Add output:flush_frequency for OptionsNetCDF

include/bout/options_io.hxx

@@ -1,3 +1,17 @@
+#pragma once
+
+#ifndef OPTIONS_IO_H
+#define OPTIONS_IO_H
+
+#include "bout/build_defines.hxx"
+#include "bout/generic_factory.hxx"
+#include "bout/options.hxx"
+
+#include <memory>
+#include <string>
+
+namespace bout {
+
 /// Parent class for IO to binary files and streams
 ///
 ///
@@ -29,29 +43,14 @@
 ///       auto file = OptionsIO::create("some_file.nc");
 ///
 ///
-
-#pragma once
-
-#ifndef OPTIONS_IO_H
-#define OPTIONS_IO_H
-
-#include "bout/build_config.hxx"
-#include "bout/generic_factory.hxx"
-#include "bout/options.hxx"
-
-#include <memory>
-#include <string>
-
-namespace bout {
-
 class OptionsIO {
 public:
   /// No default constructor, as settings are required
   OptionsIO() = delete;
 
   /// Constructor specifies the kind of file, and options to control
   /// the name of file, mode of operation etc.
-  OptionsIO(Options&) {}
+  OptionsIO(Options& /*unused*/) {}
 
   virtual ~OptionsIO() = default;
 
@@ -73,6 +72,9 @@ public:
   /// ADIOS: Indicate completion of an output step.
   virtual void verifyTimesteps() const = 0;
 
+  /// NetCDF: Flush file to disk
+  virtual void flush() {}
+
   /// Create an OptionsIO for I/O to the given file.
   /// This uses the default file type and default options.
   static std::unique_ptr<OptionsIO> create(const std::string& file);

include/bout/physicsmodel.hxx

@@ -376,6 +376,9 @@ protected:
     PhysicsModel* model;
   };
 
+  /// Set timestep counter for flushing file
+  void setFlushCounter(std::size_t iteration) { flush_counter = iteration; }
+
 private:
   /// State for outputs
   Options output_options;
@@ -399,6 +402,10 @@ private:
   bool initialised{false};
   /// write restarts and pass outputMonitor method inside a Monitor subclass
   PhysicsModelMonitor modelMonitor{this};
+  /// How often to flush to disk
+  std::size_t flush_frequency{1};
+  /// Current timestep counter
+  std::size_t flush_counter{0};
 };
 
 /*!

src/physics/physicsmodel.cxx

@@ -33,12 +33,14 @@
 #undef BOUT_NO_USING_NAMESPACE_BOUTGLOBALS
 
 #include <bout/mesh.hxx>
+#include <bout/options.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/vector2d.hxx>
 #include <bout/vector3d.hxx>
 
 #include <fmt/core.h>
 
+#include <cstddef>
 #include <string>
 using namespace std::literals;
 
@@ -66,9 +68,10 @@ PhysicsModel::PhysicsModel()
                                                     .withDefault(true)),
       restart_enabled(Options::root()["restart_files"]["enabled"]
                           .doc("Write restart files")
-                          .withDefault(true))
-
-{
+                          .withDefault(true)),
+      flush_frequency(Options::root()["output"]["flush_frequency"]
+                          .doc("How often to flush to disk")
+                          .withDefault<std::size_t>(1)) {
   if (output_enabled) {
     output_file = bout::OptionsIOFactory::getInstance().createOutput();
   }
@@ -216,9 +219,7 @@ void PhysicsModel::writeRestartFile() {
 void PhysicsModel::writeOutputFile() { writeOutputFile(output_options); }
 
 void PhysicsModel::writeOutputFile(const Options& options) {
-  if (output_enabled) {
-    output_file->write(options, "t");
-  }
+  writeOutputFile(options, "t");
 }
 
 void PhysicsModel::writeOutputFile(const Options& options,
@@ -229,13 +230,19 @@ void PhysicsModel::writeOutputFile(const Options& options,
 }
 
 void PhysicsModel::finishOutputTimestep() const {
-  if (output_enabled) {
+  Timer timer("io");
+
+  if (output_enabled and (flush_counter % flush_frequency == 0)) {
+    output_file->flush();
     output_file->verifyTimesteps();
   }
 }
 
 int PhysicsModel::PhysicsModelMonitor::call(Solver* solver, BoutReal simtime,
                                             int iteration, int nout) {
+
+  model->setFlushCounter(static_cast<std::size_t>(iteration));
+
   // Restart file variables
   solver->outputVars(model->restart_options, false);
   model->restartVars(model->restart_options);
@@ -250,6 +257,9 @@ int PhysicsModel::PhysicsModelMonitor::call(Solver* solver, BoutReal simtime,
   model->outputVars(model->output_options);
   model->writeOutputFile();
 
+  // Reset output options, this avoids rewriting time-independent data
+  model->output_options = Options{};
+
   // Call user output monitor
   return model->outputMonitor(simtime, iteration, nout);
 }

src/sys/options/options_adios.hxx

@@ -4,8 +4,7 @@
 #ifndef OPTIONS_ADIOS_H
 #define OPTIONS_ADIOS_H
 
-#include "bout/build_config.hxx"
-#include "bout/options.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/options_io.hxx"
 
 #if !BOUT_HAS_ADIOS2

src/sys/options/options_netcdf.cxx

@@ -698,10 +698,10 @@ void OptionsNetCDF::write(const Options& options, const std::string& time_dim) {
   }
 
   writeGroup(options, *data_file, time_dim);
-
-  data_file->sync();
 }
 
+void OptionsNetCDF::flush() { data_file->sync(); }
+
 } // namespace bout
 
 #endif // BOUT_HAS_NETCDF

src/sys/options/options_netcdf.hxx

@@ -4,7 +4,7 @@
 #ifndef OPTIONS_NETCDF_H
 #define OPTIONS_NETCDF_H
 
-#include "bout/build_config.hxx"
+#include "bout/build_defines.hxx"
 
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
@@ -39,24 +39,26 @@ public:
   ///  - "append"  File mode, default is false
   OptionsNetCDF(Options& options);
 
-  ~OptionsNetCDF() {}
+  ~OptionsNetCDF() override = default;
 
   OptionsNetCDF(const OptionsNetCDF&) = delete;
   OptionsNetCDF(OptionsNetCDF&&) noexcept = default;
   OptionsNetCDF& operator=(const OptionsNetCDF&) = delete;
   OptionsNetCDF& operator=(OptionsNetCDF&&) noexcept = default;
 
   /// Read options from file
-  Options read();
+  Options read() override;
 
   /// Write options to file
-  void write(const Options& options) { write(options, "t"); }
-  void write(const Options& options, const std::string& time_dim);
+  void write(const Options& options, const std::string& time_dim) override;
 
   /// Check that all variables with the same time dimension have the
   /// same size in that dimension. Throws BoutException if there are
   /// any differences, otherwise is silent
-  void verifyTimesteps() const;
+  void verifyTimesteps() const override;
+
+  /// Flush file to disk
+  void flush() override;
 
 private:
   enum class FileMode {
@@ -74,7 +76,7 @@ private:
 };
 
 namespace {
-RegisterOptionsIO<OptionsNetCDF> registeroptionsnetcdf("netcdf");
+const RegisterOptionsIO<OptionsNetCDF> registeroptionsnetcdf("netcdf");
 }
 
 } // namespace bout