Fix build with sundials 7 (#94)

modelon-community · May 17, 2024 · 214dbd6 · 214dbd6
1 parent f1e87df
commit 214dbd6
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diff --git a/CHANGELOG b/CHANGELOG
@@ -1,5 +1,8 @@
 --- CHANGELOG ---
 
+--- Assimulo-3.5.1 ---
+    * Fixed build with sundials 7.x
+
 --- Assimulo-3.5.0 ---
     * Changed "numpy.float" to equivalent "numpy.float64" due to DeprecationWarnings in numpy >= 1.20.
     * Improved examples with sparse jacobians by omitting the zeros in the jacobians.

diff --git a/examples/kinsol_ors.py b/examples/kinsol_ors.py
@@ -18,8 +18,9 @@
 import os
 import nose
 import numpy as np
-import scipy as sp
 import scipy.sparse as sps
+import scipy.sparse.linalg as spsl
+import scipy.io as spi
 from assimulo.solvers import KINSOL
 from assimulo.problem import Algebraic_Problem
 import warnings
@@ -36,7 +37,7 @@ def run_example(with_plots=True):
     Iterative Methods for Sparse Linear Systems.
     """
     #Read the original matrix
-    A_original = sp.io.mmread(os.path.join(file_path,"kinsol_ors_matrix.mtx"))
+    A_original = spi.mmread(os.path.join(file_path,"kinsol_ors_matrix.mtx"))
 
     #Scale the original matrix
     A = sps.spdiags(1.0/A_original.diagonal(), 0, len(A_original.diagonal()), len(A_original.diagonal())) * A_original
@@ -51,7 +52,7 @@ def run_example(with_plots=True):
         U = D-F
         Prec = L.dot(U)
 
-        solvePrec = sps.linalg.factorized(Prec)
+        solvePrec = spsl.factorized(Prec)
 
     #Create the RHS
     b = A.dot(np.ones(A.shape[0]))

diff --git a/setup.py b/setup.py
@@ -504,6 +504,8 @@ def cython_extensionlists(self):
 
             if self.SUNDIALS_version >= (3,0,0):
                 ext_list[-1].libraries = ["sundials_cvodes", "sundials_nvecserial", "sundials_idas", "sundials_sunlinsoldense", "sundials_sunlinsolspgmr", "sundials_sunmatrixdense", "sundials_sunmatrixsparse"]
+                if self.SUNDIALS_version >= (7,0,0):
+                    ext_list[-1].libraries.extend(["sundials_core"])
             else:
                 ext_list[-1].libraries = ["sundials_cvodes", "sundials_nvecserial", "sundials_idas"]
             if self.sundials_with_superlu and self.with_SLU: #If SUNDIALS is compiled with support for SuperLU
@@ -523,6 +525,8 @@ def cython_extensionlists(self):
             ext_list[-1].include_dirs = [np.get_include(), "assimulo","assimulo"+os.sep+"lib", self.incdirs]
             ext_list[-1].library_dirs = [self.libdirs]
             ext_list[-1].libraries = ["sundials_kinsol", "sundials_nvecserial"]
+            if self.SUNDIALS_version >= (7,0,0):
+                ext_list[-1].libraries.extend(["sundials_core"])
 
             if self.sundials_with_superlu and self.with_SLU: #If SUNDIALS is compiled with support for SuperLU
                 ext_list[-1].include_dirs.append(self.SLUincdir)
@@ -665,7 +669,7 @@ def fortran_extensionlists(self):
 NAME = "Assimulo"
 AUTHOR = u"C. Winther (Andersson), C. Führer, J. Åkesson, M. Gäfvert"
 AUTHOR_EMAIL = "[email protected]"
-VERSION = "trunk" if version_number_arg == "Default" else version_number_arg
+VERSION = "3.5.0-dev" if version_number_arg == "Default" else version_number_arg
 LICENSE = "LGPL"
 URL = "http://www.jmodelica.org/assimulo"
 DOWNLOAD_URL = "http://www.jmodelica.org/assimulo"

