sys-cluster/adios2: new package, add 2.8.1

Signed-off-by: Alessandro Barbieri <lssndrbarbieri@gmail.com>
2026-07-22 21:43:03 -04:00 · 2022-06-06 03:32:03 +02:00
parent 5888590f0a
commit 8b0667d8fb
5 changed files with 497 additions and 0 deletions
--- a/sys-cluster/adios2/files/adios2-2.8.1-sandbox.patch
+++ b/sys-cluster/adios2/files/adios2-2.8.1-sandbox.patch
@@ -0,0 +1,12 @@
+--- a/cmake/install/pre/CMakeLists.txt
+++ b/cmake/install/pre/CMakeLists.txt
+@@ -1,9 +1,3 @@
+-install(CODE "
+-  message(\"Pre-installation cleanup of CMake files\")
+-  file(REMOVE_RECURSE \"${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_CMAKEDIR}\")
+-"
+-  COMPONENT adios2_core-development
+-)
+ file(GLOB ADIOS2_MODULE_FILES 
+   "${ADIOS2_SOURCE_DIR}/cmake/Find*.cmake"
+   "${ADIOS2_SOURCE_DIR}/cmake/CMake*.cmake"
--- a/sys-cluster/adios2/files/adios2-2.8.1-system-libs.patch
+++ b/sys-cluster/adios2/files/adios2-2.8.1-system-libs.patch
@@ -0,0 +1,307 @@
+--- a/source/adios2/CMakeLists.txt
+++ b/source/adios2/CMakeLists.txt
+@@ -127,7 +127,7 @@
+     $<BUILD_INTERFACE:${ADIOS2_SOURCE_DIR}/source>
+     $<BUILD_INTERFACE:${ADIOS2_BINARY_DIR}/source>
+ )
+-target_link_libraries(adios2_core PRIVATE adios2sys_interface adios2::thirdparty::pugixml
+target_link_libraries(adios2_core PRIVATE -lkwsys adios2::thirdparty::pugixml
+   adios2::thirdparty::yaml-cpp adios2::thirdparty::nlohmann_json adios2::thirdparty::perfstubs-interface)
+ target_link_libraries(adios2_core PUBLIC ${CMAKE_THREAD_LIBS_INIT})
+ target_compile_features(adios2_core PUBLIC "$<BUILD_INTERFACE:${ADIOS2_CXX11_FEATURES}>")
+@@ -151,7 +151,7 @@
+     toolkit/format/bp5/BP5Serializer.cpp
+     toolkit/format/bp5/BP5Deserializer.cpp  toolkit/format/bp5/BP5Deserializer.tcc
+   )
+-  target_link_libraries(adios2_core PRIVATE ffs::ffs)
+  target_link_libraries(adios2_core PRIVATE ffs)
+ endif()
+ 
+ if(ADIOS2_HAVE_DAOS)
+--- a/source/adios2/core/ADIOS.cpp
+++ b/source/adios2/core/ADIOS.cpp
+@@ -19,7 +19,7 @@
+ #include "adios2/helper/adiosCommDummy.h"
+ #include "adios2/helper/adiosFunctions.h" //InquireKey, BroadcastFile
+ #include "adios2/operator/OperatorFactory.h"
+-#include <adios2sys/SystemTools.hxx>
+#include <kwsys/SystemTools.hxx>
+ 
+ #include <adios2-perfstubs-interface.h>
+ 
+@@ -53,7 +53,7 @@
+ #endif
+     if (!configFile.empty())
+     {
+-        if (!adios2sys::SystemTools::FileExists(configFile))
+        if (!kwsys::SystemTools::FileExists(configFile))
+         {
+             helper::Throw<std::logic_error>("Core", "ADIOS", "ADIOS",
+                                             "config file " + configFile +
+--- a/source/adios2/core/IO.cpp
+++ b/source/adios2/core/IO.cpp
+@@ -39,7 +39,7 @@
+ #include "adios2/helper/adiosComm.h"
+ #include "adios2/helper/adiosFunctions.h" //BuildParametersMap
+ #include "adios2/helper/adiosString.h"
+-#include <adios2sys/SystemTools.hxx> // FileIsDirectory()
