adding Adios2 io support

CMakeLists.txt

@@ -30,6 +30,7 @@ bob_input(Kokkos_PREFIX "" PATH "Path to Kokkos install")
 bob_option(Omega_h_USE_CUDA_AWARE_MPI "Assume MPI is CUDA-aware, make use of that" OFF)
 bob_option(Omega_h_USE_SimModSuite "Enable reading Simmetrix MeshSim meshes" OFF)
 bob_option(Omega_h_USE_SimDiscrete "Enable reading and creating Simmetrix Discrete models" OFF)
+bob_option(Omega_h_USE_ADIOS2 "Enable ADIOS2" OFF)
 bob_input(Omega_h_VALGRIND "" STRING "Valgrind plus arguments for testing")
 bob_option(Omega_h_EXAMPLES "Compile examples" OFF)
 
@@ -163,6 +164,7 @@ set(Omega_h_KEY_BOOLS
     Omega_h_USE_SEACASExodus
     Omega_h_USE_SimModSuite
     Omega_h_USE_SimDiscrete
+    Omega_h_USE_ADIOS2
     Omega_h_USE_DOLFIN
     Omega_h_USE_dwarf
     Omega_h_CHECK_BOUNDS

cmake/FindADIOS2.cmake

@@ -0,0 +1,104 @@
+# - Try to find ADIOS2
+# Once done this will define
+#  ADIOS2_FOUND - System has ADIOS2
+#  ADIOS2_INCLUDE_DIR - The ADIOS2 include directories
+#  ADIOS2_LIBS - The libraries needed to use ADIOS2 
+#  ADIOS2_<library>_FOUND - System has <library>
+#  ADIOS2_MAJOR_VERSION - the leading integer of the version string
+#  ADIOS2_MINOR_VERSION - the date code from the version string
+#
+# Based on input variables:
+#  ADIOS2_LIB_DIR
+#  ADIOS2_INCLUDE_DIR
+# And environment variable:
+#  CMAKE_PREFIX_PATH
+#
+# This implementation assumes an adios2 install has the following structure
+# VERSION/
+#         include/*.h
+#         lib64/*.a
+
+macro(adios2LibCheck libs isRequired)
+  foreach(lib ${libs})
+    unset(adios2lib CACHE)
+    find_library(adios2lib "${lib}" PATHS ${ADIOS2_LIB_DIR})
+    if(adios2lib MATCHES "^adios2lib-NOTFOUND$")
+      if(${isRequired})
+	      message(FATAL_ERROR "adios2 library ${lib} not found in ${ADIOS2_LIB_DIR}")
+      else()
+	      message("adios2 library ${lib} not found in ${ADIOS2_LIB_DIR}")
+      endif()
+    else()
+	    set("ADIOS2_${lib}_FOUND" TRUE CACHE INTERNAL "ADIOS2 library present")
+      set(ADIOS2_LIBS ${ADIOS2_LIBS} ${adios2lib})
+    endif()
+  endforeach()
+endmacro(adios2LibCheck)
+
+find_path(ADIOS2_INCLUDE_DIR
+  NAMES adios2_c.h  adios2.h
+  PATHS ${ADIOS2_INCLUDE_DIR})
+if(NOT EXISTS "${ADIOS2_INCLUDE_DIR}")
+  message(FATAL_ERROR "adios2 include dir not found")
+endif()
+
+string(REGEX REPLACE
+  "/include$" ""
+  ADIOS2_INSTALL_DIR
+  "${ADIOS2_INCLUDE_DIR}")
+
+string(REGEX MATCH
+  "[0-9]+[.][0-9]+-[0-9]+"
+  ADIOS2_VERSION
+  "${ADIOS2_INCLUDE_DIR}")
+
+#VERSION_LESS and VERSION_GREATER need '.' delimited version strings.
+string(REGEX REPLACE
+  "([0-9]+[.][0-9]+)-([0-9]+)"
+  "\\1.\\2" ADIOS2_DOT_VERSION
+  "${ADIOS2_VERSION}")
+string(REGEX REPLACE
+  "([0-9]+)[.]([0-9]+)-([0-9]+)"
+  "\\1" ADIOS2_MAJOR_VERSION
+  "${ADIOS2_VERSION}")
+string(REGEX REPLACE
+  "([0-9]+)[.]([0-9]+)-([0-9]+)"
+  "\\3" ADIOS2_MINOR_VERSION
+  "${ADIOS2_VERSION}")
+
+set(MIN_VALID_ADIOS2_VERSION 2.10.0)
+set(MAX_VALID_ADIOS2_VERSION 2.10.10)
+#if( ${SKIP_ADIOS2_VERSION_CHECK} )
+#	message(STATUS "Skipping ADIOS2 version check."
+#    " This may result in undefined behavior")
+#elseif( (ADIOS2_DOT_VERSION VERSION_LESS MIN_VALID_ADIOS2_VERSION) OR
+#	(ADIOS2_DOT_VERSION VERSION_GREATER MAX_VALID_ADIOS2_VERSION) )
+#  MESSAGE(FATAL_ERROR 
+#	  "invalid ADIOS2 version: ${ADIOS2_DOT_VERSION}, \
+#    valid versions are ${MIN_VALID_ADIOS2_VERSION} to ${MAX_VALID_ADIOS2_VERSION}")
+#endif()
+message(STATUS "Building with ADIOS2 ${ADIOS2_DOT_VERSION}")
+
+set(ADIOS2_LIBS "")
+
+if (Omega_h_USE_MPI)
+set(ADIOS2_LIB_NAMES
+	adios2_core_mpi
+	adios2_cxx11_mpi
+)
+else()
+set(ADIOS2_LIB_NAMES
+   	adios2_core
+    	adios2_cxx11
+)
+endif()
+
+adios2LibCheck("${ADIOS2_LIB_NAMES}" TRUE)
+
+# handle the QUIETLY and REQUIRED arguments and set ADIOS2_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(ADIOS2 DEFAULT_MSG
+  ADIOS2_LIBS ADIOS2_INCLUDE_DIR
+)
+
+mark_as_advanced(ADIOS2_INCLUDE_DIR ADIOS2_LIBS)

