Merge branch 'qss-solver-dev' into release-4.4.0

.github/workflows/c-cpp.yml

@@ -46,10 +46,11 @@ jobs:
         sudo apt-get install pkgconf
         sudo apt-get install python
         sudo apt-get install qt5-default
+        sudo apt-get install rapidjson-dev
           
     - name: Build
       working-directory: ./src
-      run: make
+      run: make repo_checkout=https
 
     - name: Install
       working-directory: ./src

.hooks/pre-commit

@@ -7,13 +7,13 @@ def get_files():
                                     '--name-only', 'HEAD']).split()
 
 def apply_code_style():
-    files = filter(lambda x: x.find('tests/system/gt_data') == -1, get_files())
+    files = filter(lambda x: x.find(b'tests/system/gt_data') == -1, get_files())
 
-    files = filter(lambda x: x.endswith('.c') or
-                             x.endswith('.h') or
-                             x.endswith('.cpp'), files)
+    files = filter(lambda x: x.endswith(b'.c') or
+                             x.endswith(b'.h') or
+                             x.endswith(b'.cpp'), files)
     for f in files:
-      print("Apply code style to: " + f)
+      print("Apply code style to: " + str(f))
       subprocess.check_output(['clang-format-7', '-i', f])
       subprocess.check_output(['git', 'add', f])
 

.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+    "sonarlint.pathToCompileCommands": "${workspaceFolder}/src/engine/compile_commands.json",
+    "files.associations": {
+        "patoh.h": "c",
+        "scotch.h": "c",
+        "utils.h": "c"
+    }
+}

deploy/linux/README.md

@@ -0,0 +1,14 @@
+**Release procedure**
+
+- Checkout `qss-solver-release` branch.
+- Create branch `release-X.X.X`.
+- Merge `qss-solver-dev` -> `qss-solver-release`.
+- Update `version` file to `X.X.X`.
+- Run `update.sh`.
+- Commit update changes with `-n`.
+- Update `CHANGELOG` and `README.md` files.
+- Commit changes with `-n`.
+- Push branch.
+- Merge pushed branch in `qss-solver-release` with `--squash`.
+- Push `qss-solver-release` branch.
+- Merge `qss-solver-release` in `qss-solver-dev`.

deploy/linux/build.sh

@@ -35,16 +35,24 @@ echo $INI_VER >> ./deploy/linux/qss-solver.ini
 # Set OS config files.
 CONTROL_FILE="control.amd64"
 SBML_LIB="libsbml.so.5.18.0"
-PACKAGE_NAME=qss-solver-$VER.deb
+PACKAGE_NAME=qss-solver-$VER
 SYSTEM_VERSION=`lsb_release -d`
 if [[ "$SYSTEM_VERSION" == *"22.04"* ]]; then
   CONTROL_FILE="control.amd64.u22"
   SBML_LIB="libsbml.so.5.19.0"
-  PACKAGE_NAME=qss-solver-$VER-u22.deb
+  PACKAGE_NAME=$PACKAGE_NAME-u22
 fi
 
 # Set solver branch
 BRANCH=`git rev-parse --abbrev-ref HEAD`
+
+# If build from development branch, update package name to unstable.
+if [ "$BRANCH" == "qss-solver-dev" ]; then
+  PACKAGE_NAME=$PACKAGE_NAME-unstable
+fi
+
+PACKAGE_NAME=$PACKAGE_NAME.deb
+
 BRANCH="branch="$BRANCH 
 echo $BRANCH >> ./deploy/linux/qss-solver.ini
 

src/Makefile

@@ -1,6 +1,9 @@
 # Target variables
 MODE ?= Debug
 DISTRO := $(shell lsb_release -r 2>/dev/null | grep Release | awk '{ print $$2 }')
+sbg_branch ?= sb-graph-dev
+build_sbg ?= True
+repo_checkout ?= ssh
 
 # Build cores.
 CORES = $(shell nproc)
@@ -18,7 +21,7 @@ mmo-interfaces: create-folders
 	@cd interfaces/sbml &&  $(MAKE) MODE=$(MODE) -j $(CORES)
 	@echo Done
 
-qss-engine: create-folders
+qss-engine: create-folders  lib-gtest
 	@echo BUILDING QSS LIBRARIES DEPS
 	@cd engine && $(MAKE) cvode
 	@cd engine && $(MAKE) ida
@@ -36,11 +39,14 @@ qss-user-libs: create-folders qss-engine
 	@echo Done
 
 mmo-compiler: create-folders lib-gtest  
+	@echo BUILDING MICROMODELICA C COMPILER DEPS
+	@cd mmoc && $(MAKE) MODE=$(MODE) lib_sbg sbg_branch=$(sbg_branch) build_sbg=$(build_sbg) repo_checkout=$(repo_checkout)
+	@echo Done
 	@echo BUILDING MICROMODELICA C COMPILER
 	@cd mmoc && $(MAKE) MODE=$(MODE) -j $(CORES) 
 	@echo Done
 
