From 3aab0facc3815338bb9209904bc96553c656d3cb Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 10 Jun 2022 18:05:01 -0400 Subject: [PATCH] ADIOS2: Update to 2.8.1 (#5015) --- A/ADIOS2/build_tarballs.jl | 17 +- A/ADIOS2/bundled/patches/fatalerror.patch | 262 ---------------------- 2 files changed, 7 insertions(+), 272 deletions(-) delete mode 100644 A/ADIOS2/bundled/patches/fatalerror.patch diff --git a/A/ADIOS2/build_tarballs.jl b/A/ADIOS2/build_tarballs.jl index 94eb5a49e86..64ff7b47ed1 100644 --- a/A/ADIOS2/build_tarballs.jl +++ b/A/ADIOS2/build_tarballs.jl @@ -6,12 +6,12 @@ const YGGDRASIL_DIR = "../.." include(joinpath(YGGDRASIL_DIR, "platforms", "mpi.jl")) name = "ADIOS2" -version = v"2.8.0" +version = v"2.8.1" # Collection of sources required to complete build sources = [ - ArchiveSource("https://github.com/ornladios/ADIOS2/archive/refs/tags/v2.8.0.tar.gz", - "5af3d950e616989133955c2430bd09bcf6bad3a04cf62317b401eaf6e7c2d479"), + ArchiveSource("https://github.com/ornladios/ADIOS2/archive/refs/tags/v$(version).tar.gz", + "3f515b442bbd52e3189866b121613fe3b59edb8845692ea86fad83d1eba35d93"), DirectorySource("./bundled"), ] @@ -22,9 +22,6 @@ cd ADIOS2-* # Don't define clock_gettime on macOS atomic_patch -p1 ${WORKSPACE}/srcdir/patches/clock_gettime.patch atomic_patch -p1 ${WORKSPACE}/srcdir/patches/shlwapi.patch -# Don't use `ERROR` as identifier; it is reserved on Windows. -# Already implemented on master. -atomic_patch -p1 ${WORKSPACE}/srcdir/patches/fatalerror.patch mkdir build cd build @@ -133,7 +130,7 @@ products = [ dependencies = [ Dependency(PackageSpec(name="Blosc_jll")), Dependency(PackageSpec(name="Bzip2_jll"); compat="1.0.8"), - Dependency(PackageSpec(name="CompilerSupportLibraries_jll", uuid="e66e0078-7015-5450-92f7-15fbd957f2ae")), + Dependency(PackageSpec(name="CompilerSupportLibraries_jll", uuid="e66e0078-7015-5450-92f7-15fbd957f2ae"), v"0.5.2"), # We cannot use HDF5 because we need an HDF5 configuration with MPI support # Dependency(PackageSpec(name="HDF5_jll")), Dependency(PackageSpec(name="ZeroMQ_jll")), @@ -143,9 +140,9 @@ dependencies = [ platforms, platform_dependencies = MPI.augment_platforms(platforms) # With MPItrampoline, select only those platforms where MPItrampoline is actually built -platforms = filter(p -> !(p["mpi"] ∈ ("mpitrampoline", "mpiwrapper") && (Sys.iswindows(p) || libc(p) == "musl")), platforms) -platforms = filter(p -> !(p["mpi"] ∈ ("mpitrampoline", "mpiwrapper") && Sys.isfreebsd(p)), platforms) -platforms = filter(p -> !(p["mpi"] ∈ ("mpitrampoline", "mpiwrapper") && libgfortran_version(p) == v"3"), platforms) +platforms = filter(p -> !(p["mpi"] == "mpitrampoline" && (Sys.iswindows(p) || libc(p) == "musl")), platforms) +platforms = filter(p -> !(p["mpi"] == "mpitrampoline" && Sys.isfreebsd(p)), platforms) +platforms = filter(p -> !(p["mpi"] == "mpitrampoline" && libgfortran_version(p) == v"3"), platforms) append!