Merge remote-tracking branch 'origin/init-point-fix'

ZocoLini · ZocoLini · commit d9fc20ce90ef · 2025-06-05T19:11:51.000+02:00
diff --git a/example-files/alpha_pinene_ess_mpi2_config.xml b/example-files/alpha_pinene_ess_mpi2_config.xml
@@ -58,9 +58,9 @@
         <ub>
             1, 1, 1, 1, 1
         </ub>
-        <initial_point>
+        <point>
             1, 1, 1, 1, 1
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/example-files/alpha_pinene_ess_serial_config.xml b/example-files/alpha_pinene_ess_serial_config.xml
@@ -58,9 +58,9 @@
         <ub>
             1, 1, 1, 1, 1
         </ub>
-        <initial_point>
+        <point>
             1, 1, 1, 1, 1
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/example-files/logistic_model_ess_mpi2_config.xml b/example-files/logistic_model_ess_mpi2_config.xml
@@ -58,9 +58,9 @@
         <ub>
             1, 200
         </ub>
-        <initial_point>
+        <point>
             1, 150
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/example-files/logistic_model_ess_mpi_config.xml b/example-files/logistic_model_ess_mpi_config.xml
@@ -58,9 +58,9 @@
         <ub>
             1, 200
         </ub>
-        <initial_point>
+        <point>
             1, 150
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/example-files/logistic_model_ess_serial_config.xml b/example-files/logistic_model_ess_serial_config.xml
@@ -58,9 +58,9 @@
         <ub>
             1, 200
         </ub>
-        <initial_point>
+        <point>
             1, 150
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/example-files/lotka_volterra_ess_mpi2_config.xml b/example-files/lotka_volterra_ess_mpi2_config.xml
@@ -58,9 +58,9 @@
         <ub>
             1.000, 1.000, 1.000, 1.000
         </ub>
-        <initial_point>
+        <point>
             0.3, 0.3, 0.3, 0.3
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/example-files/lotka_volterra_ess_mpi_config.xml b/example-files/lotka_volterra_ess_mpi_config.xml
@@ -7,7 +7,7 @@
         <verbose>0</verbose>
         <local_search>1</local_search>
         <stopping_criteria>
-            <maxevaluation>6e3</maxevaluation>
+            <maxevaluation>3e3</maxevaluation>
             <maxtime>1e10</maxtime>
             <vtr>0</vtr>
         </stopping_criteria>
@@ -58,9 +58,9 @@
         <ub>
             1.000, 1.000, 1.000, 1.000
         </ub>
-        <initial_point>
+        <point>
             0.3, 0.3, 0.3, 0.3
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/example-files/lotka_volterra_ess_serial_config.xml b/example-files/lotka_volterra_ess_serial_config.xml
@@ -7,7 +7,7 @@
         <verbose>0</verbose>
         <local_search>1</local_search>
         <stopping_criteria>
-            <maxevaluation>6e3</maxevaluation>
+            <maxevaluation>2e3</maxevaluation>
             <maxtime>1e10</maxtime>
             <vtr>0</vtr>
         </stopping_criteria>
@@ -58,9 +58,9 @@
         <ub>
             1.000, 1.000, 1.000, 1.000
         </ub>
-        <initial_point>
+        <point>
             0.3, 0.3, 0.3, 0.3
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/modules/cli/src/handlers/solve.c b/modules/cli/src/handlers/solve.c
@@ -111,7 +111,7 @@ int handle_solve(int argc, char *argv[])
     int nproc = 1;
 #endif
 
-    CuqdynResult *cuqdyn_result = cuqdyn_algo(data_file, sacess_config_file, output_dir, rank, nproc);
+    CuqdynResult *cuqdyn_result = cuqdyn_algo(data_file, sacess_config_file, output_dir);
 
     if (rank == 0)
     {
diff --git a/modules/cuqdyn-c/include/cuqdyn.h b/modules/cuqdyn-c/include/cuqdyn.h
@@ -23,7 +23,7 @@ typedef struct
 CuqdynResult* create_cuqdyn_result(SUNMatrix predicted_data_median, N_Vector predicted_params_median,
     SUNMatrix q_low, SUNMatrix q_up, N_Vector times);
 void destroy_cuqdyn_result(CuqdynResult* result);
-CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, const char *output_file, int rank, int nproc);
+CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, const char *output_file);
 
 typedef struct
 {
diff --git a/modules/cuqdyn-c/include/ess_solver.h b/modules/cuqdyn-c/include/ess_solver.h
@@ -3,10 +3,10 @@
 #include <sundials/sundials_matrix.h>
 
