Development for v7.1.0

.LSAN_suppr.txt

@@ -3,8 +3,5 @@
 
 # These are known leaks that await fixing
 
-# https://github.com/DrylandEcology/SOILWAT2/issues/205
-leak:SW_VPD_construct
-
 # on Apple arm64: https://github.com/google/sanitizers/issues/1501
 leak:realizeClassWithoutSwift

.github/workflows/main_nix.yml

@@ -32,6 +32,11 @@ jobs:
         make clean bin_run
         make clean bin_debug_severe
 
+    - name: Run binary (with sanitizers)
+      # Apple clang does not support "AddressSanitizer: detect_leaks" (at least as of clang-1200.0.32.29)
+      if: ${{ runner.os != 'macOS' }}
+      run: make clean bin_leaks
+
     - name: Unit tests (shuffle and repeat 3x)
       run: make clean test_rep3rnd
 

.gitignore

@@ -3,6 +3,9 @@
 .project
 .settings/
 
+# VS Code default folder
+.vscode/
+
 # History files
 .Rhistory
 

NEWS.md

@@ -1,5 +1,41 @@
 # NEWS
 
+# SOILWAT2 v7.1.0
+* Simulation output remains the same as the previous version.
+
+* Prepare for SOILWAT2 to become thread-safe and reentrant (#346; @N1ckP3rsl3y)
+    * Definition clarifications
+        * Thread-safe - Multiple threads (a future SOILWAT2 development)
+          will not influence each other unintentionally. Here, we implemented
+          structures to enable thread-local storage, i.e., each thread operates
+          on local data structures or with static data.
+        * Reentrant - The ability to correctly execute any part of the program
+          by multiple threads simultaneously but independently from others.
+    * All non-static variables are replaced by local variables;
+      functions gained arguments to pass local variables by reference
+      (replacing global variables).
+    * New main abstract types
+        * SW_ALL - Contains the existing structures that are relevant
+          for the simulation itself, e.g., SW_MODEL, SW_SOILWAT, SW_WEATHER.
+        * PATH_INFO - Holds information about location of input and output data,
+          e.g., directories, file paths to input data.
+        * SW_OUTPUT_POINTERS - Points to requested output subroutines.
+        * LOG_INFO - Manages information for logging warnings and errors.
+
+* Tests now require `c++14` and utilize `googletest` `v1.14.0` (issue #339).
+
+* Bugfixes
+    * Fix an error where a pointer was freed even though it was not allocated
+      (issue #356; @dschlaep).
+    * Fix memory leak in test of `SW_VPD_construct()` (issue #205; @dschlaep).
+
+## Changes to inputs
+* The output separator `OUTSEP` has been unused since the switch (`v4.0.0`)
+  from writing free-form text files to `"csv"` spreadsheets
+  (where the separator is fixed to a comma); the occurrence of
+  `OUTSEP` in `"outsetup.in"` is now deprecated and triggers a warning.
+
+
 # SOILWAT2 v7.0.0
 * This version produces nearly identical simulation output
   as the previous release under default values for the new inputs.

include/SW_Carbon.h

@@ -7,43 +7,23 @@
 #ifndef CARBON
 #define CARBON
 
-#include "include/SW_Defines.h"
+#include "include/SW_datastructs.h"
 
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-/**
- * @brief The main structure holding all CO2-related data.
- */
-typedef struct {
-  int
-    use_wue_mult,                      /**< A boolean integer indicating if WUE multipliers should be calculated. */
-    use_bio_mult;                      /**< A boolean integer indicating if biomass multipliers should be calculated. */
-
-  char
-    scenario[64];                      /**< A 64-char array holding the scenario name for which we are extracting CO2 data from the carbon.in file. */
-
-  double
-    ppm[MAX_NYEAR];                 /**< A 1D array holding atmospheric CO2 concentration values (units ppm) that are indexed by calendar year. Is typically only populated for the years that are being simulated. `ppm[index]` is the CO2 value for the calendar year `index + 1` */
-
-} SW_CARBON;
-
-
-/* =================================================== */
-/*            Externed Global Variables                */
-/* --------------------------------------------------- */
-extern SW_CARBON SW_Carbon;
-
 
