Finish de-templating sim master, make RBC cope and move path manager …

…into config where it belongs
hemelb-codes · Jun 4, 2024 · aa88ca3 · aa88ca3
1 parent 1475365
commit aa88ca3
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Showing 46 changed files with 193 additions and 261 deletions.
diff --git a/Code/CMakeLists.txt b/Code/CMakeLists.txt
@@ -123,7 +123,9 @@ if (HEMELB_USE_DEBUGGER)
   set(CMAKE_BUILD_TYPE Debug)
 endif()
 
-add_executable(${HEMELB_EXECUTABLE} SimulationMaster.cc main.cc)
+add_library(hemelb_sim OBJECT SimulationMaster.cc)
+list(APPEND heme_libraries hemelb_sim)
+add_executable(${HEMELB_EXECUTABLE} main.cc)
 codesign(${HEMELB_EXECUTABLE})
 
 include_directories(${PROJECT_SOURCE_DIR})

diff --git a/Code/SimulationMaster.cc b/Code/SimulationMaster.cc
@@ -37,23 +37,9 @@ namespace hemelb
      * Initialises member variables including the network topology
      * object.
      */
-    SimulationMaster::SimulationMaster(configuration::CommandLine & options,
-                                               const net::IOCommunicator& ioComm) :
+    SimulationMaster::SimulationMaster(const net::IOCommunicator& ioComm) :
             build_info(), ioComms(ioComm.Duplicate()), communicationNet(ioComms)
     {
-        // Start the main timer!
-        timings.total().Start();
-
-        fileManager = std::make_shared<io::PathManager>(options,
-                                                                IsCurrentProcTheIOProc(),
-                                                                GetProcessorCount());
-        log::Logger::Log<log::Info, log::Singleton>("Reading configuration from %s", fileManager->GetInputFile().c_str());
-        // Convert XML to configuration
-        simConfig = configuration::SimConfig::New(fileManager->GetInputFile());
-        // Use it to initialise self
-        auto builder = configuration::SimBuilder(simConfig);
-        log::Logger::Log<log::Info, log::Singleton>("Beginning Initialisation.");
-        builder.build<>(*this);
     }
 
   /// Destructor for the SimulationMaster class.

diff --git a/Code/SimulationMaster.h b/Code/SimulationMaster.h
@@ -16,7 +16,7 @@
 #include "util/UnitConverter.h"
 #include "configuration/SimConfig.h"
 #include "configuration/CommandLine.h"
-#include "io/PathManager.h"
+#include "configuration/PathManager.h"
 #include "reporting/Reporter.h"
 #include "reporting/Timers.h"
 #include "reporting/BuildInfo.h"
@@ -53,7 +53,7 @@ namespace hemelb
         std::shared_ptr<lb::LBMBase> latticeBoltzmannModel;
         std::shared_ptr<geometry::neighbouring::NeighbouringDataManager> neighbouringDataManager;
 
-        std::shared_ptr<io::PathManager> fileManager;
+        std::shared_ptr<configuration::PathManager> fileManager;
         std::shared_ptr<reporting::Reporter> reporter;
 
         std::shared_ptr<lb::SimulationState> simulationState;
@@ -77,9 +77,8 @@ namespace hemelb
         std::shared_ptr<net::phased::StepManager> stepManager;
         std::shared_ptr<net::phased::NetConcern> netConcern;
 
+        SimulationMaster(const net::IOCommunicator& ioComm);
     public:
-      SimulationMaster(configuration::CommandLine &options,
-                       const net::IOCommunicator& ioComms);
       virtual ~SimulationMaster();
 
       void Abort();

diff --git a/Code/configuration/CMakeLists.txt b/Code/configuration/CMakeLists.txt
@@ -5,6 +5,7 @@
 
 add_library(hemelb_configuration OBJECT
         CommandLine.cc
+        PathManager.cc
         SimConfig.cc
         SimBuilder.cc
         SimConfigReader.cc

diff --git a/Code/io/PathManager.cc → Code/configuration/PathManager.cc b/Code/io/PathManager.cc → Code/configuration/PathManager.cc
@@ -3,13 +3,13 @@
 // file AUTHORS. This software is provided under the terms of the
 // license in the file LICENSE.
 
-#include "io/PathManager.h"
+#include "configuration/PathManager.h"
 
 #include "Exception.h"
 #include "configuration/CommandLine.h"
 
 namespace fs = std::filesystem;
-namespace hemelb::io
+namespace hemelb::configuration
 {
 
     PathManager::PathManager(const configuration::CommandLine & commandLine, const bool & io,

diff --git a/Code/io/PathManager.h → Code/configuration/PathManager.h b/Code/io/PathManager.h → Code/configuration/PathManager.h
@@ -3,8 +3,8 @@
 // file AUTHORS. This software is provided under the terms of the
 // license in the file LICENSE.
 