 /// Executes the ESS solver for a given sacess config file using the given objective function.
-/// texp, yexp and initial_values are arguments needed to execute certain objective functions, like
-/// the one defined in lotka_volterra.c.
-/// rank and nproc are used to define the rank of the process and the number of processes in a MPI environment.
+/// texp, yexp and initial_condition are arguments needed to execute the objective functions, like
+/// the one defined in functions.c.
+/// rank and nproc are used to define the rank of the process and the number of processes in an MPI environment.
 N_Vector execute_ess_solver(const char *config_file, const char *output,
-  N_Vector texp, SUNMatrix yexp, N_Vector initial_values, int rank, int nproc);
+  N_Vector texp, SUNMatrix yexp, N_Vector initial_condition, N_Vector initial_params);
 
 #endif //ESS_SOLVER_H
diff --git a/modules/cuqdyn-c/src/cuqdyn.c b/modules/cuqdyn-c/src/cuqdyn.c
@@ -49,9 +49,18 @@ void destroy_cuqdyn_result(CuqdynResult *result)
     free(result);
 }
 
-CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file,
-                          const char *output_file, int rank, int nproc)
+CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, const char *output_file)
 {
+    int nproc;
+    int rank;
+
+#if defined(MPI2) || defined(MPI)
+    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+#else
+    nproc = 1;
+    rank = 0;
+#endif
     CuqdynConf *config = get_cuqdyn_conf();
 
     N_Vector times = NULL;
@@ -64,22 +73,36 @@ CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file,
     }
 
     const sunrealtype t0 = NV_Ith_S(times, 0);
-    N_Vector initial_values = copy_matrix_row(observed_data, 0, 0, SM_COLUMNS_D(observed_data));
+    N_Vector initial_condition = copy_matrix_row(observed_data, 0, 0, SM_COLUMNS_D(observed_data));
 
     const long m = SM_ROWS_D(observed_data);
     const long n = SM_COLUMNS_D(observed_data);
 
     SUNMatrix resid_loo = NULL;
     MatrixArray media_matrix = create_matrix_array(m - 1);
     SUNMatrix predicted_params_matrix = NULL;
+    N_Vector initial_params = New_Serial(get_cuqdyn_conf()->ode_expr.p_count);
 
     if (rank == 0)
     {
         resid_loo = NewDenseMatrix(m, n);
         predicted_params_matrix = NewDenseMatrix(m, config->ode_expr.p_count);
+
+        N_Vector texp = copy_vector_remove_indices(times, create_array((long[]) {}, 0));
+        SUNMatrix yexp = copy_matrix_remove_rows(observed_data, create_array((long[]) {}, 0));
+
+        N_Vector tmp_initial_condition = copy_vector_remove_indices(initial_condition, create_array((long[]) {}, 0));
+
+        N_Vector predicted_params =
+            execute_ess_solver(sacess_conf_file, output_file, texp, yexp, tmp_initial_condition, NULL);
+
+        memcpy(NV_DATA_S(initial_params), NV_DATA_S(predicted_params), NV_LENGTH_S(predicted_params) * sizeof(sunrealtype));
+        N_VDestroy(predicted_params);
     }
 
 #ifdef MPI
+    MPI_Bcast(NV_DATA_S(initial_params), NV_LENGTH_S(initial_params), MPI_DOUBLE, 0, MPI_COMM_WORLD);
+
     long iterations;
     long start_index;
 
@@ -124,15 +147,14 @@ CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file,
         N_Vector texp = copy_vector_remove_indices(times, indices_to_remove);
         SUNMatrix yexp = copy_matrix_remove_rows(observed_data, indices_to_remove);
 
-        N_Vector init_vals = New_Serial(NV_LENGTH_S(initial_values));
-        memcpy(NV_DATA_S(init_vals), NV_DATA_S(initial_values),
-               NV_LENGTH_S(initial_values) * sizeof(sunrealtype));
+        N_Vector tmp_initial_condition = copy_vector_remove_indices(initial_condition, create_array((long[]) {}, 0));
+        N_Vector tmp_initial_params = copy_vector_remove_indices(initial_params, create_array((long[]) {}, 0));
 
         N_Vector predicted_params =
-                execute_ess_solver(sacess_conf_file, output_file, texp, yexp, init_vals, rank, nproc);
+                execute_ess_solver(sacess_conf_file, output_file, texp, yexp, tmp_initial_condition, tmp_initial_params);
 
         // Saving the ode solution data obtained with the predicted params
-        SUNMatrix ode_solution = solve_ode(predicted_params, initial_values, t0, times);
+        SUNMatrix ode_solution = solve_ode(predicted_params, initial_condition, t0, times);
         SUNMatrix predicted_data = copy_matrix_remove_columns(ode_solution, create_array((long[]) {1L}, 1));
         SUNMatDestroy(ode_solution);
 