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
-void SW_CBN_construct(void);
+void SW_CBN_construct(SW_CARBON* SW_Carbon);
 void SW_CBN_deconstruct(void);
-void SW_CBN_read(void);
-void SW_CBN_init_run(void);
+void SW_CBN_read(SW_CARBON* SW_Carbon, SW_MODEL* SW_Model, char *InFiles[],
+                 LOG_INFO* LogInfo);
+void SW_CBN_init_run(VegType VegProd_veg[], SW_MODEL* SW_Model,
+                     SW_CARBON* SW_Carbon, LOG_INFO* LogInfo) ;
 
 
 #ifdef __cplusplus

include/SW_Control.h

@@ -19,6 +19,7 @@
 #define SW_CONTROL_H
 
 #include "include/generic.h" // for `Bool`, `swTRUE`, `swFALSE`
+#include "include/SW_datastructs.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -27,15 +28,19 @@ extern "C" {
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
-void SW_CTL_setup_model(const char *firstfile);
-void SW_CTL_clear_model(Bool full_reset);
-void SW_CTL_init_run(void);
-void SW_CTL_read_inputs_from_disk(void);
-void SW_CTL_main(void); /* main controlling loop for SOILWAT  */
-void SW_CTL_run_current_year(void);
+void SW_CTL_setup_model(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
+                        PATH_INFO* PathInfo, LOG_INFO* LogInfo);
+void SW_CTL_clear_model(Bool full_reset, SW_ALL* sw, PATH_INFO* PathInfo);
+void SW_CTL_init_run(SW_ALL* sw, LOG_INFO* LogInfo);
+void SW_CTL_read_inputs_from_disk(SW_ALL* sw, PATH_INFO* PathInfo,
+                                  LOG_INFO* LogInfo);
+void SW_CTL_main(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
+                 LOG_INFO* LogInfo); /* main controlling loop for SOILWAT  */
+void SW_CTL_run_current_year(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
+                             LOG_INFO* LogInfo);
 
 #ifdef DEBUG_MEM
-void SW_CTL_SetMemoryRefs(void);
+void SW_CTL_SetMemoryRefs(SW_OUTPUT SW_Output[]);
 #endif
 
 

include/SW_Defines.h

@@ -89,6 +89,9 @@ extern "C" {
 
 #define SEC_PER_DAY	86400. // the # of seconds in a day... (24 hrs * 60 mins/hr * 60 sec/min = 86400 seconds)
 
+#define OUTSTRLEN 3000 /* max output string length: in get_transp: 4*every soil layer with 14 chars */
+#define OUT_DIGITS 6 // number of floating point decimal digits written to output files
+#define _OUTSEP ',' // Separator used when generating output files
 
 //was 256 & 1024...
 #define MAX_FILENAMESIZE 512
@@ -116,6 +119,20 @@ extern "C" {
 #define SW_FORBS 2
 #define SW_GRASS 3
 
+/* Constants for number of months, weeks, and days in a year */
+  /* number of days in each week. unlikely to change, but
+  * useful as a readable indicator of usage where it occurs.
+  * On the other hand, it is conceivable that one might be
+  * interested in 4, 5, or 6 day periods, but redefine it
+  * in specific programs and take responsibility there,
+  * not here.
+  */
+#define MAX_MONTHS 12
+#define MAX_WEEKS 53
+#define MAX_DAYS 366
+
+#define SWRC_PARAM_NMAX 6 /**< Maximal number of SWRC parameters implemented */
+
 /*
    Indices to daily input flags/indices (dailyInputFlags & dailyInputIndices in SW_WEATHER)
    The order of these indices must match the order of weather input flags within `weathsetup.in`
@@ -158,17 +175,22 @@ extern "C" {
 // macro `ForEachOutPeriod` --> instead, define as type `IntUS`
 typedef IntUS OutPeriod;
 
+/*
+  * Number of output keys
+
+  * Must match number of items in output enum (minus eSW_NoKey and eSW_LastKey)
+*/
+#define SW_OUTNKEYS 32
 