+#include <kwsys/SystemTools.hxx> // FileIsDirectory()
+ 
+ #ifdef ADIOS2_HAVE_DATAMAN // external dependencies
+ #include "adios2/engine/dataman/DataManReader.h"
+@@ -559,13 +559,13 @@
+         else if ((mode_to_use == Mode::Read) ||
+                  (mode_to_use == Mode::ReadRandomAccess))
+         {
+-            if (adios2sys::SystemTools::FileIsDirectory(name))
+            if (kwsys::SystemTools::FileIsDirectory(name))
+             {
+                 char v = helper::BPVersion(name, comm, m_TransportsParameters);
+                 engineTypeLC = "bp";
+                 engineTypeLC.push_back(v);
+             }
+-            else if (adios2sys::SystemTools::FileIsDirectory(name + ".tier0"))
+            else if (kwsys::SystemTools::FileIsDirectory(name + ".tier0"))
+             {
+                 engineTypeLC = "mhs";
+             }
+--- a/source/adios2/helper/adiosDynamicBinder.cpp
+++ b/source/adios2/helper/adiosDynamicBinder.cpp
+@@ -18,8 +18,8 @@
+ #include <stdexcept> // for runtime_error
+ #include <vector>    // for vector
+ 
+-#include <adios2sys/DynamicLoader.hxx>
+-#include <adios2sys/SystemTools.hxx>
+#include <kwsys/DynamicLoader.hxx>
+#include <kwsys/SystemTools.hxx>
+ 
+ namespace adios2
+ {
+@@ -28,7 +28,7 @@
+ 
+ struct DynamicBinder::Impl
+ {
+-    adios2sys::DynamicLoader::LibraryHandle m_LibraryHandle;
+    kwsys::DynamicLoader::LibraryHandle m_LibraryHandle;
+ };
+ 
+ DynamicBinder::DynamicBinder(std::string libName) : DynamicBinder(libName, "")
+@@ -76,14 +76,14 @@
+                 // ConvertToOutputPath() will change slashes if we're running on
+                 // a Windows system
+                 fileName =
+-                    adios2sys::SystemTools::ConvertToOutputPath(fileName);
+                    kwsys::SystemTools::ConvertToOutputPath(fileName);
+             }
+             else
+             {
+                 fileName = prefix + libName + suffix;
+             }
+             m_Impl->m_LibraryHandle =
+-                adios2sys::DynamicLoader::OpenLibrary(fileName);
+                kwsys::DynamicLoader::OpenLibrary(fileName);
+             searchedLibs.push_back(fileName);
+             if (m_Impl->m_LibraryHandle)
+             {
+@@ -110,13 +110,13 @@
+ 
+ DynamicBinder::~DynamicBinder()
+ {
+-    adios2sys::DynamicLoader::CloseLibrary(m_Impl->m_LibraryHandle);
+    kwsys::DynamicLoader::CloseLibrary(m_Impl->m_LibraryHandle);
+ }
+ 
+ DynamicBinder::VoidSymbolPointer
+ DynamicBinder::GetSymbol(std::string symbolName)
+ {
+-    return adios2sys::DynamicLoader::GetSymbolAddress(m_Impl->m_LibraryHandle,
+    return kwsys::DynamicLoader::GetSymbolAddress(m_Impl->m_LibraryHandle,
+                                                       symbolName);
+ }
+ 
+--- a/source/adios2/helper/adiosPluginManager.cpp
+++ b/source/adios2/helper/adiosPluginManager.cpp
+@@ -17,7 +17,7 @@
+ #include "adios2/helper/adiosLog.h"
+ #include "adios2/helper/adiosString.h"
