Merge branch 'master' into campaign-manager-steps

* master: - Only add campaign store to file name if that is not absolute path - list command supports second argument as path flake8 fixes Update campaign manager script to handle config file, time in nanosecond format, and avoiding conflict when updating database dill 2024-03-12 (ebc98c4d) (ornladios#4091) Don't run derived test in MPI mode, it's not written for that (ornladios#4104) Fix static blosc2 build (ornladios#4093) ci: add ccache job summary (ornladios#4101) Fix typo in fortran.rst (ornladios#4102) WIP: Make Fortran tests fail with a non-zero exit code (ornladios#4097) Bison 3.8 Parser (ornladios#4062)
pnorbert · Mar 26, 2024 · 01e68ae · 01e68ae
2 parents 610633f + f046ebc
commit 01e68ae
Show file tree

Hide file tree

Showing 111 changed files with 7,832 additions and 5,076 deletions.
diff --git a/.github/workflows/everything.yml b/.github/workflows/everything.yml
@@ -188,7 +188,7 @@ jobs:
       - name: Build
         run: gha/scripts/ci/gh-actions/run.sh build
       - name: Print ccache statistics
-        run: ccache -s
+        run: ccache -s | tee $GITHUB_STEP_SUMMARY
       - name: Save cache
         uses: actions/cache/save@v3
         if: ${{ github.ref_name == 'master' && steps.restore-cache.outputs.cache-hit != 'true' }}

diff --git a/bindings/C/adios2/c/adios2_c_variable.cpp b/bindings/C/adios2/c/adios2_c_variable.cpp
@@ -79,11 +79,7 @@ adios2_error adios2_set_shape(adios2_variable *variable, const size_t ndims, con
 
 adios2::MemorySpace adios2_ToMemorySpace(const adios2_memory_space Cmem)
 {
-#ifdef ADIOS2_HAVE_GPU_SUPPORT
     adios2::MemorySpace mem = adios2::MemorySpace::Detect;
-#else
-    adios2::MemorySpace mem = adios2::MemorySpace::Host;
-#endif
     switch (Cmem)
     {
 
@@ -104,11 +100,7 @@ adios2::MemorySpace adios2_ToMemorySpace(const adios2_memory_space Cmem)
 
 adios2_memory_space adios2_FromMemorySpace(const adios2::MemorySpace mem)
 {
-#ifdef ADIOS2_HAVE_GPU_SUPPORT
     adios2_memory_space Cmem = adios2_memory_space_detect;
-#else
-    adios2_memory_space Cmem = adios2_memory_space_host;
-#endif
     switch (mem)
     {
 

diff --git a/cmake/ADIOSBisonFlexSub.cmake b/cmake/ADIOSBisonFlexSub.cmake
@@ -0,0 +1,15 @@
+FUNCTION (SETUP_ADIOS_BISON_FLEX_SUB)
+
+set (BISON_FLEX_PRECOMPILE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/toolkit/derived/parser/pregen-source")
+
+ADD_CUSTOM_COMMAND(OUTPUT parser.cpp
+        COMMAND ${CMAKE_COMMAND} -E copy ${BISON_FLEX_PRECOMPILE_DIR}/parser.cpp ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${CMAKE_COMMAND} -E copy ${BISON_FLEX_PRECOMPILE_DIR}/parser.h ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${CMAKE_COMMAND} -E copy ${BISON_FLEX_PRECOMPILE_DIR}/location.hh ${CMAKE_CURRENT_BINARY_DIR}
+	COMMENT "Using pre-generated Bison Output from ${BISON_FLEX_PRECOMPILE_DIR}")
+ADD_CUSTOM_COMMAND(OUTPUT lexer.cpp
+	COMMAND ${CMAKE_COMMAND} -E copy ${BISON_FLEX_PRECOMPILE_DIR}/lexer.cpp ${CMAKE_CURRENT_BINARY_DIR}
+	COMMENT "Using pre-generated Flex Output from ${BISON_FLEX_PRECOMPILE_DIR}")
+
+set (BISON_Parser_OUTPUT_SOURCE parser.cpp PARENT_SCOPE)
+ENDFUNCTION()
diff --git a/cmake/DetectOptions.cmake b/cmake/DetectOptions.cmake
@@ -72,31 +72,26 @@ find_package(Threads REQUIRED)
 
