Merge pull request #472 from rarutter/hold_output

When running a region with many concurrent batches, outputting at every year timestep creates a bottleneck in the run. Output at the monthly timestep is correspondingly worse.

This branch implements holding output data for a subset of our output options (specifically the outputs required for the Four Basins run, plus a few extra). Outputs for all combinations of timestep and granularity were identical to those from the current master branch for all timestep and granularity combinations.

Note that if outputs are specified for which holding is not implemented the entire run will be slowed.

The default time to hold is 1 year, so the model will behave as historically expected for yearly outputs. Monthly outputs will be held until the end of the year timestep.

config/config.js

@@ -24,7 +24,8 @@
     "output_nc_eq":       0,
     "output_nc_sp":       1,
     "output_nc_tr":       1,
-    "output_nc_sc":       1 
+    "output_nc_sc":       1, 
+    "output_interval":    1 
   },
 
   // Define storage locations for json files generated and used

config/output_spec.csv

@@ -25,6 +25,7 @@ DRIVINGTAIR,Input driving air temperature data,degree_C,invalid,invalid,,invalid
 DRIVINGVAPO,Input driving vapor pressure,hPa,invalid,invalid,,invalid,invalid,invalid,float,
 DWDC,Dead woody debris C,g/m2/time,,,invalid,invalid,invalid,invalid,double,
 DWDN,Dead woody debris N,g/m2/time,,,invalid,invalid,invalid,invalid,double,
+DWDRH,Dead woody debris HR,g/m2/time,,,invalid,invalid,invalid,invalid,double,
 EET,Actual ET,mm/m2/time,,,,,invalid,invalid,
 FRONTSDEPTH,Depth of fronts,mm,,,,invalid,invalid,,double,
 FRONTSTYPE,Front types,unitless,,,,invalid,invalid,,int,
@@ -108,5 +109,4 @@ VWCMINEB,VWC middle mineral,m3/m3,,,,invalid,invalid,invalid,double,
 VWCMINEC,VWC bottom mineral,m3/m3,,,,invalid,invalid,invalid,double,
 VWCSHLW,VWC in fibrous layer,m3/m3,,,,invalid,invalid,invalid,double,
 WATERTAB,Water table depth below surface,m,,,,invalid,invalid,invalid,double,
-WDRH,Dead woody debris HR,g/m2/time,,,invalid,invalid,invalid,invalid,double,
 YSD,Years since last disturbance,Years,,invalid,invalid,invalid,invalid,invalid,int,

include/ModelData.h

@@ -67,6 +67,7 @@ class ModelData {
   bool nc_sp;
   bool nc_tr;
   bool nc_sc;
+  int output_interval; //How many years to store for output
 
   // Maps holding data about variables to be output at specific timesteps
   // C++11 would allow the use of unordered_maps, which have a faster