-qss-solver-gui: create-folders 
+qss-solver-gui: create-folders lib-gtest
 	@echo BUILDING MMO EDITOR
 	@cd gui && $(MAKE) -f gui.makefile MODE=$(MODE) -j $(CORES)     
 	@echo Done
@@ -99,7 +105,10 @@ clean:
 	@cd interfaces/sbml && $(MAKE) clean     
 
 help:
-	@echo "make MODE=<Debug|Release> "
+	@echo "make MODE=<Debug|Release> sbg_branch=<BRANCH_NAME> build_sbg=<True|False> repo_checkout=<ssh|https>"
 	@echo "Default values:"
 	@echo ""
 	@echo "MODE=Debug"
+	@echo "sbg_branch=sb-graph-dev"
+	@echo "build_sbg=True"
+	@echo "repo_checkout=ssh"

src/engine/.vscode/launch.json

@@ -23,6 +23,25 @@
                     "ignoreFailures": true
                 }
             ]
+        },
+
+        // Advection model
+        {
+            "name": "Advection.",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "/home/joaquin/work/qss-solver/build/advection/advection",
+            "cwd": "/home/joaquin/work/qss-solver/build/advection/",
+            "environment": [],
+            "MIMode": "gdb",
+            "setupCommands": [
+                {
+                    "description": "Enable pretty-printing for gdb",
+                    "text": "-enable-pretty-printing",
+                    "ignoreFailures": true
+                }
+            ]
         }
+
     ]
 }

src/engine/.vscode/settings.json

@@ -1,6 +1,20 @@
 {
     "files.associations": {
-        "random": "cpp"
+        "random": "cpp",
+        "qss_bdf.h": "c",
+        "array": "c",
+        "compare": "c",
+        "functional": "c",
+        "istream": "c",
+        "ostream": "c",
+        "ranges": "c",
+        "tuple": "c",
+        "type_traits": "c",
+        "utility": "c",
+        "typeindex": "c",
+        "typeinfo": "c",
+        "qss_data.h": "c"
     },
-    "C_Cpp.dimInactiveRegions": true
+    "C_Cpp.dimInactiveRegions": true,
+    "sonarlint.pathToCompileCommands": "${workspaceFolder}/compile_commands.json"
 }

src/engine/classic/classic_cvode_integrator.c

@@ -233,6 +233,13 @@ void CVODE_integrate(SIM_simulator simulate)
     if (check_flag(&flag, "CVDense", 1, simulator)) return;
   }
 
+  if (simulator->data->params->CVODE_max_order != 0) {
+    flag = CVodeSetMaxOrd(cvode_mem, simulator->data->params->CVODE_max_order);
+    if (check_flag(&flag, "CVodeSetMaxOrd", 1, simulator)) {
+      return;
+    }
+  }
+
   getTime(simulator->stats->sTime);
   if (is_sampled) {
     CLC_save_step(simOutput, solution, solution_time, t, totalOutputSteps, NV_DATA_S(y), clcData->d, clcData->alg);

src/engine/classic/classic_data.c

@@ -42,7 +42,6 @@ CLC_data CLC_Data(int states, int discretes, int events, int inputs, int algebra
   strcat(fileName, ".ini");
   SET_settings settings = SET_Settings(fileName);
   CLC_data p = checkedMalloc(sizeof(*p));
-  int i;
   p->states = states;
   p->discretes = discretes;
   p->events = events;
@@ -78,14 +77,15 @@ CLC_data CLC_Data(int states, int discretes, int events, int inputs, int algebra
   cleanVector(p->nDS, 0, states);
   double sameDQMin = (settings->nDQMin == 1) ? settings->dqmin[0] : 0;
   double sameDQRel = (settings->nDQRel == 1) ? settings->dqrel[0] : 0;
-  for (i = 0; i < states; i++) {
+  for (int i = 0; i < states; i++) {
     p->nSD[i] = 0;
     p->dQMin[i] = (sameDQMin > 0) ? sameDQMin : settings->dqmin[i];
     p->dQRel[i] = (sameDQRel > 0) ? sameDQRel : settings->dqrel[i];
   }
   p->event = SD_EventData(events);
   p->params = SD_Parameters(settings->derdelta, settings->zchyst, settings->minstep, settings->symdiff, settings->lps, settings->nodesize,
-                            settings->pm, settings->dt, settings->dtSynch, settings->partitionerOptions, settings->jacobian);
+                            settings->pm, settings->dt, settings->dtSynch, settings->partitionerOptions, settings->jacobian,
+                            settings->CVODE_max_order, settings->x_output);
   p->scalarEvaluations = 0;
   p->zeroCrossings = 0;
   p->funEvaluations = 0;

src/engine/common/data.c

@@ -171,7 +171,8 @@ void SD_cleanEventData(SD_eventData events, int size)
 }
 
 SD_parameters SD_Parameters(double derDelta, double zcHyst, double minStep, int symDiff, int lps, int nodeSize, SD_PartitionMethod pm,
-                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian)
+                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian, int CVODE_max_order,
+                            int x_output)
 {
   SD_parameters p = checkedMalloc(sizeof(*p));
   p->derDelta = derDelta;
@@ -185,10 +186,12 @@ SD_parameters SD_Parameters(double derDelta, double zcHyst, double minStep, int
   p->dtSynch = synch;
   p->partitionerOptions = partitionerOptions;
   p->jacobian = jacobian;
+  p->CVODE_max_order = CVODE_max_order;
+  p->x_output = x_output;
   return p;
 }
 