 # Blosc2
 if(ADIOS2_USE_Blosc2 STREQUAL AUTO)
-  # Prefect CONFIG mode
-  find_package(Blosc2 2.4 CONFIG QUIET)
-  if(NOT Blosc2_FOUND)
-    find_package(Blosc2 2.4 MODULE QUIET)
-  endif()
+  find_package(Blosc2 2.10.1 QUIET)
 elseif(ADIOS2_USE_Blosc2)
-  # Prefect CONFIG mode
-  find_package(Blosc2 2.4 CONFIG)
-  if(NOT Blosc2_FOUND)
-    find_package(Blosc2 2.4 MODULE REQUIRED)
-  endif()
+  find_package(Blosc2 2.10.1)
 endif()
 if(Blosc2_FOUND)
   set(ADIOS2_HAVE_Blosc2 TRUE)
   if(TARGET Blosc2::blosc2_shared)
-    set(Blosc2_shlib_available ON)
+    set(blosc2_shlib_available ON)
   endif()
 
-  set(adios2_blosc2_tgt Blosc2::Blosc2)
-  if (Blosc2_VERSION VERSION_GREATER_EQUAL 2.10.1)
-    if (Blosc2_shlib_available AND ADIOS2_Blosc2_PREFER_SHARED)
-      set(adios2_blosc2_tgt Blosc2::blosc2_shared)
-    else()
-      set(adios2_blosc2_tgt Blosc2::blosc2_static)
-    endif()
+  if(TARGET Blosc2::blosc2_static)
+    set(blosc2_slib_available ON)
+  endif()
+
+  if (blosc2_shlib_available AND (NOT blosc2_slib_available OR ADIOS2_Blosc2_PREFER_SHARED))
+    set(adios2_blosc2_tgt Blosc2::blosc2_shared)
+  elseif(blosc2_slib_available)
+    set(adios2_blosc2_tgt Blosc2::blosc2_static)
+  else()
+    message(FATAL_ERROR "Blosc2 cmake package found but no targets exists inside it.")
   endif()
 
   add_library(adios2_blosc2 ALIAS ${adios2_blosc2_tgt})

diff --git a/cmake/FindBlosc2.cmake b/cmake/FindBlosc2.cmake
diff --git a/cmake/adios2-config-common.cmake.in b/cmake/adios2-config-common.cmake.in
@@ -81,6 +81,11 @@ else()
 endif()
 
 if(NOT @BUILD_SHARED_LIBS@)
+  set(ADIOS2_HAVE_Blosc2 @ADIOS2_HAVE_Blosc2@)
+  if(ADIOS2_HAVE_Blosc2)
+    find_dependency(Blosc2 2.10.1)
+  endif()
+
   set(ADIOS2_HAVE_BZip2 @ADIOS2_HAVE_BZip2@)
   if(ADIOS2_HAVE_BZip2)
     find_dependency(BZip2)

diff --git a/docs/user_guide/source/api_full/fortran.rst b/docs/user_guide/source/api_full/fortran.rst
@@ -746,11 +746,11 @@ ADIOS2 Fortran bindings handlers are mapped 1-to-1 to the ADIOS2 components desc
       integer, intent(out) :: ierr
       
 
-* :f90:`subroutine adios2_set_steps_selection` set a list of steps by specifying the starting step and the step count
+* :f90:`subroutine adios2_set_step_selection` set a list of steps by specifying the starting step and the step count
 
    .. code-block:: fortran
    
-      subroutine adios2_set_selection(variable, step_start, step_count, ierr)
+      subroutine adios2_set_step_selection(variable, step_start, step_count, ierr)
       
       ! WHERE
       

diff --git a/scripts/ci/cmake/ci-ascent-xl.cmake b/scripts/ci/cmake/ci-ascent-xl.cmake
@@ -18,7 +18,7 @@ ADIOS2_USE_SST:BOOL=ON
 ADIOS2_USE_ZeroMQ:STRING=OFF
 ADIOS2_USE_ZFP:BOOL=OFF
 ADIOS2_USE_SZ:BOOL=OFF
-ADIOS2_USE_Blosc:BOOL=OFF
+ADIOS2_USE_Blosc2:BOOL=OFF
 
 CMAKE_C_COMPILER_LAUNCHER=ccache
 CMAKE_CXX_COMPILER_LAUNCHER=ccache

diff --git a/scripts/ci/cmake/ci-crusher-cray.cmake b/scripts/ci/cmake/ci-crusher-cray.cmake
@@ -18,7 +18,7 @@ ADIOS2_USE_SST:BOOL=ON
 ADIOS2_USE_ZeroMQ:STRING=OFF
 ADIOS2_USE_ZFP:BOOL=OFF
 ADIOS2_USE_SZ:BOOL=OFF
-ADIOS2_USE_Blosc:BOOL=OFF
+ADIOS2_USE_Blosc2:BOOL=OFF
 
