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Merge branch 'develop' into pt/hu-2phase
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@paveltomin
paveltomin authored Nov 22, 2024
2 parents b0cd8ff + 70e46b3 commit 4c008c2
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Showing 7 changed files with 131 additions and 45 deletions.
2 changes: 1 addition & 1 deletion .integrated_tests.yaml
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@@ -1,6 +1,6 @@
baselines:
bucket: geosx
baseline: integratedTests/baseline_integratedTests-pr3439-8919-b09db43
baseline: integratedTests/baseline_integratedTests-pr2637-8940-3c0fc5c
allow_fail:
all: ''
streak: ''
4 changes: 4 additions & 0 deletions BASELINE_NOTES.md
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Expand Up @@ -6,6 +6,10 @@ This file is designed to track changes to the integrated test baselines.
Any developer who updates the baseline ID in the .integrated_tests.yaml file is expected to create an entry in this file with the pull request number, date, and their justification for rebaselining.
These notes should be in reverse-chronological order, and use the following time format: (YYYY-MM-DD).

PR #2637 (2024-11-21)
=====================
Added numberOfTargetProcesses.

PR #3439 (2024-11-20)
=====================
EDFM bugfixes: derivatives sign, frac/cell element volume, fix apertures inconsistency in test cases.
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15 changes: 14 additions & 1 deletion src/coreComponents/fileIO/Outputs/VTKOutput.cpp
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Expand Up @@ -18,7 +18,7 @@
*/

#include "VTKOutput.hpp"

#include "common/MpiWrapper.hpp"

#if defined(GEOS_USE_PYGEOSX)
#include "fileIO/python/PyVTKOutputType.hpp"
Expand Down Expand Up @@ -56,6 +56,11 @@ VTKOutput::VTKOutput( string const & name,
setInputFlag( InputFlags::OPTIONAL ).
setDescription( "Level detail plot. Only fields with lower of equal plot level will be output." );

registerWrapper( viewKeysStruct::numberOfTargetProcesses, &m_numberOfTargetProcesses ).
setApplyDefaultValue( MpiWrapper::commSize() ).
setInputFlag( InputFlags::OPTIONAL ).
setDescription( "Number of output aggregate files to be written." );

registerWrapper( viewKeysStruct::writeGhostCells, &m_writeGhostCells ).
setApplyDefaultValue( 0 ).
setInputFlag( InputFlags::OPTIONAL ).
Expand Down Expand Up @@ -102,6 +107,14 @@ void VTKOutput::postInputInitialization()
m_writer.setLevelNames( m_levelNames.toViewConst() );
m_writer.setOnlyPlotSpecifiedFieldNamesFlag( m_onlyPlotSpecifiedFieldNames );

GEOS_ERROR_IF_LT_MSG( m_numberOfTargetProcesses, 1,
GEOS_FMT( "{}: processes count cannot be less than 1.",
getWrapperDataContext( viewKeysStruct::numberOfTargetProcesses ) ) );
GEOS_ERROR_IF_GT_MSG( m_numberOfTargetProcesses, MpiWrapper::commSize(),
GEOS_FMT( "{}: processes count cannot exceed the launched ranks count.",
getWrapperDataContext( viewKeysStruct::numberOfTargetProcesses ) ) );
m_writer.setNumberOfTargetProcesses( m_numberOfTargetProcesses );

string const fieldNamesString = viewKeysStruct::fieldNames;
string const onlyPlotSpecifiedFieldNamesString = viewKeysStruct::onlyPlotSpecifiedFieldNames;

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4 changes: 4 additions & 0 deletions src/coreComponents/fileIO/Outputs/VTKOutput.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,7 @@ class VTKOutput : public OutputBase
static constexpr auto onlyPlotSpecifiedFieldNames = "onlyPlotSpecifiedFieldNames";
static constexpr auto fieldNames = "fieldNames";
static constexpr auto levelNames = "levelNames";
static constexpr auto numberOfTargetProcesses = "numberOfTargetProcesses";
} vtkOutputViewKeys;
/// @endcond

Expand All @@ -114,6 +115,9 @@ class VTKOutput : public OutputBase
integer m_writeFaceMesh;
integer m_plotLevel;

/// Aggregate output data to be written
integer m_numberOfTargetProcesses;

/// Should the vtk files contain the ghost cells or not.
integer m_writeGhostCells;

Expand Down
94 changes: 65 additions & 29 deletions src/coreComponents/fileIO/vtk/VTKPolyDataWriterInterface.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -33,11 +33,14 @@
#include <vtkThreshold.h>
#include <vtkUnstructuredGrid.h>
#include <vtkXMLUnstructuredGridWriter.h>

