sundials

CMakeLists.txt

@@ -21,8 +21,25 @@ endif ()
 
 if (USE_SUNDIALS)
   find_package (SUNDIALS CONFIG)
+  if (NOT SUNDIALS_FOUND)
+    # fallback to our module
+    find_package (SUNDIALS MODULE)
+    set(SUNDIALS_DIR ${SUNDIALS_INCLUDE_DIR})
+  endif ()
+
   if (SUNDIALS_FOUND)
     message(STATUS "Found SUNDIALS: ${SUNDIALS_DIR}  (found version \"${SUNDIALS_VERSION}\")")
+
+    string (REGEX REPLACE "([0-9]+)\\..*" "\\1" SUNDIALS_MAJOR_VERSION "${SUNDIALS_VERSION}")
+    string (REGEX REPLACE "[0-9]+\\.([0-9]+).*" "\\1" SUNDIALS_MINOR_VERSION "${SUNDIALS_VERSION}")
+    string (REGEX REPLACE "[0-9]+\\.[0-9]+\\.([0-9]+).*" "\\1" SUNDIALS_PATCH_VERSION "${SUNDIALS_VERSION}")
+    math(EXPR SUNDIALS_VERSION_NR "100000 * ${SUNDIALS_MAJOR_VERSION} + 100 * ${SUNDIALS_MINOR_VERSION} + ${SUNDIALS_PATCH_VERSION}")
+
+    if (SuperLU_MT_FOUND)
+      set (SUNDIALS_WITH_SUPERLU True)
+    else ()
+      set (SUNDIALS_WITH_SUPERLU False)
+    endif ()
   endif ()
 endif ()
 
@@ -82,7 +99,7 @@ macro(assimulo_add_cython_module pyx_file)
   add_custom_command(
     OUTPUT ${name}.c
     COMMENT "Making ${name}.c from ${name}.pyx"
-    COMMAND Python::Interpreter -m cython -o ${name}.c --3str --fast-fail
+    COMMAND Python::Interpreter -m cython -o ${name}.c --3str --fast-fail ${CYTHON_FLAGS}
             -I ${CMAKE_CURRENT_SOURCE_DIR}/src
             -I ${CMAKE_CURRENT_SOURCE_DIR}/src/lib
             ${CMAKE_CURRENT_BINARY_DIR}/${pyx_file}
@@ -108,9 +125,34 @@ assimulo_add_cython_module(assimulo/special_systems.pyx)
 assimulo_add_cython_module(assimulo/support.pyx)
 assimulo_add_cython_module(assimulo/solvers/euler.pyx
   DESTINATION assimulo/solvers)
-#if (SUNDIALS_FOUND)
-#  assimulo_add_cython_module(solvers/sundials.pyx)
-#endif ()
+
+if (SUNDIALS_FOUND)
+  set(CYTHON_FLAGS -E SUNDIALS_VERSION_NR=${SUNDIALS_VERSION_NR} -E SUNDIALS_VECTOR_SIZE=64 -E SUNDIALS_WITH_SUPERLU=${SUNDIALS_WITH_SUPERLU} -E SUNDIALS_CVODE_RTOL_VEC=False)
+
+  set (SUNDIALS_LIBRARIES sundials_cvodes sundials_nvecserial sundials_idas)
+  if (SUNDIALS_VERSION VERSION_GREATER_EQUAL 3)
+    list (APPEND SUNDIALS_LIBRARIES sundials_sunlinsoldense sundials_sunlinsolspgmr sundials_sunmatrixdense sundials_sunmatrixsparse)
+  endif ()
+  if (SUNDIALS_VERSION VERSION_GREATER_EQUAL 7)
+    list (APPEND SUNDIALS_LIBRARIES sundials_core)
+  endif ()
+  if (SUNDIALS_WITH_SUPERLU)
+    list (APPEND SUNDIALS_LIBRARIES sundials_sunlinsolsuperlumt)
+  endif ()
+
+  assimulo_add_cython_module(assimulo/solvers/sundials.pyx
+    DESTINATION assimulo/solvers)
+  target_link_libraries(sundials PRIVATE ${SUNDIALS_LIBRARIES})
+
+  set (SUNDIALS_LIBRARIES sundials_kinsol sundials_nvecserial)
+  if (SUNDIALS_VERSION VERSION_GREATER_EQUAL 7)
+    list (APPEND SUNDIALS_LIBRARIES sundials_core)
+  endif ()
+
+  assimulo_add_cython_module(assimulo/solvers/kinsol.pyx
+    DESTINATION assimulo/solvers)
+  target_link_libraries(kinsol PRIVATE ${SUNDIALS_LIBRARIES})
+endif ()
 
