15. Changelog
15.1. Changes to SUNDIALS in release X.Y.Z
Major Features
New Features and Enhancements
The default value of CMAKE_CUDA_ARCHITECTURES is no longer set to
70 and is now determined automatically by CMake. The previous default was
only valid for Volta GPUs while the automatically selected value will vary
across compilers and compiler versions. As such, users are encouraged to
override this value with the architecture for their system.
The Trilinos Tpetra NVector interface has been updated to utilize CMake
imported targets added in Trilinos 14 to improve support for different Kokkos
backends with Trilinos. As such, Trilinos 14 or newer is required and the
Trilinos_INTERFACE_* CMake options have been removed.
Example programs using hypre have been updated to support v2.20 and newer.
The build system has been updated to utilize the CMake LAPACK imported target which should ease building SUNDIALS with LAPACK libraries that require setting specific linker flags e.g., MKL.
Bug Fixes
Fixed a bug in the sparse
matrix implementation of SUNMatScaleAddI() which caused out of bounds
writes unless indexvals were in ascending order for each row/column.
Fixed ARKodeResize() not using the default hscale when an argument
of 0 was provided.
Fixed the loading of ARKStep’s default first order explicit method.
Fixed a CMake bug regarding usage of missing “print_warning” macro
that was only triggered when the deprecated CUDA_ARCH option was used.
Fixed a memory leak that could occur if ARKodeSetDefaults() is called
repeatedly.
Fixed compilation errors when building the Trilinos Teptra NVector with CUDA support.
Fixed a CMake configuration issue related to aliasing an ALIAS target when
using ENABLE_KLU=ON in combination with a static-only build of SuiteSparse.
Deprecation Notices
15.2. Changes to SUNDIALS in release 7.1.1
Bug Fixes
Fixed a bug in v7.1.0 with the
SYCL N_Vector N_VSpace function.
15.3. Changes to SUNDIALS in release 7.1.0
Major Features
Created shared user interface functions for ARKODE to allow more uniform control over time-stepping algorithms, improved extensibility, and simplified code maintenance. The corresponding stepper-specific user-callable functions are now deprecated and will be removed in a future major release.
Added CMake infrastructure that enables externally maintained addons/plugins to be optionally built with SUNDIALS. See Contributing for details.
New Features and Enhancements
Added support for Kokkos Kernels v4.
Added the following Runge-Kutta Butcher tables
ARKODE_FORWARD_EULER_1_1ARKODE_RALSTON_EULER_2_1_2ARKODE_EXPLICIT_MIDPOINT_EULER_2_1_2ARKODE_BACKWARD_EULER_1_1ARKODE_IMPLICIT_MIDPOINT_1_2ARKODE_IMPLICIT_TRAPEZOIDAL_2_2
Added the following MRI coupling tables
ARKODE_MRI_GARK_FORWARD_EULERARKODE_MRI_GARK_RALSTON2ARKODE_MRI_GARK_RALSTON3ARKODE_MRI_GARK_BACKWARD_EULERARKODE_MRI_GARK_IMPLICIT_MIDPOINTARKODE_IMEX_MRI_GARK_EULERARKODE_IMEX_MRI_GARK_TRAPEZOIDALARKODE_IMEX_MRI_GARK_MIDPOINT
Added ARKodeButcherTable_ERKIDToName() and
ARKodeButcherTable_DIRKIDToName() to convert a Butcher table ID to a
string representation.
Added the function ARKodeSetAutonomous() in ARKODE to indicate that the
implicit right-hand side function does not explicitly depend on time. When using
the trivial predictor, an autonomous problem may reuse implicit function
evaluations across stage solves to reduce the total number of function
evaluations.
Users may now disable interpolated output in ARKODE by passing
ARK_INTERP_NONE to ARKodeSetInterpolantType(). When interpolation is
disabled, rootfinding is not supported, implicit methods must use the trivial
predictor (the default option), and interpolation at stop times cannot be used
(interpolating at stop times is disabled by default). With interpolation
disabled, calling ARKodeEvolve() in ARK_NORMAL mode will return at
or past the requested output time (setting a stop time may still be used to halt
the integrator at a specific time). Disabling interpolation will reduce the
memory footprint of an integrator by two or more state vectors (depending on the
interpolant type and degree) which can be beneficial when interpolation is not
needed e.g., when integrating to a final time without output in between or using
an explicit fast time scale integrator with an MRI method.
Added “Resize” capability to ARKODE’s SPRKStep time-stepping module.
