Merge pull request #4374 from vicentebolea/backport-from-master

Backport from master

ReadMe.md

@@ -51,6 +51,7 @@ If you find ADIOS2 useful, please cite our [SoftwareX paper](https://doi.org/10.
 ## Releases
 
 * Latest release: [v2.10.1](https://github.com/ornladios/ADIOS2/releases/tag/v2.10.1)
+
 * Previous releases: [https://github.com/ornladios/ADIOS2/releases](https://github.com/ornladios/ADIOS2/releases)
 
 ## Packages

bindings/CXX11/adios2/cxx11/Engine.h

@@ -210,9 +210,7 @@ class Engine
         auto bufferView = static_cast<AdiosView<U>>(data);
 #if defined(ADIOS2_HAVE_KOKKOS) || defined(ADIOS2_HAVE_GPU_SUPPORT)
         auto bufferMem = bufferView.memory_space();
-        auto bufferLayout = bufferView.layout();
         variable.SetMemorySpace(bufferMem);
-        variable.SetArrayLayout(bufferLayout);
 #endif
         Put(variable, bufferView.data(), launch);
     }
@@ -416,9 +414,7 @@ class Engine
         auto bufferView = static_cast<AdiosView<U>>(data);
 #if defined(ADIOS2_HAVE_KOKKOS) || defined(ADIOS2_HAVE_GPU_SUPPORT)
         auto bufferMem = bufferView.memory_space();
-        auto bufferLayout = bufferView.layout();
         variable.SetMemorySpace(bufferMem);
-        variable.SetArrayLayout(bufferLayout);
 #endif
         Get(variable, bufferView.data(), launch);
     }

bindings/Python/py11Engine.cpp

@@ -280,7 +280,8 @@ std::vector<std::map<std::string, std::string>> Engine::BlocksInfo(std::string &
     MinVarInfo *minBlocksInfo = nullptr;
 
     auto Variable = itVariable->second.get();
-    minBlocksInfo = m_Engine->MinBlocksInfo(*Variable, 0);
+    size_t s = (m_Engine->m_OpenMode == Mode::ReadRandomAccess ? step : 0);
+    minBlocksInfo = m_Engine->MinBlocksInfo(*Variable, s);
     if (minBlocksInfo)
     {
         for (auto &info : minBlocksInfo->BlocksInfo)

python/adios2/stream.py

@@ -321,7 +321,7 @@ def _(self, name, content, shape=[], start=[], count=[], operations=None):
         if shape != [] and not variable.single_value():
             variable.set_shape(shape)
 
-        if start != [] and count != []:
+        if start != [] or count != []:
             variable.set_selection([start, count])
 
         if operations:

source/adios2/CMakeLists.txt

@@ -133,14 +133,13 @@ if (ADIOS2_HAVE_Derived_Variable)
   target_sources(adios2_core PRIVATE
       core/VariableDerived.cpp
       toolkit/derived/Expression.cpp
-      toolkit/derived/Function.cpp toolkit/derived/Function.tcc
-      toolkit/derived/ExprHelper.h)
+      toolkit/derived/Function.cpp toolkit/derived/Function.tcc)
   set_target_properties(adios2_core PROPERTIES
   				   INCLUDE_DIRECTORIES "$<BUILD_INTERFACE:${ADIOS2_SOURCE_DIR}/source/adios2/toolkit/derived/parser>;$<BUILD_INTERFACE:${ADIOS2_BINARY_DIR}/source/adios2>")
   find_package(BISON "3.8.2")
   find_package(FLEX)
 
-  if(NOT BISON_FOUND OR NOT FLEX_FOUND)
+  if(NOT BISON_FOUND OR NOT FLEX_FOUND OR (NOT BISON_VERSION VERSION_GREATER_EQUAL "3.8.2"))
     include(ADIOSBisonFlexSub)
     SETUP_ADIOS_BISON_FLEX_SUB()
   else()
@@ -156,13 +155,15 @@ if (ADIOS2_HAVE_Derived_Variable)
       DEFINES_FILE ${CMAKE_CURRENT_BINARY_DIR}/lexer.h)
     ADD_FLEX_BISON_DEPENDENCY(MyScanner MyParser)
   endif()
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/lexer.cpp PROPERTIES COMPILE_FLAGS -Wno-sign-compare)
-  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
     SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/parser.cpp PROPERTIES COMPILE_FLAGS -Wno-unused-but-set-variable)
-  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
+  elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang")
     SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/parser.cpp PROPERTIES COMPILE_FLAGS -Wno-unused-but-set-variable)
-  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+  elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "IntelLLVM")
+    SET_SOURCE_FILES_PROPERTIES(${CMAKE_CURRENT_BINARY_DIR}/parser.cpp PROPERTIES COMPILE_FLAGS -Wno-unused-but-set-variable)
+  elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
     SET_SOURCE_FILES_PROPERTIES(toolkit/derived/Expression.cpp toolkit/derived/Function.cpp PROPERTIES COMPILE_FLAGS "/wd4005 /wd4065 /wd4267 -DYY_NO_UNISTD_H")
   endif()
   add_library(adios2_core_derived