-#ifndef HEMELB_IO_PATHMANAGER_H
-#define HEMELB_IO_PATHMANAGER_H
+#ifndef HEMELB_CONFIGURATION_PATHMANAGER_H
+#define HEMELB_CONFIGURATION_PATHMANAGER_H
 
 #include <filesystem>
 #include <string>
@@ -14,12 +14,6 @@ namespace hemelb::configuration
 {
     class CommandLine;
     class SimConfig;
-}
-
-namespace hemelb::io
-{
-    // Forward declare the Writer
-    namespace writers { class Writer; }
 
     /**
      * Manage the input and output file system locations for HemeLB reports, extracted data, and input xml.
@@ -82,4 +76,4 @@ namespace hemelb::io
 
 }
 
-#endif //HEMELB_IO_PATHMANAGER_H
+#endif //HEMELB_CONFIGURATION_PATHMANAGER_H
diff --git a/Code/configuration/SimBuilder.cc b/Code/configuration/SimBuilder.cc
@@ -291,7 +291,7 @@ namespace hemelb::configuration {
     }
 
     std::shared_ptr<reporting::Reporter> SimBuilder::BuildReporter(
-            io::PathManager const& fileManager,
+            PathManager const& fileManager,
             std::vector<reporting::Reportable*>const& reps
     ) const {
         auto reporter = std::make_shared<reporting::Reporter>(fileManager.GetReportPath(),

diff --git a/Code/configuration/SimBuilder.h b/Code/configuration/SimBuilder.h
@@ -54,6 +54,31 @@ namespace hemelb::configuration {
         std::shared_ptr<util::UnitConverter> unit_converter;
 
     public:
+        template <typename TraitsT>
+        static std::unique_ptr<SimulationMaster> CreateSim(
+                CommandLine const& options,
+                net::IOCommunicator const& ioComms
+        ) {
+            auto ans = std::unique_ptr<SimulationMaster>(new SimulationMaster(ioComms));
+            // Start the main timer!
+            ans->timings.total().Start();
+
+            ans->fileManager = std::make_shared<configuration::PathManager>(
+                    options,
+                    ioComms.OnIORank(),
+                    ioComms.Size()
+            );
+            auto&& infile = ans->fileManager->GetInputFile();
+            log::Logger::Log<log::Info, log::Singleton>("Reading configuration from %s", infile.c_str());
+            // Convert XML to configuration
+            ans->simConfig = configuration::SimConfig::New(infile);
+            // Use it to initialise self
+            auto builder = configuration::SimBuilder(ans->simConfig);
+            log::Logger::Log<log::Info, log::Singleton>("Beginning Initialisation.");
+            builder.build<TraitsT>(*ans);
+            return ans;
+        }
+
         explicit SimBuilder(SimConfig const& conf, bool construct_unit_converter = true);
         virtual ~SimBuilder() = default;
 
@@ -111,7 +136,7 @@ namespace hemelb::configuration {
         ) const;
 
         [[nodiscard]] std::shared_ptr<reporting::Reporter> BuildReporter(
-                io::PathManager const& fileManager,
+                PathManager const& fileManager,
                 std::vector<reporting::Reportable*> const & reps
         ) const;
     };
@@ -299,8 +324,6 @@ namespace hemelb::configuration {
     [[nodiscard]] std::shared_ptr<net::IteratedAction> SimBuilder::BuildCellController(SimulationMaster const& control, reporting::Timers& timings) const {
         if (config.HasRBCSection()) {
 #ifdef HEMELB_BUILD_RBC
-            using traitsType = typename T::Traits;
-
             auto ccb = redblood::CellControllerBuilder(unit_converter);
 
             auto& ioComms = control.ioComms;
@@ -324,4 +347,4 @@ namespace hemelb::configuration {
         return {};
     }
 }
-#endif
+#endif
diff --git a/Code/extraction/PropertyActor.h b/Code/extraction/PropertyActor.h
@@ -7,7 +7,6 @@
 #define HEMELB_EXTRACTION_PROPERTYACTOR_H
 
 #include "extraction/PropertyWriter.h"
-#include "io/PathManager.h"
 #include "lb/MacroscopicPropertyCache.h"
 #include "lb/SimulationState.h"
 #include "net/IteratedAction.h"

diff --git a/Code/io/CMakeLists.txt b/Code/io/CMakeLists.txt
@@ -12,7 +12,6 @@ endif()
 
 add_library(hemelb_io OBJECT
   FILE.cc
-  PathManager.cc 
   writers/AsciiFileWriter.cc writers/AsciiStreamWriter.cc
   readers/XdrFileReader.cc
   readers/XdrMemReader.cc

diff --git a/Code/io/Checkpointer.h b/Code/io/Checkpointer.h
@@ -9,7 +9,7 @@
 #include <filesystem>
 #include <memory>
 