 
 assimulo_add_cython_module(thirdparty/radau5/radau5ode.pyx

cmake/FindSUNDIALS.cmake

@@ -0,0 +1,47 @@
+# - Find SUNDIALS
+# SUNDIALS, the SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
+# https://computing.llnl.gov/projects/sundials
+#
+# The module defines the following variables:
+#  SUNDIALS_VERSION, the version string
+#  SUNDIALS_INCLUDE_DIRS, where to find sundials_dense.h, etc.
+#  SUNDIALS_LIBRARIES, the libraries needed to use SUNDIALS
+#  SUNDIALS_FOUND, If false, do not try to use SUNDIALS
+# also defined, but not for general use are
+#
+
+find_path (SUNDIALS_INCLUDE_DIR sundials_config.h PATH_SUFFIXES sundials)
+
+file (STRINGS ${SUNDIALS_INCLUDE_DIR}/sundials_config.h _VERSION_DEFINE_STRING REGEX "#define SUNDIALS_VERSION .*")
+if (_VERSION_DEFINE_STRING)
+  string (REGEX REPLACE "#define SUNDIALS_VERSION \"([0-9\.]+)\"" "\\1" SUNDIALS_VERSION ${_VERSION_DEFINE_STRING})
+endif ()
+
+set(SUNDIALS_LIBRARIES)
+set(SUNDIALS_COMPONENTS sunlinsoldense sunlinsolspgmr sunmatrixdense sunmatrixsparse core sunlinsolsuperlumt kinsol nvecserial cvode cvodes)
+foreach (COMPONENT ${SUNDIALS_COMPONENTS})
+  string(TOUPPER "${COMPONENT}" COMPONENT_UPPER)
+  find_library (SUNDIALS_${COMPONENT_UPPER}_LIBRARY NAMES sundials_${COMPONENT})
+
+  if (SUNDIALS_${COMPONENT_UPPER}_LIBRARY)
+    list (APPEND SUNDIALS_LIBRARIES ${SUNDIALS_${COMPONENT_UPPER}_LIBRARY})
+  endif ()
+endforeach ()
+
+set (SUNDIALS_INCLUDE_DIRS ${SUNDIALS_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(SUNDIALS DEFAULT_MSG SUNDIALS_INCLUDE_DIRS SUNDIALS_CVODES_LIBRARY VERSION_VAR SUNDIALS_VERSION)
+
+mark_as_advanced (
+  SUNDIALS_LIBRARIES
+  SUNDIALS_INCLUDE_DIR
+  SUNDIALS_INCLUDE_DIRS)
+
+if(NOT TARGET SUNDIALS::ALL)
+  add_library(SUNDIALS::ALL UNKNOWN IMPORTED)
+  set_target_properties(SUNDIALS::ALL
+    PROPERTIES
+    INTERFACE_INCLUDE_DIRECTORIES "${SUNDIALS_INCLUDE_DIRS}")
+  target_link_libraries(SUNDIALS::ALL INTERFACE ${SUNDIALS_LIBRARIES})
+endif()

cmake/FindSuperLU_MT.cmake

@@ -3,9 +3,9 @@
 # https://github.com/xiaoyeli/superlu_mt
 #
 # The module defines the following variables:
-#  SUPERLUMT_INCLUDE_DIRS, where to find mpc.h, etc.
-#  SUPERLUMT_LIBRARIES, the libraries needed to use MPC.
-#  SUPERLUMT_FOUND, If false, do not try to use MPC.
+#  SUPERLUMT_INCLUDE_DIRS, where to find superlu.h, etc.
+#  SUPERLUMT_LIBRARIES, the libraries needed to use SuperLU_MT
+#  SUPERLUMT_FOUND, If false, do not try to use SuperLU_MT
 # also defined, but not for general use are
 #  SUPERLUMT_LIBRARY, where to find the MPC library.
 #

