Fix compiler warnings and test errors before merge.

examples/contour_tree/ContourTreeMesh2D.cxx

@@ -64,8 +64,6 @@
 //  Proceedings of the IEEE Symposium on Large Data Analysis and Visualization 
 //  (LDAV), October 2016, Baltimore, Maryland.
 
-// We first check if VTKM_DEVICE_ADAPTER is defined, so that when TBB and CUDA
-// includes this file we use the device adapter that they have set.
 #ifndef VTKM_DEVICE_ADAPTER
 #define VTKM_DEVICE_ADAPTER VTKM_DEVICE_ADAPTER_SERIAL
 #endif

examples/contour_tree/ContourTreeMesh3D.cxx

@@ -64,8 +64,6 @@
 //  Proceedings of the IEEE Symposium on Large Data Analysis and Visualization 
 //  (LDAV), October 2016, Baltimore, Maryland.
 
-// We first check if VTKM_DEVICE_ADAPTER is defined, so that when TBB and CUDA
-// includes this file we use the device adapter that they have set.
 #ifndef VTKM_DEVICE_ADAPTER
 #define VTKM_DEVICE_ADAPTER VTKM_DEVICE_ADAPTER_SERIAL
 #endif

vtkm/worklet/contourtree/CMakeLists.txt

@@ -19,9 +19,53 @@
 ##============================================================================
 
 set(headers
-#  Mesh2D_DEM_VertexOutdegreeStarter.h
+  ActiveEdgeTransferrer.h
+  ChainDoubler.h
+  ChainGraph.h
+  ContourTree.h
+  CopyJoinSplit.h
+  CopyNeighbors.h
+  CopySupernodes.h
+  DegreeDelta.h
+  DegreeSubrangeOffset.h
+  EdgePeakComparator.h
+  FillSupernodes.h
+  FindLeaves.h
+  GoverningSaddleFinder.h
+  JoinArcConnector.h
+  JoinSuperArcFinder.h
+  JoinTreeTransferrer.h
+  LinkComponentCaseTable2D.h
+  LinkComponentCaseTable3D.h
+  MergeTree.h
+  Mesh2D_DEM_SaddleStarter.h
+  Mesh2D_DEM_Triangulation.h
+  Mesh2D_DEM_Triangulation_Macros.h
+  Mesh2D_DEM_VertexOutdegreeStarter.h
   Mesh2D_DEM_VertexStarter.h
-#  ActiveEdgeTransferrer.h
+  Mesh3D_DEM_SaddleStarter.h
+  Mesh3D_DEM_Triangulation.h
+  Mesh3D_DEM_Triangulation_Macros.h
+  Mesh3D_DEM_VertexOutdegreeStarter.h
+  Mesh3D_DEM_VertexStarter.h
+  PrintVectors.h
+  RegularPointTransferrer.h
+  RegularToCandidate.h
+  RegularToCriticalDown.h
+  RegularToCriticalUp.h
+  ResetDegrees.h
+  SaddleAscentFunctor.h
+  SaddleAscentTransferrer.h
+  SetJoinAndSplitArcs.h
+  SetSupernodeInward.h
+  SkipVertex.h
+  SubrangeOffset.h
+  TrunkBuilder.h
+  Types.h
+  UpdateOutbound.h
+  VertexDegreeUpdater.h
+  VertexMergeComparator.h
+  VertexValueComparator.h
   )
 
 #-----------------------------------------------------------------------------

vtkm/worklet/contourtree/ChainDoubler.h

@@ -83,6 +83,9 @@
 #ifndef vtkm_worklet_contourtree_chain_doubler_h
 #define vtkm_worklet_contourtree_chain_doubler_h
 
+#include <vtkm/worklet/WorkletMapField.h>
+#include <vtkm/exec/ExecutionWholeArray.h>
+
 namespace vtkm {
 namespace worklet {
 namespace contourtree {

vtkm/worklet/contourtree/ChainGraph.h

@@ -92,7 +92,9 @@
 #include <vtkm/worklet/contourtree/SaddleAscentTransferrer.h>
 #include <vtkm/worklet/contourtree/TrunkBuilder.h>
 #include <vtkm/worklet/contourtree/JoinTreeTransferrer.h>
+
 #include <vtkm/cont/ArrayHandlePermutation.h>
+#include <vtkm/worklet/DispatcherMapField.h>
 