#include <vtkAggregateDataSetFilter.h>
// System includes
#include <numeric>
#include <unordered_set>

#include "mesh/generators/VTKUtilities.hpp"


namespace geos
{

Expand Down Expand Up @@ -1041,7 +1044,7 @@ void VTKPolyDataWriterInterface::writeElementFields( ElementRegionBase const & r
void VTKPolyDataWriterInterface::writeCellElementRegions( real64 const time,
ElementRegionManager const & elemManager,
NodeManager const & nodeManager,
string const & path ) const
string const & path )
{
elemManager.forElementRegions< CellElementRegion >( [&]( CellElementRegion const & region )
{
Expand All @@ -1055,15 +1058,13 @@ void VTKPolyDataWriterInterface::writeCellElementRegions( real64 const time,
writeTimestamp( ug.GetPointer(), time );
writeElementFields( region, ug->GetCellData() );
writeNodeFields( nodeManager, VTKCells.nodes, ug->GetPointData() );

string const regionDir = joinPath( path, region.getName() );
writeUnstructuredGrid( regionDir, ug.GetPointer() );
writeUnstructuredGrid( path, region, ug.GetPointer() );
} );
}

void VTKPolyDataWriterInterface::writeParticleRegions( real64 const time,
ParticleManager const & particleManager,
string const & path ) const
string const & path )
{
particleManager.forParticleRegions< ParticleRegion >( [&]( ParticleRegion const & region )
{
Expand All @@ -1077,15 +1078,15 @@ void VTKPolyDataWriterInterface::writeParticleRegions( real64 const time,
writeTimestamp( ug.GetPointer(), time );
writeParticleFields( region, ug->GetCellData() );

string const regionDir = joinPath( path, region.getName() );
writeUnstructuredGrid( regionDir, ug.GetPointer() );
// string const regionDir = joinPath( path, region.getName() );
writeUnstructuredGrid( path, region, ug.GetPointer() );
} );
}

void VTKPolyDataWriterInterface::writeWellElementRegions( real64 const time,
ElementRegionManager const & elemManager,
NodeManager const & nodeManager,
string const & path ) const
string const & path )
{
elemManager.forElementRegions< WellElementRegion >( [&]( WellElementRegion const & region )
{
Expand All @@ -1098,9 +1099,7 @@ void VTKPolyDataWriterInterface::writeWellElementRegions( real64 const time,

writeTimestamp( ug.GetPointer(), time );
writeElementFields( region, ug->GetCellData() );

string const regionDir = joinPath( path, region.getName() );
writeUnstructuredGrid( regionDir, ug.GetPointer() );
writeUnstructuredGrid( path, region, ug.GetPointer() );
} );
}

Expand All @@ -1109,7 +1108,7 @@ void VTKPolyDataWriterInterface::writeSurfaceElementRegions( real64 const time,
NodeManager const & nodeManager,
EmbeddedSurfaceNodeManager const & embSurfNodeManager,
FaceManager const & faceManager,
string const & path ) const
string const & path )
{
elemManager.forElementRegions< SurfaceElementRegion >( [&]( SurfaceElementRegion const & region )
{
Expand Down Expand Up @@ -1140,9 +1139,7 @@ void VTKPolyDataWriterInterface::writeSurfaceElementRegions( real64 const time,

writeTimestamp( ug.GetPointer(), time );
writeElementFields( region, ug->GetCellData() );

string const regionDir = joinPath( path, region.getName() );
writeUnstructuredGrid( regionDir, ug.GetPointer() );
writeUnstructuredGrid( path, region, ug.GetPointer() );
} );
}

Expand Down Expand Up @@ -1188,13 +1185,13 @@ void VTKPolyDataWriterInterface::writeVtmFile( integer const cycle,

string const meshPath = joinPath( getCycleSubFolder( cycle ), meshBodyName, meshLevelName );

int const mpiSize = MpiWrapper::commSize();
// int const mpiSize = MpiWrapper::commSize();

