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burlenburlen
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update the SENSEI in situ coupling for SENSEI v4.0.0
In this release, an install of VTK is no longer required. To compile AMReX w/ SENSEI use: ```cmake -DAMReX_SENSEI=ON -DSENSEI_DIR=<path to SENSEI install>/lib64/cmake ```
1 parent 2d931f6 commit a496c87

16 files changed

+243
-243
lines changed

‎.github/workflows/sensei.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,9 +17,9 @@ jobs:
1717
CC: clang
1818
CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code -fno-operator-names"
1919
CMAKE_GENERATOR: Ninja
20-
CMAKE_PREFIX_PATH: /root/install/sensei/develop/lib/cmake
20+
CMAKE_PREFIX_PATH: /root/install/sensei/v4.0.0/lib/cmake
2121
container:
22-
image: ryankrattiger/sensei:fedora33-vtk-mpi-20210616
22+
image: senseiinsitu/ci:fedora35-amrex-20220613
2323
steps:
2424
- uses: actions/checkout@v2
2525
- name: Setup

‎Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -30,10 +30,10 @@ public:
3030
int GetNumberOfArrays(const std::string &meshName, int association, unsigned int &numberOfArrays) override;
3131
int GetArrayName(const std::string &meshName, int association, unsigned int index, std::string &arrayName) override;
3232
#endif
33-
int GetMesh(const std::string &meshName, bool structureOnly, vtkDataObject *&mesh) override;
34-
int AddGhostNodesArray(vtkDataObject* mesh, const std::string &meshName) override;
35-
int AddGhostCellsArray(vtkDataObject* mesh, const std::string &meshName) override;
36-
int AddArray(vtkDataObject* mesh, const std::string &meshName, int association, const std::string &arrayName) override;
33+
int GetMesh(const std::string &meshName, bool structureOnly, svtkDataObject *&mesh) override;
34+
int AddGhostNodesArray(svtkDataObject* mesh, const std::string &meshName) override;
35+
int AddGhostCellsArray(svtkDataObject* mesh, const std::string &meshName) override;
36+
int AddArray(svtkDataObject* mesh, const std::string &meshName, int association, const std::string &arrayName) override;
3737
int ReleaseData() override;
3838

3939
protected:

‎Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp‎

Lines changed: 59 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,22 @@
11
#include "AMReX_AmrDataAdaptor.H"
22

3+
#include "senseiConfig.h"
34
#include "MPIUtils.h"
45
#include "STLUtils.h"
5-
#include "VTKUtils.h"
6+
#include "SVTKUtils.h"
67
#include "Profiler.h"
78
#include "Error.h"
89

9-
#include <vtkObjectFactory.h>
10-
#include <vtkOverlappingAMR.h>
11-
#include <vtkAMRBox.h>
12-
#include <vtkUniformGrid.h>
13-
#include <vtkXMLUniformGridAMRWriter.h>
14-
#include <vtkDataSetAttributes.h>
15-
#include <vtkUnsignedCharArray.h>
16-
#include <vtkFloatArray.h>
17-
#include <vtkDoubleArray.h>
18-
#include <vtkCellData.h>
19-
#include <vtkPointData.h>
10+
#include <svtkObjectFactory.h>
11+
#include <svtkOverlappingAMR.h>
12+
#include <svtkAMRBox.h>
13+
#include <svtkUniformGrid.h>
14+
#include <svtkDataSetAttributes.h>
15+
#include <svtkUnsignedCharArray.h>
16+
#include <svtkFloatArray.h>
17+
#include <svtkDoubleArray.h>
18+
#include <svtkCellData.h>
19+
#include <svtkPointData.h>
2020

2121
#include <AMReX_AmrLevel.H>
2222
#include <AMReX_BoxArray.H>
@@ -62,15 +62,15 @@ int DescriptorMap::Initialize(const DescriptorList &descriptors)
6262

