Merge pull request #1819 from stan-dev/feature/issue-1818-upgrade-sun…

…dials-520

Feature/issue 1818 upgrade sundials 520

README.md

@@ -27,7 +27,7 @@ Stan Math depends on four libraries:
 
 - Boost (version 1.72.0): [Boost Home Page](https://www.boost.org)
 - Eigen (version 3.3.3): [Eigen Home Page](https://eigen.tuxfamily.org/index.php?title=Main_Page)
-- SUNDIALS (version 5.1.0): [Sundials Home Page](https://computation.llnl.gov/projects/sundials/sundials-software)
+- SUNDIALS (version 5.2.0): [Sundials Home Page](https://computation.llnl.gov/projects/sundials/sundials-software)
 - Intel TBB (version 2019_U8): [Intel TBB Home Page](https://www.threadingbuildingblocks.org)
 
 These are distributed under the `lib/` subdirectory. Only these
@@ -91,7 +91,7 @@ The standalone makefile ensures that all the required `-I` include
 statements are given to the compiler and the necessary libraries are
 linked: `~/stan-dev/math` and `~/stan-dev/math/lib/eigen_3.3.3` and
 `~/stan-dev/math/lib/boost_1.72.0` and
-`~/stan-dev/math/lib/sundials_5.1.0/include` and
+`~/stan-dev/math/lib/sundials_5.2.0/include` and
 `~/stan-dev/math/lib/tbb_2019_U8/include`. The
 `~/stan-dev/math/lib/tbb` directory is created by the `math-libs`
 makefile target automatically and contains the dynamically loaded

lib/sundials_5.1.0/README.md → lib/sundials_5.2.0/README.md

@@ -1,5 +1,5 @@
 # SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic equation Solvers #
-### Version 5.1.0 (Jan 2020) ###
+### Version 5.2.0 (Mar 2020) ###
 
 **Center for Applied Scientific Computing, Lawrence Livermore National Laboratory**
 

lib/sundials_5.1.0/include/cvodes/cvodes_direct.h → lib/sundials_5.2.0/include/cvodes/cvodes_direct.h

@@ -38,28 +38,28 @@ typedef CVLsJacFnBS CVDlsJacFnBS;
   Exported Functions (wrappers for equivalent routines in cvodes_ls.h)
   ====================================================================*/
 
-int CVDlsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS,
-                         SUNMatrix A);
+SUNDIALS_EXPORT int CVDlsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS,
+                                         SUNMatrix A);
 
-int CVDlsSetJacFn(void *cvode_mem, CVDlsJacFn jac);
+SUNDIALS_EXPORT int CVDlsSetJacFn(void *cvode_mem, CVDlsJacFn jac);
 
-int CVDlsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
-                      long int *leniwLS);
+SUNDIALS_EXPORT int CVDlsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
+                                      long int *leniwLS);
 
-int CVDlsGetNumJacEvals(void *cvode_mem, long int *njevals);
+SUNDIALS_EXPORT int CVDlsGetNumJacEvals(void *cvode_mem, long int *njevals);
 
-int CVDlsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
+SUNDIALS_EXPORT int CVDlsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
 
-int CVDlsGetLastFlag(void *cvode_mem, long int *flag);
+SUNDIALS_EXPORT int CVDlsGetLastFlag(void *cvode_mem, long int *flag);
 
-char *CVDlsGetReturnFlagName(long int flag);
+SUNDIALS_EXPORT char *CVDlsGetReturnFlagName(long int flag);
 
-int CVDlsSetLinearSolverB(void *cvode_mem, int which,
-                          SUNLinearSolver LS, SUNMatrix A);
+SUNDIALS_EXPORT int CVDlsSetLinearSolverB(void *cvode_mem, int which,
+                                          SUNLinearSolver LS, SUNMatrix A);
 
-int CVDlsSetJacFnB(void *cvode_mem, int which, CVDlsJacFnB jacB);
+SUNDIALS_EXPORT int CVDlsSetJacFnB(void *cvode_mem, int which, CVDlsJacFnB jacB);
 
-int CVDlsSetJacFnBS(void *cvode_mem, int which, CVDlsJacFnBS jacBS);
+SUNDIALS_EXPORT int CVDlsSetJacFnBS(void *cvode_mem, int which, CVDlsJacFnBS jacBS);
 
 
 #ifdef __cplusplus

lib/sundials_5.1.0/include/cvodes/cvodes_ls.h → lib/sundials_5.2.0/include/cvodes/cvodes_ls.h

@@ -98,6 +98,8 @@ SUNDIALS_EXPORT int CVodeSetLinearSolver(void *cvode_mem,
 SUNDIALS_EXPORT int CVodeSetJacFn(void *cvode_mem, CVLsJacFn jac);
 SUNDIALS_EXPORT int CVodeSetMaxStepsBetweenJac(void *cvode_mem,
                                                long int msbj);
+SUNDIALS_EXPORT int CVodeSetLinearSolutionScaling(void *cvode_mem,
+                                                  booleantype onoff);
 SUNDIALS_EXPORT int CVodeSetEpsLin(void *cvode_mem, realtype eplifac);
 SUNDIALS_EXPORT int CVodeSetPreconditioner(void *cvode_mem,
                                            CVLsPrecSetupFn pset,
@@ -227,6 +229,9 @@ SUNDIALS_EXPORT int CVodeSetJacFnBS(void *cvode_mem, int which,
 SUNDIALS_EXPORT int CVodeSetEpsLinB(void *cvode_mem, int which,
                                     realtype eplifacB);
 
+SUNDIALS_EXPORT int CVodeSetLinearSolutionScalingB(void *cvode_mem, int which,
+                                                   booleantype onoffB);
+
 SUNDIALS_EXPORT int CVodeSetPreconditionerB(void *cvode_mem, int which,
                                             CVLsPrecSetupFnB psetB,
                                             CVLsPrecSolveFnB psolveB);

lib/sundials_5.1.0/include/cvodes/cvodes_spils.h → lib/sundials_5.2.0/include/cvodes/cvodes_spils.h

@@ -47,55 +47,55 @@ typedef CVLsJacTimesVecFnBS CVSpilsJacTimesVecFnBS;
   Exported Functions (wrappers for equivalent routines in cvodes_ls.h)
   ====================================================================*/
 
-int CVSpilsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS);
+SUNDIALS_EXPORT int CVSpilsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS);
 
-int CVSpilsSetEpsLin(void *cvode_mem, realtype eplifac);
+SUNDIALS_EXPORT int CVSpilsSetEpsLin(void *cvode_mem, realtype eplifac);
 
-int CVSpilsSetPreconditioner(void *cvode_mem, CVSpilsPrecSetupFn pset,
+SUNDIALS_EXPORT int CVSpilsSetPreconditioner(void *cvode_mem, CVSpilsPrecSetupFn pset,
                              CVSpilsPrecSolveFn psolve);
 
-int CVSpilsSetJacTimes(void *cvode_mem, CVSpilsJacTimesSetupFn jtsetup,
+SUNDIALS_EXPORT int CVSpilsSetJacTimes(void *cvode_mem, CVSpilsJacTimesSetupFn jtsetup,
                        CVSpilsJacTimesVecFn jtimes);
 
-int CVSpilsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
+SUNDIALS_EXPORT int CVSpilsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
                         long int *leniwLS);
 
-int CVSpilsGetNumPrecEvals(void *cvode_mem, long int *npevals);
+SUNDIALS_EXPORT int CVSpilsGetNumPrecEvals(void *cvode_mem, long int *npevals);
 
-int CVSpilsGetNumPrecSolves(void *cvode_mem, long int *npsolves);
+SUNDIALS_EXPORT int CVSpilsGetNumPrecSolves(void *cvode_mem, long int *npsolves);
 
-int CVSpilsGetNumLinIters(void *cvode_mem, long int *nliters);
+SUNDIALS_EXPORT int CVSpilsGetNumLinIters(void *cvode_mem, long int *nliters);
 
-int CVSpilsGetNumConvFails(void *cvode_mem, long int *nlcfails);
+SUNDIALS_EXPORT int CVSpilsGetNumConvFails(void *cvode_mem, long int *nlcfails);
 
-int CVSpilsGetNumJTSetupEvals(void *cvode_mem, long int *njtsetups);
+SUNDIALS_EXPORT int CVSpilsGetNumJTSetupEvals(void *cvode_mem, long int *njtsetups);
 
-int CVSpilsGetNumJtimesEvals(void *cvode_mem, long int *njvevals);
+SUNDIALS_EXPORT int CVSpilsGetNumJtimesEvals(void *cvode_mem, long int *njvevals);
 
-int CVSpilsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
+SUNDIALS_EXPORT int CVSpilsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
 
-int CVSpilsGetLastFlag(void *cvode_mem, long int *flag);
+SUNDIALS_EXPORT int CVSpilsGetLastFlag(void *cvode_mem, long int *flag);
 
-char *CVSpilsGetReturnFlagName(long int flag);
+SUNDIALS_EXPORT char *CVSpilsGetReturnFlagName(long int flag);
 
-int CVSpilsSetLinearSolverB(void *cvode_mem, int which,
+SUNDIALS_EXPORT int CVSpilsSetLinearSolverB(void *cvode_mem, int which,
                             SUNLinearSolver LS);
 
-int CVSpilsSetEpsLinB(void *cvode_mem, int which, realtype eplifacB);
+SUNDIALS_EXPORT int CVSpilsSetEpsLinB(void *cvode_mem, int which, realtype eplifacB);
 
-int CVSpilsSetPreconditionerB(void *cvode_mem, int which,
+SUNDIALS_EXPORT int CVSpilsSetPreconditionerB(void *cvode_mem, int which,
                               CVSpilsPrecSetupFnB psetB,
                               CVSpilsPrecSolveFnB psolveB);
 