Enabled the Fortran interfaces to build with 32-bit sunindextype.
Bug Fixes
Updated the CMake variable HIP_PLATFORM default to amd as the previous
default, hcc, is no longer recognized in ROCm 5.7.0 or newer. The new
default is also valid in older version of ROCm (at least back to version 4.3.1).
Renamed the DPCPP value for the SUNDIALS_GINKGO_BACKENDS CMake option
to SYCL to match Ginkgo’s updated naming convention.
Changed the CMake version compatibility mode for SUNDIALS to AnyNewerVersion
instead of SameMajorVersion. This fixes the issue seen here.
Fixed a CMake bug that caused an MPI linking error for our C++ examples in some instances. Fixes GitHub Issue #464.
Fixed the runtime library installation path for windows systems. This fix
changes the default library installation path from
CMAKE_INSTALL_PREFIX/CMAKE_INSTALL_LIBDIR to
CMAKE_INSTALL_PREFIX/CMAKE_INSTALL_BINDIR.
Fixed conflicting .lib files between shared and static libs when using
MSVC on Windows
Fixed invalid SUNDIALS_EXPORT generated macro when building both shared and
static libs.
Fixed a bug in some Fortran examples where c_null_ptr was passed as an
argument to a function pointer instead of c_null_funptr. This caused
compilation issues with the Cray Fortran compiler.
Fixed a bug in the HIP execution policies where WARP_SIZE would not be set
with ROCm 6.0.0 or newer.
Fixed a bug that caused error messages to be cut off in some cases. Fixes GitHub Issue #461.
Fixed a memory leak when an error handler was added to a
SUNContext. Fixes GitHub Issue #466.
Fixed a bug where MRIStepEvolve() would not handle a recoverable error
produced from evolving the inner stepper.
Added missing SetRootDirection and SetNoInactiveRootWarn functions to
ARKODE’s SPRKStep time-stepping module.
Fixed a bug in ARKodeSPRKTable_Create() where the coefficient arrays
were not allocated.
Fix bug on LLP64 platforms (like Windows 64-bit) where KLU_INDEXTYPE could be
32 bits wide even if SUNDIALS_INT64_T is defined.
Check if size of SuiteSparse_long is 8 if the size of sunindextype is 8
when using KLU.
Fixed several build errors with the Fortran interfaces on Windows systems.
Deprecation Notices
Numerous ARKODE stepper-specific functions are now deprecated in favor of ARKODE-wide functions.
Deprecated the ARKStepSetOptimalParams function. Since this function does not have an ARKODE-wide equivalent, instructions have been added to the user guide for how to retain the current functionality using other user-callable functions.
The unsupported implementations of N_VGetArrayPointer and
N_VSetArrayPointer for the hypre and PETSc vectors are now deprecated.
Users should access the underlying wrapped external library vector objects
instead with N_VGetVector_ParHyp and N_VGetVector_Petsc, respectively.
15.4. Changes to SUNDIALS in release 7.0.0
Major Feature
SUNDIALS now has more robust and uniform error handling. Non-release builds will be built with additional error checking by default. See §1.5 for details.
Breaking Changes
Minimum C Standard
SUNDIALS now requires using a compiler that supports a subset of the C99 standard. Note with the Microsoft C/C++ compiler the subset of C99 features utilized by SUNDIALS are available starting with Visual Studio 2015.
Minimum CMake Version
CMake 3.18 or newer is now required when building SUNDIALS.
Deprecated Types and Functions Removed
The previously deprecated types realtype and booleantype were removed
from sundials_types.h and replaced with sunrealtype and
sunbooleantype. The deprecated names for these types can be used by
including the header file sundials_types_deprecated.h but will be fully
removed in the next major release. Functions, types and header files that were
previously deprecated have also been removed.
Error Handling Changes
With the addition of the new error handling capability, the *SetErrHandlerFn
and *SetErrFile functions in CVODE(S), IDA(S), ARKODE, and KINSOL have been
removed. Users of these functions can use the functions
SUNContext_PushErrHandler(), and SUNLogger_SetErrorFilename()
instead. For further details see Sections §1.5 and
§1.7.
In addition the following names/symbols were replaced by SUN_ERR_* codes:
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The following functions have had their signature updated to ensure they can leverage the new SUNDIALS error handling capabilities.
