diff --git a/CMakeLists.txt b/CMakeLists.txt
index 89463224a89678ee16c84af00e469d88ec185054..0fbada3757ab7ac6375e1d974a64216b3e499a41 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -72,6 +72,7 @@ if(ADIOS_USE_MPI)
endif()
option(ADIOS_USE_BZip2 "Enable support for BZip2 transforms" OFF)
option(ADIOS_USE_ADIOS1 "Enable support for the ADIOS 1 engine" OFF)
+option(ADIOS_USE_HDF5 "Enable support for the HDF5 engine" OFF)
# DataMan is not a user-settable option. It will always be enabled if the
# platform supports it.
@@ -137,5 +138,5 @@ message(" MPI: ${ADIOS_USE_MPI}")
message(" BZip2: ${ADIOS_USE_BZip2}")
message(" ADIOS1: ${ADIOS_USE_ADIOS1}")
message(" DataMan: ${ADIOS_USE_DataMan}")
-message(" HDF5: ${ADIOS_USE_PHDF5}")
+message(" HDF5: ${ADIOS_USE_HDF5}")
message("")
diff --git a/cmake/FindADIOS1.cmake b/cmake/FindADIOS1.cmake
index 867539a498b8790715137ff3e2d7725fe493b1c7..c40191677ef30d9995f8777c4a4161e64678130d 100644
--- a/cmake/FindADIOS1.cmake
+++ b/cmake/FindADIOS1.cmake
@@ -83,159 +83,105 @@
###############################################################################
-###############################################################################
-# Required cmake version
-###############################################################################
-
-cmake_minimum_required(VERSION 2.8.5)
-
-
###############################################################################
# ADIOS
###############################################################################
# get flags for adios_config, -l is the default
#-f for fortran, -r for readonly, -s for sequential (nompi)
-set(OPTLIST "-l")
if(ADIOS1_FIND_COMPONENTS)
- foreach(COMP ${ADIOS1_FIND_COMPONENTS})
- string(TOLOWER ${COMP} comp)
- if(comp STREQUAL "fortran")
- set(OPTLIST "${OPTLIST}f")
- elseif(comp STREQUAL "readonly")
- set(OPTLIST "${OPTLIST}r")
- elseif(comp STREQUAL "sequential")
- set(OPTLIST "${OPTLIST}s")
- else()
- message("ADIOS 1.x component ${COMP} is not supported. Please use fortran, readonly, or sequential")
- endif()
- endforeach()
+ foreach(comp IN LISTS ADIOS1_FIND_COMPONENTS)
+ string(TOLOWER "${comp}" comp)
+ if(comp STREQUAL "fortran")
+ set(adios1_config_opt "-f")
+ elseif(comp STREQUAL "readonly")
+ set(adios1_config_opt "-r")
+ elseif(comp STREQUAL "sequential")
+ set(adios1_config_opt "-s")
+ else()
+ message("ADIOS 1.x component ${comp} is not supported. Please use fortran, readonly, or sequential")
+ endif()
+ endforeach()
endif()
-# we start by assuming we found ADIOS and falsify it if some
-# dependencies are missing (or if we did not find ADIOS at all)
-set(ADIOS1_FOUND TRUE)
-
+set(adios1_config_hints)
+foreach(PREFIX_VAR IN ITEMS ADIOS1_ROOT ADIOS1_DIR INSTALL_PREFIX)
+ if(${PREFIX_VAR})
+ list(APPEND adios1_config_hints "${${PREFIX_VAR}}/bin")
+ elseif("$ENV{${PREFIX_VAR}}")
+ list(APPEND adios1_config_hints "$ENV{${PREFIX_VAR}}/bin")
+ endif()
+endforeach()
# find `adios_config` program #################################################
-# check the ADIOS1_ROOT and ADIOS1_DIR hint and the normal PATH
-find_file(ADIOS1_CONFIG
- NAME adios_config
- PATHS $ENV{ADIOS1_ROOT}/bin $ENV{ADIOS1_DIR}/bin $ENV{INSTALL_PREFIX}/bin $ENV{PATH})
-
-if(ADIOS1_CONFIG)
- message(STATUS "Found 'adios_config': ${ADIOS1_CONFIG}")
-else(ADIOS1_CONFIG)
- set(ADIOS1_FOUND FALSE)
- message(STATUS "Can NOT find 'adios_config' - set ADIOS1_ROOT, ADIOS1_DIR or INSTALL_PREFIX, or check your PATH")
-endif(ADIOS1_CONFIG)
+find_program(ADIOS1_CONFIG NAME adios_config HINTS ${adios1_config_hints})
# check `adios_config` program ################################################
-if(ADIOS1_FOUND)
- execute_process(COMMAND ${ADIOS1_CONFIG} ${OPTLIST}
- OUTPUT_VARIABLE ADIOS1_LINKFLAGS
- RESULT_VARIABLE ADIOS1_CONFIG_RETURN
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- if(NOT ADIOS1_CONFIG_RETURN EQUAL 0)
- set(ADIOS1_FOUND FALSE)
- message(STATUS "Can NOT execute 'adios_config' - check file permissions")
- endif()
-
- # find ADIOS1_ROOT_DIR
- execute_process(COMMAND ${ADIOS1_CONFIG} -d
- OUTPUT_VARIABLE ADIOS1_ROOT_DIR
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- if(NOT IS_DIRECTORY "${ADIOS1_ROOT_DIR}")
