Merge pull request #680 from streeve/deprecate_cajita

Rename Cajita -> Cabana::Grid
ECP-copa · Sep 21, 2023 · 57e3263 · 57e3263
2 parents 6fe7db5 + 7a0d777
commit 57e3263
Show file tree

Hide file tree

Showing 157 changed files with 3,186 additions and 1,742 deletions.
diff --git a/.jenkins b/.jenkins
@@ -126,7 +126,7 @@ pipeline {
                             .. && \
                             make -j8 && \
                             # Exclude current failing tests (core MPI and partial Cajita)
-                            ctest --output-on-failure -E "Cabana.*MPI|Cabana_Performance_Comm|Cajita_IndexConversion|Cajita_Halo|Cajita_ParticleGridDistributor|Cajita_Interpolation|Cajita_BovWriter|valgrind"
+                            ctest --output-on-failure -E "Cabana.*MPI|Cabana_Performance_Comm|Grid_IndexConversion|Grid_Halo|Grid_ParticleGridDistributor|Grid_Interpolation|Grid_BovWriter|valgrind"
                         '''
                     }
                     post {

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -219,7 +219,7 @@ endif()
 # enable doxygen
 find_package(Doxygen)
 if(Doxygen_FOUND)
-  doxygen_add_docs(doxygen core/src cajita/src)
+  doxygen_add_docs(doxygen core/src grid/src)
 endif()
 
 ##---------------------------------------------------------------------------##
@@ -228,12 +228,22 @@ endif()
 
 add_subdirectory(core)
 
-option(Cabana_ENABLE_CAJITA "Build Cajita (grid and particle-grid)" ${Cabana_ENABLE_MPI})
-if(Cabana_ENABLE_CAJITA)
+option(Cabana_ENABLE_GRID "Build grid and particle-grid capabilities" ${Cabana_ENABLE_MPI})
+### FIXME: remove in next release.
+option(Cabana_ENABLE_CAJITA "Build grid and particle-grid capabilities" OFF)
+option(Cabana_DISABLE_CAJITA_DEPRECATION_WARNINGS "Do not warn about Cajita deprecation." OFF)
+if (Cabana_ENABLE_CAJITA)
+  if (NOT Cabana_DISABLE_CAJITA_DEPRECATION_WARNINGS)
+    message(DEPRECATION "Option Cabana_ENABLE_CAJITA is deprecated, replaced by Cabana_ENABLE_GRID")
+  endif()
+  set(Cabana_ENABLE_GRID ON)
+endif()
+
+if(Cabana_ENABLE_GRID)
   if(MPI_FOUND)
-    add_subdirectory(cajita)
+    add_subdirectory(grid)
   else()
-    message(FATAL_ERROR "Cajita requires MPI")
+    message(FATAL_ERROR "Grid subpackage requires MPI")
   endif()
 endif()
 
@@ -267,7 +277,7 @@ install(FILES "${CMAKE_CURRENT_BINARY_DIR}/CabanaConfig.cmake" "${CMAKE_CURRENT_
 ## Clang Format
 ##---------------------------------------------------------------------------##
 if(CLANG_FORMAT_FOUND)
-  file(GLOB_RECURSE FORMAT_SOURCES core/*.cpp core/*.hpp cajita/*hpp cajita/*cpp example/*cpp example/*hpp cmake/*cpp cmake/*hpp benchmark/*cpp benchmark/*hpp)
+  file(GLOB_RECURSE FORMAT_SOURCES core/*.cpp core/*.hpp grid/*hpp grid/*cpp example/*cpp example/*hpp cmake/*cpp cmake/*hpp benchmark/*cpp benchmark/*hpp)
   add_custom_target(cabana-format
     COMMAND ${CLANG_FORMAT_EXECUTABLE} -i -style=file ${FORMAT_SOURCES}
     DEPENDS ${FORMAT_SOURCES})

diff --git a/benchmark/CMakeLists.txt b/benchmark/CMakeLists.txt
@@ -11,6 +11,6 @@
 
 add_subdirectory(core)
 
-if(Cabana_ENABLE_CAJITA)
-  add_subdirectory(cajita)
+if(Cabana_ENABLE_GRID)
+  add_subdirectory(grid)
 endif()
diff --git a/benchmark/cajita/CMakeLists.txt b/benchmark/cajita/CMakeLists.txt
diff --git a/benchmark/core/CMakeLists.txt b/benchmark/core/CMakeLists.txt
@@ -10,22 +10,22 @@
 ############################################################################
 
 add_executable(BinSortPerformance Cabana_BinSortPerformance.cpp)
-target_link_libraries(BinSortPerformance cabanacore)
+target_link_libraries(BinSortPerformance Core)
 
 add_executable(NeighborVerletPerformance Cabana_NeighborVerletPerformance.cpp)
-target_link_libraries(NeighborVerletPerformance cabanacore)
+target_link_libraries(NeighborVerletPerformance Core)
 
 if(Cabana_ENABLE_ARBORX)
 add_executable(NeighborArborXPerformance Cabana_NeighborArborXPerformance.cpp)
-target_link_libraries(NeighborArborXPerformance cabanacore)
+target_link_libraries(NeighborArborXPerformance Core)
 endif()
 
 add_executable(LinkedCellPerformance Cabana_LinkedCellPerformance.cpp)
-target_link_libraries(LinkedCellPerformance cabanacore)
+target_link_libraries(LinkedCellPerformance Core)
 
 if(Cabana_ENABLE_MPI)
 add_executable(CommPerformance Cabana_CommPerformance.cpp)
-target_link_libraries(CommPerformance cabanacore)
+target_link_libraries(CommPerformance Core)
 endif()
 
 if(Cabana_ENABLE_TESTING)

diff --git a/benchmark/grid/CMakeLists.txt b/benchmark/grid/CMakeLists.txt
@@ -0,0 +1,44 @@
+############################################################################
+# Copyright (c) 2018-2023 by the Cabana authors                            #
+# All rights reserved.                                                     #
+#                                                                          #
+# This file is part of the Cabana library. Cabana is distributed under a   #
+# BSD 3-clause license. For the licensing terms see the LICENSE file in    #
+# the top-level directory.                                                 #
+#                                                                          #
+# SPDX-License-Identifier: BSD-3-Clause                                    #
+############################################################################
+
+if(NOT Kokkos_ENABLE_SYCL) #FIXME_SYCL
+  add_executable(SparseMapPerformance Cabana_Grid_SparseMapPerformance.cpp)
+  target_link_libraries(SparseMapPerformance Grid)
+
+  add_executable(SparsePartitionerPerformance Cabana_Grid_SparsePartitionerPerformance.cpp)
+  target_link_libraries(SparsePartitionerPerformance Grid)
+endif()
+
+add_executable(HaloPerformance Cabana_Grid_HaloPerformance.cpp)
+target_link_libraries(HaloPerformance Grid)
+
+add_executable(InterpolationPerformance Cabana_Grid_InterpolationPerformance.cpp)
+target_link_libraries(InterpolationPerformance Grid)
+
+if(Cabana_ENABLE_HEFFTE)
+  add_executable(FastFourierTransformPerformance Cabana_Grid_FastFourierTransformPerformance.cpp)
+  target_link_libraries(FastFourierTransformPerformance Grid)
+endif()
+
+if(Cabana_ENABLE_TESTING)
+  if(NOT Kokkos_ENABLE_SYCL) #FIXME_SYCL
+    add_test(NAME Cabana_Grid_Performance_SparseMap COMMAND ${NONMPI_PRECOMMAND} $<TARGET_FILE:SparseMapPerformance> sparsemap_output.txt)
+    add_test(NAME Cabana_Grid_Performance_SparsePartitioner COMMAND ${NONMPI_PRECOMMAND} $<TARGET_FILE:SparsePartitionerPerformance> sparsepartitioner_output.txt)
+  endif()
+
+  add_test(NAME Cabana_Grid_Performance_Halo COMMAND ${NONMPI_PRECOMMAND} $<TARGET_FILE:HaloPerformance> halo_output.txt)
+
+  add_test(NAME Cabana_Grid_Performance_Interpolation COMMAND ${NONMPI_PRECOMMAND} $<TARGET_FILE:InterpolationPerformance> interpolation_output.txt)
+
+  if (Cabana_ENABLE_HEFFTE)
+    add_test(NAME Cabana_Grid_Performance_FastFourierTransform COMMAND ${NONMPI_PRECOMMAND} $<TARGET_FILE:FastFourierTransformPerformance> fastfouriertransform_output.txt)
+  endif()
+endif()
diff --git a/...ajita_FastFourierTransformPerformance.cpp → ..._Grid_FastFourierTransformPerformance.cpp b/...ajita_FastFourierTransformPerformance.cpp → ..._Grid_FastFourierTransformPerformance.cpp
@@ -11,7 +11,7 @@
 
 #include "../Cabana_BenchmarkUtils.hpp"
 
-#include <Cajita.hpp>
+#include <Cabana_Grid.hpp>
 
 #include <Kokkos_Core.hpp>
 #include <Kokkos_Random.hpp>
@@ -25,13 +25,13 @@
 
 #include <mpi.h>
 
-using namespace Cajita;
+using namespace Cabana::Grid;
 