From
sundials_futils.hFrom
sundials_memory.hFrom
sundials_nvector.h
SUNComm Type Added
We have replaced the use of a type-erased (i.e., void*) pointer to a
communicator in place of MPI_Comm throughout the SUNDIALS API with a
SUNComm, which is just a typedef to an int in builds without MPI
and a typedef to a MPI_Comm in builds with MPI. As a result:
When MPI is enabled, all SUNDIALS libraries will include MPI symbols and applications will need to include the path for MPI headers and link against the corresponding MPI library.
All users will need to update their codes because the call to
SUNContext_Create()now takes aSUNComminstead of type-erased pointer to a communicator. For non-MPI codes, passSUN_COMM_NULLto thecommargument instead ofNULL. For MPI codes, pass theMPI_Commdirectly.The same change must be made for calls to
SUNLogger_Create()orSUNProfiler_Create().Some users will need to update their calls to
N_VGetCommunicator(), and update any customN_Vectorimplementations that provideN_VGetCommunicator(), since it now returns aSUNComm.
The change away from type-erased pointers for SUNComm fixes problems
like the one described in
GitHub Issue #275.
The SUNLogger is now always MPI-aware if MPI is enabled in SUNDIALS and the
SUNDIALS_LOGGING_ENABLE_MPI CMake option and macro definition were removed
accordingly.
SUNDIALS Core Library
Users now need to link to sundials_core in addition to the libraries already
linked to. This will be picked up automatically in projects that use the
SUNDIALS CMake target. The library sundials_generic has been superseded by
sundials_core and is no longer available. This fixes some duplicate symbol
errors on Windows when linking to multiple SUNDIALS libraries.
Fortran Interface Modules Streamlined
We have streamlined the Fortran modules that need to be included by users by
combining the SUNDIALS core into one Fortran module,
fsundials_core_mod. Modules for implementations of the core APIs still exist
(e.g., for the Dense linear solver there is fsunlinsol_dense_mod) as do the
modules for the SUNDIALS packages (e.g., fcvode_mod). The following modules
are the ones that have been consolidated into fsundials_core_mod:
fsundials_adaptcontroller_mod
fsundials_context_mod
fsundials_futils_mod
fsundials_linearsolver_mod
fsundials_logger_mod
fsundials_matrix_mod
fsundials_nonlinearsolver_mod
fsundials_nvector_mod
fsundials_profiler_mod
fsundials_types_mod
Minor Changes
The CMAKE_BUILD_TYPE defaults to RelWithDebInfo mode now i.e., SUNDIALS
will be built with optimizations and debugging symbols enabled by default.
Previously the build type was unset by default so no optimization or debugging
flags were set.
The advanced CMake options to override the inferred LAPACK name-mangling scheme
have been updated from SUNDIALS_F77_FUNC_CASE and
SUNDIALS_F77_FUNC_UNDERSCORES to SUNDIALS_LAPACK_CASE and
SUNDIALS_LAPACK_UNDERSCORES, respectively.
As a subset of C99 is now required the CMake option USE_GENERIC_MATH as been
removed.
The C++ convenience classes (e.g., sundials::Context) have been moved to
from SUNDIALS .h headers to corresponding .hpp headers (e.g.,
sundials/sundials_context.hpp) so C++ codes do not need to compile with
C++14 support when using the C API.
Converted most previous Fortran 77 and 90 examples to use SUNDIALS’ Fortran 2003 interface.
Bug Fixes
Fixed GitHub Issue #329 so that C++20 aggregate initialization can be used.
Fixed integer overflow in the internal SUNDIALS hashmap. This resolves GitHub Issues #409 and #249.
Deprecation Notice
The functions in sundials_math.h will be deprecated in the next release.
sunrealtype SUNRpowerI(sunrealtype base, int exponent);
sunrealtype SUNRpowerR(sunrealtype base, sunrealtype exponent);
sunbooleantype SUNRCompare(sunrealtype a, sunrealtype b);
sunbooleantype SUNRCompareTol(sunrealtype a, sunrealtype b, sunrealtype tol);
sunrealtype SUNStrToReal(const char* str);
Additionally, the following header files (and everything in them) will be deprecated – users who
rely on these are recommended to transition to the corresponding SUNMatrix and
SUNLinearSolver modules:
sundials_direct.h
sundials_dense.h
sundials_band.h
15.5. Changes to SUNDIALS in release 6.7.0
Major Feature
Added the SUNAdaptController base class, ported ARKODE’s internal
implementations of time step controllers to implementations of this class, and
updated ARKODE to use these objects instead of its own implementations. Added
ARKStepSetAdaptController() and ERKStepSetAdaptController()
routines so that users can modify controller parameters, or even provide custom
implementations.
