Backport from master

.github/workflows/everything.yml

@@ -40,7 +40,7 @@ jobs:
     outputs:
       num_code_changes: ${{ steps.get_code_changes.outputs.num_code_changes }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Check for appropriately named topic branch
@@ -69,10 +69,10 @@ jobs:
       image: ornladios/adios2:ci-formatting
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: gha
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           path: source
@@ -124,10 +124,10 @@ jobs:
             parallel: mpich
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: gha
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           path: source
@@ -231,10 +231,10 @@ jobs:
             compiler: xcode13_4_1
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: gha
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           path: source
@@ -280,10 +280,10 @@ jobs:
         shell: bash
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: gha
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           path: source
@@ -314,7 +314,7 @@ jobs:
         baseos: [ubuntu-bionic]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           path: ci-source
@@ -393,7 +393,7 @@ jobs:
         shell: bash -c "docker exec adios2-ci bash --login -e $(echo {0} | sed 's|/home/runner/work|/__w|g')"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           repository: ${{ matrix.repo }}
           ref: ${{ matrix.ref }}

CMakeLists.txt

@@ -196,6 +196,8 @@ if(ADIOS2_HAVE_MPI)
   add_definitions(-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX)
 endif()
 
+cmake_dependent_option(ADIOS2_Blosc2_PREFER_SHARED "Prefer shared Blosc2 libraries"
+  ON "Blosc2_shlib_available" OFF)
 
 #------------------------------------------------------------------------------#
 # POSIX O_DIRECT is only working for Unix in adios for now

CTestCustom.cmake.in

@@ -24,6 +24,7 @@ list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION
   "Warning #20208-D: '.*' is treated as '.*' in device code"
   "Warning: '.*' is treated as '.*' in device code"
   ".*was specified as both a system and non-system include directory.*"
+  "Wunused-command-line-argument"
 )
 list(APPEND CTEST_CUSTOM_COVERAGE_EXCLUDE
   ".*/thirdparty/.*"

cmake/DetectOptions.cmake

@@ -69,12 +69,35 @@ endfunction()
 
 # Blosc2
 if(ADIOS2_USE_Blosc2 STREQUAL AUTO)
-  find_package(Blosc2 2.4)
+  # Prefect CONFIG mode
+  find_package(Blosc2 2.4 CONFIG QUIET)
+  if(NOT Blosc2_FOUND)
+    find_package(Blosc2 2.4 MODULE QUIET)
+  endif()
 elseif(ADIOS2_USE_Blosc2)
-  find_package(Blosc2 2.4 REQUIRED)
+  # Prefect CONFIG mode
+  find_package(Blosc2 2.4 CONFIG)
+  if(NOT Blosc2_FOUND)
+    find_package(Blosc2 2.4 MODULE REQUIRED)
+  endif()
 endif()
-if(BLOSC2_FOUND)
+if(Blosc2_FOUND)
   set(ADIOS2_HAVE_Blosc2 TRUE)
+  if(TARGET Blosc2::blosc2_shared)
+    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)
+      set(adios2_blosc2_tgt Blosc2::blosc2_$<IF:$<BOOL:${ADIOS2_Blosc2_PREFER_SHARED}>,shared,static>)
+    else()
+      set(adios2_blosc2_tgt Blosc2::blosc2_static)
+    endif()
+  endif()
+
+  add_library(adios2_blosc2 INTERFACE)
+  target_link_libraries(adios2_blosc2 INTERFACE ${adios2_blosc2_tgt})
 endif()
 
 # BZip2
@@ -407,9 +430,11 @@ if(ADIOS2_USE_SST AND NOT WIN32)
     endif()
   endif()
   if(ADIOS2_HAVE_MPI)
-    set(CMAKE_REQUIRED_LIBRARIES MPI::MPI_C)
-    include(CheckCSourceRuns)
-    check_c_source_runs([=[
+    set(CMAKE_REQUIRED_LIBRARIES "MPI::MPI_C;Threads::Threads")
+    include(CheckCXXSourceRuns)
+    check_cxx_source_runs([=[
+        #include <chrono>
+        #include <future>
         #include <mpi.h>
         #include <stdlib.h>
 
@@ -419,9 +444,18 @@ if(ADIOS2_USE_SST AND NOT WIN32)
 
         int main()
         {
+          // Timeout after 5 second
+          auto task = std::async(std::launch::async, []() {
+                                 std::this_thread::sleep_for(std::chrono::seconds(5));
+                                 exit(EXIT_FAILURE);
+          });
+
+          char* port_name = new char[MPI_MAX_PORT_NAME];
           MPI_Init_thread(NULL, NULL, MPI_THREAD_MULTIPLE, NULL);
-          MPI_Open_port(MPI_INFO_NULL, malloc(sizeof(char) * MPI_MAX_PORT_NAME));
+          MPI_Open_port(MPI_INFO_NULL, port_name);
+          MPI_Close_port(port_name);
           MPI_Finalize();
+          exit(EXIT_SUCCESS);
         }]=]
     ADIOS2_HAVE_MPI_CLIENT_SERVER)
     unset(CMAKE_REQUIRED_LIBRARIES)