- set(ADIOS1_FOUND FALSE)
- message(STATUS "The directory provided by 'adios_config -d' does not exist: ${ADIOS1_ROOT_DIR}")
- endif()
-endif(ADIOS1_FOUND)
-
-# option: use only static libs ################################################
-if(ADIOS1_USE_STATIC_LIBS)
- # carfully: we have to restore the original path in the end
- set(_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES})
- set(CMAKE_FIND_LIBRARY_SUFFIXES .a)
-endif()
-
-
-# we found something in ADIOS1_ROOT_DIR and adios_config works #################
-if(ADIOS1_FOUND)
- # ADIOS headers
- find_path(ADIOS1_INCLUDE_DIRS adios.h
- HINTS ${ADIOS1_ROOT_DIR}/include
- NO_DEFAULT_PATHS
- )
-
- # check for compiled in dependencies, recomve ";" in ADIOS1_LINKFLAGS (from cmake build)
- string(REGEX REPLACE ";" " " ADIOS1_LINKFLAGS "${ADIOS1_LINKFLAGS}")
- message(STATUS " ADIOS1 linker flags (unparsed): ${ADIOS1_LINKFLAGS}")
-
- # find all library paths -L
- # note: this can cause trouble if some libs are specified twice from
- # different sources (quite unlikely)
- # http://www.cmake.org/pipermail/cmake/2008-November/025128.html
- set(ADIOS1_LIBRARY_DIRS "")
- string(REGEX MATCHALL " -L([A-Za-z_0-9/\\.-]+)" _ADIOS1_LIBDIRS " ${ADIOS1_LINKFLAGS}")
- foreach(_LIBDIR ${_ADIOS1_LIBDIRS})
- string(REPLACE " -L" "" _LIBDIR ${_LIBDIR})
- list(APPEND ADIOS1_LIBRARY_DIRS ${_LIBDIR})
+if(ADIOS1_CONFIG)
+ execute_process(COMMAND ${ADIOS1_CONFIG} ${adios1_config_opt}
+ OUTPUT_VARIABLE adios1_config_out
+ RESULT_VARIABLE adios1_config_ret
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ )
+ if(adios1_config_ret EQUAL 0)
+ string(REGEX MATCH "CFLAGS=([^\n]*)" adios1_match "${adios1_config_out}")
+ string(REPLACE " " ";" adios1_match "${CMAKE_MATCH_1}")
+ set(adios1_include_hints)
+ set(ADIOS1_COMPILE_OPTIONS)
+ foreach(OPT IN LISTS adios1_match)
+ if(OPT MATCHES "^-I(.*)")
+ list(APPEND adios1_include_hints "${CMAKE_MATCH_1}")
+ else()
+ list(APPEND ADIOS1_COMPILE_OPTIONS ${OPT})
+ endif()
endforeach()
- # we could append ${CMAKE_PREFIX_PATH} now but that is not really necessary
-
- #message(STATUS "ADIOS1 DIRS to look for libs: ${ADIOS1_LIBRARY_DIRS}")
-
- # parse all -lname libraries and find an absolute path for them
- string(REGEX MATCHALL " -l([A-Za-z_0-9\\.-]+)" _ADIOS1_LIBS " ${ADIOS1_LINKFLAGS}")
- foreach(_LIB ${_ADIOS1_LIBS})
- string(REPLACE " -l" "" _LIB ${_LIB})
-
- # find static lib: absolute path in -L then default
- find_library(_LIB_DIR NAMES ${_LIB} PATHS ${ADIOS1_LIBRARY_DIRS} CMAKE_FIND_ROOT_PATH_BOTH)
-
- # found?
- if(_LIB_DIR)
- if(_LIB STREQUAL "adios")
- message(STATUS " Found the main adios library in ${_LIB_DIR}")
- set(ADIOS1_LIBRARY_PATH "${_LIB_DIR}")
- #message(STATUS " ADIOS1_LIBRARY_PATH set to ${ADIOS1_LIBRARY_PATH}")
- else()
- message(STATUS " Found ${_LIB} in ${_LIB_DIR}")
- list(APPEND ADIOS1_DEPENDENCY_LIBRARIES "${_LIB_DIR}")
- endif()
- else(_LIB_DIR)
- set(ADIOS1_FOUND FALSE)
- message(STATUS "ADIOS1: Could NOT find library '${_LIB}'")
- endif(_LIB_DIR)
-
- # clean cached var
- unset(_LIB_DIR CACHE)
- unset(_LIB_DIR)
+ string(REGEX MATCH "LDFLAGS=([^\n]*)" adios1_match "${adios1_config_out}")
+ string(REPLACE " " ";" adios1_match "${CMAKE_MATCH_1}")
+ set(adios1_libs)
+ set(adios1_lib_hints)
+ set(adios1_lib_flags)
+ foreach(OPT IN LISTS adios1_match)
+ if(OPT MATCHES "^-L(.*)")
+ list(APPEND adios1_lib_hints "${CMAKE_MATCH_1}")
+ elseif(OPT MATCHES "^-l(.*)")
+ list(APPEND adios1_libs "${CMAKE_MATCH_1}")
+ else()
+ list(APPEND adios1_lib_flags "${OPT}")
+ endif()
endforeach()
+ endif()
- #add libraries which are already using cmake format
- string(REGEX MATCHALL "/([A-Za-z_0-9/\\.-]+)\\.([a|so]+)" _ADIOS1_LIBS_SUB "${ADIOS1_LINKFLAGS}")
- list(APPEND ADIOS1_DEPENDENCY_LIBRARIES "${_ADIOS1_LIBS_SUB}")
-
- # add the version string
- execute_process(COMMAND ${ADIOS1_CONFIG} -v
- OUTPUT_VARIABLE ADIOS1_VERSION
- OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-endif(ADIOS1_FOUND)
-
-# unset checked variables if not found
-if(NOT ADIOS1_FOUND)
- unset(ADIOS1_INCLUDE_DIRS)
- unset(ADIOS1_DEPENDENCY_LIBRARIES)
- unset(ADIOS1_LIBRARY_PATH)
-endif(NOT ADIOS1_FOUND)
-
+ # add the version string
+ execute_process(COMMAND ${ADIOS1_CONFIG} -v
+ OUTPUT_VARIABLE ADIOS1_VERSION
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ )
+endif()
-# restore CMAKE_FIND_LIBRARY_SUFFIXES if manipulated by this module ###########
-if(ADIOS1_USE_STATIC_LIBS)
- set(CMAKE_FIND_LIBRARY_SUFFIXES ${_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+# make suree at the very least we find libadios
+if(NOT adios1_libs)
+ set(adios1_libs adios)
endif()
+# Search for the actual libs and headers to ue based on hints from the config
+find_path(ADIOS1_INCLUDE_DIR adios.h HINTS ${adios1_include_hints})
+
+set(ADIOS1_LIBRARY)
+set(ADIOS1_DEPENDENCIES)
+foreach(lib IN LISTS adios1_libs)
+ find_library(ADIOS1_${lib}_LIBRARY NAME ${lib} HINTS ${adios1_lib_hints})
+ if(ADIOS1_${lib}_LIBRARY)
+ if(lib MATCHES "^adios")
+ set(ADIOS1_LIBRARY ${ADIOS1_${lib}_LIBRARY})
+ else()
+ list(APPEND ADIOS1_DEPENDENCIES ${ADIOS1_${lib}_LIBRARY})
+ endif()
+ else()
+ list(APPEND ADIOS1_DEPENDENCIES ${lib})
+ endif()
+endforeach()
+
+find_package(Threads REQUIRED)
+list(APPEND ADIOS1_DEPENDENCIES ${adios1_lib_flags} ${CMAKE_THREAD_LIBS_INIT})
###############################################################################
# FindPackage Options
@@ -244,20 +190,24 @@ endif()
# handles the REQUIRED, QUIET and version-related arguments for find_package
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(ADIOS1
- REQUIRED_VARS ADIOS1_LIBRARY_PATH ADIOS1_DEPENDENCY_LIBRARIES ADIOS1_INCLUDE_DIRS
- VERSION_VAR ADIOS1_VERSION
+ REQUIRED_VARS ADIOS1_LIBRARY ADIOS1_INCLUDE_DIR
+ VERSION_VAR ADIOS1_VERSION
)
-##########################################################################
-# Add target and dependencies to ADIOS2
-##########################################################################
-#message(STATUS "ADIOS1 Find ended with ${ADIOS1_FOUND}")
- if(ADIOS1_FOUND AND NOT TARGET adios1::adios)
- message(STATUS "Add library ADIOS1 to the build")
- add_library(adios1::adios UNKNOWN IMPORTED)
- set_target_properties(adios1::adios PROPERTIES
- IMPORTED_LOCATION "${ADIOS1_LIBRARY_PATH}"
- INTERFACE_LINK_LIBRARIES "${ADIOS1_DEPENDENCY_LIBRARIES}"
- INTERFACE_INCLUDE_DIRECTORIES "${ADIOS1_INCLUDE_DIRS}"
- )
- endif()
+if(ADIOS1_FOUND)
+ set(ADIOS1_INCLUDE_DIRS ${ADIOS1_INCLUDE_DIR})
+ set(ADIOS1_LIBRARIES ${ADIOS1_LIBRARY} ${ADIOS1_DEPENDENCIES})
+
+ ##########################################################################
+ # Add target and dependencies to ADIOS2
+ ##########################################################################
+ if(NOT TARGET adios1::adios)
+ add_library(adios1::adios UNKNOWN IMPORTED)
+ set_target_properties(adios1::adios PROPERTIES
+ IMPORTED_LOCATION "${ADIOS1_LIBRARY}"
+ INTERFACE_LINK_LIBRARIES "${ADIOS1_DEPENDENCIES}"
+ INTERFACE_INCLUDE_DIRECTORIES "${ADIOS1_INCLUDE_DIRS}"
+ INTERFACE_COMPILE_OPTIONS "${ADIOS1_COMPILE_OPTIONS}"
+ )
+ endif()
+endif()
diff --git a/examples/heatTransfer/read/CMakeLists.txt b/examples/heatTransfer/read/CMakeLists.txt
index 8c2486bb7397a00cc4638dfa06ca00c9392ee8c9..7f3e9c4589874abe0d85fc6b7a065ad2fbc7ed4e 100644
--- a/examples/heatTransfer/read/CMakeLists.txt
+++ b/examples/heatTransfer/read/CMakeLists.txt
@@ -15,13 +15,6 @@ if(ADIOS_USE_MPI)
target_link_libraries(heatTransfer_read_adios1
adios1::adios ${MPI_C_LIBRARIES}
)
-
- if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::heatTransfer::read::adios1
- COMMAND heatRead_adios1
- )
- endif()
endif()
endif()
diff --git a/examples/heatTransfer/write/CMakeLists.txt b/examples/heatTransfer/write/CMakeLists.txt
index eb72a2af9bd234c09be42c8b00a69ffbca7114e4..fb0b9f029cec18bc8b2e020d518254f37965f036 100644
--- a/examples/heatTransfer/write/CMakeLists.txt
+++ b/examples/heatTransfer/write/CMakeLists.txt
@@ -17,13 +17,6 @@ if(ADIOS_USE_MPI)
)
target_link_libraries(heatTransfer_write_adios2 adios2 ${MPI_C_LIBRARIES})
- if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::heatTransfer::write::adios2
- COMMAND heatTransfer_write_adios2
- )
- endif()
-
if(ADIOS_USE_ADIOS1)
find_package(ADIOS1 REQUIRED)
