Add buffer size configuration for reportinglib (#132)

- Add buffer size configuration for reportinglib
- Read buffer size from report.conf file
- Add command line option for the report buffer size (4MB as default)

Author: jorblancoa

coreneuron/nrniv/main1.cpp

@@ -408,16 +408,17 @@ extern "C" int solve_core(int argc, char** argv) {
 
         // register all reports into reportinglib
         double min_report_dt = INT_MAX;
-        int num_report_mindelay = nrnopt_get_int("--num-report-mindelay");
-
-        set_num_mindelay_to_buffer(num_report_mindelay);
-
+        int report_buffer_size = nrnopt_get_int("--report-buffer-size");
         for (size_t i = 0; i < configs.size(); i++) {
             register_report(dt, tstop, delay, configs[i]);
             if (configs[i].report_dt < min_report_dt) {
                 min_report_dt = configs[i].report_dt;
             }
         }
+        // Set the buffer size if is not the default value. Otherwise use report.conf on register_report
+        if (!nrnopt_is_default_value("--report-buffer-size")) {
+            set_report_buffer_size(report_buffer_size);
+        }
         setup_report_engine(min_report_dt, delay);
         configs.clear();
 

coreneuron/nrniv/nrnoptarg.cpp

@@ -71,7 +71,7 @@ static param_int param_int_args[] = {
     {"--extracon -x", 0, 0, 10000000,
      "Number of extra random connections in each thread to other duplicate models (int)."},
     {"--seed -s", -1, 0, 100000000, "Initialization seed for random number generator (int)."},
-    {"--num-report-mindelay", 100, 1, 10000, "Number of min delay intervals to be buffered during reporting (int)."},
+    {"--report-buffer-size", 4, 1, 8, "Size in MB of the report buffer (int)."},
     {NULL, 0, 0, 0, NULL}};
 
 static param_dbl param_dbl_args[] = {
@@ -311,6 +311,10 @@ void nrnopt_modify_dbl(const char* name, double val) {
     args.insert(args.begin(), v);
 }
 
+bool nrnopt_is_default_value(const char* name) {
+    return !opt->isSet(name);
+}
+
 // more compact display of parameters.
 // ie only first name and first value (or default or isSet).
 void nrnopt_show() {

coreneuron/nrniv/nrnoptarg.h

@@ -57,5 +57,7 @@ int nrnopt_get_int(const char* name);
 double nrnopt_get_dbl(const char* name);
 std::string nrnopt_get_str(const char* name);
 void nrnopt_modify_dbl(const char* name, double value);
+
+bool nrnopt_is_default_value(const char* name);
 }  // namespace coreneuron
 #endif

coreneuron/utils/reports/nrnreport.cpp

@@ -241,7 +241,8 @@ void register_soma_report(NrnThread& nt,
                            config.report_dt, sizemapping, (char*)config.type_str, extramapping,
                            (char*)config.unit);
 
-        /** add extra mapping */
+        records_set_report_max_buffer_size_hint ((char*)config.output_path, config.buffer_size);
+	/** add extra mapping */
         records_extra_mapping(config.output_path, gid, 5, extra);
         for (int var_idx = 0; var_idx < vars.size(); ++var_idx) {
             /** 1st key is section-id and 1st value is segment of soma */
@@ -276,7 +277,9 @@ void register_compartment_report(NrnThread& nt,
         records_add_report((char*)config.output_path, gid, gid, gid, config.start, config.stop,
                            config.report_dt, sizemapping, (char*)config.type_str, extramapping,
                            (char*)config.unit);
-        /** add extra mapping */
+        
+        records_set_report_max_buffer_size_hint ((char*)config.output_path, config.buffer_size);	
+	/** add extra mapping */
         records_extra_mapping(config.output_path, gid, 5, extra);
         for (int var_idx = 0; var_idx < vars.size(); ++var_idx) {
             mapping[0] = vars[var_idx].id;
@@ -312,7 +315,9 @@ void register_custom_report(NrnThread& nt,
         records_add_report((char*)config.output_path, gid, gid, gid, config.start, config.stop,
                            config.report_dt, sizemapping, (char*)config.type_str, extramapping,
                            (char*)config.unit);
-        /** add extra mapping : @todo api changes in reportinglib*/
+        
+        records_set_report_max_buffer_size_hint ((char*)config.output_path, config.buffer_size);	
+	/** add extra mapping : @todo api changes in reportinglib*/
         records_extra_mapping((char*)config.output_path, gid, 5, extra);
         for (int var_idx = 0; var_idx < vars.size(); ++var_idx) {
             mapping[0] = vars[var_idx].id;
@@ -350,20 +355,13 @@ std::vector<int> map_gids(NrnThread& nt) {
 }
 #endif  // ENABLE_REPORTING
 
