works and does alpha pinene faster than ever

Author: ZocoLini

deps.cmake

@@ -1,17 +1,5 @@
 include(FetchContent)
 
-# Building v7.30 of CVODES
-include(ExternalProject)
-
-FetchContent_Declare(
-        cvodes
-        URL https://github.com/LLNL/sundials/releases/download/v7.3.0/cvodes-7.3.0.tar.gz
-        DOWNLOAD_EXTRACT_TIMESTAMP TRUE
-)
-
-FetchContent_MakeAvailable(cvodes)
-
-
 # Building GSL dependency
 find_package(GSL 2.7)
 
@@ -63,6 +51,15 @@ set(HDF5_FOUND TRUE)
 set(HAVE_HDF5 TRUE CACHE BOOL "Pretend we have HDF5" FORCE)
 # set(MATIO_MAT73 ON CACHE BOOL "Enable MAT73 support" FORCE)
 
+# Building v7.30 of CVODES
+FetchContent_Declare(
+        cvodes
+        URL https://github.com/LLNL/sundials/releases/download/v7.3.0/cvodes-7.3.0.tar.gz
+        DOWNLOAD_EXTRACT_TIMESTAMP TRUE
+)
+
+FetchContent_MakeAvailable(cvodes)
+
 # Building Matio dependency
 set(MATIO_WITH_ZLIB ON CACHE BOOL "" FORCE)
 set(MATIO_WITH_HDF5 ON CACHE BOOL "" FORCE)

example-files/alpha_pinene_cuqdyn_config.xml

@@ -2,8 +2,8 @@
 
 <cuqdyn-config>
     <tolerances>
-        <rtol>1e-8</rtol>
-        <atol>1e-8, 1e-8, 1e-8, 1e-8, 1e-8</atol>
+        <rtol>1e-16</rtol>
+        <atol>1e-16, 1e-16, 1e-16, 1e-16, 1e-16</atol>
     </tolerances>
     <ode_expr y_count="5" p_count="5">
         alpha-pinene

example-files/alpha_pinene_ess_mpi_config.xml

@@ -4,10 +4,10 @@
         <id>0</id>
         <log_scale>5</log_scale>
         <output>0</output>
-        <verbose>1</verbose>
+        <verbose>0</verbose>
         <local_search>1</local_search>
         <stopping_criteria>
-            <maxevaluation>6e3</maxevaluation>
+            <maxevaluation>15e3</maxevaluation>
             <maxtime>1e10</maxtime>
             <vtr>0</vtr>
         </stopping_criteria>

example-files/alpha_pinene_paper_data.txt

@@ -1,10 +1,10 @@
 9 6
-0     1.054e+02  2.769e-01  1.409e-01   3.034e-02  3.252e-02
-1230  1.063e+02  5.842e+00  3.441e+00   6.992e-02  4.046e-01
-3060  5.875e+01  2.101e+01  5.622e+00   1.027e-01  3.011e+00
-4920  7.023e+01  2.542e+01  5.316e+00   5.430e-01  4.136e+00
-7800  5.161e+01  3.314e+01  6.977e+00   5.887e-01  9.308e+00
-10680 3.350e+01  4.389e+01  7.298e+00   9.356e-01   1.277e+01
-15030 2.510e+01  4.814e+01  5.795e+00   1.468e+00   1.797e+01
-22620 1.388e+01  5.705e+01  5.169e+00   1.443e+00   2.250e+01
-36420 5.688e+00  7.378e+01  4.175e+00   4.301e+00  2.232e+01
+0    105.4304    0.27694    0.1409    0.030344    0.032519
+1230    106.2646    5.8416    3.4414    0.069919    0.40461
+3060    58.7484    21.0121    5.6224    0.1027    3.0108
+4920    70.2255    25.4187    5.3156    0.54304    4.1355
+7800    51.6116    33.1445    6.9769    0.58873    9.3084
+10680    33.5044    43.887    7.2983    0.93556    12.7689
+15030    25.1021    48.1426    5.7949    1.4677    17.9676
+22620    13.8795    57.0451    5.1687    1.4431    22.4986
+36420    5.6877    73.7817    4.1749    4.3015    22.3218

example-files/lotka_volterra_cuqdyn_config.xml

@@ -2,8 +2,8 @@
 
 <cuqdyn-config>
     <tolerances>
-        <rtol>1e-8</rtol>
-        <atol>1e-9, 1e-10</atol>
+        <rtol>1e-9</rtol>
+        <atol>1e-9, 1e-9</atol>
     </tolerances>
     <ode_expr y_count="2" p_count="4">
         lotka-volterra

example-files/lotka_volterra_ess_mpi_config.xml

@@ -2,7 +2,7 @@
     <run>
         <typebench>customized</typebench>
         <id>0</id>
-        <log_scale>4</log_scale>
+        <log_scale>2</log_scale>
         <output>0</output>
         <verbose>0</verbose>
         <local_search>1</local_search>

modules/cli/src/handlers/solve.c

@@ -1,4 +1,4 @@
-#include <nvector_old/nvector_serial.h>
+#include <nvector//nvector_serial.h>
 #include <stdio.h>
 #include <unistd.h>
 
@@ -8,6 +8,7 @@
 #include <config.h>
 #include <stdlib.h>
 #include <string.h>
+#include <sunmatrix/sunmatrix_dense.h>
 
 #include "../../../cuqdyn-c/include/functions.h"
 #include "cuqdyn.h"

modules/cuqdyn-c/src/ode_solver.c

@@ -3,6 +3,7 @@
 #include <cvodes/cvodes.h>
 #include <ode_solver.h>
 #include <string.h>
+#include <sunlinsol/sunlinsol_dense.h>
 #include <sunmatrix/sunmatrix_dense.h>
 
 #include "cuqdyn.h"
@@ -31,6 +32,11 @@ SUNMatrix solve_ode(N_Vector parameters, N_Vector initial_values, sunrealtype t0
     retval = CVodeSetUserData(cvode_mem, parameters);
     if (check_retval(&retval, "CVodeSetUserData", 1)) { return NULL; }
 
+    SUNMatrix A = SUNDenseMatrix(cuqdyn_conf->ode_expr.y_count, cuqdyn_conf->ode_expr.y_count, get_sundials_ctx());
+    SUNLinearSolver LS = SUNLinSol_Dense(initial_values, A, get_sundials_ctx());
+    retval = CVodeSetLinearSolver(cvode_mem, LS, A);
+    if (check_retval(&retval, "CVodeSetLinearSolver", 1)) { return NULL; }
+
     retval = CVodeSetMaxNumSteps(cvode_mem, 10000000);
     if (check_retval(&retval, "CVodeSetMaxNumSteps", 1)) { return NULL; }
 

modules/sacess/libAMIGO/src/src_amigo/AMIGO_model.c

@@ -217,6 +217,11 @@ void free_AMIGO_model(AMIGO_model* amigo_model){
 	free(amigo_model);
 }
 
+int simulate_amigo_model(AMIGO_model* amigo_model, int verbose)
+{
+    return 0;
+}
+
  int simulate_AMIGO_model(AMIGO_model* amigo_model,int sens){
 
 	amigo_model->compute_sens=sens;

tests/test_data_reader.c

@@ -1,9 +1,8 @@
 #define LOTKA_VOLTERRA_MAT "data/lotka_volterra_data_homoc_noise_0.10_size_30_data_1.mat"
 #define DATA_TXT "data/test_data.txt"
 
-#include <nvector_old/nvector_serial.h>
+#include <nvector/nvector_serial.h>
 #include <stdio.h>
-#include <sundials_old/sundials_nvector.h>
 #include <assert.h>