 #define DEBUG_PRINT 1
 //#define DEBUG_FUNCTION_ENTRY 1
@@ -358,9 +360,6 @@ void ChainGraph<T,StorageType,DeviceAdapter>::TransferRegularPoints()
 		cout << "=======================" << endl;
 		cout << endl;
 #endif
-
-  vtkm::Id nActiveVertices = activeVertices.GetNumberOfValues();
-
   RegularPointTransferrer<T> regularPointTransferrer(isJoinGraph);
   vtkm::worklet::DispatcherMapField<RegularPointTransferrer<T> >
                  regularPointTransferrerDispatcher(regularPointTransferrer);
@@ -391,9 +390,6 @@ void ChainGraph<T,StorageType,DeviceAdapter>::CompactActiveVertices()
   typedef vtkm::cont::ArrayHandle<vtkm::Id> IdArrayType;
   typedef vtkm::cont::ArrayHandlePermutation<IdArrayType, IdArrayType> PermuteIndexType;
 
-  // retrieve the logical number of vertices 
-  vtkm::Id nActiveVertices = activeVertices.GetNumberOfValues();
-
   // create a temporary array the same size
   vtkm::cont::ArrayHandle<vtkm::Id> newActiveVertices;
 

vtkm/worklet/contourtree/EdgePeakComparator.h

@@ -82,6 +82,8 @@
 #ifndef vtkm_worklet_contourtree_edge_peak_comparator_h
 #define vtkm_worklet_contourtree_edge_peak_comparator_h
 
+#include <vtkm/cont/ArrayHandle.h>
+
 namespace vtkm {
 namespace worklet {
 namespace contourtree {

vtkm/worklet/contourtree/JoinSuperArcFinder.h

@@ -17,17 +17,53 @@
 //  Laboratory (LANL), the U.S. Government retains certain rights in
 //  this software.
 //============================================================================
+//  Copyright (c) 2016, Los Alamos National Security, LLC
+//  All rights reserved.
+//
+//  Copyright 2016. Los Alamos National Security, LLC. 
+//  This software was produced under U.S. Government contract DE-AC52-06NA25396 
+//  for Los Alamos National Laboratory (LANL), which is operated by 
+//  Los Alamos National Security, LLC for the U.S. Department of Energy. 
+//  The U.S. Government has rights to use, reproduce, and distribute this 
+//  software.  NEITHER THE GOVERNMENT NOR LOS ALAMOS NATIONAL SECURITY, LLC 
+//  MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE 
+//  USE OF THIS SOFTWARE.  If software is modified to produce derivative works, 
+//  such modified software should be clearly marked, so as not to confuse it 
+//  with the version available from LANL.
+//
+//  Additionally, redistribution and use in source and binary forms, with or 
+//  without modification, are permitted provided that the following conditions 
+//  are met:
+//
+//  1. Redistributions of source code must retain the above copyright notice, 
+//     this list of conditions and the following disclaimer.
+//  2. Redistributions in binary form must reproduce the above copyright notice,
+//     this list of conditions and the following disclaimer in the documentation
+//     and/or other materials provided with the distribution.
+//  3. Neither the name of Los Alamos National Security, LLC, Los Alamos 
+//     National Laboratory, LANL, the U.S. Government, nor the names of its 
+//     contributors may be used to endorse or promote products derived from 
+//     this software without specific prior written permission.
+//
+//  THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND 
+//  CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, 
+//  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
+//  FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS 
+//  NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, 
+//  INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
+//  BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF 
+//  USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 
+//  THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+//  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF 
+//  THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//============================================================================
+
+//  This code is based on the algorithm presented in the paper:  
+//  “Parallel Peak Pruning for Scalable SMP Contour Tree Computation.” 
+//  Hamish Carr, Gunther Weber, Christopher Sewell, and James Ahrens. 
+//  Proceedings of the IEEE Symposium on Large Data Analysis and Visualization 
+//  (LDAV), October 2016, Baltimore, Maryland.
 