-#include "io/PathManager.h"
+#include "configuration/SimConfig.h"
 #include "io/TimePattern.h"
 #include "lb/SimulationState.h"
 #include "net/IteratedAction.h"

diff --git a/Code/main.cc b/Code/main.cc
@@ -6,9 +6,9 @@
 #include "net/mpi.h"
 #include "net/IOCommunicator.h"
 #include "configuration/CommandLine.h"
+#include "configuration/SimBuilder.h"
 #include "io/ensure_hexfloat.h"
 #include "debug.h"
-#include "SimulationMaster.h"
 
 int main(int argc, char *argv[])
 {
@@ -40,10 +40,10 @@ int main(int argc, char *argv[])
       debug::Init(options.GetDebug(), argv[0], commWorld);
 
       // Prepare main simulation object...
-      SimulationMaster master(options, hemelbCommunicator);
+      auto master = configuration::SimBuilder::CreateSim<Traits<>>(options, hemelbCommunicator);
 
       // ..and run it.
-      master.RunSimulation();
+      master->RunSimulation();
     }
 
     // Interpose this catch to print usage before propagating the error.

diff --git a/Code/multiscale/MultiscaleSimulationMaster.h b/Code/multiscale/MultiscaleSimulationMaster.h
@@ -199,7 +199,7 @@ namespace hemelb::multiscale
           }
         }
 
-        void DoTimeStep()
+        void DoTimeStep() override
         {
           bool advance = intercomms.DoMultiscale(GetState().GetTime());
           log::Logger::Log<log::Info, log::Singleton>("At time step %i, should advance %i, time %f",

diff --git a/Code/net/IOCommunicator.h b/Code/net/IOCommunicator.h
@@ -27,6 +27,7 @@ namespace hemelb::net {
     public:
         static constexpr int IO_RANK = 0;
 
+        IOCommunicator() = default;
         explicit IOCommunicator(const MpiCommunicator& comm);
 
         inline bool OnIORank() const {

diff --git a/Code/redblood/CellArmy.h b/Code/redblood/CellArmy.h
@@ -324,8 +324,8 @@ namespace hemelb
           log::Logger::Log<log::Info, log::OnePerCore>(message.str());
 
           cellDnC.remove(*i_current);
-          cells.erase(i_current);
           auto const numErased = nodeDistributions.erase((*i_current)->GetTag());
+          cells.erase(i_current);
           assert(numErased == 1);
         }
       }

diff --git a/Code/redblood/CellControllerBuilder.cc b/Code/redblood/CellControllerBuilder.cc
@@ -5,7 +5,7 @@
 
 #include "redblood/CellControllerBuilder.h"
 
-#include "io/PathManager.h"
+#include "configuration/PathManager.h"
 #include "redblood/CellIO.h"
 #include "redblood/FaderCell.h"
 #include "redblood/MeshIO.h"
@@ -350,7 +350,7 @@ namespace hemelb::redblood {
     CellChangeListener CellControllerBuilder::build_full_cell_output(
             configuration::CellOutputConfig const& conf,
             std::shared_ptr<lb::SimulationState const> simState,
-            std::shared_ptr<io::PathManager const> fileManager,
+            std::shared_ptr<configuration::PathManager const> fileManager,
             net::IOCommunicator const& ioComms
     ) const {
         auto conv = conf.physical_units ? unit_converter : nullptr;
@@ -360,7 +360,7 @@ namespace hemelb::redblood {
     CellChangeListener CellControllerBuilder::build_summary_cell_output(
             configuration::CellOutputConfig const& conf,
             std::shared_ptr<lb::SimulationState const> simState,
-            std::shared_ptr<io::PathManager const> fileManager,
+            std::shared_ptr<configuration::PathManager const> fileManager,
             net::IOCommunicator const& ioComms
     ) const {
         auto conv = conf.physical_units ? unit_converter : nullptr;

diff --git a/Code/redblood/CellControllerBuilder.h b/Code/redblood/CellControllerBuilder.h
@@ -17,7 +17,7 @@
 #include "redblood/CellController.h"
 #include "redblood/RBCInserter.h"
 