New Features
Improved the computational complexity of the sparse matrix ScaleAddI
function from \(\mathcal{O}(M * N)\) to \(\mathcal{O}(\mathrm{NNZ})\).
Added Fortran support for the LAPACK dense linear solver implementation.
Added the routines ARKStepSetAdaptivityAdjustment() and
ERKStepSetAdaptivityAdjustment(), that allow users to adjust the
value for the method order supplied to the temporal adaptivity controllers.
The ARKODE default for this adjustment has been \(-1\) since its initial
release, but for some applications a value of \(0\) is more appropriate.
Users who notice that their simulations encounter a large number of
temporal error test failures may want to experiment with adjusting this value.
Added the third order ERK method ARKODE_SHU_OSHER_3_2_3, the fourth order
ERK method ARKODE_SOFRONIOU_SPALETTA_5_3_4, the sixth order ERK method
ARKODE_VERNER_9_5_6, the seventh order ERK method ARKODE_VERNER_10_6_7,
the eighth order ERK method ARKODE_VERNER_13_7_8, and the ninth order ERK
method ARKODE_VERNER_16_8_9.
ARKStep, ERKStep, MRIStep, and SPRKStep were updated to remove a potentially unnecessary right-hand side evaluation at the end of an integration. ARKStep was additionally updated to remove extra right-hand side evaluations when using an explicit method or an implicit method with an explicit first stage.
The MRIStepInnerStepper class in MRIStep was updated to make supplying
an MRIStepInnerFullRhsFn optional.
Bug Fixes
Changed the SUNProfiler so that it does not rely on MPI_WTime in
any case. This fixes GitHub Issue #312.
Fixed scaling bug in SUNMatScaleAddI_Sparse for non-square matrices.
Fixed a regression introduced by the stop time bug fix in v6.6.1 where ARKODE, CVODE, CVODES, IDA, and IDAS would return at the stop time rather than the requested output time if the stop time was reached in the same step in which the output time was passed.
Fixed a bug in ERKStep where methods with \(c_s = 1\) but \(a_{s,j} \neq b_j\) were incorrectly treated as having the first same as last (FSAL) property.
Fixed a bug in ARKODE where ARKStepSetInterpolateStopTime() would return
an interpolated solution at the stop time in some cases when interpolation was
disabled.
Fixed a bug in ARKStepSetTableNum() wherein it did not recognize
ARKODE_ARK2_ERK_3_1_2 and ARKODE_ARK2_DIRK_3_1_2 as a valid additive
Runge–Kutta Butcher table pair.
Fixed a bug in MRIStepCoupling_Write() where explicit coupling tables
were not written to the output file pointer.
Fixed missing soversions in some SUNLinearSolver and
SUNNonlinearSolver CMake targets.
Renamed some internal types in CVODES and IDAS to allow both packages to be built together in the same binary.
15.6. Changes to SUNDIALS in release 6.6.2
Fixed the build system support for MAGMA when using a NVIDIA HPC SDK installation of CUDA and fixed the targets used for rocBLAS and rocSPARSE.
15.7. Changes to SUNDIALS in release 6.6.1
New Features
Updated the Trilinos Tpetra N_Vector interface to support Trilinos 14.
Bug Fixes
Fixed a memory leak when destroying a CUDA, HIP, SYCL, or system
SUNMemoryHelper object.
Fixed a bug in ARKODE, CVODE, CVODES, IDA, and IDAS where the stop time may not be cleared when using normal mode if the requested output time is the same as the stop time. Additionally, with ARKODE, CVODE, and CVODES this fix removes an unnecessary interpolation of the solution at the stop time that could occur in this case.
15.8. Changes to SUNDIALS in release 6.6.0
Major Features
A new time-stepping module, SPRKStep, was added to ARKODE. This time-stepper provides explicit symplectic partitioned Runge-Kutta methods up to order 10 for separable Hamiltonian systems.
Added support for relaxation Runge-Kutta methods in ERKStep and ARKStep, see Relaxation Methods, Relaxation Methods, and Relaxation Methods for more information.
New Features
Updated the default ARKODE, CVODE, and CVODES behavior when returning the
solution when the internal time has reached a user-specified stop time.
Previously, the output solution was interpolated to the value of tstop; the
default is now to copy the internal solution vector. Users who wish to revert to
interpolation may call a new routine CVodeSetInterpolateStopTime(),
ARKStepSetInterpolateStopTime(), ERKStepSetInterpolateStopTime(),
or MRIStepSetInterpolateStopTime().
