4.1.2, repo rev: v4.1.2, Nov 24, 2021
  - HDF5 version: 1.12.1
  - Conduit version: 0.9.2
  - VTK version: 9.3.1
  - RAJA version: 2024.7.0
  - umpire version: 2024.07.0
  - chai version: 2024.7.0
  - METIS version: 5.1
  - PARAMETIS version: 4.0
  - scotch version: 7.0.3
  - superlu_dist version: 6.3.0
  - suitesparse version: 5.7.9
  - hypre version: 2.32.0
  - Python3 version: 3.10.12
Started at 2024-12-12 21:24:50.657031700
Opened XML file: /home/ptls/GEOS/GEOS/inputFiles/singlePhaseFlowFractures/fractureMatrixFlow_edfm_vtk_smoke.xml
Included additionnal XML file: /home/ptls/GEOS/GEOS/inputFiles/singlePhaseFlowFractures/fractureMatrixFlow_edfm_vtk.xml
Adding Mesh: VTKMesh, mesh1
Adding Geometric Object: Box, source
Adding Geometric Object: Box, sink
Adding Event: SoloEvent, preFracture
Adding Event: PeriodicEvent, solverApplications
Adding Event: PeriodicEvent, outputs
Adding Event: PeriodicEvent, restarts
Adding Output: VTK, vtkOutput
Adding Output: Restart, sidreRestart
Adding Solver of type SinglePhaseFVM, named SinglePhaseFlow
Adding Solver of type EmbeddedSurfaceGenerator, named SurfaceGenerator
Adding Object CellElementRegion named RockMatrix from ObjectManager::Catalog.
Adding Object SurfaceElementRegion named Fracture from ObjectManager::Catalog.
VTKMesh 'mesh1': reading mesh from /home/ptls/GEOS/GEOS/inputFiles/singlePhaseFlowFractures/main_edfm_vtk.vtm
Using global Ids defined in VTK mesh
VTKMesh 'mesh1': generating GEOSX mesh data structure
Received signal 11: Segmentation fault

** StackTrace of 11 frames **
Frame 0: /lib/x86_64-linux-gnu/libc.so.6 
Frame 1: geos::vtk::importEmbeddedFractureNetwork(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, vtkSmartPointer<vtkDataSet>, vtkSmartPointer<vtkDataSet>, geos::CellBlockManager&) 
Frame 2: geos::VTKMeshGenerator::fillCellBlockManager(geos::CellBlockManager&, geos::SpatialPartition&) 
Frame 3: geos::MeshGeneratorBase::generateMesh(geos::dataRepository::Group&, geos::SpatialPartition&) 
Frame 4: geos::MeshManager::generateMeshes(geos::DomainPartition&) 
Frame 5: geos::ProblemManager::generateMesh() 
Frame 6: geos::ProblemManager::problemSetup() 
Frame 7: geos::GeosxState::initializeDataRepository() 
Frame 8: main 
Frame 9: /lib/x86_64-linux-gnu/libc.so.6 
Frame 10: __libc_start_main 
Frame 11: _start 
=====

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Received signal 15: Terminated

** StackTrace of 19 frames **
Frame 0: /lib/x86_64-linux-gnu/libc.so.6 
Frame 1: /lib/x86_64-linux-gnu/libopen-pal.so.40 
Frame 2: /lib/x86_64-linux-gnu/libopen-pal.so.40 
Frame 3: opal_progress 
Frame 4: ompi_request_default_wait 
Frame 5: ompi_coll_base_sendrecv_actual 
Frame 6: ompi_coll_base_allreduce_intra_recursivedoubling 
Frame 7: ompi_coll_tuned_allreduce_intra_dec_fixed 
Frame 8: PMPI_Allreduce 
Frame 9: geos::vtk::printMeshStatistics(vtkDataSet&, std::map<geos::ElementType, std::unordered_map<int, std::vector<long long, std::allocator<long long> >, std::hash<int>, std::equal_to<int>, std::allocator<std::pair<int const, std::vector<long long, std::allocator<long long> > > > >, std::less<geos::ElementType>, std::allocator<std::pair<geos::ElementType const, std::unordered_map<int, std::vector<long long, std::allocator<long long> >, std::hash<int>, std::equal_to<int>, std::allocator<std::pair<int const, std::vector<long long, std::allocator<long long> > > > > > > > const&, ompi_communicator_t*) 
Frame 10: geos::VTKMeshGenerator::fillCellBlockManager(geos::CellBlockManager&, geos::SpatialPartition&) 
Frame 11: geos::MeshGeneratorBase::generateMesh(geos::dataRepository::Group&, geos::SpatialPartition&) 
Frame 12: geos::MeshManager::generateMeshes(geos::DomainPartition&) 
Frame 13: geos::ProblemManager::generateMesh() 
Frame 14: geos::ProblemManager::problemSetup() 
Frame 15: geos::GeosxState::initializeDataRepository() 
Frame 16: main 
Frame 17: /lib/x86_64-linux-gnu/libc.so.6 
Frame 18: __libc_start_main 
Frame 19: _start 
=====