-namespace hemelb::io { class PathManager; }
+namespace hemelb::configuration { class PathManager; }
 
 namespace hemelb::redblood {
 
@@ -86,13 +86,13 @@ namespace hemelb::redblood {
         CellChangeListener build_full_cell_output(
                 configuration::CellOutputConfig const& conf,
                 std::shared_ptr<lb::SimulationState const> simState,
-                std::shared_ptr<io::PathManager const> fileManager,
+                std::shared_ptr<configuration::PathManager const> fileManager,
                 net::IOCommunicator const& ioComms
         ) const;
         CellChangeListener build_summary_cell_output(
                 configuration::CellOutputConfig const& conf,
                 std::shared_ptr<lb::SimulationState const> simState,
-                std::shared_ptr<io::PathManager const> fileManager,
+                std::shared_ptr<configuration::PathManager const> fileManager,
                 net::IOCommunicator const& ioComms
         ) const;
 
@@ -104,7 +104,7 @@ namespace hemelb::redblood {
                                                    CountedIoletView const& inlets,
                                                    CountedIoletView const& outlets,
                                                    std::shared_ptr<lb::SimulationState const> simState,
-                                                   std::shared_ptr<io::PathManager const> fileManager
+                                                   std::shared_ptr<configuration::PathManager const> fileManager
         ) {
             log::Logger::Log<log::Info, log::Singleton>("Initialising RBCs.");
             timings.cellInitialisation().Start();

diff --git a/Code/redblood/CellIO.cc b/Code/redblood/CellIO.cc
@@ -9,8 +9,8 @@
 #include <cstring>
 #include <boost/uuid/uuid_io.hpp>
 
+#include "configuration/PathManager.h"
 #include "io/formats/rbc.h"
-#include "io/PathManager.h"
 #include "io/writers/XdrWriter.h"
 #include "io/readers/XdrFileReader.h"
 #include "io/readers/XdrMemReader.h"
@@ -21,6 +21,7 @@
 #include "redblood/FaderCell.h"
 #include "redblood/MeshIO.h"
 #include "util/Iterator.h"
+#include "util/span.h"
 
 namespace hemelb::redblood {
 
@@ -74,7 +75,7 @@ namespace hemelb::redblood {
     CellBarycentreOutput::CellBarycentreOutput(hemelb::LatticeTimeStep period,
                                                std::shared_ptr<const util::UnitConverter> unitConverter,
                                                std::shared_ptr<const lb::SimulationState> simState,
-                                               std::shared_ptr<const io::PathManager> fileManager,
+                                               std::shared_ptr<const configuration::PathManager> fileManager,
                                                net::IOCommunicator comms) :
             CellOutputBase{
                     period, std::move(unitConverter), std::move(simState), std::move(fileManager), comms
@@ -134,7 +135,7 @@ namespace hemelb::redblood {
         const std::size_t local_write_start = ioComms.OnIORank() ? 0 : (fmt::rbc::header_size + n_cells_before_me * fmt::rbc::row_size);
 
         auto bary_file = net::MpiFile::Open(ioComms, bary_filename, MPI_MODE_WRONLY | MPI_MODE_CREATE | MPI_MODE_EXCL);
-        bary_file.WriteAt(local_write_start, buffer);
+        bary_file.WriteAt(local_write_start, to_const_span(buffer));
         bary_file.Close();
     }
 
@@ -172,7 +173,7 @@ namespace hemelb::redblood {
         auto read_size = n * fmt::rbc::row_size;
 
         std::vector<std::byte> read_buf(read_size);
-        inputFile.ReadAt(read_start, read_buf);
+        inputFile.ReadAt(read_start, to_span(read_buf));
         auto reader = io::XdrMemReader(read_buf);
         std::vector<row> ans(n);
         boost::uuids::string_generator gen;

diff --git a/Code/redblood/CellIO.h b/Code/redblood/CellIO.h
@@ -15,7 +15,7 @@
 #include "net/IOCommunicator.h"
 #include "redblood/types_fwd.h"
 
-namespace hemelb::io { class PathManager; }
+namespace hemelb::configuration { class PathManager; }
 namespace hemelb::lb { class SimulationState; }
 namespace hemelb::util { class UnitConverter; }
 
@@ -30,7 +30,7 @@ namespace hemelb::redblood {
         // nullptr => use lattice units
         std::shared_ptr<util::UnitConverter const> unitConverter;
         std::shared_ptr<lb::SimulationState const> simState;
-        std::shared_ptr<io::PathManager const> fileManager;
+        std::shared_ptr<configuration::PathManager const> fileManager;
         net::IOCommunicator ioComms;
     };
 
@@ -46,7 +46,7 @@ namespace hemelb::redblood {
                 LatticeTimeStep period,
                 std::shared_ptr<util::UnitConverter const> unitConverter,
                 std::shared_ptr<lb::SimulationState const> simState,
-                std::shared_ptr<io::PathManager const> fileManager,
+                std::shared_ptr<configuration::PathManager const> fileManager,
                 net::IOCommunicator comms
         );