find_package(MPI COMPONENTS C REQUIRED)
@@ -40,12 +33,5 @@ if(ADIOS_USE_MPI)
target_link_libraries(heatTransfer_write_adios1
adios1::adios ${MPI_C_LIBRARIES}
)
-
- if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::heatTransfer::write::adios1
- COMMAND heatTransfer_write_adios1
- )
- endif()
endif()
endif()
diff --git a/examples/heatTransfer/write/main.cpp b/examples/heatTransfer/write/main.cpp
index ff1b6c44c9a5e0cbf836f60b475c3190d7e34e8f..657348f1d77654f6792a57c1ea0bbc0da14c8662 100644
--- a/examples/heatTransfer/write/main.cpp
+++ b/examples/heatTransfer/write/main.cpp
@@ -10,9 +10,7 @@
* Author: Norbert Podhorszki
*
*/
-#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
-#undef OMPI_SKIP_MPICXX
#include <iostream>
#include <memory>
diff --git a/examples/hello/CMakeLists.txt b/examples/hello/CMakeLists.txt
index 73fa0f560c36f0c1c0f1744cb44a90f7f7df6ba2..6719c2042ff03407a28f5e4e27c7402a2463c5d2 100644
--- a/examples/hello/CMakeLists.txt
+++ b/examples/hello/CMakeLists.txt
@@ -15,6 +15,6 @@ if(ADIOS_USE_DataMan)
add_subdirectory(datamanWriter)
endif()
-if(ADIOS_USE_PHDF5)
+if(ADIOS_USE_HDF5)
add_subdirectory(hdf5Writer)
endif()
diff --git a/examples/hello/adios1Writer/CMakeLists.txt b/examples/hello/adios1Writer/CMakeLists.txt
index b38cfb90d3a153197efaa99f88295187debcfc1b..3f7a4f8a90684c40b3e823c50bd8d75f155ec683 100644
--- a/examples/hello/adios1Writer/CMakeLists.txt
+++ b/examples/hello/adios1Writer/CMakeLists.txt
@@ -5,10 +5,16 @@
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
+
add_executable(hello_adios1Writer helloADIOS1Writer.cpp)
target_include_directories(hello_adios1Writer PRIVATE ${MPI_C_INCLUDE_PATH})
- target_link_libraries(hello_adios1Writer adios2 ${MPI_C_LIBRARIES})
+ target_link_libraries(hello_adios1Writer ${MPI_C_LIBRARIES})
+else()
+ add_executable(hello_adios1Writer helloADIOS1Writer_nompi.cpp)
+endif()
+target_link_libraries(hello_adios1Writer adios2)
+
+if(ADIOS_BUILD_TESTING)
+ add_test( NAME Example::hello::adios1::write COMMAND hello_adios1Writer)
endif()
-add_executable(hello_adios1Writer_nompi helloADIOS1Writer_nompi.cpp)
-target_link_libraries(hello_adios1Writer_nompi adios2)
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer.cpp b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
index fc6064b27b8fa5ee50be1a86f9c1b001a3227684..e2dd0bf435869c412bc5622f5d43d8357d4bb0b2 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
@@ -11,9 +11,7 @@
#include <iostream>
#include <vector>
-#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
-#undef OMPI_SKIP_MPICXX
#include "ADIOS_CPP.h"
diff --git a/examples/hello/bpWriter/CMakeLists.txt b/examples/hello/bpWriter/CMakeLists.txt
index d208c353979cc633ec57c741583831d27be03081..15de114c3a56e5bf8604b90f7f80232696516823 100644
--- a/examples/hello/bpWriter/CMakeLists.txt
+++ b/examples/hello/bpWriter/CMakeLists.txt
@@ -3,21 +3,17 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_bpWriter_nompi helloBPWriter_nompi.cpp)
-target_link_libraries(hello_bpWriter_nompi adios2_nompi)
-
-if(ADIOS_BUILD_TESTING)
- add_test( NAME Example::hello::bpWriter_nompi COMMAND hello_bpWriter_nompi)
-endif()
-
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
+
add_executable(hello_bpWriter helloBPWriter.cpp)
target_include_directories(hello_bpWriter PRIVATE ${MPI_C_INCLUDE_PATH})
- target_link_libraries(hello_bpWriter adios2 ${MPI_C_LIBRARIES})
-
- if(ADIOS_BUILD_TESTING)
- add_test( NAME Example::hello::bpWriter COMMAND hello_bpWriter)
- endif()
+ target_link_libraries(hello_bpWriter ${MPI_C_LIBRARIES})
+else()
+ add_executable(hello_bpWriter helloBPWriter_nompi.cpp)
endif()
+target_link_libraries(hello_bpWriter adios2)
+if(ADIOS_BUILD_TESTING)
+ add_test( NAME Example::hello::bp::write COMMAND hello_bpWriter)
+endif()
diff --git a/examples/hello/datamanReader/CMakeLists.txt b/examples/hello/datamanReader/CMakeLists.txt
index 34db8ffb63b807a029daa91ad67f80614170c736..41f3cb588c9c2ccd58eae67a8c21ee71ae4089d7 100644
--- a/examples/hello/datamanReader/CMakeLists.txt
+++ b/examples/hello/datamanReader/CMakeLists.txt
