Refactoring code to use namespaces and reorganizing files.

We now have a singular "sensei" library providing the "sensei"
namespace.

CMake/adios.cmake

+find_package(ADIOS 1.9 REQUIRED)
+add_library(adios INTERFACE)
+target_link_libraries(adios INTERFACE ${ADIOS_LIBRARIES})
+target_include_directories(adios SYSTEM INTERFACE ${ADIOS_INCLUDE_DIRS})
+if(ADIOS_DEFINITIONS)
+  target_compile_definitions(adios INTERFACE ${ADIOS_DEFINITIONS})
+endif()

CMakeLists.txt

@@ -42,50 +42,19 @@ cmake_dependent_option(
 
 #------------------------------------------------------------------------------
 include(mpi)
+if(ENABLE_ADIOS)
+  include(adios)
+endif()
 
 add_subdirectory(utils)
 
-# Process subdirectories.
+include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 if(ENABLE_SENSEI)
   message(STATUS "Enabled: Sensei infrastructure.")
-  add_subdirectory(core)
+  add_subdirectory(sensei)
 else()
   message(STATUS "Disabled: Sensei infrastructure.")
 endif()
 
-
-if(ENABLE_SENSEI)
-  if(VTK_HAS_GENERIC_ARRAYS)
-    add_subdirectory(analysis/histogram)
-  endif()
-  add_subdirectory(analysis/configurable)
-  add_subdirectory(analysis/autocorrelation)
-endif()
-
-if(ENABLE_PARALLEL3D)
-  message(STATUS "Enabled: Parallel3D miniapp.")
-  add_subdirectory(miniapps/parallel3d)
-else()
-  message(STATUS "Disabled: Parallel3D miniapp.")
-endif()
-
-if(ENABLE_OSCILLATORS)
-  message(STATUS "Enabled: Oscillators miniapp.")
-  add_subdirectory(miniapps/oscillators)
-else()
-  message(STATUS "Disabled: Histogram miniapp.")
-endif()
-
-if(ENABLE_CATALYST)
-  message(STATUS "Enabled: Catalyst")
-  add_subdirectory(infrastructures/catalyst)
-else()
-  message(STATUS "Disabled: Catalyst")
-endif()
-
-if(ENABLE_ADIOS)
-  message(STATUS "Enabled: ADIOS")
-  add_subdirectory(infrastructures/adios)
-else()
-  message(STATUS "Disabled: ADIOS")
-endif()
+add_subdirectory(miniapps)
+add_subdirectory(endpoints)

analysis/autocorrelation/CMakeLists.txt

-#------------------------------------------------------------------------------
-if(ENABLE_SENSEI)
-  set(sources AutocorrelationAnalysisAdaptor.cxx)
-else()
-  set(sources analysis.cpp)
-endif()
-
-add_library(autocorrelation STATIC ${sources})
-target_compile_options(autocorrelation PRIVATE "-std=c++11")
-target_include_directories(autocorrelation INTERFACE ${CMAKE_CURRENT_SOURCE_DIR})
-target_link_libraries(autocorrelation PUBLIC mpi PRIVATE diy grid)
-if (ENABLE_SENSEI)
-  target_link_libraries(autocorrelation PUBLIC core)
-endif()

analysis/configurable/CMakeLists.txt

-add_library(configurable STATIC vtkConfigurableAnalysisAdaptor.cxx)
-target_link_libraries(configurable PUBLIC mpi core PRIVATE pugixml)
-target_include_directories(configurable INTERFACE ${CMAKE_CURRENT_SOURCE_DIR})
-
-if(VTK_HAS_GENERIC_ARRAYS)
-  target_link_libraries(configurable PRIVATE histogram)
-  target_compile_options(configurable PRIVATE ENABLE_HISTOGRAM)
-endif()
-target_link_libraries(configurable PRIVATE autocorrelation)
-
-if(ENABLE_CATALYST)
-  target_link_libraries(configurable PRIVATE catalyst)
-endif()
-if(ENABLE_ADIOS)
-  target_link_libraries(configurable PRIVATE adios)
-endif()

analysis/histogram/CMakeLists.txt

-#-----------------------------------------------------------------------
-set(sources
-  HistogramAnalysisAdaptor.cxx
-  HistogramAnalysisAdaptor.h)
-
-#-----------------------------------------------------------------------
-add_library(histogram STATIC ${sources})
-target_include_directories(histogram INTERFACE ${CMAKE_CURRENT_SOURCE_DIR})
-target_link_libraries(histogram PUBLIC mpi core)