6363
if (itype.cellCentered())
6464
{
65-
this->Map[vtkDataObject::CELL][arrayName] = std::make_pair(i,j);
65+
this->Map[svtkDataObject::CELL][arrayName] = std::make_pair(i,j);
6666
}
6767
else if (itype.nodeCentered())
6868
{
69-
this->Map[vtkDataObject::POINT][arrayName] = std::make_pair(i,j);
69+
this->Map[svtkDataObject::POINT][arrayName] = std::make_pair(i,j);
7070
}
7171
else
7272
{
73-
this->Map[vtkDataObject::FIELD][arrayName] = std::make_pair(i,j);
73+
this->Map[svtkDataObject::FIELD][arrayName] = std::make_pair(i,j);
7474
}
7575
}
7676
}
@@ -156,7 +156,7 @@ struct AmrDataAdaptor::InternalsType
156156
int PinMesh;
157157
amrex::InSituUtils::DescriptorMap SimMetadata;
158158
#if SENSEI_VERSION_MAJOR < 3
159-
std::vector<vtkDataObject*> ManagedObjects;
159+
std::vector<svtkDataObject*> ManagedObjects;
160160
#endif
161161
std::vector<std::vector<unsigned char *>> Masks;
162162
};
@@ -225,11 +225,11 @@ int AmrDataAdaptor::GetMeshMetadata(unsigned int id,
225225
metadata->GlobalView = true;
226226

227227
metadata->MeshName = "mesh";
228-
metadata->MeshType = VTK_OVERLAPPING_AMR;
229-
metadata->BlockType = VTK_UNIFORM_GRID;
228+
metadata->MeshType = SVTK_OVERLAPPING_AMR;
229+
metadata->BlockType = SVTK_UNIFORM_GRID;
230230
metadata->NumBlocks = 0;
231231
metadata->NumBlocksLocal = {-1};
232-
metadata->CoordinateType = InSituUtils::amrex_tt<amrex_real>::vtk_type_enum();
232+
metadata->CoordinateType = InSituUtils::amrex_tt<amrex_real>::svtk_type_enum();
233233
metadata->StaticMesh = 0;
234234

235235
// TODO
@@ -318,14 +318,14 @@ int AmrDataAdaptor::GetMeshMetadata(unsigned int id,
318318
std::string arrayName = desc.name(j);
319319
metadata->ArrayName.push_back(arrayName);
320320
metadata->ArrayComponents.push_back(1);
321-
metadata->ArrayType.push_back(InSituUtils::amrex_tt<amrex_real>::vtk_type_enum());
321+
metadata->ArrayType.push_back(InSituUtils::amrex_tt<amrex_real>::svtk_type_enum());
322322

323323
if (itype.cellCentered())
324-
metadata->ArrayCentering.push_back(vtkDataObject::CELL);
324+
metadata->ArrayCentering.push_back(svtkDataObject::CELL);
325325
else if (itype.nodeCentered())
326-
metadata->ArrayCentering.push_back(vtkDataObject::POINT);
326+
metadata->ArrayCentering.push_back(svtkDataObject::POINT);
327327
else
328-
metadata->ArrayCentering.push_back(vtkDataObject::FIELD);
328+
metadata->ArrayCentering.push_back(svtkDataObject::FIELD);
329329
}
330330

331331
}
@@ -557,8 +557,8 @@ int AmrDataAdaptor::GetNumberOfArrays(const std::string &meshName,
557557
return -1;
558558
}
559559

560-
if ((association != vtkDataObject::POINT) &&
561-
(association != vtkDataObject::CELL))
560+
if ((association != svtkDataObject::POINT) &&
561+
(association != svtkDataObject::CELL))
562562
{
563563
SENSEI_ERROR("Invalid association " << association)
564564
return -1;
@@ -590,7 +590,7 @@ int AmrDataAdaptor::GetArrayName(const std::string &meshName,
590590
if (this->Internals->SimMetadata.GetName(association, index, arrayName))
591591
{
592592
SENSEI_ERROR("No array named \"" << arrayName << "\" in "
593-
<< sensei::VTKUtils::GetAttributesName(association)
593+
<< sensei::SVTKUtils::GetAttributesName(association)
594594
<< " data")
595595
return -1;
596596
}
@@ -603,7 +603,7 @@ int AmrDataAdaptor::GetArrayName(const std::string &meshName,
603603