Added the second order IMEX method from [57] as the
default second order IMEX method in ARKStep. The explicit table is given by
ARKODE_ARK2_ERK_3_1_2 (see ARK2-ERK-3-1-2) and the implicit
table by ARKODE_ARK2_DIRK_3_1_2 (see ARK2-DIRK-3-1-2).
Updated the F2003 utility routines SUNDIALSFileOpen() and
SUNDIALSFileClose() to support user specification of stdout and
stderr strings for the output file names.
Bug Fixes
A potential bug was fixed when using inequality constraint handling and
calling ARKStepGetEstLocalErrors() or ERKStepGetEstLocalErrors()
after a failed step in which an inequality constraint violation occurred. In
this case, the values returned by ARKStepGetEstLocalErrors() or
ERKStepGetEstLocalErrors() may have been invalid.
15.9. Changes to SUNDIALS in release 6.5.1
New Features
Added the following functions to disable a previously set stop time:
The default interpolant in ARKODE when using a first order method has been
updated to a linear interpolant to ensure values obtained by the integrator are
returned at the ends of the time interval. To restore the previous behavior of
using a constant interpolant call ARKStepSetInterpolantDegree(),
ERKStepSetInterpolantDegree(), or MRIStepSetInterpolantDegree()
and set the interpolant degree to zero before evolving the problem.
Bug Fixes
Fixed build errors when using SuperLU_DIST with ROCM enabled to target AMD GPUs.
Fixed compilation errors in some SYCL examples when using the icx compiler.
15.10. Changes to SUNDIALS in release 6.5.0
New Features
A new capability to keep track of memory allocations made through the
SUNMemoryHelper classes has been added. Memory allocation stats can be
accessed through the SUNMemoryHelper_GetAllocStats() function. See
§13.1 for more details.
Added the following functions to assist in debugging simulations utilizing matrix-based linear solvers:
Added support for CUDA 12.
Added support for the SYCL backend with RAJA 2022.x.y.
Bug Fixes
Fixed an underflow bug during root finding in ARKODE, CVODE, CVODES, IDA and IDAS. This fixes GitHub Issue #57.
Fixed an issue with finding oneMKL when using the icpx compiler with the
-fsycl flag as the C++ compiler instead of dpcpp.
Fixed the shape of the arrays returned by the Fortran interfaces to
N_VGetArrayPointer(), SUNDenseMatrix_Data(),
SUNBandMatrix_Data(), SUNSparseMatrix_Data(),
SUNSparseMatrix_IndexValues(), and
SUNSparseMatrix_IndexPointers(). Compiling and running code that uses
the SUNDIALS Fortran interfaces with bounds checking will now work.
Fixed an implicit conversion error in the Butcher table for ESDIRK5(4)7L[2]SA2.
15.11. Changes to SUNDIALS in release 6.4.1
Fixed a bug with the Kokkos interfaces that would arise when using clang.
Fixed a compilation error with the Intel oneAPI 2022.2 Fortran compiler in the
Fortran 2003 interface test for the serial N_Vector.
Fixed a bug in the LAPACK band and dense linear solvers which would cause the tests to fail on some platforms.
15.12. Changes to SUNDIALS in release 6.4.0
New Requirements
CMake 3.18.0 or newer is now required for CUDA support.
A C++14 compliant compiler is now required for C++ based features and examples e.g., CUDA, HIP, RAJA, Trilinos, SuperLU_DIST, MAGMA, Ginkgo, and Kokkos.
Major Features
Added support for the Ginkgo linear algebra library. This support includes new SUNDIALS matrix and linear solver implementations, see the sections §9.16 and §10.23.
Added new SUNDIALS vector, dense matrix, and dense linear solver implementations utilizing the Kokkos Ecosystem for performance portability, see sections §8.19, §9.17, and §10.24 for more information.
New Features
Added support for GPU enabled SuperLU_DIST and SuperLU_DIST v8.x.x. Removed support for SuperLU_DIST v6.x.x or older. Fix mismatched definition and declaration bug in SuperLU_DIST matrix constructor.
Added the functions following functions to load a Butcher table from a string:
Bug Fixes
Fixed a bug in the CUDA and HIP vectors where N_VMaxNorm() would return
the minimum positive floating-point value for the zero vector.
Fixed memory leaks/out of bounds memory accesses in the ARKODE MRIStep module that could occur when attaching a coupling table after reinitialization with a different number of stages than originally selected.