 /*------------ DON'T CHANGE ANYTHING BELOW THIS LINE ------------*/
 /* Macros to simplify and add consistency to common tasks */
 /* Note the loop var must be declared as LyrIndex */
-#define ForEachSoilLayer(i)     for((i)=0; (i) < SW_Site.n_layers;      (i)++)
-#define ForEachEvapLayer(i)     for((i)=0; (i) < SW_Site.n_evap_lyrs;   (i)++)
-#define ForEachTreeTranspLayer(i)   for((i)=0; (i) < SW_Site.n_transp_lyrs[SW_TREES]; (i)++)
-#define ForEachShrubTranspLayer(i)   for((i)=0; (i) < SW_Site.n_transp_lyrs[SW_SHRUB]; (i)++)
-#define ForEachGrassTranspLayer(i)   for((i)=0; (i) < SW_Site.n_transp_lyrs[SW_GRASS]; (i)++)
-#define ForEachForbTranspLayer(i)   for((i)=0; (i) < SW_Site.n_transp_lyrs[SW_FORBS]; (i)++)
-#define ForEachTranspRegion(r)  for((r)=0; (r) < SW_Site.n_transp_rgn;  (r)++)
+#define ForEachSoilLayer(i, n_layers)     for((i)=0; (i) < (n_layers);      (i)++)
+#define ForEachEvapLayer(i, n_evap_lyrs)     for((i)=0; (i) < (n_evap_lyrs);   (i)++)
+#ifdef STEPWAT
+#define ForEachTranspLayer(i, n_transp_lyrs, veg_index)   for((i)=0; (i) < (n_transp_lyrs)[(veg_index)]; (i)++)
+#endif
+#define ForEachTranspRegion(r, n_transp_rgn)  for((r)=0; (r) < ((unsigned int)n_transp_rgn);  (r)++)
 #define ForEachVegType(k)  for ((k) = 0; (k) < NVEGTYPES; (k)++)
 #define ForEachVegTypeBottomUp(k)  for ((k) = NVEGTYPES - 1; (k) >= 0; (k)--)
 /* define m as Months */
@@ -218,6 +240,10 @@ typedef enum { eF,   /* file management */
                eOUT  /* output */
 } ObjType;
 
+/* Types to use for time and layer-related values and make a custom flag */
+typedef unsigned int TimeInt;
+typedef unsigned int LyrIndex;
+typedef signed char flag;
 
 #ifdef __cplusplus
 }

include/SW_Files.h

@@ -16,12 +16,12 @@
 #ifndef SW_FILES_H
 #define SW_FILES_H
 
+#include "include/SW_datastructs.h"
+
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-#define SW_NFILES 23
-
 /* The number of enum elements between eNoFile and
  * eEndFile (not inclusive) must match SW_NFILES.
  * also, these elements must match the order of
@@ -49,26 +49,14 @@ typedef enum {
 	eEndFile
 } SW_FileIndex;
 
-
-/* =================================================== */
-/*            Externed Global Variables                */
-/* --------------------------------------------------- */
-extern char *InFiles[SW_NFILES];
-extern char _ProjDir[FILENAME_MAX];
-extern char weather_prefix[FILENAME_MAX];
-extern char output_prefix[FILENAME_MAX];
-
-
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
-void SW_F_read(const char *s);
-char *SW_F_name(SW_FileIndex i);
-void SW_F_construct(const char *firstfile);
-void SW_F_deconstruct(void);
-void SW_WeatherPrefix(char prefix[]);
-void SW_OutputPrefix(char prefix[]);
-void SW_CSV_F_INIT(const char *s);
+void SW_F_read(PATH_INFO* PathInfo, LOG_INFO* LogInfo);
+void SW_F_construct(char *InFiles[], const char *firstfile, char _ProjDir[],
+					LOG_INFO *LogInfo);
+void SW_F_deconstruct(char *InFiles[]);
+void SW_CSV_F_INIT(const char *s, LOG_INFO* LogInfo);
 
 #ifdef DEBUG_MEM
 void SW_F_SetMemoryRefs(void);

include/SW_Flow.h

@@ -1,6 +1,7 @@
 #ifndef SW_FLOW_H
 #define SW_FLOW_H
 
+#include "include/SW_datastructs.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -9,8 +10,8 @@ extern "C" {
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
-void SW_FLW_init_run(void);
-void SW_Water_Flow(void);
+void SW_FLW_init_run(SW_SOILWAT* SW_SoilWat);
+void SW_Water_Flow(SW_ALL* sw, LOG_INFO* LogInfo);
 
 
 #ifdef __cplusplus