-//=======================================================================================
-// 
-// Second Attempt to Compute Contour Tree in Data-Parallel Mode
-//
-// Started August 19, 2015
-//
-// Copyright Hamish Carr, University of Leeds
-//
-// JoinSuperArcFinder.h - functor that searches through the superarcs to assign each vertex
-//
 //=======================================================================================
 //
 // COMMENTS:

vtkm/worklet/contourtree/LinkComponentCaseTable2D.h

@@ -67,6 +67,7 @@
 #ifndef vtkm_worklet_contourtree_link_component_case_table_2d_h
 #define vtkm_worklet_contourtree_link_component_case_table_2d_h
 
+#include <vtkm/Types.h>
 #include <vtkm/worklet/contourtree/Mesh2D_DEM_Triangulation_Macros.h>
 
 namespace vtkm {

vtkm/worklet/contourtree/MergeTree.h

@@ -122,6 +122,8 @@
 //#define DEBUG_FUNCTION_ENTRY 1
 //#define DEBUG_TIMING 1
 
+using namespace std;
+
 namespace vtkm {
 namespace worklet {
 namespace contourtree {

vtkm/worklet/contourtree/Mesh2D_DEM_Triangulation.h

@@ -171,7 +171,7 @@ Mesh2D_DEM_Triangulation<T,StorageType,DeviceAdapter>::Mesh2D_DEM_Triangulation(
   
   // compute the number of log-jumping steps (i.e. lg_2 (nVertices))
   nLogSteps = 1;
-  for (signed long shifter = nVertices; shifter > 0; shifter >>= 1)
+  for (vtkm::Id shifter = nVertices; shifter > 0; shifter >>= 1)
     nLogSteps++;
 }
 

vtkm/worklet/contourtree/Mesh3D_DEM_Triangulation.h

@@ -159,7 +159,7 @@ Mesh3D_DEM_Triangulation<T,StorageType,DeviceAdapter>::Mesh3D_DEM_Triangulation(
   
   // compute the number of log-jumping steps (i.e. lg_2 (nVertices))
   nLogSteps = 1;
-  for (signed long shifter = nVertices; shifter > 0; shifter >>= 1)
+  for (vtkm::Id shifter = nVertices; shifter > 0; shifter >>= 1)
     nLogSteps++;
 
   linkComponentCaseTable3D = 

vtkm/worklet/contourtree/PrintVectors.h

@@ -72,8 +72,15 @@
 #include <string>
 #include <fstream>
 
+#include <vtkm/Types.h>
+#include <vtkm/cont/ArrayHandle.h>
+
 using namespace std;
 
+namespace vtkm {
+namespace worklet {
+namespace contourtree {
+
 // debug value for number of columns to print
 vtkm::Id printCols = 10;
 
@@ -227,4 +234,8 @@ void printLabelledBlock(string label, const vtkm::cont::ArrayHandle<T, StorageTy
 	cout << endl;
 } // printLabelledBlock()
 
+}
+}
+}
+
 #endif

vtkm/worklet/contourtree/VertexMergeComparator.h

@@ -79,6 +79,8 @@
 #ifndef vtkm_worklet_contourtree_vertex_merge_comparator_h
 #define vtkm_worklet_contourtree_vertex_merge_comparator_h
 
+#include <vtkm/cont/ArrayHandle.h>
+
 namespace vtkm {
 namespace worklet {
 namespace contourtree {
@@ -103,14 +105,14 @@ public:
   IdPortalType extrema;
   bool isJoinTree;
 
-  VTKM_CONT
+  VTKM_EXEC_CONT
   VertexMergeComparator(ValuePortalType Values,
                         IdPortalType Extrema,
                         bool IsJoinTree)
 		: values(Values), extrema(Extrema), isJoinTree(IsJoinTree)
 		{}
 
-  VTKM_EXEC_CONT
+  VTKM_EXEC
   bool operator() (const vtkm::Id& i, const vtkm::Id& j) const
   {
     // retrieve the pseudo-extremum the vertex belongs to

vtkm/worklet/contourtree/VertexValueComparator.h

@@ -79,6 +79,9 @@
 #ifndef vtkm_worklet_contourtree_vertex_value_comparator_h
 #define vtkm_worklet_contourtree_vertex_value_comparator_h
 
+#include <vtkm/Types.h>
+#include <vtkm/internal/ExportMacros.h>
+
 namespace vtkm {
 namespace worklet {
 namespace contourtree {
@@ -89,10 +92,10 @@ class VertexValueComparator
 public:
   const InFieldPortalType& values;
 
-  VTKM_CONT
+  VTKM_EXEC_CONT
   VertexValueComparator(const InFieldPortalType& Values) : values(Values) {}
 
-  VTKM_EXEC_CONT
+  VTKM_EXEC
   bool operator () (const vtkm::Id &i, const vtkm::Id &j, bool ascending)
   {
     if (values.Get(i) < values.Get(j))