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diff --git var/lib/mock/fedora-rawhide-x86_64/root/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src/network.cpp.orig var/lib/mock/fedora-rawhide-x86_64/root/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src/network.cpp
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index a53a138ae7..b437797ca9 100644
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--- bionetgen-BioNetGen-2.3.0/bng2/Network3/src/network.cpp.orig
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+++ bionetgen-BioNetGen-2.3.0/bng2/Network3/src/network.cpp
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@@ -2627,14 +2627,17 @@ int print_rates_network(FILE* out, int discrete) {
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#include "sundials/sundials_types.h"
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#include "cvode/cvode.h"
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+#include "cvode/cvode_direct.h"
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#include "nvector/nvector_serial.h"
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-#include "cvode/cvode_dense.h"
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#include "sundials/sundials_dense.h"
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#include "sundials/sundials_direct.h"
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+#include "sunmatrix/sunmatrix_sparse.h"
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+
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+#include "sunlinsol/sunlinsol_dense.h"
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+#include "sunlinsol/sunlinsol_spgmr.h"
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+
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-#include "cvode/cvode_spgmr.h"
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-#include "sundials/sundials_spgmr.h"
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typedef struct jacnode* jacnode_ref;
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@@ -2986,6 +2989,8 @@ int propagate_cvode_network(double* t, double delta_t, double* n_steps, double*
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static N_Vector y;
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static void* cvode_mem;
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static int initflag = 0;
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+ static SUNMatrix A;
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+ static SUNLinearSolver LS;
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long int cvode_maxnumsteps = 2000;
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/* Initializations at the beginning of new propagation */
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@@ -3018,18 +3023,26 @@ int propagate_cvode_network(double* t, double delta_t, double* n_steps, double*
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* Jacobian vs finite difference
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*/
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if (SOLVER == GMRES || SOLVER == GMRES_J) {
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- CVSpgmr(cvode_mem, PREC_NONE, 0);
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if (SOLVER == GMRES_J) {
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cout << "ERROR: Jacobian no longer supported for GMRES solver" << endl;
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exit(1);
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}
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+
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+ // CVSpgmr(cvode_mem, PREC_NONE, 0);
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+ A = SUNSparseMatrix(n_species, n_species, 0, CSC_MAT);
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+ LS = SUNSPGMR(y, PREC_NONE, 0);
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+ CVDlsSetLinearSolver(cvode_mem, LS, A);
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}
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else if (SOLVER == DENSE || SOLVER == DENSE_J) {
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- CVDense(cvode_mem, n_species);
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if (SOLVER == DENSE_J) {
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cout << "ERROR: Jacobian no longer supported for dense solver" << endl;
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exit(1);
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}
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+
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+ // CVDense(cvode_mem, n_species);
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+ A = SUNDenseMatrix(n_species, n_species);
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+ LS = SUNDenseLinearSolver(y, A);
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+ CVDlsSetLinearSolver(cvode_mem, LS, A);
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}
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else {
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fprintf(stderr, "ERROR: Invalid CVODE solver.\n");
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