cmake/adios2-config-common.cmake.in

@@ -12,6 +12,11 @@ endif()
 
 set(ADIOS2_HAVE_Fortran @ADIOS2_HAVE_Fortran@)
 set(ADIOS2_HAVE_MPI @ADIOS2_HAVE_MPI@)
+set(ADIOS2_HAVE_CUDA @ADIOS2_HAVE_CUDA@)
+set(ADIOS2_HAVE_Kokkos @ADIOS2_HAVE_Kokkos@)
+set(ADIOS2_HAVE_Kokkos_CUDA @ADIOS2_HAVE_Kokkos_CUDA@)
+set(ADIOS2_HAVE_Kokkos_HIP @ADIOS2_HAVE_Kokkos_HIP@)
+set(ADIOS2_HAVE_Kokkos_SYCL @ADIOS2_HAVE_Kokkos_SYCL@)
 
 function(adios2_add_thirdparty_target PackageName)
   add_library(adios2::thirdparty::${PackageName} INTERFACE IMPORTED)

cmake/adios2-config-install.cmake.in

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.12)
 
 set(_ADIOS2_CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH})
 list(INSERT CMAKE_MODULE_PATH 0 "${CMAKE_CURRENT_LIST_DIR}")

cmake/install/post/adios2-config-dummy/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.12)
 
 project(adios2-config-dummy C CXX)
 

cmake/install/post/generate-adios2-config.sh.in

@@ -64,6 +64,12 @@ if [ "${1:0:1}" != "/" ]
 then
   # Convert relative paths to absolute based on DESTDIR
   PREFIX="${DESTDIR:-$(pwd)}/$1"
+else
+  # check if the PREFIX directory exists and prepend DESTDIR if not
+  if [ ! -d "${PREFIX}" ]
+  then
+    PREFIX="${DESTDIR}$1"
+  fi
 fi
 
 shift

plugins/engines/CMakeLists.txt

@@ -4,7 +4,7 @@
 #------------------------------------------------------------------------------#
 
 if(ADIOS2_HAVE_Catalyst)
-  add_library(ParaViewADIOSInSituEngine
+  add_library(ParaViewADIOSInSituEngine MODULE
     ParaViewFidesEngine.cpp)
   target_link_libraries(ParaViewADIOSInSituEngine
     PUBLIC

plugins/operators/CMakeLists.txt

@@ -4,7 +4,7 @@
 #------------------------------------------------------------------------------#
 
 if(ADIOS2_HAVE_Sodium)
-  add_library(EncryptionOperator
+  add_library(EncryptionOperator MODULE
     EncryptionOperator.cpp
   )
   target_link_libraries(EncryptionOperator adios2_core sodium)

readthedocs.yml

@@ -10,7 +10,7 @@ build:
         python: "miniconda3-4.7"
     jobs:
         pre_install:
-            - cmake -B build -S . -DADIOS2_USE_PYTHON=ON -DBUILD_TESTING=OFF -DADIOS2_BUILD_EXAMPLES=OFF
+            - cmake -B build -S . -DADIOS2_USE_PYTHON=ON
             - cmake --build build
             - cmake --install build --prefix "$HOME/.local"
 formats:

scripts/ci/cmake-v2/ci-el8-gcc10-mpi.cmake

@@ -14,6 +14,7 @@ ADIOS2_USE_Blosc:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON
+ADIOS2_USE_MGARD:BOOL=OFF
 ADIOS2_USE_MPI:BOOL=ON
 ADIOS2_USE_Python:BOOL=ON
 ADIOS2_USE_SZ:BOOL=ON

scripts/ci/cmake-v2/ci-el8-gcc11-mpi.cmake

@@ -14,6 +14,7 @@ ADIOS2_USE_Blosc:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON
+ADIOS2_USE_MGARD:BOOL=OFF
 ADIOS2_USE_MPI:BOOL=ON
 ADIOS2_USE_Python:BOOL=ON
 ADIOS2_USE_SZ:BOOL=ON

source/adios2/CMakeLists.txt

@@ -258,9 +258,11 @@ if(ADIOS2_HAVE_DataSpaces)
   target_link_libraries(adios2_core_mpi PRIVATE DataSpaces::DataSpaces)
 endif()
 
+set(maybe_adios2_blosc2)
 if(ADIOS2_HAVE_Blosc2)
   target_sources(adios2_core PRIVATE operator/compress/CompressBlosc.cpp)
-  target_link_libraries(adios2_core PRIVATE Blosc2::Blosc2)
+  target_link_libraries(adios2_core PRIVATE adios2_blosc2)
+  set(maybe_adios2_blosc2 adios2_blosc2)
 endif()
 
 if(ADIOS2_HAVE_BZip2)
@@ -399,11 +401,6 @@ install(FILES common/ADIOSMacros.h common/ADIOSTypes.h common/ADIOSTypes.inl
 install(DIRECTORY core/
   DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/adios2/core COMPONENT adios2_core-development
   FILES_MATCHING PATTERN "*.h"
-  PATTERN "Info.h" EXCLUDE
-)
-
-install(FILES core/Info.h
-  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} COMPONENT adios2_core-development
 )
 
 install(DIRECTORY engine/
@@ -433,7 +430,7 @@ install(DIRECTORY toolkit/
 )
 