@@ -203,7 +225,7 @@ N_VDestroy(residuals);
 
     if (rank != 0)
     {
-        N_VDestroy(initial_values);
+        N_VDestroy(initial_condition);
         SUNMatDestroy(observed_data);
         return NULL;
     }
@@ -218,8 +240,8 @@ N_VDestroy(residuals);
 
     for (int i = 0; i < n; ++i)
     {
-        SM_ELEMENT_D(q_low, 0, i) = NV_Ith_S(initial_values, i);
-        SM_ELEMENT_D(q_up, 0, i) = NV_Ith_S(initial_values, i);
+        SM_ELEMENT_D(q_low, 0, i) = NV_Ith_S(initial_condition, i);
+        SM_ELEMENT_D(q_up, 0, i) = NV_Ith_S(initial_condition, i);
     }
 
     MatrixArray m_low = create_matrix_array(m - 1);
@@ -252,7 +274,7 @@ N_VDestroy(residuals);
     destroy_matrix_array(m_low);
     destroy_matrix_array(m_up);
     destroy_matrix_array(media_matrix);
-    N_VDestroy(initial_values);
+    N_VDestroy(initial_condition);
     SUNMatDestroy(observed_data);
     SUNMatDestroy(resid_loo);
     SUNMatDestroy(predicted_params_matrix);
diff --git a/modules/cuqdyn-c/src/ess_solver.c b/modules/cuqdyn-c/src/ess_solver.c
@@ -10,26 +10,31 @@
 #include <../include/functions.h>
 
 #include "cuqdyn.h"
-#if defined(MPI2) && !defined(MPI)
+#if defined(MPI2) || defined(MPI)
 #include <mpi.h>
 #endif
 
 #ifdef OPENMP
 #include <omp.h>
 #endif
 
-N_Vector execute_ess_solver(const char *file, const char *path, N_Vector texp, SUNMatrix yexp, N_Vector initial_values,
-    int rank, int nproc
-    )
+N_Vector execute_ess_solver(const char *file, const char *path, N_Vector texp, SUNMatrix yexp,
+    N_Vector initial_condition, N_Vector initial_params)
 {
-    int error, i, NPROC_OPENMP;
+    int error, NPROC_OPENMP;
     experiment_total *exptotal;
     result_solver result;
     int first, init;
 
-#if defined(MPI2) && !defined(MPI)
+    int nproc;
+    int rank;
+
+#if defined(MPI2) || defined(MPI)
     MPI_Comm_size(MPI_COMM_WORLD, &nproc);
     MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+#else
+    nproc = 1;
+    rank = 0;
 #endif
 
 #ifdef OPENMP
@@ -40,10 +45,17 @@ N_Vector execute_ess_solver(const char *file, const char *path, N_Vector texp, S
 
     exptotal = (experiment_total *) malloc(NPROC_OPENMP * sizeof(experiment_total));
     init = 1;
-    for (i = 0; i < NPROC_OPENMP; i++)
+    for (int i = 0; i < NPROC_OPENMP; i++)
     {
         // PARSE THE OPTIONS OF THE SOLVER
-        create_expetiment_struct(file, &(exptotal[i]), nproc, rank, path, init, texp, yexp, initial_values);
+        create_expetiment_struct(file, &(exptotal[i]), nproc, rank, path, init, texp, yexp, initial_condition);
+        if (initial_params != NULL)
+        {
+            for (int i = 0; i < NV_LENGTH_S(initial_params); i++)
+            {
+                exptotal[0].test.bench.X0[0][i] = NV_Ith_S(initial_params, i);
+            }
+        }
         init = 0;
     }
 
@@ -64,12 +76,15 @@ N_Vector execute_ess_solver(const char *file, const char *path, N_Vector texp, S
 #else
     exptotal = (experiment_total *) malloc(sizeof(experiment_total));
     init = 1;
-    create_expetiment_struct(file, &exptotal[0], nproc, rank, path, init, texp, yexp, initial_values);
+    create_expetiment_struct(file, &exptotal[0], nproc, rank, path, init, texp, yexp, initial_condition);
 
-    // INIT MESSAGE
-    NPROC_OPENMP = 1;
-    // INIT BENCHMARK
-    first = 1;
+    if (initial_params != NULL)
+    {
+        for (int i = 0; i < NV_LENGTH_S(initial_params); i++)
+        {
+            exptotal[0].test.bench.X0[0][i] = NV_Ith_S(initial_params, i);
+        }
+    }
 