setup.py

@@ -376,7 +376,7 @@ def check_SUNDIALS(self):
         if os.path.exists(os.path.join(os.path.join(self.incdirs,'cvodes'), 'cvodes.h')):
             self.with_SUNDIALS=True
             logging.debug('SUNDIALS found.')
-            sundials_version = None
+            sundials_version_tuple = None
             sundials_vector_type_size = None
             sundials_with_superlu = False
             sundials_with_msvc = False
@@ -386,8 +386,8 @@ def check_SUNDIALS(self):
                     with open(os.path.join(os.path.join(self.incdirs,'sundials'), 'sundials_config.h')) as f:
                         for line in f:
                             if "SUNDIALS_PACKAGE_VERSION" in line or "SUNDIALS_VERSION" in line:
-                                sundials_version = tuple([int(f) for f in line.split()[-1][1:-1].split('-dev')[0].split(".")])
-                                logging.debug('SUNDIALS %d.%d found.'%(sundials_version[0], sundials_version[1]))
+                                sundials_version_tuple = tuple([int(f) for f in line.split()[-1][1:-1].split('-dev')[0].split(".")])
+                                logging.debug('SUNDIALS %d.%d found.'%(sundials_version_tuple[0], sundials_version_tuple[1]))
                                 break
                     with open(os.path.join(os.path.join(self.incdirs,'sundials'), 'sundials_config.h')) as f:
                         for line in f:
@@ -418,13 +418,13 @@ def check_SUNDIALS(self):
                         sundials_with_msvc = True
             except Exception:
                 if os.path.exists(os.path.join(os.path.join(self.incdirs,'arkode'), 'arkode.h')): #This was added in 2.6
-                    sundials_version = (2,6,0)
+                    sundials_version_tuple = (2,6,0)
                     logging.debug('SUNDIALS 2.6 found.')
                 else:
-                    sundials_version = (2,5,0)
+                    sundials_version_tuple = (2,5,0)
                     logging.debug('SUNDIALS 2.5 found.')
-                
-            self.SUNDIALS_version = sundials_version
+
+            self.SUNDIALS_version_nr = 100000 * sundials_version_tuple[0] + 100 * sundials_version_tuple[1] + sundials_version_tuple[2]
             self.SUNDIALS_vector_size = sundials_vector_type_size
             self.sundials_with_superlu = sundials_with_superlu
             self.sundials_with_msvc = sundials_with_msvc
@@ -489,7 +489,7 @@ def cython_extensionlists(self):
 
         # SUNDIALS
         if self.with_SUNDIALS:
-            compile_time_env = {'SUNDIALS_VERSION': self.SUNDIALS_version,
+            compile_time_env = {'SUNDIALS_VERSION_NR': self.SUNDIALS_version_nr,
                                 'SUNDIALS_WITH_SUPERLU': self.sundials_with_superlu and self.with_SLU,
                                 'SUNDIALS_VECTOR_SIZE': self.SUNDIALS_vector_size,
                                 'SUNDIALS_CVODE_RTOL_VEC': self.sundials_cvode_with_rtol_vec}
@@ -502,14 +502,14 @@ 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]
 
-            if self.SUNDIALS_version >= (3,0,0):
+            if self.SUNDIALS_version_nr >= 300000:
                 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):
+                if self.SUNDIALS_version_nr >= 700000:
                     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
-                if self.SUNDIALS_version >= (3,0,0):
+                if self.SUNDIALS_version_nr >= 300000:
                     ext_list[-1].libraries.extend(["sundials_sunlinsolsuperlumt"])
 
                 ext_list[-1].include_dirs.append(self.SLUincdir)
@@ -525,7 +525,7 @@ 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):
+            if self.SUNDIALS_version_nr >= 700000:
                 ext_list[-1].libraries.extend(["sundials_core"])
 
             if self.sundials_with_superlu and self.with_SLU: #If SUNDIALS is compiled with support for SuperLU

src/lib/sundials_callbacks.pxi

@@ -22,9 +22,9 @@ from numpy cimport PyArray_DATA
 #=================
 
 cdef N_Vector N_VNewEmpty_Euclidean(long int n) noexcept:
-    IF SUNDIALS_VERSION >= (6,0,0):
+    IF SUNDIALS_VERSION_NR >= 600000:
         cdef SUNDIALS.SUNContext ctx = NULL
-        IF SUNDIALS_VERSION >= (7,0,0):
+        IF SUNDIALS_VERSION_NR >= 700000:
             cdef SUNDIALS.SUNComm comm = 0
         ELSE:
             cdef void* comm = NULL
@@ -40,9 +40,9 @@ cdef inline N_Vector arr2nv(x) noexcept:
     cdef long int n = len(x)
     cdef np.ndarray[realtype, ndim=1,mode='c'] ndx=x
     cdef void* data_ptr=PyArray_DATA(ndx)
-    IF SUNDIALS_VERSION >= (6,0,0):
+    IF SUNDIALS_VERSION_NR >= 600000:
         cdef SUNDIALS.SUNContext ctx = NULL
-        IF SUNDIALS_VERSION >= (7,0,0):
+        IF SUNDIALS_VERSION_NR >= 700000:
             cdef SUNDIALS.SUNComm comm = 0
         ELSE:
             cdef void* comm = NULL

src/lib/sundials_callbacks_ida_cvode.pxi

@@ -89,7 +89,7 @@ cdef int cv_sens_rhs_all(int Ns, realtype t, N_Vector yv, N_Vector yvdot,
         return CV_UNREC_RHSFUNC_ERR 
 
