lanl · rfbird · Dec 30, 2018 · Jan 7, 2019 · Jan 11, 2019 · Jan 31, 2019
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -84,13 +84,20 @@ option(USE_LEGACY_SORT "Enable Legacy Sort Implementation" OFF)
 
 option(VPIC_PRINT_MORE_DIGITS "Print more digits in VPIC timer info" OFF)
 
-option(ENABLE_OPENSSL "Enable OpenSSL support for checksums" OFF)
-
 option(DISABLE_DYNAMIC_RESIZING "Prevent particle arrays from dynamically resizing during a run" OFF)
 
+option(USE_HDF5 "Enable HDF5 for use during IO. VPIC does not help you install HDF5" OFF)
+
+option(USE_OPENPMD "Enable OpenPMD for use during IO. VPIC does not help you install OpenPM" OFF)
+
+option(OUTPUT_CONVERT_GLOBAL_ID "Convert particle cell id to be global, such that it tells  you  a unique global location instead of a local offset" ON)
+
 # option to set minimum number of particles
 set(SET_MIN_NUM_PARTICLES AUTO CACHE STRING "Select minimum number of particles to use, if using dynamic particle array resizing")
 
+# TODO: better name for this?
+set(PMD_MAX_IO_CHUNK AUTO CACHE STRING "Select the maxiumum IO write size to use when writing -- applies to particles only, and is specified as number of particles. currently only honored by OpenPMD backend")
+
 
 #------------------------------------------------------------------------------#
 # Create include and link aggregates
@@ -125,31 +132,22 @@ if(NOT SET_MIN_NUM_PARTICLES STREQUAL "AUTO")
     add_definitions(-DMIN_NP=${SET_MIN_NUM_PARTICLES})
 endif()
 
-#------------------------------------------------------------------------------#
-# OpenSSL
-#------------------------------------------------------------------------------#
-
-if(ENABLE_OPENSSL)
-  find_package(OpenSSL REQUIRED)
-
-  include_directories(${OPENSSL_INCLUDE_DIR})
-  string(REPLACE ";" " " string_libraries "${OPENSSL_LIBRARIES}")
-  set(VPIC_CXX_LIBRARIES "${VPIC_CXX_LIBRARIES} ${string_libraries}")
-endif(ENABLE_OPENSSL)
+if(NOT PMD_MAX_IO_CHUNK STREQUAL "AUTO")
+    add_definitions(-DPMD_MAX_IO_CHUNK=${PMD_MAX_IO_CHUNK})
+endif()
 
 find_package(Threads REQUIRED)
 
 #------------------------------------------------------------------------------#
 # Act on build options set in project.cmake
 #------------------------------------------------------------------------------#
-
 #------------------------------------------------------------------------------#
 # Add options for building with the legacy particle sort implementation.
 #------------------------------------------------------------------------------#
 
 if(USE_LEGACY_SORT)
   add_definitions(-DVPIC_USE_LEGACY_SORT)
-    set(VPIC_CXX_FLAGS "${VPIC_CXX_FLAGS} -DVPIC_USE_LEGACY_SORT")
+  set(VPIC_CXX_FLAGS "${VPIC_CXX_FLAGS} -DVPIC_USE_LEGACY_SORT")
 endif(USE_LEGACY_SORT)
 
 #------------------------------------------------------------------------------#
@@ -164,7 +162,7 @@ endif()
 
 if(USE_PTHREADS)
   add_definitions(-DVPIC_USE_PTHREADS)
-    set(VPIC_CXX_FLAGS "${VPIC_CXX_FLAGS} -DVPIC_USE_PTHREADS")
+  set(VPIC_CXX_FLAGS "${VPIC_CXX_FLAGS} -DVPIC_USE_PTHREADS")
 endif(USE_PTHREADS)
 
 if(USE_OPENMP)
@@ -288,15 +286,23 @@ endif()
 # Miscellaneous options.
 #------------------------------------------------------------------------------#
 