-int CVSpilsSetPreconditionerBS(void *cvode_mem, int which,
+SUNDIALS_EXPORT int CVSpilsSetPreconditionerBS(void *cvode_mem, int which,
                                CVSpilsPrecSetupFnBS psetBS,
                                CVSpilsPrecSolveFnBS psolveBS);
 
-int CVSpilsSetJacTimesB(void *cvode_mem, int which,
+SUNDIALS_EXPORT int CVSpilsSetJacTimesB(void *cvode_mem, int which,
                         CVSpilsJacTimesSetupFnB jtsetupB,
                         CVSpilsJacTimesVecFnB jtimesB);
 
-int CVSpilsSetJacTimesBS(void *cvode_mem, int which,
+SUNDIALS_EXPORT int CVSpilsSetJacTimesBS(void *cvode_mem, int which,
                          CVSpilsJacTimesSetupFnBS jtsetupBS,
                          CVSpilsJacTimesVecFnBS jtimesBS);
 

lib/sundials_5.1.0/include/idas/idas_direct.h → lib/sundials_5.2.0/include/idas/idas_direct.h

@@ -38,28 +38,28 @@ typedef IDALsJacFnBS IDADlsJacFnBS;
   Exported Functions (wrappers for equivalent routines in idas_ls.h)
   ===================================================================*/
 
-int IDADlsSetLinearSolver(void *ida_mem, SUNLinearSolver LS,
-                          SUNMatrix A);
+SUNDIALS_EXPORT int IDADlsSetLinearSolver(void *ida_mem, SUNLinearSolver LS,
+                                          SUNMatrix A);
 
-int IDADlsSetJacFn(void *ida_mem, IDADlsJacFn jac);
+SUNDIALS_EXPORT int IDADlsSetJacFn(void *ida_mem, IDADlsJacFn jac);
 
-int IDADlsGetWorkSpace(void *ida_mem, long int *lenrwLS,
-                       long int *leniwLS);
+SUNDIALS_EXPORT int IDADlsGetWorkSpace(void *ida_mem, long int *lenrwLS,
+                                       long int *leniwLS);
 
-int IDADlsGetNumJacEvals(void *ida_mem, long int *njevals);
+SUNDIALS_EXPORT int IDADlsGetNumJacEvals(void *ida_mem, long int *njevals);
 
-int IDADlsGetNumResEvals(void *ida_mem, long int *nrevalsLS);
+SUNDIALS_EXPORT int IDADlsGetNumResEvals(void *ida_mem, long int *nrevalsLS);
 
-int IDADlsGetLastFlag(void *ida_mem, long int *flag);
+SUNDIALS_EXPORT int IDADlsGetLastFlag(void *ida_mem, long int *flag);
 
 char *IDADlsGetReturnFlagName(long int flag);
 
-int IDADlsSetLinearSolverB(void *ida_mem, int which,
-                           SUNLinearSolver LS, SUNMatrix A);
+SUNDIALS_EXPORT int IDADlsSetLinearSolverB(void *ida_mem, int which,
+                                           SUNLinearSolver LS, SUNMatrix A);
 
-int IDADlsSetJacFnB(void *ida_mem, int which, IDADlsJacFnB jacB);
+SUNDIALS_EXPORT int IDADlsSetJacFnB(void *ida_mem, int which, IDADlsJacFnB jacB);
 
-int IDADlsSetJacFnBS(void *ida_mem, int which, IDADlsJacFnBS jacBS);
+SUNDIALS_EXPORT int IDADlsSetJacFnBS(void *ida_mem, int which, IDADlsJacFnBS jacBS);
 
 
 

lib/sundials_5.1.0/include/idas/idas_ls.h → lib/sundials_5.2.0/include/idas/idas_ls.h

@@ -104,6 +104,8 @@ SUNDIALS_EXPORT int IDASetJacTimes(void *ida_mem,
                                    IDALsJacTimesSetupFn jtsetup,
                                    IDALsJacTimesVecFn jtimes);
 SUNDIALS_EXPORT int IDASetEpsLin(void *ida_mem, realtype eplifac);
+SUNDIALS_EXPORT int IDASetLinearSolutionScaling(void *ida_mem,
+                                                booleantype onoff);
 SUNDIALS_EXPORT int IDASetIncrementFactor(void *ida_mem,
                                           realtype dqincfac);
 
@@ -232,6 +234,8 @@ SUNDIALS_EXPORT int IDASetJacFnBS(void *ida_mem, int which,
 
 SUNDIALS_EXPORT int IDASetEpsLinB(void *ida_mem, int which,
                                   realtype eplifacB);
+SUNDIALS_EXPORT int IDASetLinearSolutionScalingB(void *ida_mem, int which,
+                                                 booleantype onoffB);
 SUNDIALS_EXPORT int IDASetIncrementFactorB(void *ida_mem, int which,
                                            realtype dqincfacB);
 SUNDIALS_EXPORT int IDASetPreconditionerB(void *ida_mem, int which,