auto addElementRegion = [&]( ElementRegionBase const & region )
{
std::vector< string > const blockPath{ meshBody.getName(), meshLevel.getName(), region.getCatalogName(), region.getName() };
string const regionPath = joinPath( meshPath, region.getName() );
for( int i = 0; i < mpiSize; i++ )
for( const auto & i : m_targetProcessesId.at( region.getName()) )
{
string const dataSetName = getRankFileName( i );
string const dataSetFile = joinPath( regionPath, dataSetName + ".vtu" );
Expand All @@ -1207,7 +1204,7 @@ void VTKPolyDataWriterInterface::writeVtmFile( integer const cycle,
string const & regionName = region.getName();
std::vector< string > const blockPath{ meshBodyName, meshLevelName, region.getCatalogName(), regionName };
string const regionPath = joinPath( meshPath, regionName );
for( int i = 0; i < mpiSize; i++ )
for( const auto & i : m_targetProcessesId.at( region.getName()) )
{
string const dataSetName = getRankFileName( i );
string const dataSetFile = joinPath( regionPath, dataSetName + ".vtu" );
Expand Down Expand Up @@ -1256,8 +1253,11 @@ int toVtkOutputMode( VTKOutputMode const mode )
}

void VTKPolyDataWriterInterface::writeUnstructuredGrid( string const & path,
vtkUnstructuredGrid * ug ) const
ObjectManagerBase const & region,
vtkUnstructuredGrid * ug )
{
string const regionDir = joinPath( path, region.getName() );

vtkSmartPointer< vtkAlgorithm > filter;

// If we want to get rid of the ghost ranks, we use the appropriate `vtkThreshold` filter.
Expand All @@ -1279,15 +1279,51 @@ void VTKPolyDataWriterInterface::writeUnstructuredGrid( string const & path,
}

filter->SetInputDataObject( ug );
filter->Update();

makeDirectory( path );
string const vtuFilePath = joinPath( path, getRankFileName( MpiWrapper::commRank() ) + ".vtu" );
auto const vtuWriter = vtkSmartPointer< vtkXMLUnstructuredGridWriter >::New();
vtuWriter->SetInputData( filter->GetOutputDataObject( 0 ) );
vtuWriter->SetFileName( vtuFilePath.c_str() );
vtuWriter->SetDataMode( toVtkOutputMode( m_outputMode ) );
vtuWriter->Write();

vtkSmartPointer< vtkMultiProcessController > controller = vtk::getController();
vtkMultiProcessController::SetGlobalController( controller );

// In case of m_numberOfTargetProcesses == GetNumberOfProcesses the filter returns a shallow copy
// The behavior is the same as previously in this case. The rank number is computed instead of implicitly written
vtkNew< vtkAggregateDataSetFilter > aggregate;
aggregate->SetInputConnection( filter->GetOutputPort());
aggregate->SetNumberOfTargetProcesses( m_numberOfTargetProcesses );
aggregate->SetMergePoints( false );
aggregate->Update();

int localCommRank = -1;
if( vtkDataSet::SafeDownCast( aggregate->GetOutput())->GetNumberOfPoints() != 0 )
{
localCommRank = MpiWrapper::commRank();
makeDirectory( regionDir );
string const vtuFilePath = joinPath( regionDir, getRankFileName( localCommRank ) + ".vtu" );
auto const vtuWriter = vtkSmartPointer< vtkXMLUnstructuredGridWriter >::New();
vtuWriter->SetInputData( aggregate->GetOutput() );
vtuWriter->SetFileName( vtuFilePath.c_str() );
vtuWriter->SetDataMode( toVtkOutputMode( m_outputMode ) );
vtuWriter->Write();
}

const int size = MpiWrapper::commSize( MPI_COMM_GEOS );
std::vector< int > globalValues( size );

// Everything is done on rank 0
MpiWrapper::gather( &localCommRank,
1,
globalValues.data(),
1,
0,
MPI_COMM_GEOS );

if( MpiWrapper::commRank() == 0 )
{
// any rank that does not hold data will not participate in the output
globalValues.erase( std::remove_if( globalValues.begin(),
globalValues.end(),
[]( int x ) { return x == -1; } ),
globalValues.end());
m_targetProcessesId[region.getName()] = globalValues;
}
}

void VTKPolyDataWriterInterface::write( real64 const time,
Expand Down
55 changes: 41 additions & 14 deletions src/coreComponents/fileIO/vtk/VTKPolyDataWriterInterface.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
#define GEOS_FILEIO_VTK_VTKPOLYDATAWRITERINTERFACE_HPP_

#include "common/DataTypes.hpp"
#include "mesh/ObjectManagerBase.hpp"
#include "dataRepository/WrapperBase.hpp"
#include "dataRepository/Wrapper.hpp"
#include "fileIO/vtk/VTKPVDWriter.hpp"
Expand Down Expand Up @@ -167,6 +168,14 @@ class VTKPolyDataWriterInterface
{
m_levelNames.insert( levelNames.begin(), levelNames.end() );
}
/**
* @brief Set the Number Of Target Processes
* @param[in] numberOfTargetProcesses the number of processes
*/
void setNumberOfTargetProcesses( integer const numberOfTargetProcesses )
{
m_numberOfTargetProcesses = numberOfTargetProcesses;
}