 
-IF SUNDIALS_VERSION >= (3,0,0):
+IF SUNDIALS_VERSION_NR >= 300000:
     @cython.boundscheck(False)
     @cython.wraparound(False)
     cdef int cv_jac_sparse(realtype t, N_Vector yv, N_Vector fy, SUNMatrix Jac,
@@ -163,7 +163,7 @@ ELSE:
         cdef np.ndarray[int, ndim=1, mode='c'] jindices
         cdef np.ndarray[int, ndim=1, mode='c'] jindptr
 
-        IF SUNDIALS_VERSION >= (2,6,3):
+        IF SUNDIALS_VERSION_NR >= 200603:
             cdef int* rowvals = Jacobian.rowvals[0]
             cdef int* colptrs = Jacobian.colptrs[0]
         ELSE:
@@ -212,7 +212,7 @@ ELSE:
             return CVDLS_JACFUNC_UNRECVR
 
 
-IF SUNDIALS_VERSION >= (3,0,0):
+IF SUNDIALS_VERSION_NR >= 300000:
     cdef int cv_jac(realtype t, N_Vector yv, N_Vector fy, SUNMatrix Jac, 
                 void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
@@ -363,7 +363,7 @@ cdef int cv_jacv(N_Vector vv, N_Vector Jv, realtype t, N_Vector yv, N_Vector fyv
             traceback.print_exc()
             return SPGMR_PSOLVE_FAIL_UNREC
 
-IF SUNDIALS_VERSION >= (3,0,0):
+IF SUNDIALS_VERSION_NR >= 300000:
     cdef int cv_prec_setup(realtype t, N_Vector yy, N_Vector fyy,
                       bint jok, bint *jcurPtr,
                       realtype gamma, void *problem_data) noexcept:
@@ -558,7 +558,7 @@ cdef int ida_res(realtype t, N_Vector yv, N_Vector yvdot, N_Vector residual, voi
             traceback.print_exc()
             return IDA_RES_FAIL
 
-IF SUNDIALS_VERSION >= (3,0,0):
+IF SUNDIALS_VERSION_NR >= 300000:
     cdef int ida_jac(realtype t, realtype c, N_Vector yv, N_Vector yvdot, N_Vector residual, SUNMatrix Jac,
                  void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
@@ -744,7 +744,7 @@ cdef int ida_jacv(realtype t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector vv
 
 # Error handling callback functions
 # =================================
-IF SUNDIALS_VERSION >= (7,0,0):
+IF SUNDIALS_VERSION_NR >= 700000:
     cdef extern from "sundials/sundials_context.h":
         ctypedef _SUNContext * SUNContext
         cdef struct _SUNContext:
@@ -776,7 +776,7 @@ ELSE:
             if error_code < 0: #Error
                 print('[CVode Error]', msg)
 
-IF SUNDIALS_VERSION >= (7,0,0):
+IF SUNDIALS_VERSION_NR >= 700000:
     cdef void ida_err(int line, const char* func, const char* file, const char* msg, SUNErrCode error_code, void* problem_data, SUNContext sunctx) noexcept:
         """
         This method overrides the default handling of error messages.

src/lib/sundials_callbacks_kinsol.pxi

@@ -19,7 +19,7 @@ import cython
 import traceback
 from assimulo.exception import AssimuloRecoverableError
 
-IF SUNDIALS_VERSION >= (3,0,0):
+IF SUNDIALS_VERSION_NR >= 300000:
     cdef int kin_jac(N_Vector xv, N_Vector fval, SUNMatrix Jac, 
                     void *problem_data, N_Vector tmp1, N_Vector tmp2) noexcept:
         """
@@ -67,7 +67,7 @@ ELSE:
         except Exception:
             return KINDLS_JACFUNC_RECVR #Recoverable Error (See Sundials description)
 
-IF SUNDIALS_VERSION >= (6,0,0):
+IF SUNDIALS_VERSION_NR >= 600000:
     ctypedef bint kin_jacv_bool
 ELSE:
     ctypedef int kin_jacv_bool
@@ -115,7 +115,7 @@ cdef int kin_res(N_Vector xv, N_Vector fval, void *problem_data) noexcept:
         traceback.print_exc()
         return KIN_SYSFUNC_FAIL
 
-IF SUNDIALS_VERSION >= (3,0,0):
+IF SUNDIALS_VERSION_NR >= 300000:
     cdef int kin_prec_solve(N_Vector u, N_Vector uscaleN, N_Vector fval, 
              N_Vector fscaleN, N_Vector v, void *problem_data) noexcept:
         """
@@ -221,7 +221,7 @@ ELSE:
 
         return KIN_SUCCESS
 
-IF SUNDIALS_VERSION >= (7,0,0):
+IF SUNDIALS_VERSION_NR >= 700000:
     cdef extern from "sundials/sundials_context.h":
         ctypedef _SUNContext * SUNContext
         cdef struct _SUNContext: