chore: Update blt, RAJA, CHAI, Caliper, adiak, conduit (#3218)

* update blt to 0.6.2

* update RAJA and CHAI to v2024.02.2

* update Caliper to 2.11.0

*update adiak to 0.4.0

* update conduit to 0.9.2

* change to new HDF import. use umpires fmt and add extra dependency to executable

* changes for change in raja interface

* move src/coreComponents/unitTests/dataRepository/testPacking.cpp to src/coreComponents/dataRepository/unitTests

* switched to syncronous packing/upacking to avoid test failures on CI image running on streak

.devcontainer/devcontainer.json

@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "273-460"
+            "GEOS_TPL_TAG": "275-480"
         }
     },
     "runArgs": [

host-configs/apple/darwin-clang.cmake

@@ -20,7 +20,7 @@ set(ENABLE_OPENMP "OFF" CACHE PATH "" FORCE)
 
 set(ENABLE_CALIPER "OFF" CACHE PATH "" FORCE )
 
-set(GEOSX_BUILD_OBJ_LIBS ON CACHE BOOL "" FORCE)
+#set(GEOSX_BUILD_OBJ_LIBS ON CACHE BOOL "" FORCE)
 
 set( BLAS_LIBRARIES /usr/local/opt/openblas/lib/libblas.dylib CACHE PATH "" FORCE )
 set( LAPACK_LIBRARIES /usr/local/opt/openblas/lib/liblapack.dylib CACHE PATH "" FORCE )

host-configs/tpls.cmake

@@ -53,7 +53,9 @@ if(EXISTS ${GEOSX_TPL_DIR}/vtk)
 endif()
 
 if(EXISTS ${GEOSX_TPL_DIR}/fmt)
-  set(FMT_DIR ${GEOSX_TPL_DIR}/fmt CACHE PATH "" FORCE)
+#  set(FMT_DIR ${GEOSX_TPL_DIR}/fmt CACHE PATH "" FORCE)
+  set(FMT_DIR ${GEOSX_TPL_DIR}/chai CACHE PATH "" FORCE)
+#  /Users/settgast1/Codes/geos/thirdPartyLibs/install-macOS_arm-release/chai/lib/cmake/fmt/fmt-targets.cmake
 endif()
 
 #

scripts/ci_build_and_test_in_container.sh

@@ -330,4 +330,4 @@ if [[ ! -z "${INTEGRATED_TEST_EXIT_STATUS+x}" ]]; then
 else
   echo "Exiting the build process with exit status 0."
   exit 0
-fi
+fi

src/CMakeLists.txt

@@ -144,16 +144,21 @@ endif()
 blt_add_executable( NAME geosx
                     SOURCES main/main.cpp
                     DEPENDS_ON ${extraComponentsLinkList}
-                               ${externalComponentsLinkList} )
+                               ${externalComponentsLinkList} fmt::fmt-header-only HDF5::HDF5 )
+
+# blt_print_target_properties(TARGET               geosx
+#                             CHILDREN             TRUE
+#                             PROPERTY_NAME_REGEX  "LINK_LIBRARIES"
+#                             )
+
+# blt_print_target_properties(TARGET               HDF5::HDF5
+#                             CHILDREN             TRUE )
 
 # Seems to be required on some CMake versions (e.g. 3.16) to get enforce device linking
 if( ${ENABLE_HYPRE_DEVICE} STREQUAL "CUDA"  )
   set_target_properties( geosx PROPERTIES CUDA_RESOLVE_DEVICE_SYMBOLS TRUE )
 endif()
 
-# Removing all transitive link dependencies from geosx_core target to circumvent
-# the BLT behavior which imposes all dependencies to be public
-#set_target_properties(geosx_core PROPERTIES INTERFACE_LINK_LIBRARIES "")
 
 target_include_directories( geosx PUBLIC ${CMAKE_SOURCE_DIR}/coreComponents )
 

src/cmake/thirdparty/SetupGeosxThirdParty.cmake

@@ -216,27 +216,16 @@ endif()
 if(DEFINED HDF5_DIR)
     message(STATUS "HDF5_DIR = ${HDF5_DIR}")
 
-    set(HDF5_ROOT ${HDF5_DIR})
-    set(HDF5_USE_STATIC_LIBRARIES FALSE)
-    set(HDF5_NO_FIND_PACKAGE_CONFIG_FILE ON)
-    include(FindHDF5)
-
-    # On some platforms (Summit) HDF5 lists /usr/include in it's list of include directories.
-    # When this happens you can get really opaque include errors.
-    list(REMOVE_ITEM HDF5_INCLUDE_DIRS /usr/include)
-
-    blt_import_library(NAME hdf5
-                       INCLUDES ${HDF5_INCLUDE_DIRS}
-                       LIBRARIES ${HDF5_LIBRARIES}
-                       TREAT_INCLUDES_AS_SYSTEM ON)
+    find_package(HDF5 REQUIRED
+                 PATHS ${HDF5_DIR}
+                 NO_DEFAULT_PATH)
 
-    file(READ "${HDF5_DIR}/include/H5public.h" header_file )
-    string(REGEX MATCH "version: *([0-9]+.[0-9]+.[0-9]+)" _ ${header_file})
-    set( HDF5_VERSION "${CMAKE_MATCH_1}" CACHE STRING "" FORCE )
     message( " ----> HDF5 version ${HDF5_VERSION}")
 
+    blt_convert_to_system_includes(TARGET HDF5::HDF5)
+
     set(ENABLE_HDF5 ON CACHE BOOL "")
-    set(thirdPartyLibs ${thirdPartyLibs} hdf5)
+    set(thirdPartyLibs ${thirdPartyLibs} HDF5::HDF5 )
 else()
     mandatory_tpl_doesnt_exist("hdf5" HDF5_DIR)
 endif()
@@ -252,7 +241,7 @@ if(DEFINED SILO_DIR AND ENABLE_SILO)
                       LIBRARY_DIRECTORIES ${SILO_DIR}/lib
                       HEADER silo.h
                       LIBRARIES siloh5
-                      DEPENDS hdf5)
+                      DEPENDS HDF5::HDF5 )
 
 
     set(ENABLE_SILO ON CACHE BOOL "")
@@ -344,7 +333,7 @@ endif()
 if(DEFINED FMT_DIR)
     message(STATUS "FMT_DIR = ${FMT_DIR}")
 
-    find_package(fmt REQUIRED
+    find_package(FMT REQUIRED
                  PATHS ${FMT_DIR}
                  NO_DEFAULT_PATH)
 
@@ -356,6 +345,7 @@ if(DEFINED FMT_DIR)
                  APPEND PROPERTY INTERFACE_SYSTEM_INCLUDE_DIRECTORIES
                  ${includeDirs})
 
+
     set(ENABLE_FMT ON CACHE BOOL "")
 
     set(thirdPartyLibs ${thirdPartyLibs} fmt::fmt-header-only )

src/coreComponents/CMakeLists.txt

@@ -73,7 +73,7 @@ if( GEOSX_BUILD_SHARED_LIBS AND GEOSX_BUILD_OBJ_LIBS )
   message( "Building shared geosx_core library with object coreComponents, executables link to geosx_core" )
   blt_add_library ( NAME geosx_core
                     SOURCES dummy.cpp
-                    DEPENDS_ON  mainInterface physicsSolvers
+                    DEPENDS_ON  mainInterface physicsSolvers HDF5::HDF5
                     SHARED TRUE )
 
 elseif( GEOSX_BUILD_SHARED_LIBS AND NOT GEOSX_BUILD_OBJ_LIBS )

