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Updated TreeGrafter for parallel hypersweep
This commit is contained in:
Oliver Ruebel
Gunther H. Weber
parent
76d88db157
commit
7506068236
@ -66,6 +66,7 @@
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#include <vtkm/worklet/contourtree_augmented/ContourTree.h>
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#include <vtkm/worklet/contourtree_distributed/HierarchicalContourTree.h>
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#include <vtkm/worklet/contourtree_distributed/InteriorForest.h>
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#include <vtkm/worklet/contourtree_distributed/tree_grafter/CalculateAttachementCounterWorklet.h>
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#include <vtkm/worklet/contourtree_distributed/tree_grafter/CollapseRegularChainsWorklet.h>
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#include <vtkm/worklet/contourtree_distributed/tree_grafter/CopyFirstHypernodePerIterationWorklet.h>
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#include <vtkm/worklet/contourtree_distributed/tree_grafter/CopyFirstSupernodePerIterationWorklet.h>
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@ -354,7 +355,18 @@ void TreeGrafter<MeshType, FieldType>::GraftInteriorForests(
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// count the number of iterations
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this->NumTransferIterations = 0;
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// Now loop to transfer one iteration at a time
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// There are several cases we need to handle properly
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// 1. We could have a round with no superarcs to add (in which case we are
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// guaranteed not to have attachment points)
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// 2. We could have a round with some superarcs but no attachment points
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// (because we attach to existing supernodes)
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// 3. We could have a round with attachment points to add
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// Attachment points are interior, so are never added to the active superarc
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// list in the first place. This means that we need to have an extra round
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// some of the time to transfer attachment points. So the logic is:
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// first we transfer all active superarcs, then we test (somehow) for having
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// attachment points to transfer
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// Loop to transfer active superarcs with a variation of the PPP transfer phase
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// We stop when all that is left are attachment points (which aren't included in the active list)
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while (this->ActiveSuperarcs.GetNumberOfValues() > 0)
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{ // loop to transfer
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@ -381,18 +393,34 @@ void TreeGrafter<MeshType, FieldType>::GraftInteriorForests(
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DebugPrint("Finished Transfer Iterations", __FILE__, __LINE__));
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#endif
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// Now set the transfer iteration for all attachment points
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// If there were no supernodes to transfer, their types are all NO_SUCH_ELEMENT
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auto setTransferIterationWorklet = vtkm::worklet::contourtree_distributed::tree_grafter::
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GraftInteriorForestsSetTransferIterationWorklet(this->NumTransferIterations);
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this->Invoke(setTransferIterationWorklet,
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this->SupernodeType, // input
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this->HierarchicalSuperId, // input
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this->WhenTransferred // output
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// At this point, we can check to see whether all supernodes in the residue have already been transferred
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// length of the attachementCounter will be set to (this->ContourTree->Supernodes.GetNumberOfValue());
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// as a result of the worklet
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vtkm::worklet::contourtree_augmented::IdArrayType attachmentCounter;
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vtkm::worklet::contourtree_distributed::tree_grafter::CalculateAttachementCounterWorklet
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calculateAttachementCounterWorklet;
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this->Invoke(calculateAttachementCounterWorklet, // worklet
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this->SupernodeType, // input
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this->HierarchicalSuperId, // input
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attachmentCounter // output
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);
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vtkm::Id numAttachmentPoints = vtkm::cont::Algorithm::Reduce(attachmentCounter, 0, vtkm::Sum());
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// and increment the number of iterations
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this->NumTransferIterations++;
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// if there are any at all, we need an extra iteration
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if (numAttachmentPoints > 0)
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{ // attachment points needing transfer
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// Now set the transfer iteration for all attachment points
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// If there were no supernodes to transfer, their types are all NO_SUCH_ELEMENT
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auto setTransferIterationWorklet = vtkm::worklet::contourtree_distributed::tree_grafter::
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GraftInteriorForestsSetTransferIterationWorklet(this->NumTransferIterations);
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this->Invoke(setTransferIterationWorklet,
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this->SupernodeType, // input
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this->HierarchicalSuperId, // input
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this->WhenTransferred // output
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);
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// and increment the number of iterations
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this->NumTransferIterations++;
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} // attachment points needing transfer
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#ifdef DEBUG_PRINT
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VTKM_LOG_S(vtkm::cont::LogLevel::Info,
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@ -1397,8 +1425,8 @@ void TreeGrafter<MeshType, FieldType>::CopyIterationDetails(
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this->NewSupernodes.GetNumberOfValues());
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hierarchicalTree.NumHypernodesInRound.WritePortal().Set(theRound,
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this->NewHypernodes.GetNumberOfValues());
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// the -1 is because the last iteration is just setting attachment points
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hierarchicalTree.NumIterations.WritePortal().Set(theRound, this->NumTransferIterations - 1);
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// last iteration is just setting attachment points (but we are including this now) (previously added -1)
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hierarchicalTree.NumIterations.WritePortal().Set(theRound, this->NumTransferIterations);
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#ifdef DEBUG_PRINT
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VTKM_LOG_S(vtkm::cont::LogLevel::Info,
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@ -1424,7 +1452,7 @@ void TreeGrafter<MeshType, FieldType>::CopyIterationDetails(
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// and set the per round iteration counts. There may be smarter ways of doing this, but . . .