 # Library installation
-install(TARGETS adios2_core ${maybe_adios2_core_mpi} ${maybe_adios2_core_cuda} ${maybe_adios2_core_kokkos} EXPORT adios2Exports
+install(TARGETS adios2_core ${maybe_adios2_core_mpi} ${maybe_adios2_core_cuda} ${maybe_adios2_core_kokkos} ${maybe_adios2_blosc2} EXPORT adios2Exports
   RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT adios2_core-runtime
   LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT adios2_core-libraries NAMELINK_COMPONENT adios2_core-development
   ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT adios2_core-development

source/adios2/toolkit/sst/dp/mpi_dp.c

@@ -42,8 +42,6 @@
 #define QUOTE(name) #name
 #define MACRO_TO_STR(name) QUOTE(name)
 
-static pthread_once_t OnceMpiInitializer = PTHREAD_ONCE_INIT;
-
 /*****Stream Basic Structures ***********************************************/
 
 typedef struct _MpiReaderContactInfo
@@ -249,40 +247,6 @@ static void MpiReadReplyHandler(CManager cm, CMConnection conn, void *msg_v,
 static void MpiReadRequestHandler(CManager cm, CMConnection conn, void *msg_v,
                                   void *client_Data, attr_list attrs);
 
-/**
- * Initialize MPI in the mode that it is required for MPI_DP to work.
- *
- * It can be called multiple times.
- */
-static void MpiInitialize()
-{
-    int IsInitialized = 0;
-    int provided;
-
-    MPI_Initialized(&IsInitialized);
-    if (!IsInitialized)
-    {
-        MPI_Init_thread(NULL, NULL, MPI_THREAD_MULTIPLE, &provided);
-    }
-    else
-    {
-        MPI_Query_thread(&provided);
-    }
-
-    if (provided != MPI_THREAD_MULTIPLE)
-    {
-        int rank;
-        MPI_Comm_rank(MPI_COMM_WORLD, &rank);
-        if (!rank)
-        {
-            fprintf(stderr,
-                    "MPI init without MPI_THREAD_MULTIPLE (Externally "
-                    "initialized:%s)\n",
-                    IsInitialized ? "true" : "false");
-        }
-    }
-}
-
 /*****Public accessible functions********************************************/
 
 /**
@@ -301,8 +265,6 @@ static DP_RS_Stream MpiInitReader(CP_Services Svcs, void *CP_Stream,
                                   struct _SstParams *Params,
                                   attr_list WriterContact, SstStats Stats)
 {
-    pthread_once(&OnceMpiInitializer, MpiInitialize);
-
     MpiStreamRD Stream = calloc(sizeof(struct _MpiStreamRD), 1);
     CManager cm = Svcs->getCManager(CP_Stream);
     SMPI_Comm comm = Svcs->getMPIComm(CP_Stream);
@@ -344,8 +306,6 @@ static DP_WS_Stream MpiInitWriter(CP_Services Svcs, void *CP_Stream,
                                   struct _SstParams *Params, attr_list DPAttrs,
                                   SstStats Stats)
 {
-    pthread_once(&OnceMpiInitializer, MpiInitialize);
-
     MpiStreamWR Stream = calloc(sizeof(struct _MpiStreamWR), 1);
     CManager cm = Svcs->getCManager(CP_Stream);
     SMPI_Comm comm = Svcs->getMPIComm(CP_Stream);
@@ -848,16 +808,30 @@ static void MpiReleaseTimeStep(CP_Services Svcs, DP_WS_Stream Stream_v,
 static int MpiGetPriority(CP_Services Svcs, void *CP_Stream,
                           struct _SstParams *Params)
 {
-#if defined(MPICH)
-    // Only enabled when MPI_THREAD_MULTIPLE and using MPICH
+    int IsInitialized = 0;
     int provided = 0;
-    pthread_once(&OnceMpiInitializer, MpiInitialize);
-    MPI_Query_thread(&provided);
-    if (provided == MPI_THREAD_MULTIPLE)
+    int IsMPICH = 0;
+#if defined(MPICH)
+    IsMPICH = 1;
+
+    MPI_Initialized(&IsInitialized);
+    if (IsInitialized)
     {
-        return 100;
+        MPI_Query_thread(&provided);
+        // Only enabled when MPI_THREAD_MULTIPLE and using MPICH
+        if (provided == MPI_THREAD_MULTIPLE)
+        {
+            return 100;
+        }
     }
 #endif
+
+    Svcs->verbose(CP_Stream, DPTraceVerbose,
+                  "MPI DP disabled since the following predicate is false: "
+                  "(MPICH=%s AND MPI_initialized=%s AND MPI_THREAD_MULTIPLE=%s)",
+                  IsMPICH ? "true" : "false", IsInitialized ? "true" : "false",
+                  provided == MPI_THREAD_MULTIPLE ? "true" : "false");
+
     return -100;
 }