src/coreComponents/common/GEOS_RAJA_Interface.hpp

@@ -170,8 +170,8 @@ struct PolicyMap< RAJA::omp_parallel_for_exec >
 #endif
 
 #if defined(GEOS_USE_CUDA)
-template< typename X, typename Y, size_t BLOCK_SIZE, bool ASYNC >
-struct PolicyMap< RAJA::policy::cuda::cuda_exec_explicit< X, Y, BLOCK_SIZE, ASYNC > >
+template< typename X, typename Y, typename C, size_t BLOCK_SIZE, bool ASYNC >
+struct PolicyMap< RAJA::policy::cuda::cuda_exec_explicit< X, Y, C, BLOCK_SIZE, ASYNC > >
 {
   using atomic = RAJA::cuda_atomic;
   using reduce = RAJA::cuda_reduce;

src/coreComponents/common/unitTests/CMakeLists.txt

@@ -11,7 +11,7 @@ if ( ENABLE_CALIPER )
         testCaliperSmoke.cpp )
 endif()
 
-set( dependencyList ${parallelDeps} common hdf5 gtest )
+set( dependencyList ${parallelDeps} common HDF5::HDF5 gtest )
 
 # Add gtest C++ based tests
 foreach(test ${gtest_geosx_tests})

src/coreComponents/common/unitTests/testLifoStorage.cpp

@@ -58,8 +58,8 @@ struct RAJAHelper< parallelHostPolicy >
 template< unsigned long THREADS_PER_BLOCK >
 using devicePolicy = RAJA::cuda_exec< THREADS_PER_BLOCK >;
 
-template< typename X, typename Y, size_t BLOCK_SIZE, bool ASYNC >
-struct RAJAHelper< RAJA::policy::cuda::cuda_exec_explicit< X, Y, BLOCK_SIZE, ASYNC > >
+template< typename X, typename Y, typename C, size_t BLOCK_SIZE, bool ASYNC >
+struct RAJAHelper< RAJA::policy::cuda::cuda_exec_explicit< X, Y, C, BLOCK_SIZE, ASYNC > >
 {
   using ReducePolicy = RAJA::cuda_reduce;
   using AtomicPolicy = RAJA::cuda_atomic;

src/coreComponents/dataRepository/BufferOpsDevice.cpp

@@ -87,15 +87,16 @@ template< bool DO_PACKING, typename T, int NDIM, int USD >
 typename std::enable_if< can_memcpy< T >, localIndex >::type
 PackDataDevice( buffer_unit_type * & buffer,
                 ArrayView< T const, NDIM, USD > const & var,
-                parallelDeviceEvents & events )
+                parallelDeviceEvents & GEOS_UNUSED_PARAM( events ) )
 {
   if( DO_PACKING )
   {
-    parallelDeviceStream stream;
-    events.emplace_back( forAll< parallelDeviceAsyncPolicy<> >( stream, var.size(), [=] GEOS_DEVICE ( localIndex ii )
+//    parallelDeviceStream stream;
+//    events.emplace_back( forAll< parallelDeviceAsyncPolicy<> >( stream, var.size(), [=] GEOS_DEVICE ( localIndex ii )
+    forAll< parallelDevicePolicy<> >( var.size(), [=] GEOS_DEVICE ( localIndex ii )
     {
       reinterpret_cast< std::remove_const_t< T > * >( buffer )[ ii ] = var.data()[ ii ];
-    } ) );
+    } );
   }
   localIndex packedSize = var.size() * sizeof(T);
   if( DO_PACKING )
@@ -121,13 +122,14 @@ template< typename T, int NDIM, int USD >
 typename std::enable_if< can_memcpy< T >, localIndex >::type
 UnpackDataDevice( buffer_unit_type const * & buffer,
                   ArrayView< T, NDIM, USD > const & var,
-                  parallelDeviceEvents & events )
+                  parallelDeviceEvents & GEOS_UNUSED_PARAM( events ) )
 {
-  parallelDeviceStream stream;
-  events.emplace_back( forAll< parallelDeviceAsyncPolicy<> >( stream, var.size(), [=] GEOS_DEVICE ( localIndex ii )
+  // parallelDeviceStream stream;
+  // events.emplace_back( forAll< parallelDeviceAsyncPolicy<> >( stream, var.size(), [=] GEOS_DEVICE ( localIndex ii )
+  forAll< parallelDevicePolicy<> >( var.size(), [=] GEOS_DEVICE ( localIndex ii )
   {
     var.data()[ ii ] = reinterpret_cast< const T * >( buffer )[ ii ];
-  } ) );
+  } );
   localIndex packedSize = var.size() * sizeof(T);
   buffer += var.size() * sizeof(T);
   return packedSize;

