Merge branch 'develop' into fix_1949_notrun

AMICI-dev · Feb 13, 2023 · a72fe96 · a72fe96
2 parents 47c399c + e51815d
commit a72fe96
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Showing 4 changed files with 12 additions and 10 deletions.
diff --git a/documentation/rtd_requirements.txt b/documentation/rtd_requirements.txt
@@ -12,7 +12,7 @@ sphinx_rtd_theme>=1.0.0
 petab>=0.1.20
 sphinx-autodoc-typehints==1.19.2
 git+https://github.com/readthedocs/sphinx-hoverxref@main
-ipython==8.4.0
+ipython==8.10.0
 breathe==4.34.0
 #exhale>=0.3.5
 -e git+https://github.com/mithro/sphinx-contrib-mithro#egg=sphinx-contrib-exhale-multiproject&subdirectory=sphinx-contrib-exhale-multiproject

diff --git a/include/amici/solver.h b/include/amici/solver.h
@@ -7,6 +7,7 @@
 #include "amici/logging.h"
 
 #include <cmath>
+#include <ctime>
 #include <functional>
 #include <memory>
 #include <chrono>
@@ -487,7 +488,7 @@ class Solver {
     double getMaxTime() const;
 
     /**
-     * @brief Set the maximum time allowed for integration
+     * @brief Set the maximum CPU time allowed for integration
      * @param maxtime Time in seconds
      */
     void setMaxTime(double maxtime);
@@ -1607,11 +1608,11 @@ class Solver {
     /** maximum number of allowed integration steps */
     long int maxsteps_ {10000};
 
-    /** Maximum wall-time for integration in seconds */
+    /** Maximum CPU-time for integration in seconds */
     std::chrono::duration<double, std::ratio<1>> maxtime_ {std::chrono::duration<double>::max()};
 
     /** Time at which solver timer was started */
-    mutable std::chrono::time_point<std::chrono::system_clock> starttime_;
+    mutable std::clock_t starttime_;
 
     /** linear solver for the forward problem */
     mutable std::unique_ptr<SUNLinSolWrapper> linear_solver_;

diff --git a/src/model.cpp b/src/model.cpp
@@ -1476,7 +1476,7 @@ int Model::checkFinite(gsl::span<const realtype> array,
         if(hasObservableIds())
             row_id += " " + getObservableIds()[row];
         if(hasParameterIds())
-            col_id += " " + getParameterIds()[plist(col)];
+            col_id += " " + getParameterIds()[plist(gsl::narrow<int>(col))];
         break;
     case ModelQuantity::dydx:
         if(hasObservableIds())
@@ -1488,7 +1488,7 @@ int Model::checkFinite(gsl::span<const realtype> array,
         if(hasStateIds())
             row_id += " " + getStateIdsSolver()[row];
         if(hasParameterIds())
-            col_id += " " + getParameterIds()[plist(col)];
+            col_id += " " + getParameterIds()[plist(gsl::narrow<int>(col))];
         break;
     case ModelQuantity::dJydy:
     case ModelQuantity::dJydy_matlab:
@@ -1510,7 +1510,7 @@ int Model::checkFinite(gsl::span<const realtype> array,
     case ModelQuantity::drzdp:
     case ModelQuantity::dsigmazdp:
         if(hasParameterIds())
-            col_id += " " + getParameterIds()[plist(col)];
+            col_id += " " + getParameterIds()[plist(gsl::narrow<int>(col))];
         break;
     case ModelQuantity::dsigmaydy:
         if(hasObservableIds()) {
@@ -1610,7 +1610,7 @@ int Model::checkFinite(SUNMatrix m, ModelQuantity model_quantity, realtype t) co
         if(hasExpressionIds())
             row_id += " " + getExpressionIds()[row];
         if(hasParameterIds())
-            col_id += " " + getParameterIds()[plist(col)];
+            col_id += " " + getParameterIds()[plist(gsl::narrow<int>(col))];
         break;
     default:
         break;

diff --git a/src/solver.cpp b/src/solver.cpp
@@ -859,12 +859,13 @@ void Solver::setMaxTime(double maxtime)
 
 void Solver::startTimer() const
 {
-    starttime_ = std::chrono::system_clock::now();
+    starttime_ = std::clock();
 }
 
 bool Solver::timeExceeded() const
 {
-    return std::chrono::system_clock::now() - starttime_ > maxtime_;
+    auto cputime_exceed = static_cast<double>(std::clock() - starttime_) / CLOCKS_PER_SEC;
+    return std::chrono::duration<double>(cputime_exceed) > maxtime_;
 }
 
 void Solver::setMaxSteps(const long int maxsteps) {