@@ -3,26 +3,17 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_datamanReader_nompi helloDataManReader_nompi.cpp)
-target_link_libraries(hello_datamanReader_nompi adios2_nompi)
-
-if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::hello::datamanReader_nompi
- COMMAND hello_datamanReader_nompi
- )
-endif()
-
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
add_executable(hello_datamanReader helloDataManReader.cpp)
- target_link_libraries(hello_datamanReader adios2)
target_include_directories(hello_datamanReader PRIVATE ${MPI_C_INCLUDE_PATH})
- target_link_libraries(hello_datamanReader adios2 ${MPI_C_LIBRARIES})
+ target_link_libraries(hello_datamanReader ${MPI_C_LIBRARIES})
+else()
+ add_executable(hello_datamanReader helloDataManReader_nompi.cpp)
+endif()
+target_link_libraries(hello_datamanReader adios2)
- if(ADIOS_BUILD_TESTING)
- add_test(NAME Example::hello::datamanReader COMMAND hello_datamanReader)
- endif()
+if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::dataman::read COMMAND hello_datamanReader)
endif()
-
diff --git a/examples/hello/datamanWriter/CMakeLists.txt b/examples/hello/datamanWriter/CMakeLists.txt
index c9268d31c761aac93069bee68adcae9fa2289530..eac85b42342826010cd4ee8a03c98f3902b375c7 100644
--- a/examples/hello/datamanWriter/CMakeLists.txt
+++ b/examples/hello/datamanWriter/CMakeLists.txt
@@ -3,26 +3,17 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_datamanWriter_nompi helloDataManWriter_nompi.cpp)
-target_link_libraries(hello_datamanWriter_nompi adios2_nompi)
-
-if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::hello::datamanWriter_nompi
- COMMAND hello_datamanWriter_nompi
- )
-endif()
-
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
add_executable(hello_datamanWriter helloDataManWriter.cpp)
- target_link_libraries(hello_datamanWriter adios2)
target_include_directories(hello_datamanWriter PRIVATE ${MPI_C_INCLUDE_PATH})
- target_link_libraries(hello_datamanWriter adios2 ${MPI_C_LIBRARIES})
-
- if(ADIOS_BUILD_TESTING)
- add_test(NAME Example::hello::datamanWriter COMMAND hello_datamanWriter)
- endif()
+ target_link_libraries(hello_datamanWriter ${MPI_C_LIBRARIES})
+else()
+ add_executable(hello_datamanWriter helloDataManWriter_nompi.cpp)
endif()
+target_link_libraries(hello_datamanWriter adios2)
+if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::dataman::write COMMAND hello_datamanWriter)
+endif()
diff --git a/examples/hello/hdf5Writer/CMakeLists.txt b/examples/hello/hdf5Writer/CMakeLists.txt
index 2f7d7fc0cbc69fc167f32a60b4aa030b44174bd1..1c3b030382190579703d21034077d99ed91f929e 100644
--- a/examples/hello/hdf5Writer/CMakeLists.txt
+++ b/examples/hello/hdf5Writer/CMakeLists.txt
@@ -3,28 +3,17 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-#add_executable(hello_hdf5Writer_nompi helloHDF5Writer_nompi.cpp)
-message(" HDF5: ${HDF5_INCLUDE_DIRS}")
-include_directories(${HDF5_INCLUDE_DIRS})
-#target_link_libraries(hello_hdf5Writer_nompi adios2_nompi)
-
-if(ADIOS_BUILD_TESTING)
- #add_test(
- # NAME Example::hello::hdf5Writer_nompi
- # COMMAND hello_hdf5Writer_nompi
- #)
-endif()
-
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
add_executable(hello_hdf5Writer helloHDF5Writer.cpp)
- target_link_libraries(hello_hdf5Writer adios2)
target_include_directories(hello_hdf5Writer PRIVATE ${MPI_C_INCLUDE_PATH})
- target_link_libraries(hello_hdf5Writer adios2 ${MPI_C_LIBRARIES})
-
- if(ADIOS_BUILD_TESTING)
- add_test(NAME Example::hello::hdf5Writer COMMAND hello_hdf5Writer)
- endif()
+ target_link_libraries(hello_hdf5Writer ${MPI_C_LIBRARIES})
+else()
+ add_executable(hello_hdf5Writer helloHDF5Writer_nompi.cpp)
endif()
+target_link_libraries(hello_hdf5Writer adios2)
+if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::hdf5::write COMMAND hello_hdf5Writer)
+endif()
diff --git a/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp b/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6f19e961f16d0cdb4b02e9507f3fb5fbc3309a2e
--- /dev/null
+++ b/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
@@ -0,0 +1,130 @@
+/*
+ * HDF5Writer.cpp
+ *
+ * Created on: March 20, 2017
+ * Author: Junmin
+ */
+
+#include <iostream>