604604
//-----------------------------------------------------------------------------
605605
int AmrDataAdaptor::GetMesh(const std::string &meshName,
606-
bool structureOnly, vtkDataObject *&mesh)
606+
bool structureOnly, svtkDataObject *&mesh)
607607
{
608608
amrex::ignore_unused(structureOnly);
609609

@@ -626,8 +626,8 @@ int AmrDataAdaptor::GetMesh(const std::string &meshName,
626626

627627
unsigned int nLevels = InSituUtils::NumActiveLevels(levels);
628628

629-
// initialize new vtk datasets
630-
vtkOverlappingAMR *amrMesh = vtkOverlappingAMR::New();
629+
// initialize new svtk datasets
630+
svtkOverlappingAMR *amrMesh = svtkOverlappingAMR::New();
631631
#if SENSEI_VERSION_MAJOR < 3
632632
Internals->ManagedObjects.push_back(amrMesh);
633633
#endif
@@ -685,12 +685,12 @@ int AmrDataAdaptor::GetMesh(const std::string &meshName,
685685
int cboxLo[3] = {AMREX_ARLIM(cbox.loVect())};
686686
int cboxHi[3] = {AMREX_ARLIM(cbox.hiVect())};
687687

688-
// vtk's representation of box metadata
689-
vtkAMRBox block(cboxLo, cboxHi);
688+
// svtk's representation of box metadata
689+
svtkAMRBox block(cboxLo, cboxHi);
690690
amrMesh->SetAMRBox(i, j, block);
691691
amrMesh->SetAMRBlockSourceIndex(i, j, gid++);
692692

693-
// skip building a vtk amrMesh for the non local boxes
693+
// skip building a svtk amrMesh for the non local boxes
694694
if (dmap[j] != rank)
695695
continue;
696696

@@ -705,14 +705,14 @@ int AmrDataAdaptor::GetMesh(const std::string &meshName,
705705
int nboxLo[3] = {AMREX_ARLIM(nbox.loVect())};
706706
int nboxHi[3] = {AMREX_ARLIM(nbox.hiVect())};
707707

708-
// new vtk uniform amrMesh, node centered
709-
vtkUniformGrid *ug = vtkUniformGrid::New();
708+
// new svtk uniform amrMesh, node centered
709+
svtkUniformGrid *ug = svtkUniformGrid::New();
710710
ug->SetOrigin(origin);
711711
ug->SetSpacing(spacing);
712712
ug->SetExtent(nboxLo[0], nboxHi[0],
713713
nboxLo[1], nboxHi[1], nboxLo[2], nboxHi[2]);
714714

715-
// pass the block into vtk
715+
// pass the block into svtk
716716
amrMesh->SetDataSet(i, j, ug);
717717
ug->Delete();
718718
}
@@ -722,7 +722,7 @@ int AmrDataAdaptor::GetMesh(const std::string &meshName,
722722
}
723723

724724
//-----------------------------------------------------------------------------
725-
int AmrDataAdaptor::AddGhostCellsArray(vtkDataObject* mesh,
725+
int AmrDataAdaptor::AddGhostCellsArray(svtkDataObject* mesh,
726726
const std::string &meshName)
727727
{
728728
sensei::TimeEvent<64> event("AmrDataAdaptor::AddGhostCellsArray");
@@ -733,7 +733,7 @@ int AmrDataAdaptor::AddGhostCellsArray(vtkDataObject* mesh,
733733
return -1;
734734
}
735735

736-
vtkOverlappingAMR *amrMesh = dynamic_cast<vtkOverlappingAMR*>(mesh);
736+
svtkOverlappingAMR *amrMesh = dynamic_cast<svtkOverlappingAMR*>(mesh);
737737
if (!amrMesh)
738738
{
739739
SENSEI_ERROR("Invalid mesh type "
@@ -780,7 +780,7 @@ int AmrDataAdaptor::AddGhostCellsArray(vtkDataObject* mesh,
780780
if (dMap[j] != rank)
781781
continue;
782782

783-
vtkUniformGrid *blockMesh = amrMesh->GetDataSet(i, j);
783+
svtkUniformGrid *blockMesh = amrMesh->GetDataSet(i, j);
784784