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this->ResizeVector<vtkm::Id>(
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hierarchicalTree.FirstSupernodePerIteration[static_cast<std::size_t>(theRound)],
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this->NumTransferIterations,
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this->NumTransferIterations + 1,
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vtkm::worklet::contourtree_augmented::NO_SUCH_ELEMENT);
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{
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auto copyFirstSupernodePerIterationWorklet =
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@ -1445,11 +1473,16 @@ void TreeGrafter<MeshType, FieldType>::CopyIterationDetails(
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hierarchicalTree.DebugPrint("Supernode Iteration Counts Set", __FILE__, __LINE__));
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#endif
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// Initalize hierarchicalTree.FirstHypernodePerIteration with NO_SUCH_ELEMENT
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// we add one so we don't need special cases when establishing subranges
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// There's a tricky case to be dealt with due to attachment points - the last (extra) iteration transfers supernodes
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// with a "virtual" superarc but no hyperarc. This can only occur in the final iteration, in which case the correct value is
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// the "off the end" sentinel. But it is also possible for there to be no attachment points, in which case the final iteration
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// will have some other value. Also, we need to set the "off the end" for the extra entry in any event.
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// THEREFORE, instead of instantiating to NO_SUCH_ELEMENT for safety, we instantiate to the hypernodes.size()
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this->ResizeVector<vtkm::Id>(
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hierarchicalTree.FirstHypernodePerIteration[static_cast<std::size_t>(theRound)],
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this->NumTransferIterations,
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vtkm::worklet::contourtree_augmented::NO_SUCH_ELEMENT);
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this->NumTransferIterations + 1,
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hierarchicalTree.Hypernodes.GetNumberOfValues());
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// copy the approbriat hierarchicalTree.FirstHypernodePerIteration values
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{
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auto copyFirstHypernodePerIterationWorklet =
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@ -1466,9 +1499,9 @@ void TreeGrafter<MeshType, FieldType>::CopyIterationDetails(
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);
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}
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// force the extra one to be one-off-the end for safety
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hierarchicalTree.FirstHypernodePerIteration[static_cast<size_t>(theRound)].WritePortal().Set(
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this->NumTransferIterations - 1, hierarchicalTree.Hypernodes.GetNumberOfValues());
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// force the extra one to be one-off-the end for safety; REMOVED - SEE ABOVE FOR LOGIC
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//hierarchicalTree.FirstHypernodePerIteration[static_cast<size_t>(theRound)].WritePortal().Set(
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// this->NumTransferIterations, hierarchicalTree.Hypernodes.GetNumberOfValues());
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#ifdef DEBUG_PRINT
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VTKM_LOG_S(vtkm::cont::LogLevel::Info,
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@ -32,6 +32,7 @@ set(headers
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CopyNewNodesSetSuperparentsWorklet.h
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CopyFirstSupernodePerIterationWorklet.h
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CopyFirstHypernodePerIterationWorklet.h
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CalculateAttachementCounterWorklet.h
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)
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vtkm_declare_headers(${headers})
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105
vtkm/worklet/contourtree_distributed/tree_grafter/CalculateAttachementCounterWorklet.h
Normal file
105
vtkm/worklet/contourtree_distributed/tree_grafter/CalculateAttachementCounterWorklet.h
Normal file
@ -0,0 +1,105 @@
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//============================================================================
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// Copyright (c) Kitware, Inc.