analysis/histogram/vtk_histogram.cxx

-#include "vtk_histogram.h"
-
-#include <vtkAOSDataArrayTemplate.h>
-#include <vtkArrayDispatch.h>
-#include <vtkSOADataArrayTemplate.h>
-
-namespace {
-// Private worker for histogram method. Computes the local histogram on
-// array (passed to operator()). To be used with vtkArrayDispatch.
-//
-// Inputs:
-// range: Global range of data
-// bins: Number of histogram bins
-// array: Local data.
-//
-// Outputs:
-// Histogram: The histogram of the local data.
-struct HistogramWorker
-{
-  const double *Range;
-  int Bins;
-  std::vector<unsigned int> Histogram;
-  HistogramWorker(const double *range, int bins) : Range(range), Bins(bins) {}
-
-  template <typename ArrayT>
-  void operator()(ArrayT *array)
-  {
-    assert(array);
-    assert(array->GetNumberOfComponents() == 1);
-
-    typedef typename ArrayT::ValueType ValueType;
-    ValueType width = static_cast<ValueType>((this->Range[1] - this->Range[0]) / this->Bins);
-    ValueType min = static_cast<ValueType>(this->Range[0]);
-    vtkIdType numTuples = array->GetNumberOfTuples();
-
-    this->Histogram.clear();
-    // + 1 to store val == max. These will be moved to this last bin before
-    // returning (Avoids having to branch in the loop below);
-    this->Histogram.resize(this->Bins + 1, 0);
-    for (vtkIdType tIdx = 0; tIdx < numTuples; ++tIdx)
-      {
-      int bin = static_cast<int>((array->GetComponent(tIdx, 0) - min) / width);
-      ++this->Histogram[bin];
-      }
-
-    // Merge the last two bins (the last is only when val == max)
-    this->Histogram[this->Bins-1] += this->Histogram[this->Bins];
-    this->Histogram.resize(this->Bins);
-  }
-};
-
-} // end anon namespace
-
-void vtk_histogram(MPI_Comm comm, vtkDataArray* array, int bins)
-{
-  int rank;
-  MPI_Comm_rank(comm, &rank);
-
-  // find max and min.
-  double range[2];
-  array->GetRange(range);
-
-  double g_range[2];
-  // Find the global max/min
-  MPI_Allreduce(&range[0], &g_range[0], 1, MPI_DOUBLE, MPI_MIN, comm);
-  MPI_Allreduce(&range[1], &g_range[1], 1, MPI_DOUBLE, MPI_MAX, comm);
-
-  // Compute local histogram
-  HistogramWorker worker(g_range, bins);
-  // vtkArrayDispatch downcasts the array to a concrete typed implementation
-  // that provides faster access methods.
-  if (!vtkArrayDispatch::Dispatch::Execute(array, worker))
-    {
-    // This happens if vtkArrayDispatch doesn't know about the array subclass
-    // in use.
-    std::cerr << "HistogramWorker dispatch failed on rank " << rank << "!\n";
-    worker.Histogram.resize(bins, 0);
-    }
-
-  // Global histogram:
-  std::vector<unsigned int> gHist(bins, 0);
-  MPI_Reduce(&worker.Histogram[0], &gHist[0], bins, MPI_UNSIGNED, MPI_SUM, 0, comm);
-  if (rank == 0)
-    {
-    std::cout << "Histogram '" << array->GetName() << "' (VTK):\n";
-    double width = (g_range[1] - g_range[0]) / bins;
-    for (int i = 0; i < bins; ++i)
-      {
-      printf("  %f-%f: %d\n", g_range[0] + i*width, g_range[0] + (i+1)*width, gHist[i]);
-      }
-    }
-}
-
-

analysis/histogram/vtk_histogram.h

-#ifndef VTK_HISTOGRAM_H
-#define VTK_HISTOGRAM_H
-
-#include <mpi.h>
-
-class vtkDataArray;
-
-/// Parallel histogram implementation using array-layout independent
-/// VTK's Generic Array infrastructure.
-void vtk_histogram(MPI_Comm comm, vtkDataArray* array, int bins);
-
-#endif

core/CMakeLists.txt

-#-----------------------------------------------------------------------
-set (sources
-  vtkInsituAnalysisAdaptor.cxx
-  vtkInsituAnalysisAdaptor.h
-  vtkInsituDataAdaptor.cxx
-  vtkInsituDataAdaptor.h
-  )
-
-#-----------------------------------------------------------------------
-find_package(VTK QUIET COMPONENTS vtkCommonDataModel)
-if(NOT VTK_FOUND)
-  message(FATAL_ERROR "VTK (vtkCommonDataModel) is required for Sensei core "
-    "even when not using any infrastructures. Please set VTK_DIR to point to a "
-    "directory containing `VTKConfig.cmake`.")
-endif()
-
-add_library(core STATIC ${sources})
-target_include_directories(core SYSTEM PUBLIC ${VTK_INCLUDE_DIRS}
-                                INTERFACE ${CMAKE_CURRENT_SOURCE_DIR})
-target_compile_definitions(core PUBLIC ${VTK_DEFINITIONS}
-                                INTERFACE ENABLE_SENSEI)
-target_link_libraries(core PUBLIC ${VTK_LIBRARIES})

core/vtkInsituAnalysisAdaptor.cxx

-/*=========================================================================
-
-  Program:   Visualization Toolkit
-  Module:    vtkInsituAnalysisAdaptor.cxx
-
-  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
-  All rights reserved.
-  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
-
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notice for more information.
-
-=========================================================================*/
-#include "vtkInsituAnalysisAdaptor.h"
-
-#include "vtkObjectFactory.h"
-
-//----------------------------------------------------------------------------
-vtkInsituAnalysisAdaptor::vtkInsituAnalysisAdaptor()
-{
-}
-
-//----------------------------------------------------------------------------
-vtkInsituAnalysisAdaptor::~vtkInsituAnalysisAdaptor()
-{
-}
-
-//----------------------------------------------------------------------------
-void vtkInsituAnalysisAdaptor::PrintSelf(ostream& os, vtkIndent indent)
-{
-  this->Superclass::PrintSelf(os, indent);
-}

core/vtkInsituAnalysisAdaptor.h

-/*=========================================================================
-
-  Program:   Visualization Toolkit
-  Module:    vtkInsituAnalysisAdaptor.h
-
-  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
-  All rights reserved.
-  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
-
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notice for more information.
-
-=========================================================================*/
-// .NAME vtkInsituAnalysisAdaptor
-// .SECTION Description
-// vtkInsituAnalysisAdaptor is an adaptor for any insitu analysis framework or
-// algorithm. Concrete subclasses use vtkInsituDataAdaptor instance passed to
-// the Execute() method to access simulation data for further processing.
-#ifndef vtkInsituAnalysisAdaptor_h
-#define vtkInsituAnalysisAdaptor_h
-
-#include "vtkObjectBase.h"
-#include "vtkSetGet.h"
-
-class vtkInsituDataAdaptor;
-class vtkInsituAnalysisAdaptor : public vtkObjectBase
-{
-public:
-  vtkTypeMacro(vtkInsituAnalysisAdaptor, vtkObjectBase);
-  void PrintSelf(ostream& os, vtkIndent indent);
-
-  virtual bool Execute(vtkInsituDataAdaptor* data) = 0;
-
-protected:
-  vtkInsituAnalysisAdaptor();
-  ~vtkInsituAnalysisAdaptor();
-
-private:
-  vtkInsituAnalysisAdaptor(const vtkInsituAnalysisAdaptor&); // Not implemented.
-  void operator=(const vtkInsituAnalysisAdaptor&); // Not implemented.
-};
-
-#endif

infrastructures/adios/ADIOSAnalysisEndPoint.cxx → endpoints/ADIOSAnalysisEndPoint.cxx

@@ -9,10 +9,8 @@
 #include <opts/opts.h>
 #include <mpi.h>
 #include <iostream>
-#include <adios.h>
-#include <adios_read.h>
-#include <vtkADIOSDataAdaptor.h>
-#include <vtkConfigurableAnalysisAdaptor.h>
+#include <sensei/adios/DataAdaptor.h>
+#include <sensei/ConfigurableAnalysis.h>
 #include <vtkNew.h>
 #include <vtkDataSet.h>
 
@@ -55,10 +53,10 @@ int main(int argc, char** argv)
   readmethods["dimes"] = ADIOS_READ_METHOD_DIMES;
   readmethods["flexpath"] = ADIOS_READ_METHOD_FLEXPATH;
 