785785
if (!blockMesh)
786786
{
@@ -790,24 +790,24 @@ int AmrDataAdaptor::AddGhostCellsArray(vtkDataObject* mesh,
790790

791791
long nCells = blockMesh->GetNumberOfCells();
792792

793-
// transfer mask array into vtk
794-
vtkUnsignedCharArray *ga = vtkUnsignedCharArray::New();
795-
ga->SetName("vtkGhostType");
793+
// transfer mask array into svtk
794+
svtkUnsignedCharArray *ga = svtkUnsignedCharArray::New();
795+
ga->SetName("svtkGhostType");
796796
ga->SetArray(mask[j], nCells, 0);
797797
blockMesh->GetCellData()->AddArray(ga);
798798
ga->Delete();
799799

800800
// for debug can visualize the ghost cells
801801
// FIXME -- a bug in Catalyst ignores internal ghost zones
802-
// when using the VTK writrer. Until that bug gets fixed, one
802+
// when using the SVTK writrer. Until that bug gets fixed, one
803803
// can manually inject this copy using a PV Python filter
804-
ga = vtkUnsignedCharArray::New();
804+
ga = svtkUnsignedCharArray::New();
805805
ga->SetName("GhostType");
806806
ga->SetArray(mask[j], nCells, 1);
807807
blockMesh->GetCellData()->AddArray(ga);
808808
ga->Delete();
809809

810-
// because VTK takes ownership
810+
// because SVTK takes ownership
811811
mask[j] = nullptr;
812812
}
813813
}
@@ -816,7 +816,7 @@ int AmrDataAdaptor::AddGhostCellsArray(vtkDataObject* mesh,
816816
}
817817

818818
//-----------------------------------------------------------------------------
819-
int AmrDataAdaptor::AddGhostNodesArray(vtkDataObject *mesh,
819+
int AmrDataAdaptor::AddGhostNodesArray(svtkDataObject *mesh,
820820
const std::string &meshName)
821821
{
822822
amrex::ignore_unused(mesh);
@@ -834,7 +834,7 @@ int AmrDataAdaptor::AddGhostNodesArray(vtkDataObject *mesh,
834834
}
835835

836836
//-----------------------------------------------------------------------------
837-
int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
837+
int AmrDataAdaptor::AddArray(svtkDataObject* mesh, const std::string &meshName,
838838
int association, const std::string &arrayName)
839839
{
840840
sensei::TimeEvent<64> event("AmrDataAdaptor::AddArray");
@@ -848,7 +848,7 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
848848
return -1;
849849
}
850850

851-
vtkOverlappingAMR *amrMesh = dynamic_cast<vtkOverlappingAMR*>(mesh);
851+
svtkOverlappingAMR *amrMesh = dynamic_cast<svtkOverlappingAMR*>(mesh);
852852
if (!amrMesh)
853853
{
854854
SENSEI_ERROR("Invalid mesh type "
@@ -861,8 +861,8 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
861861
return -1;
862862
}
863863

864-
if ((association != vtkDataObject::CELL) &&
865-
(association != vtkDataObject::POINT))
864+
if ((association != svtkDataObject::CELL) &&
865+
(association != svtkDataObject::POINT))
866866
{
867867
SENSEI_ERROR("Invalid association " << association)
868868
return -1;
@@ -878,7 +878,7 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
878878
if (this->Internals->SimMetadata.GetIndex(arrayName, association, fab, comp))
879879
{
880880
SENSEI_ERROR("Failed to locate descriptor for "
881-
<< sensei::VTKUtils::GetAttributesName(association)
881+
<< sensei::SVTKUtils::GetAttributesName(association)
882882
<< " data array \"" << arrayName << "\"")
883883
return -1;
884884
}
@@ -894,8 +894,8 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
894894
amrex::MultiFab& state = levels[i]->get_new_data(fab);
895895
unsigned int ng = state.nGrow();
896896