src/coreComponents/dataRepository/unitTests/CMakeLists.txt

@@ -1,6 +1,7 @@
 # Specify list of tests
 set( dataRepository_tests
      testDefaultValue.cpp
+     testPacking.cpp
      testWrapper.cpp
      testXmlWrapper.cpp
      testBufferOps.cpp )

src/coreComponents/unitTests/dataRepositoryTests/testPacking.cpp → src/coreComponents/dataRepository/unitTests/testPacking.cpp

@@ -17,13 +17,11 @@
 #include "LvArray/src/Array.hpp"
 #include "dataRepository/BufferOps.hpp"
 #include "dataRepository/BufferOpsDevice.hpp"
-#include "mainInterface/initialization.hpp"
-#include "mesh/mpiCommunications/CommunicationTools.hpp"
-
 #include "dataRepository/wrapperHelpers.hpp"
 
 #include <ctime>
 #include <cstdlib>
+#include <unistd.h>
 
 using namespace geos;
 
@@ -116,6 +114,32 @@ TEST( testPacking, testTensorPacking )
     EXPECT_TRUE( tns[0][ii] = unp[0][ii] );
 }
 
+// void printArray( arrayView1d< R1Tensor const > const & arr,
+//                  arrayView1d< R1Tensor const > const & unpackArray )
+// {
+//   printf( "arr.size() = %d\n", arr.size() );
+//   printf( "unpackArray.size() = %d\n", unpackArray.size() );
+
+//   for( localIndex ii = 0; ii < unpackArray.size(); ++ii )
+//   {
+//     if( !( arr[ii] == unpackArray[ii] ) )
+//     {
+//       printf( "arr[%d]         = ( %f, %f, %f )\n", ii, arr[ii][0], arr[ii][1], arr[ii][2] );
+//       printf( "unPackarray[%d] = ( %f, %f, %f ) : ", ii, unpackArray[ii][0], unpackArray[ii][1], unpackArray[ii][2] );
+
+//       forAll< geos::parallelDevicePolicy<1> >( 1, [=] GEOS_DEVICE ( localIndex )
+//       {
+//         printf( "( %f, %f, %f ) : ", unpackArray[ii][0], unpackArray[ii][1], unpackArray[ii][2] );
+//       } );
+
+//       forAll< serialPolicy >( 1, [=]( localIndex )
+//       {
+//         printf( "( %f, %f, %f )\n", unpackArray[ii][0], unpackArray[ii][1], unpackArray[ii][2] );
+//       } );
+//       }
+//   }
+// }
+
 TEST( testPacking, testPackingDevice )
 {
   std::srand( std::time( nullptr ));
@@ -134,15 +158,32 @@ TEST( testPacking, testPackingDevice )
   buffer_type buf( calc_size );
   buffer_unit_type * buffer = &buf[0];
   bufferOps::PackDevice< true >( buffer, veloc.toViewConst(), packEvents );
-  waitAllDeviceEvents( packEvents );
+  // waitAllDeviceEvents( packEvents );
+
+  // R1Tensor const * const castedBuffer = reinterpret_cast< R1Tensor const * >( &buf[16] );
+  // for( localIndex ii = 0; ii < size; ++ii )
+  // {
+  //   printf( " %d = ( %f, %f, %f ) != ( %f, %f, %f )\n", ii, veloc[ii][0], veloc[ii][1], veloc[ii][2], castedBuffer[ii][0],
+  // castedBuffer[ii][1], castedBuffer[ii][2] );
+  // }
 