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// All rights reserved.
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// See LICENSE.txt for details.
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//
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// This software is distributed WITHOUT ANY WARRANTY; without even
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// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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// PURPOSE. See the above copyright notice for more information.
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//============================================================================
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// Copyright (c) 2018, The Regents of the University of California, through
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// Lawrence Berkeley National Laboratory (subject to receipt of any required approvals
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// from the U.S. Dept. of Energy). All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without modification,
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// are permitted provided that the following conditions are met:
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//
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// (1) Redistributions of source code must retain the above copyright notice, this
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// list of conditions and the following disclaimer.
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//
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// (2) Redistributions in binary form must reproduce the above copyright notice,
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// this list of conditions and the following disclaimer in the documentation
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// and/or other materials provided with the distribution.
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//
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// (3) Neither the name of the University of California, Lawrence Berkeley National
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// Laboratory, U.S. Dept. of Energy nor the names of its contributors may be
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// used to endorse or promote products derived from this software without
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// specific prior written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
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// IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
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// INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
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// OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
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// OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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//=============================================================================
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//
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// This code is an extension of the algorithm presented in the paper:
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// Parallel Peak Pruning for Scalable SMP Contour Tree Computation.
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// Hamish Carr, Gunther Weber, Christopher Sewell, and James Ahrens.
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// Proceedings of the IEEE Symposium on Large Data Analysis and Visualization
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// (LDAV), October 2016, Baltimore, Maryland.
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//
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// The PPP2 algorithm and software were jointly developed by
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// Hamish Carr (University of Leeds), Gunther H. Weber (LBNL), and
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// Oliver Ruebel (LBNL)
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//==============================================================================
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#ifndef vtk_m_worklet_contourtree_distributed_tree_grafter_calculate_attachement_counter_worklet_h
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#define vtk_m_worklet_contourtree_distributed_tree_grafter_calculate_attachement_counter_worklet_h
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#include <vtkm/worklet/WorkletMapField.h>
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#include <vtkm/worklet/contourtree_augmented/Types.h>
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namespace vtkm
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{
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namespace worklet
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{
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namespace contourtree_distributed
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{
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namespace tree_grafter
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{
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// In TreeGrafter.GraftInteriorForests to compute attachmentCounter to
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// check whether additional attachement points need to be transferred
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class CalculateAttachementCounterWorklet : public vtkm::worklet::WorkletMapField
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{
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public:
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using ControlSignature = void(FieldIn supernodeType, // input
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FieldIn hierarchicalSuperId, // input
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FieldOut attachmentCounter // output
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);
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using ExecutionSignature = _3(_1, _2);
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using InputDomain = _1;
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// Default Constructor
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VTKM_EXEC_CONT
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CalculateAttachementCounterWorklet() {}
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VTKM_EXEC vtkm::Id operator()(const vtkm::Id& supernodeType,
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const vtkm::Id& hierarchicalSuperId) const
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{ // operator ()
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return (supernodeType == vtkm::worklet::contourtree_augmented::IS_ATTACHMENT) &&
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vtkm::worklet::contourtree_augmented::NoSuchElement(hierarchicalSuperId);
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// In serial this worklet implements the following operation
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/*
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for (indexType supernode = 0; supernode < contourTree->supernodes.size(); supernode++)
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attachmentCounter[supernode] = (supernodeType[supernode] == IS_ATTACHMENT) && noSuchElement(hierarchicalSuperID[supernode]);
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*/
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} // operator ()
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}; // CalculateAttachementCounterWorklet
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} // namespace tree_grafter
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} // namespace contourtree_distributed
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} // namespace worklet
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} // namespace vtkm
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#endif
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