897-
if (!((association == vtkDataObject::CELL) && state.is_cell_centered()) &&
898-
!((association == vtkDataObject::POINT) && state.is_nodal()))
897+
if (!((association == svtkDataObject::CELL) && state.is_cell_centered()) &&
898+
!((association == svtkDataObject::POINT) && state.is_nodal()))
899899
{
900900
SENSEI_ERROR("association does not match MultiFAB centering")
901901
return -1;
@@ -926,7 +926,7 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
926926
int cboxLo[3] = {AMREX_ARLIM(cbox.loVect())};
927927
int cboxHi[3] = {AMREX_ARLIM(cbox.hiVect())};
928928

929-
// skip building a vtk mesh for the non local boxes
929+
// skip building a svtk mesh for the non local boxes
930930
if (dmap[j] != rank)
931931
continue;
932932

@@ -938,7 +938,7 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
938938
int nboxHi[3] = {AMREX_ARLIM(nbox.hiVect())};
939939

940940
// get the block mesh
941-
vtkUniformGrid *ug = amrMesh->GetDataSet(i, j);
941+
svtkUniformGrid *ug = amrMesh->GetDataSet(i, j);
942942

943943
// node centered size
944944
long nlen = 1;
@@ -953,9 +953,9 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
953953
// pointer to the data
954954
amrex_real *pcd = state[j].dataPtr(comp);
955955

956-
// allocate vtk array
957-
InSituUtils::amrex_tt<amrex_real>::vtk_type *da =
958-
InSituUtils::amrex_tt<amrex_real>::vtk_type::New();
956+
// allocate svtk array
957+
InSituUtils::amrex_tt<amrex_real>::svtk_type *da =
958+
InSituUtils::amrex_tt<amrex_real>::svtk_type::New();
959959

960960
// set component name
961961
da->SetName(arrayName.c_str());
@@ -981,15 +981,15 @@ int AmrDataAdaptor::AddArray(vtkDataObject* mesh, const std::string &meshName,
981981

982982
#if defined(SENSEI_DEBUG)
983983
// mark level id
984-
vtkFloatArray *la = vtkFloatArray::New();
984+
svtkFloatArray *la = svtkFloatArray::New();
985985
la->SetName("amrex_level_id");
986986
la->SetNumberOfTuples(clen);
987987
la->Fill(i);
988988
ug->GetCellData()->AddArray(la);
989989
la->Delete();
990990

991991
// mark mpi rank
992-
vtkFloatArray *ra = vtkFloatArray::New();
992+
svtkFloatArray *ra = svtkFloatArray::New();
993993
ra->SetName("amrex_mpi_rank");
994994
ra->SetNumberOfTuples(clen);
995995
ra->Fill(rank);

‎Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@ AmrInSituBridge::update(Amr *dataSource)
2929
data_adaptor->SetDataSource(dataSource);
3030
data_adaptor->SetDataTime(dataSource->cumTime());
3131
data_adaptor->SetDataTimeStep(dataSource->levelSteps(0));
32-
ret = analysis_adaptor->Execute(data_adaptor) ? 0 : -1;
32+
ret = analysis_adaptor->Execute(data_adaptor, nullptr) ? 0 : -1;
3333
data_adaptor->ReleaseData();
3434
data_adaptor->Delete();
3535

‎Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -34,10 +34,10 @@ public:
3434
int GetNumberOfArrays(const std::string &meshName, int association, unsigned int &numberOfArrays) override;
3535
int GetArrayName(const std::string &meshName, int association, unsigned int index, std::string &arrayName) override;
3636
#endif
37-
int GetMesh(const std::string &meshName, bool structureOnly, vtkDataObject *&mesh) override;
38-
int AddGhostNodesArray(vtkDataObject* mesh, const std::string &meshName) override;
39-
int AddGhostCellsArray(vtkDataObject* mesh, const std::string &meshName) override;
40-
int AddArray(vtkDataObject* mesh, const std::string &meshName, int association, const std::string &arrayName) override;
37+
int GetMesh(const std::string &meshName, bool structureOnly, svtkDataObject *&mesh) override;
38+
int AddGhostNodesArray(svtkDataObject* mesh, const std::string &meshName) override;
39+
int AddGhostCellsArray(svtkDataObject* mesh, const std::string &meshName) override;
40+
int AddArray(svtkDataObject* mesh, const std::string &meshName, int association, const std::string &arrayName) override;
4141
int ReleaseData() override;
4242

4343
protected:

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