Conduit Data Adaptor and small conduit multi-domain example.

CMake/FindConduit.cmake

+###############################################################################
+# Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+# 
+# Produced at the Lawrence Livermore National Laboratory
+# 
+# LLNL-CODE-716457
+# 
+# All rights reserved.
+# 
+# This file is part of Ascent. 
+# 
+# For details, see: http://ascent.readthedocs.io/.
+# 
+# Please also read ascent/LICENSE
+# 
+# Redistribution and use in source and binary forms, with or without 
+# modification, are permitted provided that the following conditions are met:
+# 
+# * Redistributions of source code must retain the above copyright notice, 
+#   this list of conditions and the disclaimer below.
+# 
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the disclaimer (as noted below) in the
+#   documentation and/or other materials provided with the distribution.
+# 
+# * Neither the name of the LLNS/LLNL 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 THE COPYRIGHT HOLDERS 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 LAWRENCE LIVERMORE NATIONAL SECURITY,
+# LLC, THE U.S. DEPARTMENT OF ENERGY 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.
+# 
+###############################################################################
+
+###############################################################################
+#
+# Setup Conduit
+#
+###############################################################################
+#
+#  Expects CONDUIT_DIR to point to a Conduit installations.
+#
+# This file defines the following CMake variables:
+#  CONDUIT_FOUND - If Conduit was found
+#  CONDUIT_INCLUDE_DIRS - The Conduit include directories
+#
+#  If found, the conduit CMake targets will also be imported.
+#  The main conduit library targets are:
+#   conduit
+#   conduit_relay
+#   conduit_relay_mpi (if conduit was built with mpi support)
+#   conduit_blueprint
+#
+###############################################################################
+
+###############################################################################
+# Check for CONDUIT_DIR
+###############################################################################
+if(NOT CONDUIT_DIR)
+    MESSAGE(FATAL_ERROR "Could not find Conduit. Conduit requires explicit CONDUIT_DIR.")
+endif()
+
+if(NOT EXISTS ${CONDUIT_DIR}/lib/cmake/conduit.cmake)
+    MESSAGE(FATAL_ERROR "Could not find Conduit CMake include file (${CONDUIT_DIR}/lib/cmake/conduit.cmake)")
+endif()
+
+###############################################################################
+# Import Conduit's CMake targets
+###############################################################################
+include(${CONDUIT_DIR}/lib/cmake/conduit.cmake)
+
+###############################################################################
+# Set remaning CMake variables 
+###############################################################################
+# we found Conduit
+set(CONDUIT_FOUND TRUE)
+# provide location of the headers in CONDUIT_INCLUDE_DIRS
+set(CONDUIT_INCLUDE_DIRS ${CONDUIT_DIR}/include/conduit)
+
+
+
+

CMake/SENSEIConfig.cmake.in

@@ -31,6 +31,7 @@ set(ENABLE_CATALYST @ENABLE_CATALYST@)
 set(ENABLE_CATALYST_PYTHON @ENABLE_CATALYST_PYTHON@)
 set(ENABLE_LIBSIM @ENABLE_LIBSIM@)
 set(ENABLE_ADIOS @ENABLE_ADIOS@)
+set(ENABLE_CONDUIT @ENABLE_CONDUIT@)
 set(ENABLE_VTK_GENERIC_ARRAYS @ENABLE_VTK_GENERIC_ARRAYS@)
 set(ENABLE_VTK_MPI @ENABLE_VTK_MPI@)
 set(ENABLE_VTK_IO @ENABLE_VTK_IO@)
@@ -68,6 +69,9 @@ endif()
 if(ENABLE_ADIOS)
   include(adios)
 endif()
+if(ENABLE_CONDUIT)
+  include(sconduit)
+endif()
 include(senseiCore)
 if(ENABLE_PYTHON)
   include(python)

CMake/conduit.cmake

+if(ENABLE_CONDUIT)
+  find_package(Conduit REQUIRED)
+
+  add_library(sconduit INTERFACE)
+
+  target_link_libraries(sconduit INTERFACE conduit conduit_relay conduit_blueprint)
+
+  target_include_directories(sconduit SYSTEM INTERFACE ${CONDUIT_INCLUDE_DIRS})
+
+  install(TARGETS sconduit EXPORT sconduit)
+  install(EXPORT sconduit DESTINATION lib/cmake EXPORT_LINK_INTERFACE_LIBRARIES)
+endif()

CMake/options.cmake

@@ -20,6 +20,10 @@ cmake_dependent_option(ENABLE_ADIOS
   "Enable analysis methods that use ADIOS" OFF
   "ENABLE_SENSEI" OFF)
 