(dependencies, platform_dependencies) # Build the tarballs, and possibly a `build.jl` as well. diff --git a/A/ADIOS2/bundled/patches/fatalerror.patch b/A/ADIOS2/bundled/patches/fatalerror.patch deleted file mode 100644 index 1389d389ea2..00000000000 --- a/A/ADIOS2/bundled/patches/fatalerror.patch +++ /dev/null @@ -1,262 +0,0 @@ -diff --git a/source/adios2/engine/ssc/SscReader.cpp b/source/adios2/engine/ssc/SscReader.cpp -index e8461258b..ff13c69c2 100644 ---- a/source/adios2/engine/ssc/SscReader.cpp -+++ b/source/adios2/engine/ssc/SscReader.cpp -@@ -150,7 +150,7 @@ StepStatus SscReader::BeginStep(const StepMode stepMode, - { - helper::Log("Engine", "SSCReader", "BeginStep", - "unknown data type", 0, m_Comm.Rank(), 0, -- m_Verbosity, helper::LogMode::ERROR); -+ m_Verbosity, helper::LogMode::FATALERROR); - } - } - } -@@ -252,7 +252,7 @@ void SscReader::PerformGets() - { - helper::Log("Engine", "SSCReader", "PerformGets", - "unknown data type", 0, m_Comm.Rank(), -- 0, m_Verbosity, helper::LogMode::ERROR); -+ 0, m_Verbosity, helper::LogMode::FATALERROR); - } - } - } -diff --git a/source/adios2/engine/ssc/SscReader.tcc b/source/adios2/engine/ssc/SscReader.tcc -index 6271b69b9..9dd70e191 100644 ---- a/source/adios2/engine/ssc/SscReader.tcc -+++ b/source/adios2/engine/ssc/SscReader.tcc -@@ -154,7 +154,7 @@ void SscReader::GetDeferredCommon(Variable &variable, T *data) - { - helper::Log("Engine", "SSCReader", "GetDeferredCommon", - "unknown ShapeID", 0, m_Comm.Rank(), 0, -- m_Verbosity, helper::LogMode::ERROR); -+ m_Verbosity, helper::LogMode::FATALERROR); - } - } - } -diff --git a/source/adios2/helper/adiosCommDummy.cpp b/source/adios2/helper/adiosCommDummy.cpp -index 9c0234952..2f09b97ce 100644 ---- a/source/adios2/helper/adiosCommDummy.cpp -+++ b/source/adios2/helper/adiosCommDummy.cpp -@@ -25,7 +25,7 @@ void CommDummyError(const std::string &msg) - helper::Log("Helper", "adiosCommDummy", "CommDummyError", - "CommDummy: a function returned error code '" + msg + - "'. Aborting!", -- helper::LogMode::ERROR); -+ helper::LogMode::FATALERROR); - std::abort(); - } - } -diff --git a/source/adios2/helper/adiosLog.cpp b/source/adios2/helper/adiosLog.cpp -index f080797b3..f13769b84 100644 ---- a/source/adios2/helper/adiosLog.cpp -+++ b/source/adios2/helper/adiosLog.cpp -@@ -54,7 +54,7 @@ std::string MakeMessage(const std::string &component, const std::string &source, - { - m << warningColor << " [ADIOS2 WARNING]" << defaultColor; - } -- else if (mode == ERROR) -+ else if (mode == FATALERROR) - { - m << errorColor << " [ADIOS2 ERROR]" << defaultColor; - } -@@ -102,7 +102,7 @@ void Log(const std::string &component, const std::string &source, - if ((logRank >= 0 && commRank >= 0 && logRank != commRank) || - priority > verbosity || - (messages.find(message) != messages.end() && -- (mode == LogMode::ERROR || mode == LogMode::WARNING))) -+ (mode == LogMode::FATALERROR || mode == LogMode::WARNING))) - { - return; - } -@@ -115,7 +115,7 @@ void Log(const std::string &component, const std::string &source, - { - std::cout << m; - } -- else if (mode == ERROR) -+ else if (mode == FATALERROR) - { - std::cerr << m; - } -diff --git a/source/adios2/helper/adiosLog.h b/source/adios2/helper/adiosLog.h -index 570ffd68a..74dc73da9 100644 ---- a/source/adios2/helper/adiosLog.h -+++ b/source/adios2/helper/adiosLog.h -@@ -21,7 +21,7 @@ namespace helper - enum LogMode : char - { - EXCEPTION = 'x', -- ERROR = 'e', -+ FATALERROR = 'e', - WARNING = 'w', - INFO = 'i' - }; -@@ -36,7 +36,7 @@ std::string MakeMessage(const std::string &component, const std::string &source, - * @param source: class name of component - * @param activity: function name where this is called - * @param message: text message -- * @param mode: INFO, WARNING or ERROR -+ * @param mode: INFO, WARNING or FATALERROR - */ - void