 CMAKE_C_COMPILER_LAUNCHER=ccache
 CMAKE_CXX_COMPILER_LAUNCHER=ccache

diff --git a/scripts/ci/cmake/ci-el7-spack.cmake b/scripts/ci/cmake/ci-el7-spack.cmake
@@ -13,7 +13,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON
@@ -22,7 +22,7 @@ ADIOS2_USE_Python:BOOL=ON
 ADIOS2_USE_SZ:BOOL=ON
 ADIOS2_USE_ZeroMQ:STRING=ON
 ADIOS2_USE_ZFP:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_DataSpaces:BOOL=OFF
 
 ADIOS2_USE_EXTERNAL_DEPENDENCIES:BOOL=ON

diff --git a/scripts/ci/cmake/ci-el8-icc-mpich.cmake b/scripts/ci/cmake/ci-el8-icc-mpich.cmake
@@ -11,7 +11,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=OFF
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_DataSpaces:BOOL=OFF
 ADIOS2_USE_Fortran:BOOL=OFF

diff --git a/scripts/ci/cmake/ci-el8-icc-ompi.cmake b/scripts/ci/cmake/ci-el8-icc-ompi.cmake
@@ -7,7 +7,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_DataSpaces:BOOL=OFF
 ADIOS2_USE_Fortran:BOOL=OFF

diff --git a/scripts/ci/cmake/ci-el8-icc-serial.cmake b/scripts/ci/cmake/ci-el8-icc-serial.cmake
@@ -7,7 +7,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=OFF
+ADIOS2_USE_Blosc2:BOOL=OFF
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_DataSpaces:BOOL=OFF
 ADIOS2_USE_Fortran:BOOL=OFF

diff --git a/scripts/ci/cmake/ci-el8-oneapi-mpich.cmake b/scripts/ci/cmake/ci-el8-oneapi-mpich.cmake
@@ -11,7 +11,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=OFF
+ADIOS2_USE_Blosc2:BOOL=OFF
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_DataSpaces:BOOL=OFF
 ADIOS2_USE_Fortran:BOOL=OFF

diff --git a/scripts/ci/cmake/ci-el8-oneapi-ompi.cmake b/scripts/ci/cmake/ci-el8-oneapi-ompi.cmake
@@ -7,7 +7,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=OFF
+ADIOS2_USE_Blosc2:BOOL=OFF
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_DataSpaces:BOOL=OFF
 ADIOS2_USE_Fortran:BOOL=OFF

diff --git a/scripts/ci/cmake/ci-el8-oneapi-serial.cmake b/scripts/ci/cmake/ci-el8-oneapi-serial.cmake
@@ -7,7 +7,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=OFF
+ADIOS2_USE_Blosc2:BOOL=OFF
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_DataSpaces:BOOL=OFF
 ADIOS2_USE_Fortran:BOOL=OFF

diff --git a/scripts/ci/cmake/ci-macos-12-xcode13_4_1-static-serial.cmake b/scripts/ci/cmake/ci-macos-12-xcode13_4_1-static-serial.cmake
@@ -11,7 +11,7 @@ ADIOS2_BUILD_EXAMPLES:BOOL=OFF
 
 ADIOS2_USE_AWSSDK:STRING=OFF
 ADIOS2_USE_Blosc2:STRING=OFF
-ADIOS2_USE_Blosc:BOOL=OFF
+ADIOS2_USE_Blosc2:BOOL=OFF
 ADIOS2_USE_BZip2:BOOL=OFF
 ADIOS2_USE_Catalyst:STRING=OFF
 ADIOS2_USE_CUDA:STRING=OFF

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang10-mpich.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang10-mpich.cmake
@@ -15,7 +15,7 @@ set(dashboard_cache "
 BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang10-ompi.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang10-ompi.cmake
@@ -11,7 +11,7 @@ set(dashboard_cache "
 BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang10-serial.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang10-serial.cmake
@@ -11,7 +11,7 @@ set(dashboard_cache "
 BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang6-mpich.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang6-mpich.cmake
@@ -15,7 +15,7 @@ set(dashboard_cache "
 BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang6-ompi.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang6-ompi.cmake
@@ -11,7 +11,7 @@ set(dashboard_cache "
 BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang6-serial.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang6-serial.cmake
@@ -11,7 +11,7 @@ set(dashboard_cache "
 BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang6-static-ompi.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang6-static-ompi.cmake
@@ -13,7 +13,7 @@ BUILD_TESTING:BOOL=OFF
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-gcc10-mpich.cmake b/scripts/ci/cmake/ci-ubuntu20.04-gcc10-mpich.cmake
@@ -16,7 +16,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-gcc10-ompi.cmake b/scripts/ci/cmake/ci-ubuntu20.04-gcc10-ompi.cmake
@@ -12,7 +12,7 @@ BUILD_TESTING:BOOL=ON
 ADIOS2_BUILD_EXAMPLES:BOOL=ON
 
 ADIOS2_USE_BZip2:BOOL=ON
-ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_Blosc2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON