Merge pull request #212 from DrylandEcology/bugfix_211

Better compilation and use in rSOILWAT2

we have three documented and suppressed/ignored problems:
- memory leak (use of a suppression file): #205
- compile warning #208: treating c input as c++
- compile warning #214: variable array length

.LSAN_suppr.txt

@@ -0,0 +1,7 @@
+# Suppression of memory leaks
+# https://github.com/google/sanitizers/wiki/AddressSanitizerLeakSanitizer#suppressions
+
+# These are known leaks that await fixing
+
+# https://github.com/DrylandEcology/SOILWAT2/issues/205
+leak:SW_VPD_construct

.travis.yml

@@ -1,13 +1,44 @@
 language: cpp
 
+# We want to run the `*_severe` debug and test targets; thus, we need
+# to enable ptrace capability for (L/A)SAN which is currently not possible
+# with container-based builds on travis-ci
+# TODO: revert to `sudo: false` once the following are fixed/made possible
+# - https://github.com/google/sanitizers/issues/764
+# - https://github.com/travis-ci/travis-ci/issues/9033
+sudo: required
+
+matrix:
+  fast_finish: true
+
+# We want to run the `*_severe` debug and test targets; thus, we need
+# g++ >= 4.9 and clang++ >= 3.5
 compiler:
   - clang
   - gcc
 
+addons:
+  apt:
+    sources:
+      - ubuntu-toolchain-r-test
+    packages:
+      - gcc-4.9
+      - g++-4.9
+
+before_install:
+  - if [[ $CXX = g++ ]]; then export CXX="g++-4.9" CC="gcc-4.9"; fi
+
 script:
-  - export CPPFLAGS=-DSWDEBUG && make cleaner bint_run
-  - make cleaner cov test_run
+  # compile and run optimized binary
+  - make clean bin bint_run
+  # compile and run debug binary
+  - make clean bin_debug_severe bint_run
+  # compile and run (severe) unit tests
+  - ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe test_run
+  # determine code coverage of unit tests
+  - make clean cov test_run
 
 after_success:
   - bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"
-  - make cleaner
+  # clean up
+  - make clean

README.md

@@ -49,6 +49,16 @@ You can help us in different ways:
    [pull request](https://github.com/DrylandEcology/SOILWAT2/pulls)
 
 
+__Compilation__:
+  * Requirements:
+    - the `gcc` or `clang/llvm` toolchains
+      - `gcc >= v4.9` and `clang >= v3.3` for the `*_severe` test/debug targets
+    - POSIX- or GNU-compliant `make`
+    - On Windows OS: an installation of `cygwin`
+  * Build with `make` (see `make help` to print information about all
+    available targets)
+
+
 __SOILWAT2 code is used as part of three applications__:
   * stand-alone (code flag `SOILWAT` is defined if neither `STEPWAT` nor
     `RSOILWAT` exist),
@@ -75,25 +85,35 @@ __Tests, documentation, and code__ form a trinity
   * Note: `SOILWAT2` is written in C whereas `GoogleTest` is a C++ framework.
   * Run unit tests locally on the command-line with
     ```
-    make test     # compiles the unit-test binary/executable (with `-DSWDEBUG`)
-    make test_run # executes the unit-test binary
-    make cleaner
+    make test test_run         # compiles and executes the unit-tests
+    make test_severe test_run  # compiles/executes with strict/severe flags
+    make clean                 # cleans build artifacts
     ```
   * Development/feature branches can only be merged into master if they pass
-    all checks
+    all checks on `appveyor` and `travis` continuous integration servers, i.e.,
+    run the following locally to prepare a pull-request or commit to be reviewed
+    ```
+    make clean bin_debug_severe bint_run
+    make clean test_severe test_run
+    ```
+  * Note that you may want/need to exclude known memory leaks from severe
+    testing (see https://github.com/DrylandEcology/SOILWAT2/issues/205):
+    ```
+    ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe test_run
+    ```
   * Informal and local integration tests example:
     1. Before coding, run `testing/` and produce reference output
         ```
         git checkout master
-        make cleaner bint_run
+        make bin bint_run
         cp -r testing/Output testing/Output_ref
         ```
     2. Develop your code and keep "testing/Output_ref" locally, i.e., don't
     include "testing/Output_ref" in commits
     3. Regularly, e.g., before finalizing a commit, check that new code produces
     identical output (that is unless you work on output...)
         ```
-        make cleaner bint_run
+        make bin bint_run
         diff testing/Output/ testing/Output_ref/ -qs
         ```
 
@@ -116,19 +136,21 @@ __Tests, documentation, and code__ form a trinity
       ...
     }
     ```
-  * Clean, compile and run SOILWAT2-standalone in debugging mode with, e.g.,
+  * Clean, compile and run optimized SOILWAT2-standalone in debugging mode
+    with, e.g.,
     ```
-    make cleaner bint_run CPPFLAGS=-DSWDEBUG
+    make bin bint_run CPPFLAGS=-DSWDEBUG
     ```
-  * Alternatively, you can use the pre-configured debugging targets
-    `bin_debug` and `bind`, for instance, with
+  * Alternatively and potentially preferably, you can use the pre-configured
+    debugging targets
+    `bin_debug` and `bin_debug_severe`, for instance, with
     ```
-    make cleaner bind bint_run
+    make bin_debug_severe bint_run
     ```
   * If **valgrind** is installed, then you can call the target `bind_valgrind`
     (see description in `makefile`) with
     ```
-    make cleaner bind_valgrind
+    make bind_valgrind
     ```
 