/**
* @brief Main method of this class. Write all the files for one time step.
Expand Down Expand Up @@ -223,33 +232,38 @@ class VTKPolyDataWriterInterface
* @brief Writes the files for all the CellElementRegions.
* @details There will be one file written per CellElementRegion and per rank.
* @param[in] time the time-step
* @param[in] cycle the current cycle number
* @param[in] elemManager the ElementRegionManager containing the CellElementRegions to be output
* @param[in] nodeManager the NodeManager containing the nodes of the domain to be output
* @param[in] meshLevelName the name of the MeshLevel containing the nodes and elements to be output
* @param[in] meshBodyName the name of the MeshBody containing the nodes and elements to be output
* @param[in] path the root path where the mesh will be written
*/
void writeCellElementRegions( real64 time,
ElementRegionManager const & elemManager,
NodeManager const & nodeManager,
string const & path ) const;

void writeParticleRegions( real64 const time,
ParticleManager const & particleManager,
string const & path ) const;
string const & path );

/**
* @brief Writes the files containing the well representation
* @details There will be one file written per WellElementRegion and per rank
* @param[in] time the time-step
* @param[in] cycle the current cycle number
* @param[in] elemManager the ElementRegionManager containing the WellElementRegions to be output
* @param[in] nodeManager the NodeManager containing the nodes of the domain to be output
* @param[in] path the root path where the mesh will be written
*/
void writeWellElementRegions( real64 time,
ElementRegionManager const & elemManager,
NodeManager const & nodeManager,
string const & path ) const;
string const & path );

/**
* @brief Writes the files containing the particle representation
* @details There will be one file written per ParticleRegion and per rank
* @param[in] time the time-step
* @param[in] particleManager the ParticleManager containing the ParticleRegions to be output
* @param[in] path the root path where the mesh will be written
*/
void writeParticleRegions( real64 const time,
ParticleManager const & particleManager,
string const & path );

/**
* @brief Writes the files containing the faces elements
Expand All @@ -266,13 +280,13 @@ class VTKPolyDataWriterInterface
NodeManager const & nodeManager,
EmbeddedSurfaceNodeManager const & embSurfNodeManager,
FaceManager const & faceManager,
string const & path ) const;
string const & path );

/**
* @brief Writes a VTM file for the time-step \p time.
* @details a VTM file is a VTK Multiblock file. It contains relative path to different files organized in blocks.
* @param[in] cycle the current cycle number
* @param[in] elemManager the ElementRegionManager containing all the regions to be output and referred to in the VTM file
* @param[in] domain the DomainPartition containing all the regions to be output and referred to in the VTM file
* @param[in] vtmWriter a writer specialized for the VTM file format
*/

Expand All @@ -297,6 +311,11 @@ class VTKPolyDataWriterInterface
void writeElementFields( ElementRegionBase const & subRegion,
vtkCellData * cellData ) const;

/**
* @brief Writes all the fields associated to the elements of \p er if their plotlevel is <= m_plotLevel
* @param[in] region ParticleRegion being written
* @param[in] cellData a VTK object containing all the fields associated with the elements
*/
void writeParticleFields( ParticleRegionBase const & region,
vtkCellData * cellData ) const;

Expand All @@ -305,11 +324,13 @@ class VTKPolyDataWriterInterface
* @details The unstructured grid is the last element in the hierarchy of the output,
* it contains the cells connectivities and the vertices coordinates as long as the
* data fields associated with it
* @param[in] ug a VTK SmartPointer to the VTK unstructured grid.
* @param[in] path directory path for the grid file
* @param[in] region ElementRegionBase beeing written
* @param[in] ug a VTK SmartPointer to the VTK unstructured grid.
*/
void writeUnstructuredGrid( string const & path,
vtkUnstructuredGrid * ug ) const;
ObjectManagerBase const & region,
vtkUnstructuredGrid * ug );

private:

Expand Down Expand Up @@ -352,6 +373,12 @@ class VTKPolyDataWriterInterface

/// Defines whether to plot a faceElement as a 3D volumetric element or not.
bool m_writeFaceElementsAs3D;

/// Number of target processes to aggregate the data to be written
integer m_numberOfTargetProcesses;

/// Map a region name to the array of ranks outputed for it
std::map< string, std::vector< integer > > m_targetProcessesId;
};

} // namespace vtk
Expand Down
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