include/OutputHolder.h

@@ -0,0 +1,91 @@
+
+/* When running a region with many concurrent batches, outputting at every
+ * year timestep creates a bottleneck in the run. Output at the monthly
+ * timestep is correspondingly worse.
+ *
+ * This class is a basic repository for output data to be held until
+ * outputting is triggered based on the user's specifications.
+ * */
+
+
+#ifndef OUTPUTHOLDER_H
+#define OUTPUTHOLDER_H
+
+#include "temconst.h"
+#include "layerconst.h"
+
+class OutputHolder{
+public:
+
+//  OutputHolder();
+//  ~OutputHolder();
+
+  void clear();
+
+  int months_held;
+  int years_held;
+
+  std::vector<int> ysd_for_output;
+
+  std::vector<double> ald_for_output;
+  std::vector<double> burnsoic_for_output;
+  std::vector<double> burnthick_for_output;
+  std::vector<double> burnveg2airc_for_output;
+  std::vector<double> burnveg2deadc_for_output;
+  std::vector<double> burnveg2soiabvc_for_output;
+  std::vector<double> burnveg2soiblwc_for_output;
+  std::vector<double> deadc_for_output;
+  std::vector<double> deepc_for_output;
+  std::vector<double> dwdc_for_output;
+  std::vector<double> dwdrh_for_output;
+  std::vector<double> minec_for_output;
+  std::vector<double> qdrain_for_output;
+  std::vector<double> qinfil_for_output;
+  std::vector<double> qrunoff_for_output;
+  std::vector<double> shlwc_for_output;
+  std::vector<double> snowthick_for_output;
+  std::vector<double> swe_for_output;
+  std::vector<double> watertab_for_output;
+
+  //Variables by layer
+  std::vector<double> rh_tot_for_output;
+  std::vector<std::array<double, MAX_SOI_LAY>> rh_for_output;
+
+  std::vector<std::array<double, MAX_SOI_LAY>> tlayer_for_output;
+  std::vector<std::array<double, MAX_SOI_LAY>> vwclayer_for_output;
+
+  //Variables by PFT
+  std::vector<double> eet_tot_for_output;
+  std::vector<std::array<double, NUM_PFT>> eet_for_output;
+
+  std::vector<double> pet_tot_for_output;
+  std::vector<std::array<double, NUM_PFT>> pet_for_output;
+
+  std::vector<double> trans_tot_for_output;
+  std::vector<std::array<double, NUM_PFT>> trans_for_output;
+
+  //Variables by PFT and Compartment both
+  std::vector<double> gpp_tot_for_output;
+  std::vector<std::array<double, NUM_PFT_PART>> gpp_part_for_output;
+  std::vector<std::array<double, NUM_PFT>> gpp_pft_for_output;
+  std::vector<std::array<std::array<double, NUM_PFT>, NUM_PFT_PART>> gpp_for_output; 
+
+  std::vector<double> ltrfalc_tot_for_output;
+  std::vector<std::array<double, NUM_PFT_PART>> ltrfalc_part_for_output;
+  std::vector<std::array<double, NUM_PFT>> ltrfalc_pft_for_output;
+  std::vector<std::array<std::array<double, NUM_PFT>, NUM_PFT_PART>> ltrfalc_for_output; 
+
+  std::vector<double> npp_tot_for_output;
+  std::vector<std::array<double, NUM_PFT_PART>> npp_part_for_output;
+  std::vector<std::array<double, NUM_PFT>> npp_pft_for_output;
+  std::vector<std::array<std::array<double, NUM_PFT>, NUM_PFT_PART>> npp_for_output; 
+
+  std::vector<double> vegc_tot_for_output;
+  std::vector<std::array<double, NUM_PFT_PART>> vegc_part_for_output;
+  std::vector<std::array<double, NUM_PFT>> vegc_pft_for_output;
+  std::vector<std::array<std::array<double, NUM_PFT>, NUM_PFT_PART>> vegc_for_output; 
+
+};
+
+
+#endif /* OUTPUTHOLDER_H */

include/Runner.h

@@ -28,6 +28,7 @@
 #include "CalController.h"
 #include "ArgHandler.h"
 #include "util_structs.h"
+#include "OutputHolder.h"
 
 using namespace std;
 
@@ -61,9 +62,9 @@ class Runner {
   void output_debug_daily_drivers(int iy, boost::filesystem::path p);
 
   //void output_netCDF(int year, boost::filesystem::path p);
-  void output_netCDF_monthly(int year, int month, std::string stage);
-  void output_netCDF_yearly(int year, std::string stage);
-  void output_netCDF(std::map<std::string, OutputSpec> &outputs, int year, int month, std::string stage);
+  void output_netCDF_monthly(int year, int month, std::string stage, int endyr);
+  void output_netCDF_yearly(int year, std::string stage, int endyr);
+  void output_netCDF(std::map<std::string, OutputSpec> &outputs, int year, int month, std::string stage, int endyr);
 
 
   template<typename PTYPE>
@@ -95,7 +96,9 @@ class Runner {
 
   deque<RestartData> mlyres;
 
-  void monthly_output(const int year, const int month, const std::string& runstage);
+  OutputHolder outhold;
+
+  void monthly_output(const int year, const int month, const std::string& runstage, int endyr);
   void yearly_output(const int year, const std::string& stage, const int startyr, const int endyr);
 
 };

src/ModelData.cpp

@@ -57,6 +57,7 @@ ModelData::ModelData(Json::Value controldata):force_cmt(-1) {
   nc_sp             = controldata["IO"]["output_nc_sp"].asBool();
   nc_tr             = controldata["IO"]["output_nc_tr"].asBool();
   nc_sc             = controldata["IO"]["output_nc_sc"].asBool();
+  output_interval   = controldata["IO"]["output_interval"].asInt();
 
   pid_tag           = controldata["calibration-IO"]["pid_tag"].asString();
   caldata_tree_loc  = controldata["calibration-IO"]["caldata_tree_loc"].asString();