-if(ENABLE_OPENSSL)
-  add_definitions(-DENABLE_OPENSSL)
-endif(ENABLE_OPENSSL)
-
 if(VPIC_PRINT_MORE_DIGITS)
   add_definitions(-DVPIC_PRINT_MORE_DIGITS)
   set(VPIC_CXX_FLAGS "${VPIC_CXX_FLAGS} -DVPIC_PRINT_MORE_DIGITS")
 endif(VPIC_PRINT_MORE_DIGITS)
 
+if(USE_HDF5)
+    # Enable HDF5, and the relevant defines
+    find_package(HDF5 REQUIRED)
+    if (NOT HDF5_IS_PARALLEL)
+        message(FATAL_ERROR "HDF5 Parallel support is required: ${HDF5_IS_PARALLEL}")
+    endif()
+    add_definitions(-DVPIC_ENABLE_HDF5)
+    string(REPLACE ";" " " string_libraries "${HDF5_C_LIBRARIES}")
+    set(VPIC_CXX_LIBRARIES "${VPIC_CXX_LIBRARIES} ${string_libraries}")
+    include_directories(${HDF5_INCLUDE_DIRS})
+endif(USE_HDF5)
+
 #------------------------------------------------------------------------------#
 # Handle vpic compile script last.
 #------------------------------------------------------------------------------#
@@ -312,48 +318,12 @@ if(ENABLE_COVERAGE_BUILD)
     set(VPIC_CXX_FLAGS "${VPIC_CXX_FLAGS} --coverage")
 endif(ENABLE_COVERAGE_BUILD)
 
-# process Makefile.run.in to get a simple Makefile.run for a run. Points to
-# local built exe wrapper, and has example deck/platform.
-configure_file(${CMAKE_SOURCE_DIR}/sample/Makefile.run.in
-  ${CMAKE_BINARY_DIR}/bin/Makefile.run)
-
-# Append all defines to VPIC_DEFINES, so it can be seen during input deck building
-get_directory_property(ALL_DEFINES DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
-#string(REPLACE ";" " -D" EEK "${ALL_DEFINES}")
-foreach(d ${ALL_DEFINES})
-    set(VPIC_DEFINES "${VPIC_DEFINES} -D${d}")
-endforeach()
-
-# install script
-configure_file(${CMAKE_SOURCE_DIR}/bin/vpic.in
-  ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic-install)
-install(FILES ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic-install
-  DESTINATION bin
-  RENAME vpic
-  PERMISSIONS
-    OWNER_READ OWNER_WRITE OWNER_EXECUTE
-    GROUP_READ GROUP_EXECUTE
-    WORLD_READ WORLD_EXECUTE
-    )
-
 install(FILES deck/main.cc deck/wrapper.cc DESTINATION share/vpic)
 install(FILES deck/wrapper.h DESTINATION include/vpic)
 install(DIRECTORY src/ DESTINATION include/vpic
          FILES_MATCHING PATTERN "*.h")
 
 
-# local script
-configure_file(${CMAKE_SOURCE_DIR}/bin/vpic-local.in
-  ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic)
-
-file(COPY ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic
-  DESTINATION ${CMAKE_BINARY_DIR}/bin
-  FILE_PERMISSIONS
-    OWNER_READ OWNER_WRITE OWNER_EXECUTE
-    GROUP_READ GROUP_EXECUTE
-    WORLD_READ WORLD_EXECUTE
-)
-
 #------------------------------------------------------------------------------#
 # Add library target
 #------------------------------------------------------------------------------#
@@ -377,10 +347,49 @@ else()
   set(VPIC_SRC)
   install(TARGETS vpic LIBRARY DESTINATION lib ARCHIVE DESTINATION lib)
 endif()
+
 target_include_directories(vpic INTERFACE ${CMAKE_SOURCE_DIR}/src)
-target_link_libraries(vpic ${VPIC_EXPOSE} ${MPI_CXX_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${OPENSSL_LIBRARIES} ${CMAKE_DL_LIBS})
+target_link_libraries(vpic ${VPIC_EXPOSE} ${MPI_CXX_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${CMAKE_DL_LIBS} ${HDF5_C_LIBRARIES})
 target_compile_options(vpic ${VPIC_EXPOSE} ${MPI_C_COMPILE_FLAGS})
 