paveltomin · 2024-12-12T21:53:42Z

src/coreComponents/mesh/generators/VTKEmbeddedSurfaceBlockUtilities.cpp

+  //1.Get EDFM vertices
+  vtkUnstructuredGrid * grid = vtkUnstructuredGrid::SafeDownCast( embeddedSurfaceMesh );
+  vtkPoints * const nodes = grid->GetPoints();
+  vtkIdType numNodes = nodes->GetNumberOfPoints();


parallel crash seems to happen here

for some reason GetPoints is null for one of the two ranks

Rank 1: grid->GetPoints() = 0x7fffca3fb8f0 Rank 0: grid->GetPoints() = 0

ouassimkh · 2024-12-16T14:32:49Z

Just wondering why was the branch closed? is it merged ?

ouassimkh requested review from TotoGaz and CusiniM April 16, 2024 15:04

TotoGaz removed their request for review July 5, 2024 17:08

ouassimkh and others added 18 commits October 21, 2024 08:41

initial embedded surface block abc

d77d082

minor change

35196c8

start concrete implementation

2135a21

add the cpp

7eb79a5

add embedded surfaces to CellBlockManager

b20dd27

this should not be commited

738c14a

upate cellBlock Manger and embedded Ruface block

2fcdeed

Correct edfm to cell type

186a222

corrections

2401cc7

create edfm patches in bulk

e2346e7

small changes

c42b37f

add flag to enable experimentation

55239bd

missed files

4b2363e

add bulk edfm fracs

0fde8c6

All is running

dd8d49e

uncrustify pass

2e43180

start VTK edfm support

cd555e0

Finish EDFM loading from VTK (no parallel)

041d290

ouassimkh force-pushed the Feature/ouassim/edfm_loader_new branch from 8dc1a32 to 041d290 Compare October 21, 2024 14:34

ouassimkh changed the title ~~Feature/ouassim/edfm loader new~~ [Feat] Implement 2.5D EDFM loading from VTK (serial only) Oct 21, 2024

ouassimkh changed the title ~~[Feat] Implement 2.5D EDFM loading from VTK (serial only)~~ feat: Implement 2.5D EDFM loading from VTK (serial only) Oct 21, 2024

ouassimkh added 5 commits October 31, 2024 16:26

builds after master rebase issues

3bda862

working serial run

256efee

clearning

2d6583d

cleraning

8d52abc

bug

c718d96

paveltomin requested review from untereiner, corbett5, castelletto1 and paveltomin as code owners November 20, 2024 00:20

paveltomin and others added 3 commits November 19, 2024 18:20

Merge branch 'develop' into Feature/ouassim/edfm_loader_new

29a20e8

Merge branch 'develop' into Feature/ouassim/edfm_loader_new

7b9014e

Merge branch 'develop' into Feature/ouassim/edfm_loader_new

31118bb

paveltomin added flag: ready for review ci: run integrated tests Allows to run the integrated tests in GEOS CI labels Dec 9, 2024

Merge branch 'develop' into Feature/ouassim/edfm_loader_new

5caf9aa

paveltomin reviewed Dec 9, 2024

View reviewed changes

Pavel Tomin added 2 commits December 9, 2024 17:52

build fix

c84e27a

remove

b4a5df4

Merge branch 'develop' into Feature/ouassim/edfm_loader_new

cec6ed2

paveltomin removed the ci: run integrated tests Allows to run the integrated tests in GEOS CI label Dec 12, 2024

paveltomin changed the title ~~feat: Implement 2.5D EDFM loading from VTK (serial only)~~ feat: Implement EDFM loading from VTK (serial only) Dec 12, 2024

paveltomin reviewed Dec 12, 2024

View reviewed changes

MelReyCG closed this Dec 16, 2024

MelReyCG deleted the Feature/ouassim/edfm_loader_new branch December 16, 2024 14:22

ouassimkh restored the Feature/ouassim/edfm_loader_new branch December 16, 2024 14:30

paveltomin reopened this Dec 16, 2024

paveltomin and others added 4 commits December 16, 2024 08:34

Merge branch 'develop' into Feature/ouassim/edfm_loader_new

b079426

doxygen fix

3e0357e

fix one crash and introduce another

1388970

just to see if test fail because of this

ef54e9c

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feat: Implement EDFM loading from VTK (serial only) #3082

feat: Implement EDFM loading from VTK (serial only) #3082

ouassimkh commented Apr 16, 2024

ouassimkh commented Oct 21, 2024 •

edited

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paveltomin commented Dec 2, 2024

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ouassimkh commented Dec 16, 2024

feat: Implement EDFM loading from VTK (serial only) #3082

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feat: Implement EDFM loading from VTK (serial only) #3082

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ouassimkh commented Dec 16, 2024

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