source/adios2/common/ADIOSConfig.h.in

@@ -31,7 +31,16 @@
 
 @ADIOS2_CONFIG_DEFINES@
 
-#define ADIOS2_FEATURE_LIST @ADIOS2_CONFIG_FEATURE_LIST@
+/*
+ * Constant defines: These are available unconditionally
+ * in the current version of ADIOS2.
+ */
+
+#define ADIOS2_HAVE_BP3
+#define ADIOS2_HAVE_BP4
+#define ADIOS2_HAVE_BP5
+
+#define ADIOS2_FEATURE_LIST "BP3" "BP4" "BP5" @ADIOS2_CONFIG_FEATURE_LIST@
 
 /* Everything between here and the note above is programatically generated */
 

source/adios2/core/VariableBase.cpp

@@ -55,6 +55,8 @@ void VariableBase::SetArrayLayout(const ArrayOrdering layout)
         UpdateLayout(m_Shape);
         UpdateLayout(m_Count);
         UpdateLayout(m_Start);
+        UpdateLayout(m_MemoryStart);
+        UpdateLayout(m_MemoryCount);
         return;
     }
     if (m_ArrayLayout != layout)
@@ -101,6 +103,9 @@ MemorySpace VariableBase::GetMemorySpace(const void *ptr)
 
 void VariableBase::SetMemorySpace(const MemorySpace mem)
 {
+#if defined(ADIOS2_HAVE_KOKKOS) || defined(ADIOS2_HAVE_GPU_SUPPORT)
+    ArrayOrdering layout = m_BaseLayout;
+#endif
 #ifdef ADIOS2_HAVE_GPU_SUPPORT
     if (m_MemSpace != MemorySpace::Detect && m_MemSpace != mem)
     {
@@ -115,6 +120,14 @@ void VariableBase::SetMemorySpace(const MemorySpace mem)
                                                  ExistingMemSpace + " and cannot received a " +
                                                  NewMemSpace + " buffer");
     }
+    if (mem == MemorySpace::GPU)
+        layout = ArrayOrdering::ColumnMajor;
+#endif
+#if defined(ADIOS2_HAVE_KOKKOS) || defined(ADIOS2_HAVE_GPU_SUPPORT)
+    // set the layout based on the buffer memory space
+    // skipping throwing an exception for a mismatch
+    if (m_ArrayLayout == ArrayOrdering::Auto)
+        SetArrayLayout(layout);
 #endif
     m_MemSpace = mem;
 }

source/adios2/core/VariableDerived.h

@@ -1,9 +1,7 @@
 #ifndef ADIOS2_CORE_VARIABLE_DERIVED_H_
 #define ADIOS2_CORE_VARIABLE_DERIVED_H_
 
-#include "adios2/common/ADIOSTypes.h"
 #include "adios2/core/VariableBase.h"
-#include "adios2/helper/adiosType.h"
 #include "adios2/toolkit/derived/Expression.h"
 
 namespace adios2

source/adios2/engine/campaign/CampaignData.h

@@ -12,6 +12,7 @@
 #ifndef ADIOS2_ENGINE_CAMPAIGNDATA_H_
 #define ADIOS2_ENGINE_CAMPAIGNDATA_H_
 
+#include <cstdint>
 #include <fstream>
 #include <iostream>
 #include <map>

source/adios2/helper/kokkos/adiosKokkos.cpp

@@ -85,7 +85,7 @@ bool IsGPUbuffer(const void *ptr)
     hipError_t ret;
     hipPointerAttribute_t attr;
     ret = hipPointerGetAttributes(&attr, ptr);
-#if defined(ROCM_VERSION_MAJOR) && ROCM_VERSION_MAJOR < 6
+#if defined(HIP_VERSION_MAJOR) && HIP_VERSION_MAJOR < 6
     if (ret == hipSuccess && attr.memoryType == hipMemoryTypeDevice)
 #else
     if (ret == hipSuccess && attr.type == hipMemoryTypeDevice)

source/adios2/operator/compress/CompressMGARD.cpp

@@ -151,10 +151,13 @@ size_t CompressMGARD::Operate(const char *dataIn, const Dims &blockStart, const
         return 0;
     }
 