   buffer_unit_type const * cbuffer = &buf[0];
   parallelDeviceEvents unpackEvents;
   bufferOps::UnpackDevice( cbuffer, unpacked.toView(), unpackEvents );
   waitAllDeviceEvents( unpackEvents );
   unpacked.move( hostMemorySpace );
+
+//  printArray( veloc, unpacked.toViewConst() );
+
   for( localIndex ii = 0; ii < size; ++ii )
+  {
     EXPECT_EQ( veloc[ii], unpacked[ii] );
+//    if( !(veloc[ii] == unpacked[ii]) )
+//    {
+//      printf( " veloc[%d]    = ( %f, %f, %f )\n", ii, veloc[ii][0], veloc[ii][1], veloc[ii][2] );
+//      printf( " unpacked[%d] = ( %f, %f, %f )\n", ii, unpacked[ii][0], unpacked[ii][1], unpacked[ii][2] );
+//    }
+  }
 }
 
 TEST( testPacking, testPackingDeviceHelper )
@@ -221,8 +262,6 @@ TEST( testPacking, testPackByIndexDevice )
 int main( int ac, char * av[] )
 {
   ::testing::InitGoogleTest( &ac, av );
-  geos::basicSetup( ac, av );
   int const result = RUN_ALL_TESTS();
-  geos::basicCleanup();
   return result;
 }

src/coreComponents/fileIO/CMakeLists.txt

@@ -34,7 +34,7 @@ set( fileIO_sources
      timeHistory/PackCollection.cpp
      timeHistory/HDFHistoryIO.cpp )
 
-set( dependencyList ${parallelDeps} mesh constitutive hdf5 )
+set( dependencyList ${parallelDeps} mesh constitutive HDF5::HDF5 )
 if( ENABLE_PYGEOSX )
   list( APPEND fileIO_headers
         python/PyHistoryCollectionType.hpp
@@ -50,13 +50,13 @@ endif()
 
 if( ENABLE_MPI )
   add_subdirectory( coupling/hdf5_interface )
-  list( APPEND dependencyList mpi hdf5_interface )
+  list( APPEND dependencyList mpi hdf5_interface HDF5::HDF5 )
   list( APPEND fileIO_headers coupling/ChomboCoupler.hpp Outputs/ChomboIO.hpp )
   list( APPEND fileIO_sources coupling/ChomboCoupler.cpp Outputs/ChomboIO.cpp )
 endif()
 
 if( ENABLE_SILO )
-  list( APPEND dependencyList silo )
+  list( APPEND dependencyList silo HDF5::HDF5)
   list( APPEND fileIO_headers 
                silo/SiloFile.hpp 
                Outputs/SiloOutput.hpp )

src/coreComponents/unitTests/constitutiveTests/CMakeLists.txt

@@ -35,9 +35,9 @@ set( gtest_reactivefluid_xmls
 set( dependencyList ${parallelDeps} gtest )
 
 if ( GEOSX_BUILD_SHARED_LIBS )
-  list( APPEND dependencyList geosx_core )
+  list( APPEND dependencyList geosx_core HDF5::HDF5 )
 else()
-  list( APPEND dependencyList ${geosx_core_libs} )
+  list( APPEND dependencyList ${geosx_core_libs} HDF5::HDF5 )
 endif()
 
 if( ENABLE_PVTPackage )

src/coreComponents/unitTests/dataRepositoryTests/CMakeLists.txt

@@ -3,16 +3,15 @@ set( dataRepository_tests
      testObjectCatalog.cpp
      testRestartBasic.cpp
      testRestartExtended.cpp
-     testPacking.cpp
      testWrapperHelpers.cpp
      testGroupPath.cpp )
 
 set( dependencyList ${parallelDeps} gtest )
 
 if ( GEOSX_BUILD_SHARED_LIBS )
-  list( APPEND dependencyList geosx_core )
+  list( APPEND dependencyList geosx_core HDF5::HDF5 )
 else()
-  list( APPEND dependencyList ${geosx_core_libs} )
+  list( APPEND dependencyList ${geosx_core_libs} HDF5::HDF5 )
 endif()
 
 if (TARGET pugixml::pugixml)