Support reading Array/Matrix/Tensor<int> in OptionsAdios2

.clang-tidy

@@ -18,6 +18,9 @@ CheckOptions:
 
   - key: readability-qualified-auto.AllowedTypes
     value: 'MPI_Comm'
+
+  - key: misc-include-cleaner.IgnoreHeaders
+    value: 'adios2/.*;bits/.*'
 ---
 
 Disabled checks and reasons:

include/bout/adios_object.hxx

@@ -16,6 +16,8 @@
 
 #if BOUT_HAS_ADIOS2
 
+#include "bout/boutexception.hxx"
+
 #include <adios2.h>
 #include <memory>
 #include <mpi.h>
@@ -36,14 +38,12 @@ IOPtr GetIOPtr(const std::string IOName);
 class ADIOSStream {
 public:
   adios2::IO io;
-  adios2::Engine engine;
   adios2::Variable<double> vTime;
   adios2::Variable<int> vStep;
   int adiosStep = 0;
-  bool isInStep = false; // true if BeginStep was called and EndStep was not yet called
 
   /** create or return the ADIOSStream based on the target file name */
-  static ADIOSStream& ADIOSGetStream(const std::string& fname);
+  static ADIOSStream& ADIOSGetStream(const std::string& fname, adios2::Mode mode);
 
   ~ADIOSStream();
 
@@ -74,14 +74,63 @@ public:
     return v;
   }
 
+  auto engine() -> adios2::Engine& {
+    if (not engine_) {
+      engine_ = io.Open(fname, file_mode);
+      if (not engine_) {
+        throw BoutException("Could not open ADIOS file '{:s}' for writing", fname);
+      }
+    }
+    return engine_;
+  }
+
+  void beginStep() {
+    if (not isInStep) {
+      engine().BeginStep();
+      isInStep = true;
+      adiosStep = static_cast<int>(engine().CurrentStep());
+    }
+  }
+
+  void endStep() {
+    if (isInStep) {
+      engine().EndStep();
+      isInStep = false;
+    }
+  }
+
+  void finish() {
+    if (engine_) {
+      engine().EndStep();
+      engine().Close();
+    }
+  }
+
 private:
-  ADIOSStream(const std::string fname) : fname(fname){};
+  ADIOSStream(const std::string& fname, adios2::Mode mode)
+      : fname(fname), file_mode(mode) {
+
+    ADIOSPtr adiosp = GetADIOSPtr();
+    std::string ioname = "write_" + fname;
+    try {
+      io = adiosp->AtIO(ioname);
+    } catch (const std::invalid_argument& e) {
+      io = adiosp->DeclareIO(ioname);
+      io.SetEngine("BP5");
+    }
+  };
+
   std::string fname;
+  adios2::Mode file_mode;
+  adios2::Engine engine_;
+
+  /// true if BeginStep was called and EndStep was not yet called
+  bool isInStep = false;
 };
 
 /** Set user parameters for an IO group */
-void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
-                        const char delimItem, adios2::IO& io);
+void ADIOSSetParameters(const std::string& input, char delimKeyValue, char delimItem,
+                        adios2::IO& io);
 
 } // namespace bout
 

src/sys/adios_object.cxx

@@ -5,8 +5,8 @@
 #include "bout/adios_object.hxx"
 #include "bout/boutexception.hxx"
 
-#include <exception>
-#include <iostream>
+#include <adios2.h>
+
 #include <unordered_map>
 
 namespace bout {
@@ -48,25 +48,25 @@ IOPtr GetIOPtr(const std::string IOName) {
 }
 
 ADIOSStream::~ADIOSStream() {
-  if (engine) {
+  if (engine_) {
     if (isInStep) {
-      engine.EndStep();
+      engine_.EndStep();
       isInStep = false;
     }
-    engine.Close();
+    engine_.Close();
   }
 }
 
-ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname) {
+ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode mode) {
   auto it = adiosStreams.find(fname);
   if (it == adiosStreams.end()) {
-    it = adiosStreams.emplace(fname, ADIOSStream(fname)).first;
+    it = adiosStreams.emplace(fname, ADIOSStream(fname, mode)).first;
   }
   return it->second;
 }
 
-void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
-                        const char delimItem, adios2::IO& io) {
+void ADIOSSetParameters(const std::string& input, char delimKeyValue, char delimItem,
+                        adios2::IO& io) {
   auto lf_Trim = [](std::string& input) {
     input.erase(0, input.find_first_not_of(" \n\r\t")); // prefixing spaces
     input.erase(input.find_last_not_of(" \n\r\t") + 1); // suffixing spaces
@@ -76,7 +76,7 @@ void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
   std::string parameter;
   while (std::getline(inputSS, parameter, delimItem)) {
     const size_t position = parameter.find(delimKeyValue);
-    if (position == parameter.npos) {
+    if (position == std::string::npos) {
       throw BoutException("ADIOSSetParameters(): wrong format for IO parameter "
                           + parameter + ", format must be key" + delimKeyValue
                           + "value for each entry");