src/CMakeLists.txt

@@ -171,6 +171,17 @@ if(Omega_h_USE_SimModSuite)
     "${CMAKE_CURRENT_BINARY_DIR}/Omega_h_simConfig.h")
 endif()
 
+message(STATUS "Omega_h_USE_ADIOS2: ${Omega_h_USE_ADIOS2}")
+if(Omega_h_USE_ADIOS2)
+  list(APPEND Omega_h_SOURCES Omega_h_adios2.cpp)
+  #Is there a better way? I assume CMAKE_MODULE_PATH was purposely not set in
+  # the top level CMakeLists.txt
+  set(OLD_CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH})
+  set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/")
+  find_package(ADIOS2 MODULE REQUIRED)
+  set(CMAKE_MODULE_PATH ${OLD_CMAKE_MODULE_PATH})
+endif()
+
 if(Omega_h_USE_SEACASExodus)
   set(Omega_h_SOURCES ${Omega_h_SOURCES} Omega_h_exodus.cpp)
 endif()
@@ -226,6 +237,16 @@ if(Omega_h_USE_SimModSuite)
   target_link_libraries(omega_h PUBLIC "${SIMMODSUITE_LIBS}")
 endif()
 
+if(Omega_h_USE_ADIOS2)
+  set(ADIOS_REQUIRED_VERSION 2.10)
+  if (Omega_h_USE_MPI)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DADIOS2_USE_MPI")
+    target_include_directories(omega_h PUBLIC "${ADIOS2_INCLUDE_DIR}")
+    target_link_libraries(omega_h PUBLIC "${ADIOS2_LIBS}")
+  else()
+    message("set Omega_h_USE_MPI to use ADIOS2")
+  endif()
+endif()
 
 bob_link_dependency(omega_h PUBLIC SEACASExodus)
 
@@ -629,6 +650,15 @@ if(BUILD_TESTING)
   else()
     test_func(describe_serial 1 ./describe ${CMAKE_SOURCE_DIR}/meshes/box_3d.osh)
   endif()
+
+  if (Omega_h_USE_ADIOS2)
+    osh_add_util(bp2osh)
+    osh_add_util(osh2bp)
+    osh_add_exe(adios2_io)
+    test_basefunc(adios2_io 1 ./adios2_io
+	  ${CMAKE_SOURCE_DIR}/meshes/unitbox_cutTriCube_1k.osh
+	  output.bp)
+  endif()
 endif()
 
 bob_config_header("${CMAKE_CURRENT_BINARY_DIR}/Omega_h_config.h")
@@ -744,6 +774,10 @@ else()
   list(APPEND Omega_h_HEADERS Omega_h_array_default.hpp)
 endif()
 
+if(Omega_h_USE_ADIOS2)
+  list(APPEND Omega_h_HEADERS Omega_h_adios2.hpp)
+endif()
+
 install(FILES ${Omega_h_HEADERS} DESTINATION include)
 
 if (Omega_h_USE_pybind11)