+cmake_dependent_option(ENABLE_CONDUIT
+  "Enable analysis methods that use Conduit" OFF
+  "ENABLE_SENSEI" OFF)
+
 cmake_dependent_option(ENABLE_LIBSIM
   "Enable analysis methods that use Libsim" OFF
   "ENABLE_SENSEI" OFF)
@@ -39,6 +43,7 @@ cmake_dependent_option(ENABLE_VTK_M
 
 option(ENABLE_PARALLEL3D "Enable Parallel3D miniapp" ON)
 option(ENABLE_OSCILLATORS "Enable Oscillators miniapp" ON)
+option(ENABLE_CONDUITTEST "Enable Conduit miniapp" OFF)
 
 message(STATUS "ENABLE_SENSEI=${ENABLE_SENSEI}")
 message(STATUS "ENABLE_PYTHON=${ENABLE_PYTHON}")
@@ -46,8 +51,10 @@ message(STATUS "ENABLE_VTK_GENERIC_ARRAYS=${ENABLE_VTK_GENERIC_ARRAYS}")
 message(STATUS "ENABLE_CATALYST=${ENABLE_CATALYST}")
 message(STATUS "ENABLE_CATALYST_PYTHON=${ENABLE_CATALYST}")
 message(STATUS "ENABLE_ADIOS=${ENABLE_ADIOS}")
+message(STATUS "ENABLE_CONDUIT=${ENABLE_CONDUIT}")
 message(STATUS "ENABLE_LIBSIM=${ENABLE_LIBSIM}")
 message(STATUS "ENABLE_VTK_IO=${ENABLE_VTK_IO}")
 message(STATUS "ENABLE_VTK_MPI=${ENABLE_VTK_MPI}")
 message(STATUS "ENABLE_PARALLEL3D=${ENABLE_PARALLEL3D}")
 message(STATUS "ENABLE_OSCILLATORS=${ENABLE_OSCILLATORS}")
+message(STATUS "ENABLE_CONDUITTEST=${ENABLE_CONDUITTEST}")

CMakeLists.txt

@@ -12,6 +12,7 @@ include(adios)
 include(vtk)
 include(libsim)
 include(catalyst)
+include(conduit)
 include(python)
 include(version)
 include(config)

miniapps/CMakeLists.txt

@@ -5,6 +5,13 @@ else()
   message(STATUS "Disabled: Parallel3D miniapp.")
 endif()
 
+if(ENABLE_CONDUITTEST)
+  message(STATUS "Enabled: CONDUIT TEST miniapp.")
+  add_subdirectory(conduit_test)
+else()
+  message(STATUS "Disabled: conduit_test miniapp.")
+endif()
+
 if(ENABLE_OSCILLATORS)
   message(STATUS "Enabled: Oscillators miniapp.")
   add_subdirectory(oscillators)

miniapps/conduit_test/CMakeLists.txt

+set(sources conduitTest.cpp bridge.cpp)
+set(libs mpi diy grid opts thread timer util sconduit sensei)
+
+add_executable(conduitTest ${sources})
+target_link_libraries(conduitTest ${libs})

miniapps/conduit_test/bridge.cpp

+#include <conduit.hpp>
+#include <ConduitDataAdaptor.h>
+#include "bridge.h"
+#include <Error.h>
+#include <mpi.h>
+#include <string>
+
+#include <ConfigurableAnalysis.h>
+#include <vtkNew.h>
+#include <vtkSmartPointer.h>
+#include <vtkDataObject.h>
+#include <vtkObjectBase.h>
+#include <iostream>
+
+namespace BridgeGuts
+{
+  static vtkSmartPointer<sensei::ConduitDataAdaptor> DataAdaptor;
+  static vtkSmartPointer<sensei::ConfigurableAnalysis> AnalysisAdaptor;
+  static MPI_Comm comm;
+}
+
+void initialize(MPI_Comm comm, 
+                conduit::Node* node, 
+                const std::string& config_file)
+{
+  //setup communication
+  BridgeGuts::comm = comm;
+    
+  //data adaptor
+  BridgeGuts::DataAdaptor = vtkSmartPointer<sensei::ConduitDataAdaptor>::New();
+  BridgeGuts::DataAdaptor->Initialize(node); 
+
+  //analysis adaptor
+  BridgeGuts::AnalysisAdaptor = vtkSmartPointer<sensei::ConfigurableAnalysis>::New();
+  BridgeGuts::AnalysisAdaptor->Initialize(config_file); 
+}
+
+void analyze(conduit::Node* node)
+{
+  BridgeGuts::DataAdaptor->SetNode(node);
+  if(!BridgeGuts::AnalysisAdaptor->Execute(BridgeGuts::DataAdaptor))
+  {
+    SENSEI_ERROR("ERROR: Failed to execute analysis")
+    abort();
+  }
+    
+  BridgeGuts::DataAdaptor->ReleaseData();
+}
+
+void finalize()
+{
+  BridgeGuts::AnalysisAdaptor->Finalize();
+  BridgeGuts::AnalysisAdaptor = NULL;
+  BridgeGuts::DataAdaptor     = NULL;
+}