+# get absolute paths to linked libraries, and their transitive dependencies
+function(openpmdreclibs tgtname outname)
+    get_target_property(PC_PRIVATE_LIBS_TGT ${tgtname} INTERFACE_LINK_LIBRARIES)
+    foreach(PC_LIB IN LISTS PC_PRIVATE_LIBS_TGT)
+       if(TARGET ${PC_LIB})
+           openpmdreclibs(${PC_LIB} ${outname})
+       else()
+           if(PC_LIB)
+               string(APPEND ${outname} " ${PC_LIB}")
+           endif()
+       endif()
+    endforeach()
+    set(${outname} ${${outname}} PARENT_SCOPE)
+endfunction()
+
+if(USE_OPENPMD)
+    # Enable openPMD, and the relevant defines
+    find_package(openPMD REQUIRED CONFIG COMPONENTS MPI)
+    target_link_libraries(vpic PRIVATE openPMD::openPMD)
+    target_compile_definitions(vpic PRIVATE "-DVPIC_ENABLE_OPENPMD")
+
+    add_definitions(-DVPIC_ENABLE_OPENPMD)
+
+    # legacy stuff for 2-phase compile
+    get_target_property(openPMD_LIBRARIES openPMD::openPMD LOCATION)
+    string(REPLACE ";" " " string_libraries "${openPMD_LIBRARIES}")
+    set(VPIC_CXX_LIBRARIES "${VPIC_CXX_LIBRARIES} ${string_libraries}")
+    get_target_property(openPMD_TYPE openPMD::openPMD TYPE)
+    if("${openPMD_TYPE}" STREQUAL "STATIC_LIBRARY")
+        openpmdreclibs(openPMD openPMD_TRANSITIVE_LIBS)
+        set(VPIC_CXX_LIBRARIES "${VPIC_CXX_LIBRARIES} ${openPMD_TRANSITIVE_LIBS}")
+    endif()
+endif(USE_OPENPMD)
+
+if(OUTPUT_CONVERT_GLOBAL_ID)
+    add_definitions(-DOUTPUT_CONVERT_GLOBAL_ID)
+endif(OUTPUT_CONVERT_GLOBAL_ID)
+
 macro(build_a_vpic name deck)
   if(NOT EXISTS ${deck})
     message(FATAL_ERROR "Could not find deck '${deck}'")
@@ -438,6 +447,40 @@ if(ENABLE_PERFORMANCE_TESTS)
   include_directories(${CATCH_DIR})
   add_subdirectory(test/performance)
 endif(ENABLE_PERFORMANCE_TESTS)
-#~---------------------------------------------------------------------------~-#
-# vim: set tabstop=2 shiftwidth=2 expandtab :
-#~---------------------------------------------------------------------------~-#
+
+# process Makefile.run.in to get a simple Makefile.run for a run. Points to
+# local built exe wrapper, and has example deck/platform.
+configure_file(${CMAKE_SOURCE_DIR}/sample/Makefile.run.in
+  ${CMAKE_BINARY_DIR}/bin/Makefile.run)
+
+# Append all defines to VPIC_DEFINES, so it can be seen during input deck building
+get_directory_property(ALL_DEFINES DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
+#string(REPLACE ";" " -D" EEK "${ALL_DEFINES}")
+foreach(d ${ALL_DEFINES})
+    set(VPIC_DEFINES "${VPIC_DEFINES} -D${d}")
+endforeach()
+
+# install script
+configure_file(${CMAKE_SOURCE_DIR}/bin/vpic.in
+  ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic-install)
+install(FILES ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic-install
+  DESTINATION bin
+  RENAME vpic
+  PERMISSIONS
+    OWNER_READ OWNER_WRITE OWNER_EXECUTE
+    GROUP_READ GROUP_EXECUTE
+    WORLD_READ WORLD_EXECUTE
+)
+
+# Configure local script to generate bin/vpic
+configure_file(${CMAKE_SOURCE_DIR}/bin/vpic-local.in
+  ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic)
+
+file(COPY ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/vpic
+  DESTINATION ${CMAKE_BINARY_DIR}/bin
+  FILE_PERMISSIONS
+    OWNER_READ OWNER_WRITE OWNER_EXECUTE
+    GROUP_READ GROUP_EXECUTE
+    WORLD_READ WORLD_EXECUTE
+)
+
diff --git a/bin/vpic-local.in b/bin/vpic-local.in
@@ -2,6 +2,6 @@
 