 //---------------------------------------------------------------------------//
 // Performance test.
 template <class Device>
 void performanceTest( std::ostream& stream,
-                      const Cajita::DimBlockPartitioner<3> partitioner,
+                      const DimBlockPartitioner<3> partitioner,
                       std::vector<double> grid_sizes_per_dim_per_rank,
                       MPI_Comm comm, const std::string& test_prefix )
 {
@@ -172,7 +172,7 @@ int main( int argc, char* argv[] )
     MPI_Comm_size( MPI_COMM_WORLD, &comm_size );
 
     // Get partitioner
-    Cajita::DimBlockPartitioner<3> partitioner;
+    DimBlockPartitioner<3> partitioner;
     // Get ranks per dimension
     std::array<int, 3> ranks_per_dimension =
         partitioner.ranksPerDimension( MPI_COMM_WORLD, { 0, 0, 0 } );
@@ -186,7 +186,7 @@ int main( int argc, char* argv[] )
         file.open( filename + "_" + std::to_string( comm_size ),
                    std::fstream::out );
         file << "\n";
-        file << "Cajita FFT Performance Benchmark"
+        file << "Cabana::Grid FFT Performance Benchmark"
              << "\n";
         file << "----------------------------------------------"
              << "\n";

diff --git a/benchmark/cajita/Cajita_HaloPerformance.cpp → ...mark/grid/Cabana_Grid_HaloPerformance.cpp b/benchmark/cajita/Cajita_HaloPerformance.cpp → ...mark/grid/Cabana_Grid_HaloPerformance.cpp
@@ -12,7 +12,7 @@
 #include "../Cabana_BenchmarkUtils.hpp"
 
 #include <Cabana_Core.hpp>
-#include <Cajita.hpp>
+#include <Cabana_Grid.hpp>
 
 #include <Kokkos_Core.hpp>
 
@@ -26,11 +26,13 @@
 
 #include <mpi.h>
 
+using namespace Cabana::Grid;
+
 //---------------------------------------------------------------------------//
 // Performance test.
 template <class Device>
 void performanceTest( std::ostream& stream,
-                      const Cajita::DimBlockPartitioner<3> partitioner,
+                      const DimBlockPartitioner<3> partitioner,
                       std::vector<int> grid_sizes_per_dim_per_rank,
                       const std::string& test_prefix,
                       std::vector<int> halo_widths, MPI_Comm comm )
@@ -83,20 +85,19 @@ void performanceTest( std::ostream& stream,
                     grid_sizes_per_dim_per_rank[p] * ranks_per_dim[d];
             }
 
-            auto global_mesh = Cajita::createUniformGlobalMesh(
+            auto global_mesh = createUniformGlobalMesh(
                 global_low_corner, global_high_corner, grid_sizes_per_dim );
             auto global_grid = createGlobalGrid( comm, global_mesh,
                                                  is_dim_periodic, partitioner );
 
             // Create a cell array.
             auto layout =
-                createArrayLayout( global_grid, halo_width, 4, Cajita::Cell() );
-            auto array =
-                Cajita::createArray<double, device_type>( "array", layout );
+                createArrayLayout( global_grid, halo_width, 4, Cell() );
+            auto array = createArray<double, device_type>( "array", layout );
 
             // Assign the owned cells a value of 1 and ghosted 0.
-            Cajita::ArrayOp::assign( *array, 0.0, Cajita::Ghost() );
-            Cajita::ArrayOp::assign( *array, 1.0, Cajita::Own() );
+            ArrayOp::assign( *array, 0.0, Ghost() );
+            ArrayOp::assign( *array, 1.0, Own() );
 
             // create host mirror view
             auto array_view = array->view();
@@ -105,8 +106,8 @@ void performanceTest( std::ostream& stream,
             {
                 // create halo
                 halo_create_timer.start( pid );
-                auto halo = createHalo( Cajita::NodeHaloPattern<3>(),
-                                        halo_width, *array );
+                auto halo =
+                    createHalo( NodeHaloPattern<3>(), halo_width, *array );
                 halo_create_timer.stop( pid );
 
                 // gather
@@ -116,8 +117,7 @@ void performanceTest( std::ostream& stream,
 
                 // scatter
                 halo_scatter_timer.start( pid );
-                halo->scatter( exec_space(), Cajita::ScatterReduce::Sum(),
-                               *array );
+                halo->scatter( exec_space(), ScatterReduce::Sum(), *array );
                 halo_scatter_timer.stop( pid );
             }
             // Increment the problem id.
@@ -177,7 +177,7 @@ int main( int argc, char* argv[] )
     MPI_Comm_size( MPI_COMM_WORLD, &comm_size );
 