miniapps/conduit_test/bridge.h

+#ifndef _CONDUIT_SENSI_BRIDGE_H
+#define _CONDUIT_SENSI_BRIDGE_H
+
+#include <mpi.h>
+#include <string>
+#include <conduit.hpp>
+
+  //called before the simulation loops
+  void initialize(MPI_Comm world, 
+                  conduit::Node* node, 
+                  const std::string& config_file);
+
+  //called during simulation loop to update node
+  void analyze(conduit::Node* node); 
+
+  //called for cleanup
+  void finalize();
+
+#endif

miniapps/conduit_test/conduitTest.cpp

+#include <conduit.hpp>
+#include <cstring>
+#include <conduit_blueprint.hpp>
+#include <mpi.h>
+#include "bridge.h"
+
+int main(int argc, char* argv[])
+{
+  int rank, size;
+  MPI_Init(&argc, &argv);
+  MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+  MPI_Comm_size(MPI_COMM_WORLD, &size);
+    
+  conduit::Node res;
+  conduit::blueprint::mesh::examples::spiral( 7, res);
+  initialize(MPI_COMM_WORLD, &res, argv[1]);
+
+  analyze(&res);
+
+  finalize();
+
+  MPI_Finalize();
+    
+  return 0;
+}

sensei/CMakeLists.txt

@@ -10,6 +10,11 @@ if (ENABLE_SENSEI)
 
   set(senseiCore_libs mpi pugixml vtk thread ArrayIO timer diy grid)
 
+  if(ENABLE_CONDUIT)
+    list(APPEND senseiCore_sources ConduitDataAdaptor.cxx)
+    list(APPEND senseiCore_libs sconduit)
+  endif()
+
   if(ENABLE_CATALYST)
     list(APPEND senseiCore_sources CatalystAnalysisAdaptor.cxx
       CatalystSlice.cxx CatalystUtilities.cxx)

sensei/ConduitDataAdaptor.h

+#ifndef CONDUIT_DATAADAPTOR_H
+#define CONDUIT_DATAADAPTOR_H
+
+#include <vector>
+#include <vtkDataArray.h>
+#include <vtkSmartPointer.h>
+#include <vtkMultiBlockDataSet.h>
+#include <sensei/DataAdaptor.h>
+#include <conduit.hpp>
+
+
+namespace sensei
+{
+
+class ConduitDataAdaptor : public sensei::DataAdaptor
+{
+public:
+  static ConduitDataAdaptor* New();
+  senseiTypeMacro(ConduitDataAdaptor, sensei::DataAdaptor);
+
+  /// @brief Initialize the data adaptor.
+  ///
+  /// This initializes the data adaptor. This must be called once per simulation run.
+  /// @param node contains the current data that will be visualized. 
+  void Initialize(conduit::Node* node);
+
+  void SetNode(conduit::Node* node);
+
+  int GetMeshName(unsigned int id, std::string &meshName) override;
+  
+  int GetNumberOfMeshes(unsigned int &numMeshes) override;
+
+  int GetMesh(const std::string &meshName, 
+              bool structureOnly, 
+              vtkDataObject* &mesh) override;
+  int AddArray(vtkDataObject* mesh, 
+               const std::string &meshName, 
+               int association, 
+               const std::string& arrayname) override;
+  int GetNumberOfArrays(const std::string &meshName, 
+                        int association, 
+                        unsigned int &numberOfArrays) override;
+  int GetArrayName(const std::string &meshName, 
+                   int association, 
+                   unsigned int index,
+                   std::string &arrayName) override;
+  int ReleaseData() override;
+
+  void UpdateFields();
+
+protected:
+  ConduitDataAdaptor();
+  ~ConduitDataAdaptor();
+  typedef std::map<std::string, std::vector<std::string>> Fields;
+  Fields FieldNames;
+  int *GlobalBlockDistribution;
+
+private:
+  ConduitDataAdaptor(const ConduitDataAdaptor&)=delete; // not implemented.
+  void operator=(const ConduitDataAdaptor&)=delete; // not implemented.
+  conduit::Node* Node;
+};
+
+}
+#endif