+ 
+-#include <adios2sys/SystemTools.hxx>
+#include <kwsys/SystemTools.hxx>
+ 
+ #include <memory>
+ #include <stdexcept>
+@@ -110,13 +110,13 @@
+     }
+ 
+     std::string allPluginPaths;
+-    adios2sys::SystemTools::GetEnv(pluginEnvVarName, allPluginPaths);
+    kwsys::SystemTools::GetEnv(pluginEnvVarName, allPluginPaths);
+     if (allPluginPaths.empty())
+     {
+         return OpenPlugin(pluginName, pluginLibrary, "");
+     }
+     auto pathsSplit =
+-        adios2sys::SystemTools::SplitString(allPluginPaths, ':', false);
+        kwsys::SystemTools::SplitString(allPluginPaths, ':', false);
+ 
+     bool loaded = false;
+     auto pathIt = pathsSplit.begin();
+--- a/source/adios2/helper/adiosSystem.cpp
+++ b/source/adios2/helper/adiosSystem.cpp
+@@ -13,7 +13,7 @@
+ #include <stdexcept> // std::runtime_error, std::exception
+ #include <system_error>
+ 
+-#include <adios2sys/SystemTools.hxx>
+#include <kwsys/SystemTools.hxx>
+ 
+ #include "adios2/common/ADIOSTypes.h"
+ #include "adios2/helper/adiosComm.h"
+@@ -37,7 +37,7 @@
+ 
+ bool CreateDirectory(const std::string &fullPath) noexcept
+ {
+-    return static_cast<bool>(adios2sys::SystemTools::MakeDirectory(fullPath));
+    return static_cast<bool>(kwsys::SystemTools::MakeDirectory(fullPath));
+ }
+ 
+ bool IsLittleEndian() noexcept
+@@ -168,7 +168,7 @@
+     if (!comm.Rank())
+     {
+         std::string mmdFileName = name + PathSeparator + "mmd.0";
+-        if (adios2sys::SystemTools::PathExists(mmdFileName))
+        if (kwsys::SystemTools::PathExists(mmdFileName))
+         {
+             version = '5';
+         }
+--- a/source/adios2/operator/plugin/PluginOperator.cpp
+++ b/source/adios2/operator/plugin/PluginOperator.cpp
+@@ -21,7 +21,7 @@
+ #include "adios2/helper/adiosPluginManager.h"
+ #include "adios2/helper/adiosString.h"
+ 
+-#include <adios2sys/SystemTools.hxx>
+#include <kwsys/SystemTools.hxx>
+ 
+ namespace adios2
+ {
+--- a/source/utils/bpls/bpls.cpp
+++ b/source/utils/bpls/bpls.cpp
+@@ -57,8 +57,8 @@
+ 
+ #include "adios2/helper/adiosString.h" // EndsWith
+ #include "adios2/helper/adiosSystem.h" //isHDF5File
+-#include <adios2sys/CommandLineArguments.hxx>
+-#include <adios2sys/SystemTools.hxx>
+#include <kwsys/CommandLineArguments.hxx>
+#include <kwsys/SystemTools.hxx>
+ #include <pugixml.hpp>
+ 
+ namespace adios2
+@@ -202,8 +202,8 @@
+ bool option_help_was_called = false;
+ int optioncb_help(const char *argument, const char *value, void *call_data)
+ {
+-    // adios2sys::CommandLineArguments *arg =
+-    // static_cast<adios2sys::CommandLineArguments *>(call_data);
+    // kwsys::CommandLineArguments *arg =
+    // static_cast<kwsys::CommandLineArguments *>(call_data);
+     // printf("%s\n", arg->GetHelp());
+     display_help();
+     option_help_was_called = true;
+@@ -431,7 +431,7 @@
+ 
+ void introspect_file(const char *filename) noexcept
+ {
+-    if (adios2sys::SystemTools::FileIsDirectory(filename))