Log(const std::string &component, const std::string &source, - const std::string &activity, const std::string &message, -@@ -50,7 +50,7 @@ void Log(const std::string &component, const std::string &source, - * @param message: text message - * @param priority: only print if(priority<=verbosity) - * @param verbosity: engine parameter for engine wide verbosity level -- * @param mode: INFO, WARNING or ERROR -+ * @param mode: INFO, WARNING or FATALERROR - */ - void Log(const std::string &component, const std::string &source, - const std::string &activity, const std::string &message, -@@ -66,7 +66,7 @@ void Log(const std::string &component, const std::string &source, - * @param commRank: current MPI rank - * @param priority: only print if(priority<=verbosity) - * @param verbosity: engine parameter for engine wide verbosity level -- * @param mode: INFO, WARNING or ERROR -+ * @param mode: INFO, WARNING or FATALERROR - */ - void Log(const std::string &component, const std::string &source, - const std::string &activity, const std::string &message, -diff --git a/source/adios2/helper/adiosSystem.cpp b/source/adios2/helper/adiosSystem.cpp -index 7ff903b84..92e6f040b 100644 ---- a/source/adios2/helper/adiosSystem.cpp -+++ b/source/adios2/helper/adiosSystem.cpp -@@ -97,25 +97,25 @@ int ExceptionToError(const std::string &function) - catch (std::invalid_argument &e) - { - helper::Log("Helper", "adiosSystem", "ExceptionToError", -- function + ": " + e.what(), helper::LogMode::ERROR); -+ function + ": " + e.what(), helper::LogMode::FATALERROR); - return 1; - } - catch (std::system_error &e) - { - helper::Log("Helper", "adiosSystem", "ExceptionToError", -- function + ": " + e.what(), helper::LogMode::ERROR); -+ function + ": " + e.what(), helper::LogMode::FATALERROR); - return 2; - } - catch (std::runtime_error &e) - { - helper::Log("Helper", "adiosSystem", "ExceptionToError", -- function + ": " + e.what(), helper::LogMode::ERROR); -+ function + ": " + e.what(), helper::LogMode::FATALERROR); - return 3; - } - catch (std::exception &e) - { - helper::Log("Helper", "adiosSystem", "ExceptionToError", -- function + ": " + e.what(), helper::LogMode::ERROR); -+ function + ": " + e.what(), helper::LogMode::FATALERROR); - return 4; - } - } -diff --git a/source/adios2/operator/compress/CompressBlosc.cpp b/source/adios2/operator/compress/CompressBlosc.cpp -index 8233fc3f3..e414b64ac 100644 ---- a/source/adios2/operator/compress/CompressBlosc.cpp -+++ b/source/adios2/operator/compress/CompressBlosc.cpp -@@ -141,7 +141,7 @@ size_t CompressBlosc::Operate(const char *dataIn, const Dims &blockStart, - "ADIOS WARNING: Unknown parameter keyword '" + key + - "' with value '" + value + - "' passed to Blosc compression operator.", -- helper::ERROR); -+ helper::FATALERROR); - } - } - -diff --git a/source/adios2/toolkit/burstbuffer/FileDrainerSingleThread.cpp b/source/adios2/toolkit/burstbuffer/FileDrainerSingleThread.cpp -index a0452d64c..8e4f6c5a1 100644 ---- a/source/adios2/toolkit/burstbuffer/FileDrainerSingleThread.cpp -+++ b/source/adios2/toolkit/burstbuffer/FileDrainerSingleThread.cpp -@@ -220,7 +220,7 @@ void FileDrainerSingleThread::DrainThread() - helper::Log("BurstBuffer", "FileDrainerSingleThread", - "DrainThread", - "ADIOS THREAD ERROR: " + std::string(e.what()), -- helper::LogMode::ERROR); -+ helper::LogMode::FATALERROR); - } - } - break; -diff --git a/source/adios2/toolkit/query/JsonWorker.cpp b/source/adios2/toolkit/query/JsonWorker.cpp -index 4b842267f..8b0fc3d1a 100644 ---- a/source/adios2/toolkit/query/JsonWorker.cpp -+++ b/source/adios2/toolkit/query/JsonWorker.cpp -@@ -105,7 +105,7 @@ void JsonWorker::ParseJson() - { - helper::Log("Query", "JsonWorker", "ParseJson", - "No such variable: " + varName.dump(), -- helper::LogMode::ERROR); -+ helper::LogMode::FATALERROR); - return nullptr; - } - -diff --git a/source/adios2/toolkit/query/Query.cpp b/source/adios2/toolkit/query/Query.cpp -index 0ed551a03..54d48c7a6 100644 ---- a/source/adios2/toolkit/query/Query.cpp -+++ b/source/adios2/toolkit/query/Query.cpp -@@ -244,7 +244,7 @@ bool QueryVar::IsSelectionValid(adios2::Dims &shape) const - helper::Log( - "Query", "QueryVar", "IsSelectionValid", - "Query selection dimension is different from shape dimension", -- helper::LogMode::ERROR); -+ helper::LogMode::FATALERROR); - return false; // different dimension - } - -diff --git a/source/adios2/toolkit/query/Worker.cpp b/source/adios2/toolkit/query/Worker.cpp -index 8541cbadb..be6787c8d 100644 ---- a/source/adios2/toolkit/query/Worker.cpp -+++ b/source/adios2/toolkit/query/Worker.cpp -@@ -73,7 +73,7 @@ QueryVar *Worker::GetBasicVarQuery(adios2::core::IO ¤tIO, - { - helper::Log("Query", "Worker", "GetBasicVarQuery", - "No such variable: " + variableName, -- helper::LogMode::ERROR); -+ helper::LogMode::FATALERROR); - return nullptr; - } - #define declare_type(T) \ -diff --git a/source/adios2/toolkit/query/XmlWorker.cpp b/source/adios2/toolkit/query/XmlWorker.cpp -index 40e7c855d..d49c8b6a0 100644 ---- a/source/adios2/toolkit/query/XmlWorker.cpp -+++ b/source/adios2/toolkit/query/XmlWorker.cpp -@@ -150,7 +150,7 @@ QueryVar *XmlWorker::ParseVarNode(const pugi::xml_node &node, - { - helper::Log("Query", "XmlWorker", "ParseVarNode", - "No such variable: " + variableName, -- helper::LogMode::ERROR); -+ helper::LogMode::FATALERROR); - helper::Throw( - "Toolkit", "query::XmlWorker", "ParseVarNode", - "variable: " + variableName + " not found"); -diff --git a/source/utils/adios_reorganize/Reorganize.cpp b/source/utils/adios_reorganize/Reorganize.cpp -index 80db2a04f..d8bb1348c 100644 ---- a/source/utils/adios_reorganize/Reorganize.cpp -+++ b/source/utils/adios_reorganize/Reorganize.cpp -@@ -597,7 +597,7 @@ int Reorganize::ProcessMetadata(core::Engine &rStream, core::IO &io, - "write buffer size needs to hold about " + - std::to_string(bufsize) + " bytes but max is set to " + - std::to_string(max_write_buffer_size), -- m_Rank, m_Rank, 0, 0, helper::LogMode::ERROR); -+ m_Rank, m_Rank, 0, 0, helper::LogMode::FATALERROR); - return 1; - } - -@@ -608,7 +608,7 @@ int Reorganize::ProcessMetadata(core::Engine &rStream, core::IO &io, - std::to_string(largest_block) + - " bytes but max is set to " + - std::to_string(max_read_buffer_size), -- m_Rank, m_Rank, 0, 0, helper::LogMode::ERROR); -+ m_Rank, m_Rank, 0, 0, helper::LogMode::FATALERROR); - return 1; - } - return retval; -@@ -628,7 +628,7 @@ int Reorganize::ReadWrite(core::Engine &rStream, core::Engine &wStream, - std::to_string(nvars) + - ") to read does not match the number of processed variables (" + - std::to_string(varinfo.size()) + ")", -- m_Rank, m_Rank, 0, 0, helper::LogMode::ERROR); -+ m_Rank, m_Rank, 0, 0, helper::LogMode::FATALERROR); - } - - /*