-  vtkNew<vtkConfigurableAnalysisAdaptor> analysis;
+  vtkNew<sensei::ConfigurableAnalysis> analysis;
   analysis->Initialize(comm, config_file);
 
-  vtkNew<vtkADIOSDataAdaptor> dataAdaptor;
+  vtkNew<sensei::adios::DataAdaptor> dataAdaptor;
   dataAdaptor->Open(comm, readmethods[readmethod], input);
   do
     {

endpoints/CMakeLists.txt

+if (ENABLE_ADIOS)
+  #------------------------------------------------------------------------------
+  add_executable(ADIOSAnalysisEndPoint ADIOSAnalysisEndPoint.cxx)
+  target_link_libraries(ADIOSAnalysisEndPoint PRIVATE opts mpi adios sensei)
+endif()

infrastructures/catalyst/CMakeLists.txt

-set(sources
-  vtkCatalystAnalysisAdaptor.cxx
-  vtkCatalystSlicePipeline.cxx)
-
-#------------------------------------------------------------------------------
-find_package(ParaView QUIET COMPONENTS vtkPVCatalyst)
-if(NOT ParaView_FOUND)
-  message(FATAL_ERROR "Catalyst analysis components require Catalyst build (or "
-                      "install directory. Please set ParaView_DIR to point to "
-                      "directory containing `ParaViewConfig.cmake`.")
-endif()
-add_library(catalyst STATIC ${sources})
-target_include_directories(catalyst
-                            SYSTEM PUBLIC ${PARAVIEW_INCLUDE_DIRS}
-                            INTERFACE ${CMAKE_CURRENT_SOURCE_DIR})
-target_compile_definitions(catalyst
-                            PUBLIC ${VTK_DEFINITIONS}
-                            INTERFACE ENABLE_CATALYST)
-target_link_libraries(catalyst
-                        PUBLIC ${VTK_LIBRARIES}
-                        PUBLIC core)

miniapps/CMakeLists.txt

+if(ENABLE_PARALLEL3D)
+  message(STATUS "Enabled: Parallel3D miniapp.")
+  add_subdirectory(parallel3d)
+else()
+  message(STATUS "Disabled: Parallel3D miniapp.")
+endif()
+
+if(ENABLE_OSCILLATORS)
+  message(STATUS "Enabled: Oscillators miniapp.")
+  add_subdirectory(oscillators)
+else()
+  message(STATUS "Disabled: Oscillators miniapp.")
+endif()
+

miniapps/oscillators/CMakeLists.txt

@@ -26,5 +26,5 @@ find_package(Threads)
 target_link_libraries(oscillator PRIVATE util ${CMAKE_THREAD_LIBS_INIT})
 
 if(ENABLE_SENSEI)
-  target_link_libraries(oscillator PRIVATE core configurable)
+  target_link_libraries(oscillator PRIVATE sensei)
 endif()

miniapps/oscillators/bridge.cpp

@@ -3,16 +3,15 @@
 #include "dataadaptor.h"
 
 #include <vector>
-#include <vtkConfigurableAnalysisAdaptor.h>
+#include <sensei/ConfigurableAnalysis.h>
 #include <vtkDataObject.h>
-#include <vtkInsituAnalysisAdaptor.h>
 #include <vtkNew.h>
 #include <vtkSmartPointer.h>
 
 namespace bridge
 {
 static vtkSmartPointer<oscillators::DataAdaptor> GlobalDataAdaptor;
-static vtkSmartPointer<vtkConfigurableAnalysisAdaptor> GlobalAnalysisAdaptor;
+static vtkSmartPointer<sensei::ConfigurableAnalysis> GlobalAnalysisAdaptor;
 
 //-----------------------------------------------------------------------------
 void initialize(MPI_Comm world,
@@ -36,7 +35,7 @@ void initialize(MPI_Comm world,
       from_z[cc], to_z[cc]);
     }
 