 <br>

SW_Carbon.h

@@ -5,30 +5,40 @@
  * @date   23 January 2017
  */
 #ifndef CARBON
-  #define CARBON             /**< A macro that only lets the variables in @f SW_Carbon.h be defined once. */
+#define CARBON             /**< A macro that only lets the variables in @f SW_Carbon.h be defined once. */
 
-  #include "SW_Defines.h"
+#include "SW_Defines.h"
 
 
-  /**
-   * @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. */
+#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. */
+  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` */
+  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;
+} SW_CARBON;
+
+/* Function Declarations */
+void SW_CBN_construct(void);
+void SW_CBN_deconstruct(void);
+void SW_CBN_read(void);
+void calculate_CO2_multipliers(void);
+
+
+#ifdef __cplusplus
+}
+#endif
 
-  /* Function Declarations */
-  void SW_CBN_construct(void);
-  void SW_CBN_deconstruct(void);
-  void SW_CBN_read(void);
-  void calculate_CO2_multipliers(void);
 #endif

SW_Control.h

@@ -18,6 +18,10 @@
 #ifndef SW_CONTROL_H
 #define SW_CONTROL_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 void SW_CTL_init_model(const char *firstfile);
 void SW_CTL_clear_model(Bool full_reset);
 void SW_CTL_obtain_inputs(void);
@@ -29,4 +33,9 @@ void SW_CTL_run_current_year(void);
 void SW_CTL_SetMemoryRefs(void);
 #endif
 
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif

SW_Defines.h

@@ -17,11 +17,15 @@
 /********************************************************/
 
 #ifndef SOILW_DEF_H
-	#define SOILW_DEF_H
+#define SOILW_DEF_H
 
 #include <math.h>  /* for atan() in tanfunc() below */
 #include "generic.h"
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /* Not sure if this parameter is variable or a consequence of algebra,
  * but it's different in the FORTRAN version than in the ELM doc.
  * If deemed to need changing, might as well recompile rather than
@@ -150,4 +154,9 @@ typedef enum { eF,   /* file management */
                eOUT  /* output */
 } ObjType;
 
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif

SW_Files.h

@@ -14,7 +14,11 @@
 /********************************************************/
 /********************************************************/
 #ifndef SW_FILES_H
-	#define SW_FILES_H
+#define SW_FILES_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
 
 #define SW_NFILES 23
 
@@ -43,4 +47,9 @@ void SW_CSV_F_INIT(const char *s);
 void SW_F_SetMemoryRefs(void);
 #endif
 
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif

SW_Flow.h

@@ -1,3 +1,18 @@
+#ifndef SW_FLOW_H
+#define SW_FLOW_H
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 void SW_FLW_construct(void);
 void SW_FLW_deconstruct(void);
 void SW_Water_Flow(void);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

SW_Flow_lib.h

@@ -37,6 +37,10 @@
 #ifndef SW_WATERSUBS_H
 #define SW_WATERSUBS_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /* Standing crop can only intercept so much precip
  * This is the limiter used inside stdcrop_intercepted()
  */
@@ -179,4 +183,9 @@ void soil_temperature_today(double *ptr_dTime, double deltaX, double sT1, double
 	int nRgr, double sTempR[], double oldsTempR[], double vwcR[], double wpR[], double fcR[],
 	double bDensityR[], double csParam1, double csParam2, double shParam, Bool *ptr_stError);
 
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif

SW_Main_lib.c

@@ -36,7 +36,7 @@
 /* --------------------------------------------------- */
 
 /* see generic.h and filefuncs.h for more info on these vars */
-char inbuf[1024]; /* buffer used by input statements */
+char inbuf[MAX_FILENAMESIZE]; /* buffer used by input statements */
 char errstr[MAX_ERROR]; /* used to compose an error msg    */
 FILE *logfp; /* file handle for logging messages */
 int logged; /* boolean: true = we logged a msg */
@@ -62,7 +62,7 @@ void usage(void) {
   sw_error(0, "%s", s1);
 }
 
-char _firstfile[1024];
+char _firstfile[MAX_FILENAMESIZE];
 
 void init_args(int argc, char **argv) {
 	/* =================================================== */

SW_Markov.h

@@ -13,6 +13,10 @@
 #ifndef SW_MARKOV_H
 #define SW_MARKOV_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 typedef struct {
 
 	/* pointers to arrays of probabilities for each day saves some space */
@@ -42,4 +46,10 @@ void SW_MKV_today(TimeInt doy, RealD *tmax, RealD *tmin, RealD *rain);
 void SW_MKV_SetMemoryRefs( void);
 #endif
 
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif
+

SW_Model.h

@@ -23,6 +23,10 @@
 #include "Times.h"
 #include "SW_Defines.h"
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 typedef struct {
 	TimeInt /* controlling dates for model run */
 	startyr, /* beginning year for model run */
@@ -54,4 +58,9 @@ void SW_MDL_deconstruct(void);
 void SW_MDL_new_year(void);
 void SW_MDL_new_day(void);
 
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif

SW_Output.c

@@ -1826,6 +1826,8 @@ int SW_OUT_read_onekey(OutKey k, OutSum sumtype, char period[], int first,
 		last = 366;
 		#ifndef RSOILWAT
 		strcpy(period, "YR");
+		#else
+		if (period) {} // avoid `-Wunused-parameter`
 		#endif
 
 	} else if ((k == eSW_AllVeg || k == eSW_ET || k == eSW_AllWthr || k == eSW_AllH2O))