+#include <vector>
+
+#include "ADIOS_CPP.h"
+
+int main(int argc, char *argv[])
+{
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adios::Verbose::INFO, adiosDebug);
+
+ // Application variable
+ const std::size_t intDim1 = 4;
+ const std::size_t intDim2 = 3;
+ std::vector<int> myInts = {10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21};
+
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
+
+ std::vector<std::complex<float>> myCFloats;
+ const std::size_t CFloatSize = 3;
+ myCFloats.reserve(CFloatSize);
+ myCFloats.emplace_back(1, 3);
+ myCFloats.emplace_back(2, 2);
+ myCFloats.emplace_back(3, 1);
+
+ std::vector<std::complex<double>> myCDoubles;
+ const std::size_t CDoubleSize = 3;
+ myCDoubles.reserve(CDoubleSize);
+ myCDoubles.emplace_back(1, 3);
+ myCDoubles.emplace_back(2, 2);
+ myCDoubles.emplace_back(3, 1);
+
+ std::size_t doubleVCount = Nx / size;
+ std::size_t floatCount = CFloatSize / size;
+ std::size_t intCountDim1 = intDim1 / size;
+
+ std::size_t doubleVOffset = rank * doubleVCount;
+ std::size_t floatOffset = rank * floatCount;
+ std::size_t intOffsetDim1 = rank * intCountDim1;
+ std::size_t intOffsetDim2 = 0;
+
+ if ((size > 1) && (rank == size - 1))
+ {
+ doubleVCount = Nx - rank * (Nx / size);
+ floatCount = CFloatSize - rank * (CFloatSize / size);
+ intCountDim1 = intDim1 - rank * (intDim1 / size);
+ }
+
+ try
+ {
+ // Define variable and local size
+ // auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {Nx},
+ // {Nx} );
+ // auto& ioMyCFloats = adios.DefineVariable<std::complex<float>>(
+ // "myCFloats", {3}, {3} );
+ // auto& ioMyInts = adios.DefineVariable<int>( "myInts", {4,3}, {4,3} );
+
+ auto &ioMyDoubles = adios.DefineVariable<double>(
+ "myDoubles", {doubleVCount}, {Nx}, {doubleVOffset});
+ auto &ioMyCFloats = adios.DefineVariable<std::complex<float>>(
+ "myCFloats", {floatCount}, {3}, {floatOffset});
+ auto &ioMyCDoubles = adios.DefineVariable<std::complex<double>>(
+ "myCDoubles", {floatCount}, {3}, {floatOffset});
+ auto &ioMyInts =
+ adios.DefineVariable<int>("myInts", {intCountDim1, intDim2}, {4, 3},
+ {intOffsetDim1, intOffsetDim2});
+
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &HDF5Settings =
+ adios.DeclareMethod("HDF5Writer"); // default method type is Writer
+ HDF5Settings.SetParameters("chunck=yes", "collectiveIO=yes");
+ // HDF5Settings.AddTransport( "Mdtm", "localIP=128.0.0.0.1",
+ // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+
+ // Create engine smart pointer to HDF5 Engine due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // HDF5
+ auto HDF5Writer = adios.Open("test.bp", "w", HDF5Settings);
+
+ if (HDF5Writer == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to create HDF5 I/O engine at Open\n");
+
+ HDF5Writer->Write(ioMyDoubles, myDoubles.data() +
+ doubleVOffset); // Base class Engine
+ // own the Write<T>
+ // that will call
+ // overloaded Write
+ // from Derived
+ HDF5Writer->Write(ioMyInts,
+ myInts.data() + (intOffsetDim1 * intDim2 * rank));
+ HDF5Writer->Write(ioMyCFloats, myCFloats.data());
+ HDF5Writer->Write(ioMyCDoubles, myCDoubles.data());
+ HDF5Writer->Close();
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch (std::ios_base::failure &e)
+ {
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+
+ return 0;
+}
diff --git a/examples/hello/timeBP/CMakeLists.txt b/examples/hello/timeBP/CMakeLists.txt
index 949e8145e18683463df84e4b555e065901bc9e03..f077e9e80ab72e6174b342938ed6add902eb1dae 100644
--- a/examples/hello/timeBP/CMakeLists.txt
+++ b/examples/hello/timeBP/CMakeLists.txt
@@ -3,24 +3,17 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_timeBPWriter_nompi timeBPWriter_nompi.cpp)
-target_link_libraries(hello_timeBPWriter_nompi adios2_nompi)
-
-if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::hello::timeBPWriter_nompi
- COMMAND hello_timeBPWriter_nompi
- )
-endif()
-
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
+
add_executable(hello_timeBPWriter timeBPWriter.cpp)
- target_link_libraries(hello_timeBPWriter adios2)
target_include_directories(hello_timeBPWriter PRIVATE ${MPI_C_INCLUDE_PATH})