-SD_parameters SD_copyParameters(SD_parameters parameters)
+SD_parameters SD_copyParameters(const_SD_parameters parameters)
 {
   SD_parameters p = checkedMalloc(sizeof(*p));
   p->derDelta = parameters->derDelta;
@@ -199,6 +202,7 @@ SD_parameters SD_copyParameters(SD_parameters parameters)
   p->nodeSize = parameters->nodeSize;
   p->pm = parameters->pm;
   p->dt = parameters->dt;
+  p->x_output = parameters->x_output;
   return p;
 }
 
@@ -436,8 +440,8 @@ SD_jacMatrix SD_JacMatrix(int variables)
 
 void SD_allocJacMatrix(SD_jacMatrix jac_matrix)
 {
-  int i, variables = jac_matrix->variables;
-  for (i = 0; i < variables; i++) {
+  int variables = jac_matrix->variables;
+  for (int i = 0; i < variables; i++) {
     int size = jac_matrix->size[i];
     if (size > 0) {
       jac_matrix->index[i] = (int *)malloc(size * sizeof(int));
@@ -452,8 +456,8 @@ void SD_allocJacMatrix(SD_jacMatrix jac_matrix)
 
 void SD_cleanJacMatrix(SD_jacMatrix jac_matrix)
 {
-  int i, variables = jac_matrix->variables;
-  for (i = 0; i < variables; i++) {
+  int variables = jac_matrix->variables;
+  for (int i = 0; i < variables; i++) {
     if (jac_matrix->size[i] > 0) {
       cleanDoubleVector(jac_matrix->value[i], 0, jac_matrix->size[i]);
     }
@@ -462,13 +466,13 @@ void SD_cleanJacMatrix(SD_jacMatrix jac_matrix)
 
 void SD_freeJacMatrix(SD_jacMatrix jac_matrix)
 {
-  int i, variables = jac_matrix->variables;
+  int variables = jac_matrix->variables;
   free(jac_matrix->size);
-  for (i = 0; i < variables; i++) {
+  for (int i = 0; i < variables; i++) {
     free(jac_matrix->index[i]);
   }
   free(jac_matrix->index);
-  for (i = 0; i < variables; i++) {
+  for (int i = 0; i < variables; i++) {
     free(jac_matrix->value[i]);
   }
   free(jac_matrix->value);

src/engine/common/data.h

@@ -21,6 +21,7 @@
 
 #include <stdio.h>
 
+#include <common/macros.h>
 #include "utils.h"
 
 typedef void (*SD_eq)(int, double *, double *, double *, double, double *);
@@ -158,7 +159,7 @@ void SD_freeEventData(SD_eventData events, int size);
 
 void SD_cleanEventData(SD_eventData events, int size);
 
-typedef struct SD_parameters_ *SD_parameters;
+TYPE_DEF(SD_parameters)
 
 struct SD_parameters_ {
   double derDelta;
@@ -169,15 +170,18 @@ struct SD_parameters_ {
   int lps;       //!< Number of LPs defined for parallel simulations.
   int nodeSize;  //!< Node size used in the memory list for output simulation values.
   int jacobian;
+  int CVODE_max_order;
   SD_PartitionMethod pm;  //!< Partition method used to obtain a model partition for parallel simulations.
   SD_DtSynch dtSynch;     //!< \f $ \delta t $ \f synchronization policy.
   SD_partitionerOptions partitionerOptions;
+  int x_output;
 };
 
 SD_parameters SD_Parameters(double derDelta, double zcHyst, double minStep, int symDiff, int lps, int nodeSize, SD_PartitionMethod pm,
-                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian);
+                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian, int CVODE_max_order,
+                            int x_output);
 
-SD_parameters SD_copyParameters(SD_parameters parameters);
+SD_parameters SD_copyParameters(const_SD_parameters parameters);
 
 void SD_freeParameters(SD_parameters params);
 
@@ -204,7 +208,7 @@ SD_outputVariable SD_OutputVariable(int outputs);
 
 void SD_freeOutputVariable(SD_outputVariable variable);
 
-typedef struct SD_output_ *SD_output;
+TYPE_DEF(SD_output)
 
 struct SD_output_ {
   char *name;