+    if (kwsys::SystemTools::FileIsDirectory(filename))
+     {
+         if (!introspectAsBPDir(filename))
+         {
+@@ -460,7 +460,7 @@
+     }
+ }
+ 
+-int process_unused_args(adios2sys::CommandLineArguments &arg)
+int process_unused_args(kwsys::CommandLineArguments &arg)
+ {
+     int nuargs;
+     char **uargs;
+@@ -541,9 +541,9 @@
+ 
+     init_globals();
+ 
+-    adios2sys::CommandLineArguments arg;
+    kwsys::CommandLineArguments arg;
+     arg.Initialize(argc, argv);
+-    typedef adios2sys::CommandLineArguments argT;
+    typedef kwsys::CommandLineArguments argT;
+     arg.StoreUnusedArguments(true);
+     arg.AddCallback("-v", argT::NO_ARGUMENT, optioncb_verbose, nullptr, "");
+     arg.AddCallback("--verbose", argT::NO_ARGUMENT, optioncb_verbose, nullptr,
+@@ -1521,7 +1521,7 @@
+     if (verbose > 1)
+         printf("\nADIOS Open: read header info from %s\n", path);
+ 
+-    if (!adios2sys::SystemTools::FileExists(path))
+    if (!kwsys::SystemTools::FileExists(path))
+     {
+         fprintf(stderr, "\nError: input path %s does not exist\n", path);
+         return 4;
+--- a/source/utils/CMakeLists.txt
+++ b/source/utils/CMakeLists.txt
+@@ -11,7 +11,7 @@
+ 
+ # BPLS
+ add_executable(bpls ./bpls/bpls.cpp)
+-target_link_libraries(bpls adios2_core adios2sys adios2::thirdparty::pugixml)
+target_link_libraries(bpls adios2_core -lkwsys adios2::thirdparty::pugixml)
+ target_include_directories(bpls PRIVATE ${PROJECT_BINARY_DIR})
+ set_property(TARGET bpls PROPERTY OUTPUT_NAME bpls${ADIOS2_EXECUTABLE_SUFFIX})
+ install(TARGETS bpls EXPORT adios2
+@@ -30,7 +30,7 @@
+ 
+ # BPSPLIT
+ #add_executable(bpsplit ./bpsplit/bpsplit.cpp)
+-#target_link_libraries(bpsplit adios2::cxx11 adios2sys_interface adios2::thirdparty::pugixml)
+#target_link_libraries(bpsplit adios2::cxx11 -lkwsys adios2::thirdparty::pugixml)
+ #install(TARGETS bpsplit EXPORT adios2
+ #  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+ #)
+--- a/thirdparty/CMakeLists.txt
+++ b/thirdparty/CMakeLists.txt
+@@ -33,8 +33,6 @@
+ option(ADIOS2_USE_EXTERNAL_YAMLCPP
+   "Use an externally supplied yaml-cpp library" "${ADIOS2_USE_EXTERNAL_DEPENDENCIES}")
+ 
+-add_subdirectory(KWSys)
+-
+ add_subdirectory(perfstubs)
+ adios2_add_thirdparty_target(perfstubs-interface perfstubs-interface)
+ 
+--- a/thirdparty/perfstubs/CMakeLists.txt
+++ b/thirdparty/perfstubs/CMakeLists.txt
+@@ -1,12 +1,3 @@
+-message_start_thirdparty()
+-
+-if (NOT WIN32 AND BUILD_SHARED_LIBS AND ADIOS2_HAVE_Profiling)
+-  set(PERFSTUBS_USE_TIMERS ON CACHE INTERNAL "")
+-  add_subdirectory(perfstubs)
+-else()
+-  set(PERFSTUBS_USE_TIMERS OFF CACHE INTERNAL "")
+-endif()
+-
+ add_library(perfstubs-interface INTERFACE)
+ 
+ configure_file(
+@@ -19,7 +10,6 @@
+ )
+ 
+ if (PERFSTUBS_USE_TIMERS)
+  find_package(perfstubs REQUIRED)
+   target_link_libraries(perfstubs-interface INTERFACE perfstubs)
+ endif()
+-
+-message_end_thirdparty()