-  GlobalAnalysisAdaptor = vtkSmartPointer<vtkConfigurableAnalysisAdaptor>::New();
+  GlobalAnalysisAdaptor = vtkSmartPointer<sensei::ConfigurableAnalysis>::New();
   GlobalAnalysisAdaptor->Initialize(world, config_file);
 }
 

miniapps/oscillators/dataadaptor.h

 #ifndef OSCILLATORS_DATAADAPTOR_H
 #define OSCILLATORS_DATAADAPTOR_H
 
-#include <vtkInsituDataAdaptor.h>
+#include <sensei/DataAdaptor.h>
 
 namespace oscillators
 {
-class DataAdaptor : public vtkInsituDataAdaptor
+class DataAdaptor : public sensei::DataAdaptor
 {
 public:
   static DataAdaptor* New();
-  vtkTypeMacro(DataAdaptor, vtkInsituDataAdaptor);
+  vtkTypeMacro(DataAdaptor, sensei::DataAdaptor);
 
   /// @brief Initialize the data adaptor.
   ///

miniapps/parallel3d/Bridge.cxx

 #include "Bridge.h"
-
 #include "DataAdaptor.h"
-#include "vtkInsituAnalysisAdaptor.h"
-#include "vtkNew.h"
-#include "vtkDataObject.h"
-#include "vtkConfigurableAnalysisAdaptor.h"
 
+#include <sensei/ConfigurableAnalysis.h>
+#include <vtkNew.h>
+#include <vtkDataObject.h>
 #include <vector>
+
 namespace BridgeInternals
 {
   static vtkSmartPointer<parallel3d::DataAdaptor> GlobalDataAdaptor;
-  static vtkSmartPointer<vtkConfigurableAnalysisAdaptor> GlobalAnalysisAdaptor;
+  static vtkSmartPointer<sensei::ConfigurableAnalysis> GlobalAnalysisAdaptor;
 }
 
 //-----------------------------------------------------------------------------
@@ -33,7 +32,7 @@ void bridge_initialize(MPI_Comm comm,
     tot_blocks_x, tot_blocks_y, tot_blocks_z,
     block_id_x, block_id_y, block_id_z);
 
-  BridgeInternals::GlobalAnalysisAdaptor = vtkSmartPointer<vtkConfigurableAnalysisAdaptor>::New();
+  BridgeInternals::GlobalAnalysisAdaptor = vtkSmartPointer<sensei::ConfigurableAnalysis>::New();
   BridgeInternals::GlobalAnalysisAdaptor->Initialize(comm, config_file);
 }
 

miniapps/parallel3d/CMakeLists.txt

@@ -17,5 +17,5 @@ target_compile_definitions(3D_Grid PRIVATE _FILE_OFFSET_BITS=64 _LARGEFILE64_SOU
 target_link_libraries(3D_Grid PRIVATE m mpi)
 
 if(ENABLE_SENSEI)
-  target_link_libraries(3D_Grid PRIVATE core configurable)
+  target_link_libraries(3D_Grid PRIVATE sensei)
 endif()

miniapps/parallel3d/DataAdaptor.h

 #ifndef PARALLEL3D_DATAADAPTOR_H
 #define PARALLEL3D_DATAADAPTOR_H
 
-#include "vtkInsituDataAdaptor.h"
+#include <sensei/DataAdaptor.h>
 #include "vtkSmartPointer.h"
 #include <map>
 #include <string>
@@ -14,11 +14,11 @@ namespace parallel3d
 /// DataAdaptor is an adaptor for the parallel_3d simulation (miniapp).
 /// Its purpose is to map the simulation datastructures to VTK
 /// data model.
-class DataAdaptor : public vtkInsituDataAdaptor
+class DataAdaptor : public sensei::DataAdaptor
 {
 public:
   static DataAdaptor* New();
-  vtkTypeMacro(DataAdaptor, vtkInsituDataAdaptor);
+  vtkTypeMacro(DataAdaptor, sensei::DataAdaptor);
 
   /// Initialize the data adaptor.
   void Initialize(

sensei/AnalysisAdaptor.cxx

+#include "AnalysisAdaptor.h"
+
+#include "vtkObjectFactory.h"
+
+namespace sensei
+{
+
+//----------------------------------------------------------------------------
+AnalysisAdaptor::AnalysisAdaptor()
+{
+}
+
+//----------------------------------------------------------------------------
+AnalysisAdaptor::~AnalysisAdaptor()
+{
+}
+
+//----------------------------------------------------------------------------
+void AnalysisAdaptor::PrintSelf(ostream& os, vtkIndent indent)
+{
+  this->Superclass::PrintSelf(os, indent);
+}
+
+} // end of namespace sensei

sensei/AnalysisAdaptor.h

+#ifndef sensei_AnalysisAdaptor_h
+#define sensei_AnalysisAdaptor_h