+    mgard_x::Config config;
+    config.lossless = mgard_x::lossless_type::Huffman_Zstd;
+
     PutParameter(bufferOut, bufferOutOffset, true);
     void *compressedData = bufferOut + bufferOutOffset;
     mgard_x::compress(mgardDim, mgardType, mgardCount, tolerance, s, errorBoundType, dataIn,
-                      compressedData, sizeOut, true);
+                      compressedData, sizeOut, config, true);
     bufferOutOffset += sizeOut;
 
     return bufferOutOffset;

source/adios2/toolkit/derived/DerivedData.h

@@ -0,0 +1,18 @@
+#ifndef ADIOS2_DERIVED_Data_H_
+#define ADIOS2_DERIVED_Data_H_
+
+#include "adios2/common/ADIOSTypes.h"
+
+namespace adios2
+{
+namespace derived
+{
+struct DerivedData
+{
+    void *Data;
+    Dims Start;
+    Dims Count;
+};
+}
+}
+#endif

source/adios2/toolkit/derived/Expression.cpp

@@ -2,14 +2,49 @@
 #define ADIOS2_DERIVED_Expression_CPP_
 
 #include "Expression.h"
+#include "Function.h"
+#include "adios2/helper/adiosLog.h"
 #include "parser/ASTDriver.h"
 
 namespace adios2
 {
 namespace detail
 {
+struct OperatorProperty
+{
+    std::string name;
+    bool is_associative;
+};
+
+const std::map<ExpressionOperator, OperatorProperty> op_property = {
+    {ExpressionOperator::OP_NULL, {"NULL", false}},
+    {ExpressionOperator::OP_ALIAS, {"ALIAS", false}}, /* Parser-use only */
+    {ExpressionOperator::OP_PATH, {"PATH", false}},   /* Parser-use only */
+    {ExpressionOperator::OP_NUM, {"NUM", false}},     /* Parser-use only */
+    {ExpressionOperator::OP_INDEX, {"INDEX", false}},
+    {ExpressionOperator::OP_ADD, {"ADD", true}},
+    {ExpressionOperator::OP_SQRT, {"SQRT", false}},
+    {ExpressionOperator::OP_POW, {"POW", false}},
+    {ExpressionOperator::OP_CURL, {"CURL", false}},
+    {ExpressionOperator::OP_MAGN, {"MAGNITUDE", false}}};
+
+const std::map<std::string, ExpressionOperator> string_to_op = {
+    {"ALIAS", ExpressionOperator::OP_ALIAS}, /* Parser-use only */
+    {"PATH", ExpressionOperator::OP_PATH},   /* Parser-use only */
+    {"NUM", ExpressionOperator::OP_NUM},     /* Parser-use only */
+    {"INDEX", ExpressionOperator::OP_INDEX},    {"+", ExpressionOperator::OP_ADD},
+    {"add", ExpressionOperator::OP_ADD},        {"ADD", ExpressionOperator::OP_ADD},
+    {"SQRT", ExpressionOperator::OP_SQRT},      {"sqrt", ExpressionOperator::OP_SQRT},
+    {"POW", ExpressionOperator::OP_POW},        {"^", ExpressionOperator::OP_POW},
+    {"CURL", ExpressionOperator::OP_CURL},      {"curl", ExpressionOperator::OP_CURL},
+    {"MAGNITUDE", ExpressionOperator::OP_MAGN}, {"magnitude", ExpressionOperator::OP_MAGN}};
+
+inline std::string get_op_name(ExpressionOperator op) { return op_property.at(op).name; }
+
+inline ExpressionOperator get_op(std::string op) { return string_to_op.at(op); }
+
 // helper function
-adios2::detail::ExpressionOperator convert_op(std::string opname)
+ExpressionOperator convert_op(std::string opname)
 {
     adios2::detail::ExpressionOperator op;
     try
@@ -77,6 +112,16 @@ adios2::derived::ExpressionTree ASTNode_to_ExpressionTree(adios2::detail::ASTNod
 
 namespace derived
 {
+struct OperatorFunctions
+{
+    std::function<DerivedData(std::vector<DerivedData>, DataType)> ComputeFct;
+    std::function<Dims(std::vector<Dims>)> DimsFct;
+};
+
+std::map<adios2::detail::ExpressionOperator, OperatorFunctions> OpFunctions = {
+    {adios2::detail::ExpressionOperator::OP_ADD, {AddFunc, SameDimsFunc}},
+    {adios2::detail::ExpressionOperator::OP_CURL, {Curl3DFunc, CurlDimsFunc}},
+    {adios2::detail::ExpressionOperator::OP_MAGN, {MagnitudeFunc, SameDimsFunc}}};
 
 Expression::Expression(std::string string_exp)
 : m_Shape({0}), m_Start({0}), m_Count({0}), ExprString(string_exp)