 deck=`echo $1 | sed 's,\.cxx,,g;s,\.cc,,g;s,\.cpp,,g;s,.*\/,,g'`
 
-echo "${CMAKE_CXX_COMPILER} ${CMAKE_CXX_FLAGS} -I. -I${CMAKE_SOURCE_DIR}/src ${VPIC_CXX_FLAGS} -DINPUT_DECK=$1 ${CMAKE_SOURCE_DIR}/deck/main.cc ${CMAKE_SOURCE_DIR}/deck/wrapper.cc -o $deck.${CMAKE_SYSTEM_NAME} -Wl,-rpath,${CMAKE_BINARY_DIR} -L${CMAKE_BINARY_DIR} -lvpic ${VPIC_CXX_LIBRARIES} -lpthread -ldl"
+echo "${CMAKE_CXX_COMPILER} ${VPIC_DEFINES} ${CMAKE_CXX_FLAGS} -I. -I${CMAKE_SOURCE_DIR}/src ${VPIC_CXX_FLAGS} -DINPUT_DECK=$1 ${CMAKE_SOURCE_DIR}/deck/main.cc ${CMAKE_SOURCE_DIR}/deck/wrapper.cc -o $deck.${CMAKE_SYSTEM_NAME} -Wl,-rpath,${CMAKE_BINARY_DIR} -L${CMAKE_BINARY_DIR} -lvpic ${VPIC_CXX_LIBRARIES} -lpthread -ldl"
 
-${CMAKE_CXX_COMPILER} ${CMAKE_CXX_FLAGS} -I. -I${CMAKE_SOURCE_DIR}/src ${VPIC_CXX_FLAGS} -DINPUT_DECK=$1 ${CMAKE_SOURCE_DIR}/deck/main.cc ${CMAKE_SOURCE_DIR}/deck/wrapper.cc -o $deck.${CMAKE_SYSTEM_NAME} -Wl,-rpath,${CMAKE_BINARY_DIR} -L${CMAKE_BINARY_DIR} -lvpic ${VPIC_CXX_LIBRARIES} -lpthread -ldl
+${CMAKE_CXX_COMPILER} ${VPIC_DEFINES} ${CMAKE_CXX_FLAGS} -I. -I${CMAKE_SOURCE_DIR}/src ${VPIC_CXX_FLAGS} -DINPUT_DECK=$1 ${CMAKE_SOURCE_DIR}/deck/main.cc ${CMAKE_SOURCE_DIR}/deck/wrapper.cc -o $deck.${CMAKE_SYSTEM_NAME} -Wl,-rpath,${CMAKE_BINARY_DIR} -L${CMAKE_BINARY_DIR} -lvpic ${VPIC_CXX_LIBRARIES} -lpthread -ldl
diff --git a/deck/main.cc b/deck/main.cc
@@ -98,6 +98,12 @@ int main(int argc, char** argv)
         }
         simulation = new vpic_simulation();
         simulation->initialize( argc, argv );
+
+        // do post init setup to consume deck values
+        // which includes setting dump starts steps, as we didn't know it sooner
+        // TODO: make this use sane functions
+        simulation->dump_strategy->num_step = simulation->num_step;
+
         REGISTER_OBJECT( &simulation, checkpt_main, restore_main, NULL );
     }