diff --git a/src/lib/sundials_callbacks.pxi b/src/lib/sundials_callbacks.pxi
@@ -24,7 +24,10 @@ from numpy cimport PyArray_DATA
 cdef N_Vector N_VNewEmpty_Euclidean(long int n) noexcept:
     IF SUNDIALS_VERSION >= (6,0,0):
         cdef SUNDIALS.SUNContext ctx = NULL
-        cdef void * comm = NULL
+        IF SUNDIALS_VERSION >= (7,0,0):
+            cdef SUNDIALS.SUNComm comm = 0
+        ELSE:
+            cdef void* comm = NULL
         SUNDIALS.SUNContext_Create(comm, &ctx)
         cdef N_Vector v = N_VNew_Serial(n, ctx)
     ELSE:
@@ -39,7 +42,10 @@ cdef inline N_Vector arr2nv(x) noexcept:
     cdef void* data_ptr=PyArray_DATA(ndx)
     IF SUNDIALS_VERSION >= (6,0,0):
         cdef SUNDIALS.SUNContext ctx = NULL
-        cdef void * comm = NULL
+        IF SUNDIALS_VERSION >= (7,0,0):
+            cdef SUNDIALS.SUNComm comm = 0
+        ELSE:
+            cdef void* comm = NULL
         SUNDIALS.SUNContext_Create(comm, &ctx)
         cdef N_Vector v = N_VNew_Serial(n, ctx)
     ELSE:
@@ -63,7 +69,7 @@ cdef inline void arr2nv_inplace(x, N_Vector out) noexcept:
     cdef void* data_ptr=PyArray_DATA(ndx)
     memcpy((<N_VectorContent_Serial>out.content).data, data_ptr, n*sizeof(realtype))
 
-cdef inline np.ndarray nv2arr(N_Vector v) noexcept:
+cdef inline np.ndarray nv2arr(N_Vector v):
     cdef long int n = (<N_VectorContent_Serial>v.content).length
     cdef realtype* v_data = (<N_VectorContent_Serial>v.content).data
     cdef np.ndarray[realtype, ndim=1, mode='c'] x=np.empty(n)
@@ -82,7 +88,7 @@ cdef inline void nv2mat_inplace(int Ns, N_Vector *v, np.ndarray o) noexcept:
         for j in range(Nf):
             o[j,i] = (<N_VectorContent_Serial>v[i].content).data[j]
 
-cdef inline realtype2arr(realtype *data, int n) noexcept:
+cdef inline realtype2arr(realtype *data, int n):
     """Create new numpy array from realtype*"""
     cdef np.ndarray[realtype, ndim=1, mode='c'] x=np.empty(n)
     memcpy(PyArray_DATA(x), data, n*sizeof(realtype))

diff --git a/src/lib/sundials_callbacks_kinsol.pxi b/src/lib/sundials_callbacks_kinsol.pxi
@@ -256,41 +256,40 @@ ELSE:
         #print("<functionNorm: %g, scaledStepLength: %g, tolerance: %g>"%(fnorm, snorm, pData.TOL))
 
 
-cdef void kin_info(const char *module, const char *function, char *msg, void *eh_data) noexcept:
-    cdef ProblemDataEquationSolver pData = <ProblemDataEquationSolver>eh_data
-    cdef int flag
-    cdef realtype fnorm
-
-    if str(function) == "KINSol" and "fnorm" in str(msg):
-        #fnorm = float(msg.split("fnorm = ")[-1].strip())
-        flag = SUNDIALS.KINGetFuncNorm(pData.KIN_MEM, &fnorm)
-        pData.nl_fnorm.append(fnorm)
-
-    pData.log.append([module, function, msg])
-
-    #print("KinsolInfo <calling_function:%s>"%function)
-    #print("<message: %s>"%msg)
-    """
-    # Get the number of iterations
-    KINGetNumNonlinSolvIters(kin_mem, &nniters)
-    
-    
-    /* Only output an iteration under certain conditions:
-     *  1. nle_solver_log > 2
-     *  2. The calling function is either KINSolInit or KINSol
-     *  3. The message string starts with "nni"
-     *
-     *  This approach gives one printout per iteration
-    
-    
-    if ("KINSolInit" in function or "KINSol" in function) and "nni" in msg:
-        print("<iteration_index:%d>"%nniters)
-        print("ivs", N_VGetArrayPointer(kin_mem->kin_uu), block->n))
-        print("<scaled_residual_norm:%E>", kin_mem->kin_fnorm))
-        print("residuals", 
-            realtype* f = N_VGetArrayPointer(kin_mem->kin_fval);
-            f[i]*residual_scaling_factors[i])
-    """
+
+    cdef void kin_info(const char *module, const char *function, char *msg, void *eh_data) noexcept:
+        cdef ProblemDataEquationSolver pData = <ProblemDataEquationSolver>eh_data
+        cdef int flag
+        cdef realtype fnorm
+
+        if str(function) == "KINSol" and "fnorm" in str(msg):
+            #fnorm = float(msg.split("fnorm = ")[-1].strip())
+            flag = SUNDIALS.KINGetFuncNorm(pData.KIN_MEM, &fnorm)
+            pData.nl_fnorm.append(fnorm)
+
+        pData.log.append([module, function, msg])
+
+        #print("KinsolInfo <calling_function:%s>"%function)
+        #print("<message: %s>"%msg)
+        """
+        # Get the number of iterations
+        KINGetNumNonlinSolvIters(kin_mem, &nniters)
+
+        /* Only output an iteration under certain conditions:
+        *  1. nle_solver_log > 2
+        *  2. The calling function is either KINSolInit or KINSol
+        *  3. The message string starts with "nni"
+        *
+        *  This approach gives one printout per iteration
+
+        if ("KINSolInit" in function or "KINSol" in function) and "nni" in msg:
+            print("<iteration_index:%d>"%nniters)
+            print("ivs", N_VGetArrayPointer(kin_mem->kin_uu), block->n))
+            print("<scaled_residual_norm:%E>", kin_mem->kin_fnorm))
+            print("residuals",
+                realtype* f = N_VGetArrayPointer(kin_mem->kin_fval);
+                f[i]*residual_scaling_factors[i])
+        """
 
