Fix container and image issues

neuland/application/R3BNeulandAnalysisApp.h

@@ -112,7 +112,7 @@
         void print_json_options() override;
         void dump_json_options(const std::string& filename) override;
         void setup_application_options(CLI::App& program_options) override;
-        void ParseApplicationOption(const std::string& filename) override
+        void ParseApplicationOption(const std::vector<std::string>& filename) override
         {
             ParseApplicationOptionImp(filename, options_);
         }

neuland/application/R3BNeulandApp.cxx

@@ -1,6 +1,6 @@
-#include "R3BFileSource2.h"
 #include "R3BNeulandApp.h"
+#include "R3BFileSource2.h"
 #include <CLI/CLI.hpp>
 #include <FairParRootFileIo.h>
 #include <FairRootFileSink.h>
 #include <FairRun.h>
@@ -96,7 +96,7 @@
             dump_json_filename_ = filename;
         };
 
-        auto use_config_callback = [this](const std::string& filename)
+        auto use_config_callback = [this](const std::vector<std::string>& filename)
         {
             if (not is_already_parsed_)
             {
@@ -107,10 +107,10 @@
 
         auto& options = option_.get();
         program_options
-            .add_option_function<std::string>("-c, --config-file", use_config_callback, "Set the json config file")
+            .add_option_function<std::vector<std::string>>(
+                "-c, --config-file", use_config_callback, "Set the json config file")
             ->default_val(fmt::format("{}_{}", app_name_, DEFAULT_JSON_FILENAME))
             ->run_callback_for_default()
-            ->expected(0, 1)
             ->trigger_on_parse();
         program_options.add_flag("--print-config", has_print_default_options_, "Print default option value");
         program_options
@@ -150,7 +150,6 @@
     void Application::add_inout_files()
     {
         const auto& option = option_.get();
-        // output files:
         const auto output_name =
             option.enable_mpi ? fmt::format("{}.{}", option.output.data, rank_num_) : option.output.data;
         if (not option_.get().output.data.empty())
@@ -164,6 +163,7 @@
         if (option_.get().run_id >= 0)
         {
             file_source->SetInitRunID(option_.get().run_id);
+            run_->SetRunId(option_.get().run_id);
             R3BLOG(info, fmt::format("Filesource2: Set to run id {}", option_.get().run_id));
         }
         add_input_filename(file_source.get());
@@ -191,8 +191,11 @@
 
         if (not option_.get().output.par.empty())
         {
+            const auto& option = option_.get();
+            const auto output_name =
+                option.enable_mpi ? fmt::format("{}.{}", option.output.par, rank_num_) : option.output.par;
             auto fileio = std::make_unique<FairParRootFileIo>(true);
-            fileio->open(option_.get().output.par.c_str(), "RECREATE");
+            fileio->open(output_name.c_str(), "RECREATE");
             auto* rtdb = run_->GetRuntimeDb();
             rtdb->setOutput(fileio.release());
         }

neuland/application/R3BNeulandApp.h

@@ -108,7 +108,7 @@ namespace R3B::Neuland
 
       protected:
         template <typename OptionType>
-        void ParseApplicationOptionImp(const std::string& filename, OptionType& option);
+        void ParseApplicationOptionImp(const std::vector<std::string>& filename, OptionType& option);
 
       private:
         bool is_failed_ = false;
@@ -127,7 +127,7 @@ namespace R3B::Neuland
 
         // private virtual methods:
         virtual void pre_init(FairRun* run) = 0;
-        virtual void ParseApplicationOption(const std::string& filename) = 0;
+        virtual void ParseApplicationOption(const std::vector<std::string>& filename) = 0;
         virtual void post_init(FairRun* run) {}
         void add_input_filename(R3BFileSource2* filesource);
         virtual void print_json_options() {}
@@ -175,11 +175,17 @@ namespace R3B::Neuland
     }
 
     template <typename OptionType>
-    void Application::ParseApplicationOptionImp(const std::string& filename, OptionType& option)
+    void Application::ParseApplicationOptionImp(const std::vector<std::string>& filenames, OptionType& option)
     {
-        auto file = std::ifstream{ filename };
-        auto json_obj = nlohmann::json{};
-        file >> json_obj;
+        auto json_obj = nlohmann::ordered_json{ option };
+        for (const auto& filename : filenames)
+        {
+            auto json_file_obj = nlohmann::ordered_json{};
+            auto file = std::ifstream{ filename };
+            file >> json_file_obj;
+            R3BLOG(info, fmt::format("Reading the configuration from the json file {:?}", filename));
+            json_obj.merge_patch(json_file_obj);
+        }
         json_obj.get_to(option);
     }
 } // namespace R3B::Neuland

neuland/application/R3BNeulandSimApp.h

@@ -68,7 +68,7 @@
         void print_json_options() override;
         void dump_json_options(const std::string& filename) override;
         void run_action(FairRun* run, int num_of_events) override;
-        void ParseApplicationOption(const std::string& filename) override
+        void ParseApplicationOption(const std::vector<std::string>& filename) override
         {
             ParseApplicationOptionImp(filename, options_);
         }

neuland/executables/neuland_cli.cxx

@@ -60,6 +60,8 @@ auto main(int argc, char** argv) -> int
             return EXIT_SUCCESS;
         }
 
+        app->set_rank_num(num_rank);
+        app->set_num_of_procs(num_proc);
         app->init();
         app->run();
     }