Add ReturnData::cpu_time_total to track total time spent in runAmic…

…iS… (#1743) Add `ReturnData::cpu_time_total` to track total time spent in `runAmiciSimulation`
AMICI-dev · Mar 25, 2022 · 3683d3e · 3683d3e
1 parent 3bbf6e4
commit 3683d3e
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Showing 6 changed files with 14 additions and 2 deletions.
diff --git a/include/amici/rdata.h b/include/amici/rdata.h
@@ -225,6 +225,9 @@ class ReturnData: public ModelDimensions {
     /** computation time of backward solve [ms] */
     double cpu_timeB = 0.0;
 
+    /** total CPU time from entering runAmiciSimulation until exiting [ms] */
+    double cpu_time_total = 0.0;
+
     /** flags indicating success of steady state solver (preequilibration) */
     std::vector<SteadyStateStatus> preeq_status;
 

diff --git a/include/amici/serialization.h b/include/amici/serialization.h
@@ -207,6 +207,7 @@ void serialize(Archive &ar, amici::ReturnData &r, const unsigned int /*version*/
     ar &r.order;
     ar &r.cpu_time;
     ar &r.cpu_timeB;
+    ar &r.cpu_time_total;
     ar &r.preeq_cpu_time;
     ar &r.preeq_cpu_timeB;
     ar &r.preeq_status;

diff --git a/python/amici/numpy.py b/python/amici/numpy.py
@@ -158,7 +158,7 @@ class ReturnDataView(SwigPtrView):
         'posteq_cpu_timeB', 'numsteps', 'numrhsevals',
         'numerrtestfails', 'numnonlinsolvconvfails', 'order', 'cpu_time',
         'numstepsB', 'numrhsevalsB', 'numerrtestfailsB',
-        'numnonlinsolvconvfailsB', 'cpu_timeB'
+        'numnonlinsolvconvfailsB', 'cpu_timeB', 'cpu_time_total'
     ]
 
     def __init__(self, rdata: Union[ReturnDataPtr, ReturnData]):

diff --git a/python/tests/test_pysb.py b/python/tests/test_pysb.py
@@ -67,7 +67,7 @@ def test_compare_to_sbml_import(pysb_example_presimulation_module,
     skip_attrs = ['ptr', 'preeq_t', 'numsteps', 'preeq_numsteps',
                   'numrhsevals', 'numerrtestfails', 'order', 'J', 'xdot',
                   'preeq_wrms', 'preeq_cpu_time', 'cpu_time',
-                  'cpu_timeB', 'w']
+                  'cpu_timeB', 'cpu_time_total', 'w']
 
     for field in rdata_pysb:
         if field in skip_attrs:

diff --git a/src/amici.cpp b/src/amici.cpp
@@ -104,6 +104,7 @@ AmiciApplication::runAmiciSimulation(Solver& solver,
                                      Model& model,
                                      bool rethrow)
 {
+    auto start_time_total = clock();
     solver.startTimer();
 
     /* Applies condition-specific model settings and restores them when going
@@ -233,6 +234,10 @@ AmiciApplication::runAmiciSimulation(Solver& solver,
         preeq.get(), fwd.get(),
         bwd_success ? bwd.get() : nullptr,
         posteq.get(), model, solver, edata);
+
+    rdata->cpu_time_total = static_cast<double>(clock() - start_time_total)
+                            * 1000.0 / CLOCKS_PER_SEC;
+
     return rdata;
 }
 

diff --git a/src/hdf5.cpp b/src/hdf5.cpp
@@ -452,6 +452,9 @@ void writeReturnDataDiagnosis(const ReturnData &rdata,
     H5LTset_attribute_double(file.getId(), hdf5Location.c_str(),
                              "cpu_timeB", &rdata.cpu_timeB, 1);
 
+    H5LTset_attribute_double(file.getId(), hdf5Location.c_str(),
+                             "cpu_time_total", &rdata.cpu_time_total, 1);
+
     if (!rdata.J.empty())
         createAndWriteDouble2DDataset(file, hdf5Location + "/J", rdata.J,
                                       rdata.nx, rdata.nx);