 cdef class ProblemDataEquationSolver:
     cdef:

diff --git a/src/lib/sundials_includes.pxd b/src/lib/sundials_includes.pxd
@@ -36,7 +36,11 @@ IF SUNDIALS_VERSION >= (6,0,0):
         ctypedef _SUNContext * SUNContext
         cdef struct _SUNContext:
             pass
-        int SUNContext_Create(void* comm, SUNContext* ctx) noexcept
+        IF SUNDIALS_VERSION >= (7,0,0):
+            ctypedef int SUNComm
+            int SUNContext_Create(SUNComm comm, SUNContext* ctx) noexcept
+        ELSE:
+            int SUNContext_Create(void* comm, SUNContext* ctx) noexcept
 
 IF SUNDIALS_VERSION >= (7,0,0):
     cdef extern from "sundials/sundials_context.h":
@@ -48,6 +52,8 @@ IF SUNDIALS_VERSION >= (6,0,0):
     cdef extern from "sundials/sundials_types.h":
         ctypedef double sunrealtype
         ctypedef bint sunbooleantype
+        IF SUNDIALS_VERSION >= (7,0,0):
+            cdef int SUN_COMM_NULL
     ctypedef double realtype
     ctypedef bint booleantype
 ELSE:
@@ -494,7 +500,7 @@ ELSE:
                                         N_Vector tmp2, N_Vector tmp3) noexcept
             int CVSlsSetSparseJacFn(void *cvode_mem, CVSlsSparseJacFn jac) noexcept
             int CVSlsGetNumJacEvals(void *cvode_mem, long int *njevals) noexcept
-        cdef inline tuple version() noexcept: return (2,6,0)
+        cdef inline tuple version(): return (2,6,0)
         IF SUNDIALS_WITH_SUPERLU:
             cdef extern from "cvodes/cvodes_superlumt.h":
                 int CVSuperLUMT(void *cvode_mem, int numthreads, int n, int nnz) noexcept
@@ -579,7 +585,7 @@ cdef extern from "idas/idas.h":
     int IDAGetNumResEvals(void *ida_mem, long int *nrevals)             #Number of res evals
     IF SUNDIALS_VERSION >= (4,0,0):
         int IDAGetNumJacEvals(void *ida_mem, long int *njevals)          #Number of jac evals
-        int IDAGetNumResEvals(void *ida_mem, long int *nrevalsLS)        #Number of res evals due to jac evals
+        int IDAGetNumLinResEvals(void *ida_mem, long int *nrevalsLS)        #Number of res evals due to jac evals
     ELSE:
         int IDADlsGetNumJacEvals(void *ida_mem, long int *njevals)          #Number of jac evals
         int IDADlsGetNumResEvals(void *ida_mem, long int *nrevalsLS)        #Number of res evals due to jac evals

diff --git a/src/solvers/dasp3.py b/src/solvers/dasp3.py
@@ -44,8 +44,8 @@ class DASP3ODE(Explicit_ODE):
     
     .. math::
       
-      \\frac{\mathrm{d}y}{\mathrm{d}t} &=  f(t,y,z) \;\;\;  \\text{(N equations)} \\\\
-      \\varepsilon\\frac{\mathrm{d}z}{\mathrm{d}t} &= G(t,y,z)\;\;\;  \\text{(M equations)}       
+      \\frac{\\mathrm{d}y}{\\mathrm{d}t} &=  f(t,y,z) \\;\\;\\;  \\text{(N equations)} \\\\
+      \\varepsilon\\frac{\\mathrm{d}z}{\\mathrm{d}t} &= G(t,y,z)\\;\\;\\;  \\text{(M equations)}
     