     // INIT RESULT STRUCT
     init_result_data(&result, exptotal->test.bench.dim);
diff --git a/modules/sacess/src/input_module/input_module.c b/modules/sacess/src/input_module/input_module.c
@@ -1036,6 +1036,7 @@ int extract_element_problem(xmlDocPtr doc, xmlNodePtr *root, experiment_total *e
 	     vector_char[i] = (char *) malloc(100000* sizeof(char));
 	     test->bench.X0[i] = (double *) malloc(test->bench.dim*sizeof(double));
 	}
+
 	extract_element_multi(doc,cur,name_sol,vector_char);
         for (i=0;i<test->bench.number_init_sol;i++) {
     		counter=0;
diff --git a/mpi_toolchain.cmake b/mpi_toolchain.cmake
@@ -1,8 +1,8 @@
 set(CMAKE_C_COMPILER mpicc)
 set(CMAKE_CXX_COMPILER mpic++)
 set(CMAKE_Fortran_COMPILER mpifort)
-set(CMAKE_C_FLAGS "-O3 -cpp -DGNU -fPIC -no-pie -DOPENMP -DMPI -fopenmp -w")
-set(CMAKE_Fortran_FLAGS "-O3 -cpp -DGNU -w -fallow-argument-mismatch -std=gnu -DOPENMP -DMPI -DGNU -fopenmp")
+set(CMAKE_C_FLAGS "-O3 -cpp -DGNU -fPIC -no-pie -DMPI -w")
+set(CMAKE_Fortran_FLAGS "-O3 -cpp -DGNU -w -fallow-argument-mismatch -std=gnu -DGNU")
 
 set(MISQP_LIBRARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/deps/misqp/gnu")
 set(LIBRARIES mpi)
diff --git a/tests/data/alpha_pinene_ess_config_nl2sol.dn2fb.xml b/tests/data/alpha_pinene_ess_config_nl2sol.dn2fb.xml
@@ -58,9 +58,9 @@
         <ub>
             1, 1, 1, 1, 1
         </ub>
-        <initial_point>
+        <point>
             1, 1, 1, 1, 1
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/tests/data/logistic_model_ess_config_nl2sol.dn2fb.xml b/tests/data/logistic_model_ess_config_nl2sol.dn2fb.xml
@@ -58,9 +58,9 @@
         <ub>
             1, 200
         </ub>
-        <initial_point>
+        <point>
             1, 150
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/tests/data/lotka_volterra_ess_config_dhc.xml b/tests/data/lotka_volterra_ess_config_dhc.xml
@@ -58,9 +58,9 @@
         <ub>
             1.000, 1.000, 1.000, 1.000
         </ub>
-        <initial_point>
+        <point>
             0.3, 0.3, 0.3, 0.3
-        </initial_point>
+        </point>
     </problem>
 
 </xml>
diff --git a/tests/data/lotka_volterra_ess_config_misqp.xml b/tests/data/lotka_volterra_ess_config_misqp.xml
diff --git a/tests/data/lotka_volterra_ess_config_nl2sol.dn2fb.xml b/tests/data/lotka_volterra_ess_config_nl2sol.dn2fb.xml
diff --git a/tests/data/lotka_volterra_ess_config_nl2sol.dn2gb.xml b/tests/data/lotka_volterra_ess_config_nl2sol.dn2gb.xml
diff --git a/tests/data/lotka_volterra_ess_mpi_config_nl2sol.dn2gb.xml b/tests/data/lotka_volterra_ess_mpi_config_nl2sol.dn2gb.xml
diff --git a/tests/data/lotka_volterra_ess_serial_config_nl2sol.dn2gb.xml b/tests/data/lotka_volterra_ess_serial_config_nl2sol.dn2gb.xml
diff --git a/tests/test_cuqdyn_algo.c b/tests/test_cuqdyn_algo.c
diff --git a/tests/test_ess_solver.c b/tests/test_ess_solver.c

Original file line number	Diff line number	Diff line change
`@@ -111,7 +111,7 @@ int handle_solve(int argc, char *argv[])`
`111`	`111`	`int nproc = 1;`
`112`	`112`	`#endif`
`113`	`113`
`114`		`- CuqdynResult *cuqdyn_result = cuqdyn_algo(data_file, sacess_config_file, output_dir, rank, nproc);`
	`114`	`+ CuqdynResult *cuqdyn_result = cuqdyn_algo(data_file, sacess_config_file, output_dir);`
`115`	`115`
`116`	`116`	`if (rank == 0)`
`117`	`117`	`{`
Original file line number	Diff line number	Diff line change
`@@ -23,7 +23,7 @@ typedef struct`
`23`	`23`	`CuqdynResult* create_cuqdyn_result(SUNMatrix predicted_data_median, N_Vector predicted_params_median,`
`24`	`24`	`SUNMatrix q_low, SUNMatrix q_up, N_Vector times);`
`25`	`25`	`void destroy_cuqdyn_result(CuqdynResult* result);`
`26`		`-CuqdynResult cuqdyn_algo(const char data_file, const char sacess_conf_file, const char output_file, int rank, int nproc);`
	`26`	`+CuqdynResult cuqdyn_algo(const char data_file, const char sacess_conf_file, const char output_file);`
`27`	`27`
`28`	`28`	`typedef struct`
`29`	`29`	`{`