     // Get partitioner
-    Cajita::DimBlockPartitioner<3> partitioner;
+    DimBlockPartitioner<3> partitioner;
     // Get ranks per dimension
     std::array<int, 3> ranks_per_dimension =
         partitioner.ranksPerDimension( MPI_COMM_WORLD, { 0, 0, 0 } );
@@ -190,7 +190,7 @@ int main( int argc, char* argv[] )
         file.open( filename + "_" + std::to_string( comm_size ),
                    std::fstream::out );
         file << "\n";
-        file << "Cajita Halo Performance Benchmark"
+        file << "Cabana::Grid Halo Performance Benchmark"
              << "\n";
         file << "----------------------------------------------"
              << "\n";

diff --git a/...ajita/Cajita_InterpolationPerformance.cpp → .../Cabana_Grid_InterpolationPerformance.cpp b/...ajita/Cajita_InterpolationPerformance.cpp → .../Cabana_Grid_InterpolationPerformance.cpp
@@ -11,14 +11,14 @@
 
 #include "../Cabana_BenchmarkUtils.hpp"
 
-#include <Cajita.hpp>
+#include <Cabana_Grid.hpp>
 
 #include <Kokkos_Core.hpp>
 #include <Kokkos_Random.hpp>
 
 #include <mpi.h>
 
-using namespace Cajita;
+using namespace Cabana::Grid;
 
 // This is an example fused kernel version of p2g. It is not intended to be
 // physical, but only to compare performance.
@@ -201,7 +201,7 @@ void performanceTest( std::ostream& stream, const std::string& test_prefix,
     using aosoa_type = Cabana::AoSoA<member_types, memory_space>;
 
     // Define properties that do not depend on mesh size.
-    Cajita::DimBlockPartitioner<3> partitioner;
+    DimBlockPartitioner<3> partitioner;
     int halo_width = 1;
     uint64_t seed = 1938347;
 
@@ -323,7 +323,7 @@ void performanceTest( std::ostream& stream, const std::string& test_prefix,
             auto position = Cabana::slice<2>( aosoa, "position" );
             auto scalar = Cabana::slice<3>( aosoa, "scalar" );
 
-            Cajita::grid_parallel_for(
+            grid_parallel_for(
                 "particles_init", exec_space{}, *local_grid, Own(), Cell(),
                 KOKKOS_LAMBDA( const int i, const int j, const int k ) {
                     int i_own = i - owned_cells.min( Dim::I );
@@ -340,14 +340,12 @@ void performanceTest( std::ostream& stream, const std::string& test_prefix,
                     // Get the coordinates of the low cell node.
                     int low_node[3] = { i, j, k };
                     double low_coords[3];
-                    local_mesh.coordinates( Cajita::Node(), low_node,
-                                            low_coords );
+                    local_mesh.coordinates( Node(), low_node, low_coords );
 
                     // Get the coordinates of the high cell node.
                     int high_node[3] = { i + 1, j + 1, k + 1 };
                     double high_coords[3];
-                    local_mesh.coordinates( Cajita::Node(), high_node,
-                                            high_coords );
+                    local_mesh.coordinates( Node(), high_node, high_coords );
 
                     for ( int ip = 0; ip < num_ppc; ++ip )
                     {

diff --git a/...rk/cajita/Cajita_SparseMapPerformance.cpp → ...grid/Cabana_Grid_SparseMapPerformance.cpp b/...rk/cajita/Cajita_SparseMapPerformance.cpp → ...grid/Cabana_Grid_SparseMapPerformance.cpp
@@ -12,7 +12,7 @@
 #include "../Cabana_BenchmarkUtils.hpp"
 #include "Cabana_ParticleInit.hpp"
 
-#include <Cajita_SparseIndexSpace.hpp>
+#include <Cabana_Grid.hpp>
 
 #include <Kokkos_Core.hpp>
 
@@ -75,14 +75,14 @@ void performanceTest( std::ostream& stream, const std::string& test_prefix,
     {
         std::array<int, 3> global_num_cell = {
             num_cells_per_dim[c], num_cells_per_dim[c], num_cells_per_dim[c] };
-        auto global_mesh = Cajita::createSparseGlobalMesh(
+        auto global_mesh = Cabana::Grid::createSparseGlobalMesh(
             global_low_corner, global_high_corner, global_num_cell );
         float cell_size = 1.0 / num_cells_per_dim[c];
 
         // create sparse map
         int pre_alloc_size = num_cells_per_dim[c] * num_cells_per_dim[c];
-        auto sis =
-            Cajita::createSparseMap<exec_space>( global_mesh, pre_alloc_size );
+        auto sis = Cabana::Grid::createSparseMap<exec_space>( global_mesh,
+                                                              pre_alloc_size );
 
         // Create insertion timers
         std::stringstream insert_time_name;