     If is assumed that the first system is non-stiff and that
     the stiffness of the second system is due to the parameter

diff --git a/src/solvers/kinsol.pyx b/src/solvers/kinsol.pyx
@@ -183,7 +183,10 @@ cdef class KINSOL(Algebraic):
         cdef int flag #Used for return
         IF SUNDIALS_VERSION >= (6,0,0):
             cdef SUNDIALS.SUNContext ctx = NULL
-            cdef void * comm = NULL
+            IF SUNDIALS_VERSION >= (7,0,0):
+                cdef SUNDIALS.SUNComm comm = SUNDIALS.SUN_COMM_NULL
+            ELSE:
+                cdef void* comm = NULL
             SUNDIALS.SUNContext_Create(comm, &ctx)
 
         self.y_temp  = arr2nv(self.y)
@@ -230,7 +233,10 @@ cdef class KINSOL(Algebraic):
     cpdef add_linear_solver(self):
         IF SUNDIALS_VERSION >= (6,0,0):
             cdef SUNDIALS.SUNContext ctx = NULL
-            cdef void * comm = NULL
+            IF SUNDIALS_VERSION >= (7,0,0):
+                cdef SUNDIALS.SUNComm comm = SUNDIALS.SUN_COMM_NULL
+            ELSE:
+                cdef void* comm = NULL
             SUNDIALS.SUNContext_Create(comm, &ctx)
         if self.options["linear_solver"] == "DENSE":
             IF SUNDIALS_VERSION >= (3,0,0):

diff --git a/src/solvers/odepack.py b/src/solvers/odepack.py
@@ -48,7 +48,7 @@ class LSODAR(Explicit_ODE):
         
         .. math::
     
-            \dot{y} = f(t,y), \quad y(t_0) = y_0.
+            \\dot{y} = f(t,y), \\quad y(t_0) = y_0.
             
         LSODAR automatically switches between using an ADAMS method
         or an BDF method and is also able to monitor events.

diff --git a/src/solvers/radau5.py b/src/solvers/radau5.py
@@ -16,7 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import scipy as sp
+import scipy.linalg as spl
 import scipy.sparse as sps
 
 from assimulo.exception import (
@@ -707,9 +707,9 @@ def newton(self,t,y):
                 self._g = self._gamma/self.h
                 self._B = self._g*self.I - self._jac
 
-                self._P1,self._L1,self._U1 = sp.linalg.lu(self._B) #LU decomposition
-                self._P2,self._L2,self._U2 = sp.linalg.lu(self._a*self.I-self._jac)
-                self._P3,self._L3,self._U3 = sp.linalg.lu(self._b*self.I-self._jac)
+                self._P1,self._L1,self._U1 = spl.lu(self._B) #LU decomposition
+                self._P2,self._L2,self._U2 = spl.lu(self._a*self.I-self._jac)
+                self._P3,self._L3,self._U3 = spl.lu(self._b*self.I-self._jac)
 
                 self._needLU = False
 
@@ -1526,9 +1526,9 @@ def newton(self,t,y,yd):
                 self._g = self._gamma/self.h
                 self._B = self._g*self.M - self._jac
 
-                self._P1,self._L1,self._U1 = sp.linalg.lu(self._B) #LU decomposition
-                self._P2,self._L2,self._U2 = sp.linalg.lu(self._a*self.M-self._jac)
-                self._P3,self._L3,self._U3 = sp.linalg.lu(self._b*self.M-self._jac)
+                self._P1,self._L1,self._U1 = spl.lu(self._B) #LU decomposition
+                self._P2,self._L2,self._U2 = spl.lu(self._a*self.M-self._jac)
+                self._P3,self._L3,self._U3 = spl.lu(self._b*self.M-self._jac)
 
                 self._needLU = False
 

diff --git a/src/solvers/runge_kutta.py b/src/solvers/runge_kutta.py
@@ -753,7 +753,7 @@ class RungeKutta4(Explicit_ODE):
     
     .. math::
 
-        \dot{y} = f(t,y), \quad y(t_0) = y_0 .
+        \\dot{y} = f(t,y), \\quad y(t_0) = y_0 .
         
     Using a Runge-Kutta method of order 4, the approximation is defined as 
     follow,