-// number of min-delay intervals to buffer
-static int num_min_delay_to_buffer = 100;
-
-/// number of min-delays completed since last flush
-static int num_min_delays_completed = 0;
+// Size in MB of the report buffer
+static int size_report_buffer = 4;
 
 void nrn_flush_reports(double t) {
 #ifdef ENABLE_REPORTING
     // flush before buffer is full
-    if (num_min_delays_completed >= (num_min_delay_to_buffer - 2)) {
-        records_flush(t);
-        num_min_delays_completed = 0;
-    }
-    num_min_delays_completed++;
+    records_end_iteration(t);
 #endif
 }
 
@@ -376,20 +374,18 @@ void nrn_flush_reports(double t) {
  */
 void setup_report_engine(double dt_report, double mindelay) {
 #ifdef ENABLE_REPORTING
-    int timesteps_to_buffer = mindelay / dt_report + 2;
-    timesteps_to_buffer *= num_min_delay_to_buffer;
-
-    records_set_steps_to_buffer(timesteps_to_buffer);
     /** reportinglib setup */
     records_setup_communicator();
     records_finish_and_share();
 #endif  // ENABLE_REPORTING
 }
 
-// number of min delay intervals that will be buffered with reports
-// @todo : this will be replaced by buffer size in MB
-void set_num_mindelay_to_buffer(int n) {
-    num_min_delay_to_buffer = n;
+// Size in MB of the report buffers
+void set_report_buffer_size(int n) {
+    size_report_buffer = n;
+#ifdef ENABLE_REPORTING
+    records_set_max_buffer_size_hint(size_report_buffer);
+#endif
 }
 
 // TODO: we can have one ReportEvent per register_report_call generated by MPI rank

coreneuron/utils/reports/nrnreport.h

@@ -68,6 +68,7 @@ struct ReportConfiguration {
     double start;                           // start time of report
     double stop;                            // stop time of report
     int num_gids;                           // total number of gids
+    size_t buffer_size;                     // hint on buffer size used for this report
     std::set<int> target;                   // list of gids for this report
 };
 
@@ -78,7 +79,7 @@ std::vector<ReportConfiguration> create_report_configurations(const char* filena
 void setup_report_engine(double dt_report, double mindelay);
 void finalize_report();
 void nrn_flush_reports(double t);
-void set_num_mindelay_to_buffer(int n);
+void set_report_buffer_size(int n);
 
 }  // namespace coreneuron
 #endif  //_H_NRN_REPORT_

coreneuron/utils/reports/report_configuration_parser.cpp

@@ -79,10 +79,11 @@ std::vector<ReportConfiguration> create_report_configurations(const char* conf_f
         ReportConfiguration& report = reports[reports.size() - 1];
         // mechansim id registered in coreneuron
         report.mech_id = -1;
+        report.buffer_size = 4; //default size to 4 Mb
         fgets(raw_line, MAX_FILEPATH_LEN, fp);
-        sscanf(raw_line, "\n%s %s %s %s %s %s %d %lf %lf %lf %d\n", report.name, report.target_name,
-               report.type_str, report_on, report.unit, report.format, &is_soma, &report.report_dt,
-               &report.start, &report.stop, &report.num_gids);
+        sscanf(raw_line, "\n%s %s %s %s %s %s %d %lf %lf %lf %d %d\n", report.name, report.target_name,
+                report.type_str, report_on, report.unit, report.format, &is_soma, &report.report_dt,
+                &report.start, &report.stop, &report.num_gids, &report.buffer_size);
         for (int i = 0; i < MAX_REPORT_NAME_LEN; i++) {
             report.type_str[i] = tolower(report.type_str[i]);
         }