- target_link_libraries(hello_timeBPWriter adios2 ${MPI_C_LIBRARIES})
+ target_link_libraries(hello_timeBPWriter ${MPI_C_LIBRARIES})
+else()
+ add_executable(hello_timeBPWriter timeBPWriter_nompi.cpp)
+endif()
+target_link_libraries(hello_timeBPWriter adios2)
- if(ADIOS_BUILD_TESTING)
- add_test(NAME Example::hello::timeBPWriter COMMAND hello_timeBPWriter)
- endif()
+if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::timeBP::write COMMAND hello_timeBPWriter)
endif()
diff --git a/include/engine/adios1/ADIOS1Writer.h b/include/engine/adios1/ADIOS1Writer.h
index 11a9eb313440eda2e2deba1c820d1f61989bc05a..c13eee78201bc3b797e7bbe654c1fe7d1a3e9be1 100644
--- a/include/engine/adios1/ADIOS1Writer.h
+++ b/include/engine/adios1/ADIOS1Writer.h
@@ -18,13 +18,7 @@
namespace adios
{
-#ifndef ADIOS_HAVE_MPI
-#define _NOMPI
-#endif
#include "adios.h" // this is adios 1.x header file
-#ifndef ADIOS_HAVE_MPI
-#undef _NOMPI
-#endif
class ADIOS1Writer : public Engine
{
diff --git a/source/ADIOS.cpp b/source/ADIOS.cpp
index 30aac797cd4d6533626106baef0dcab3eeed529b..ac6eb562639c56fd3b43fc904a026e00ce6ca4f8 100644
--- a/source/ADIOS.cpp
+++ b/source/ADIOS.cpp
@@ -36,12 +36,10 @@
#include "engine/adios1/ADIOS1Writer.h"
#endif
-#ifdef ADIOS_HAVE_PHDF5 // external dependencies
-#ifdef ADIOS_HAVE_MPI
+#ifdef ADIOS_HAVE_HDF5 // external dependencies
#include "engine/hdf5/HDF5ReaderP.h"
#include "engine/hdf5/HDF5WriterP.h"
#endif
-#endif
namespace adios
{
@@ -194,7 +192,7 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
}
else if (type == "HDF5Writer") // -junmin
{
-#if defined(ADIOS_HAVE_PHDF5) && defined(ADIOS_HAVE_MPI)
+#ifdef ADIOS_HAVE_HDF5
return std::make_shared<HDF5Writer>(*this, name, accessMode, mpiComm,
method);
#else
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
index 62a642e966648cd5d2d73c4473146429920fa58a..993366d5fcc6656a64a47c24699aeb3d6805843f 100644
--- a/source/CMakeLists.txt
+++ b/source/CMakeLists.txt
@@ -3,107 +3,104 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-set(adios2_targets adios2_nompi)
-if(ADIOS_USE_MPI)
- list(APPEND adios2_targets adios2)
-endif()
-
-foreach(adios2_target IN LISTS adios2_targets)
- add_library(${adios2_target}
- ADIOS.cpp ADIOS.tcc
- #ADIOS_C.cpp
+add_library(adios2
+ ADIOS.cpp ADIOS.tcc
+ #ADIOS_C.cpp
- capsule/heap/STLVector.cpp
- capsule/shmem/ShmSystemV.cpp
+ capsule/heap/STLVector.cpp
+ capsule/shmem/ShmSystemV.cpp
- core/Capsule.cpp
- core/Engine.cpp
- core/Method.cpp
- core/Support.cpp
- core/Transform.cpp
- core/Transport.cpp
+ core/Capsule.cpp
+ core/Engine.cpp
+ core/Method.cpp
+ core/Support.cpp
+ core/Transform.cpp
+ core/Transport.cpp
- engine/bp/BPFileReader.cpp
- engine/bp/BPFileWriter.cpp
+ engine/bp/BPFileReader.cpp
+ engine/bp/BPFileWriter.cpp
- utilities/format/bp1/BP1Base.cpp
- utilities/format/bp1/BP1Aggregator.cpp
- utilities/format/bp1/BP1Writer.cpp
+ utilities/format/bp1/BP1Base.cpp
+ utilities/format/bp1/BP1Aggregator.cpp
+ utilities/format/bp1/BP1Writer.cpp
- utilities/profiling/iochrono/Timer.cpp
-
- functions/adiosFunctions.cpp
+ utilities/profiling/iochrono/Timer.cpp
+
+ functions/adiosFunctions.cpp
- transport/file/FStream.cpp
- transport/file/FileDescriptor.cpp
- transport/file/FilePointer.cpp
+ transport/file/FStream.cpp
+ transport/file/FileDescriptor.cpp
+ transport/file/FilePointer.cpp
- utilities/format/bp1/BP1Base.cpp
- utilities/format/bp1/BP1Aggregator.cpp
- utilities/format/bp1/BP1Writer.cpp
- utilities/format/bp1/BP1Writer.tcc
+ utilities/format/bp1/BP1Base.cpp
+ utilities/format/bp1/BP1Aggregator.cpp
+ utilities/format/bp1/BP1Writer.cpp
+ utilities/format/bp1/BP1Writer.tcc
- utilities/profiling/iochrono/Timer.cpp
- )
- target_include_directories(${adios2_target}
- PUBLIC ${ADIOS_SOURCE_DIR}/include
- )
+ utilities/profiling/iochrono/Timer.cpp
+)
+target_include_directories(adios2
+ PUBLIC ${ADIOS_SOURCE_DIR}/include
+)
- if(ADIOS_USE_DataMan)
- target_sources(${adios2_target} PRIVATE
- engine/dataman/DataManReader.cpp
- engine/dataman/DataManWriter.cpp
- transport/wan/MdtmMan.cpp
- utilities/realtime/dataman/DataManBase.cpp
- utilities/realtime/dataman/DataMan.cpp
- )
- target_compile_definitions(${adios2_target} PRIVATE ADIOS_HAVE_DATAMAN)
- target_link_libraries(${adios2_target} PRIVATE ${CMAKE_DL_LIBS})
- endif()
+if(ADIOS_USE_DataMan)
+ target_sources(adios2 PRIVATE
+ engine/dataman/DataManReader.cpp
+ engine/dataman/DataManWriter.cpp
+ transport/wan/MdtmMan.cpp
+ utilities/realtime/dataman/DataManBase.cpp
+ utilities/realtime/dataman/DataMan.cpp
+ )
+ target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_DATAMAN)
+ target_link_libraries(adios2 PRIVATE ${CMAKE_DL_LIBS})
+endif()
- if(ADIOS_USE_BZip2)
- find_package(BZip2 REQUIRED)
- target_sources(${adios2_target} PRIVATE transform/BZip2.cpp)
- target_compile_definitions(${adios2_target} PRIVATE ADIOS_HAVE_BZIP2)
- target_link_libraries(${adios2_target} PRIVATE BZip2::BZip2)
- endif()
-endforeach()
-
-target_sources(adios2_nompi PRIVATE mpidummy.cpp)
-if(CMAKE_CXX_COMPILER_WRAPPER STREQUAL CrayPrgEnv)
- target_compile_options(adios2_nompi PRIVATE --cray-bypass-pkgconfig)
+if(ADIOS_USE_BZip2)
+ find_package(BZip2 REQUIRED)
+ target_sources(adios2 PRIVATE transform/BZip2.cpp)
+ target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_BZIP2)
+ target_link_libraries(adios2 PRIVATE BZip2::BZip2)
endif()
+
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
target_include_directories(adios2 PUBLIC ${MPI_C_INCLUDE_PATH})
target_compile_definitions(adios2 PUBLIC ADIOS_HAVE_MPI)
target_link_libraries(adios2 PUBLIC ${MPI_C_LIBRARIES})
+else()
+ target_sources(adios2 PRIVATE mpidummy.cpp)
+endif()
- if(ADIOS_USE_ADIOS1)
+if(ADIOS_USE_ADIOS1)
+ if(ADIOS_USE_MPI)
find_package(ADIOS1 REQUIRED)
- target_sources(adios2 PRIVATE
- engine/adios1/ADIOS1Reader.cpp
- engine/adios1/ADIOS1Writer.cpp
- )
- target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_ADIOS1)
- target_link_libraries(adios2 PRIVATE adios1::adios)
+ else()
+ find_package(ADIOS1 COMPONENTS sequential REQUIRED)
endif()
- if(ADIOS_USE_PHDF5)
- find_package(HDF5 REQUIRED)
- message(" HDF5 ROOT: ${HDF5_ROOT}")
- message(" HDF5 include: ${HDF5_INCLUDE_DIRS} is paralle? ${HDF5_IS_PARALLEL}")
-
- target_include_directories(adios2 PRIVATE ${HDF5_INCLUDE_DIRS})
+ target_sources(adios2 PRIVATE
+ engine/adios1/ADIOS1Reader.cpp
+ engine/adios1/ADIOS1Writer.cpp
+ )
+ target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_ADIOS1)
+ target_link_libraries(adios2 PRIVATE adios1::adios)
+endif()
- target_sources(adios2 PRIVATE
- engine/hdf5/HDF5ReaderP.cpp
- engine/hdf5/HDF5WriterP.cpp
- )
- target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_PHDF5)
- target_link_libraries(adios2 PRIVATE ${HDF5_C_LIBRARIES})
+if(ADIOS_USE_HDF5)
+ find_package(HDF5 REQUIRED)
+ if(ADIOS_USE_MPI AND (NOT HDF5_IS_PARALLEL))
+ message(FATAL_ERROR "A sequential version of HDF5 was detected but the parallel version of ADIOS is being built, which requires a parallel HDF5.")
+ elseif((NOT ADIOS_USE_MPI) AND HDF5_IS_PARALLEL)
+ message(FATAL_ERROR "A parallel version of HDF5 was detected but the sequential version of ADIOS is being built, which requires a sequential HDF5.")
endif()
+ target_include_directories(adios2 PRIVATE ${HDF5_INCLUDE_DIRS})
+ target_sources(adios2 PRIVATE
+ engine/hdf5/HDF5ReaderP.cpp
+ engine/hdf5/HDF5WriterP.cpp
+ )
+ target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_HDF5)
+ target_link_libraries(adios2 PRIVATE ${HDF5_C_LIBRARIES})
endif()
diff --git a/source/engine/hdf5/HDF5WriterP.cpp b/source/engine/hdf5/HDF5WriterP.cpp
index 05656e2babf1170f368702b2cd0d309d47800a8c..b75a447b4b9383575f58e0e36d9275f2a494bef7 100644
--- a/source/engine/hdf5/HDF5WriterP.cpp
+++ b/source/engine/hdf5/HDF5WriterP.cpp
@@ -78,7 +78,9 @@ void HDF5Writer::Init()
_plist_id = H5Pcreate(H5P_FILE_ACCESS);
+#ifdef ADIOS_HAVE_MPI
H5Pset_fapl_mpio(_plist_id, m_MPIComm, MPI_INFO_NULL);
+#endif
/*
* Create a new file collectively and release property list identifier.
@@ -340,8 +342,9 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
// Create property list for collective dataset write.
_plist_id = H5Pcreate(H5P_DATASET_XFER);
+#ifdef ADIOS_HAVE_MPI
H5Pset_dxpl_mpio(_plist_id, H5FD_MPIO_COLLECTIVE);
-
+#endif
herr_t status;
status =