Fixed a memory leak where the projection memory would not be deallocated when
calling CVodeFree().
15.13. Changes to SUNDIALS in release 6.3.0
New Features
Added the following functions to retrieve the user data pointer provided with
SetUserData functions:
Added a variety of embedded DIRK methods from [83] and [84].
Updated MRIStepReset() to call the corresponding
MRIStepInnerResetFn with the same tR and yR arguments for the
MRIStepInnerStepper object that is used to evolve the MRI “fast” time
scale subproblems.
Added a new example (examples/cvode/serial/cvRocket_dns.c) which
demonstrates using CVODE with a discontinuous right-hand-side function and
rootfinding.
Bug Fixes
Fixed a bug in ERKStepReset(), ERKStepReInit(),
ARKStepReset(), ARKStepReInit(), MRIStepReset(), and
MRIStepReInit() where a previously-set value of tstop (from
a call to ERKStepSetStopTime(), ARKStepSetStopTime(), or
MRIStepSetStopTime(), respectively) would not be cleared.
Fixed the unituitive behavior of the USE_GENERIC_MATH CMake option which
caused the double precision math functions to be used regardless of the value of
SUNDIALS_PRECISION. Now, SUNDIALS will use precision appropriate math
functions when they are available and the user may provide the math library to
link to via the advanced CMake option SUNDIALS_MATH_LIBRARY.
Changed SUNDIALS_LOGGING_ENABLE_MPI CMake option default to be OFF. This
fixes GitHub Issue #177.
15.14. Changes to SUNDIALS in release 6.2.0
Major Features
Added the SUNLogger API which provides a SUNDIALS-wide mechanism for
logging of errors, warnings, informational output, and debugging output.
Added support to CVODES for integrating IVPs with constraints using BDF methods and projecting the solution onto the constraint manifold with a user defined projection function. This implementation is accompanied by additions to the CVODES user documentation and examples.
New Features
Added the function SUNProfiler_Reset() to reset the region timings and
counters to zero.
Added the following functions to output all of the integrator, nonlinear solver, linear solver, and other statistics in one call:
The file scripts/sundials_csv.py contains functions for parsing the
comma-separated value (CSV) output files when using the CSV output format.
Added functions to CVODE, CVODES, IDA, and IDAS to change the default step size adaptivity parameters. For more information see the documentation for:
Added the functions ARKStepSetDeduceImplicitRhs() and
MRIStepSetDeduceImplicitRhs() to optionally remove an evaluation of the
implicit right-hand side function after nonlinear solves. See
Nonlinear solver methods, for considerations on using this
optimization.
Added the function MRIStepSetOrder() to select the default MRI method of
a given order.
Added the functions CVodeSetDeltaGammaMaxLSetup() and
CVodeSetDeltaGammaMaxBadJac() in CVODE and CVODES to adjust the
\(\gamma\) change thresholds to require a linear solver setup or
Jacobian/precondition update, respectively.
Added the function IDASetDeltaCjLSetup() in IDA and IDAS to adjust the
parameter that determines when a change in \(c_j\) requires calling the
linear solver setup function.
Added the function IDASetMinStep() to set a minimum step size.
Bug Fixes
Fixed the SUNContext convenience class for C++ users to disallow copy
construction and allow move construction.
The behavior of N_VSetKernelExecPolicy_Sycl() has been updated to be
consistent with the CUDA and HIP vectors. The input execution policies are now
cloned and may be freed after calling
N_VSetKernelExecPolicy_Sycl(). Additionally, NULL inputs are now
allowed and, if provided, will reset the vector execution policies to the
defaults.
A memory leak in the SYCL vector was fixed where the execution policies were not freed when the vector was destroyed.
The include guard in nvector_mpimanyvector.h has been corrected to enable
using both the ManyVector and MPIManyVector vector implementations
in the same simulation.
A bug was fixed in the ARKODE, CVODE(S), and IDA(S) functions to retrieve the number of nonlinear solver failures. The failure count returned was the number of failed steps due to a nonlinear solver failure i.e., if a nonlinear solve failed with a stale Jacobian or preconditioner but succeeded after updating the Jacobian or preconditioner, the initial failure was not included in the nonlinear solver failure count. The following functions have been updated to return the total number of nonlinear solver failures:
As a result of this change users may see an increase in the number of failures reported from the above functions. The following functions have been added to retrieve the number of failed steps due to a nonlinear solver failure i.e., the counts previously returned by the above functions:
Changed exported SUNDIALS PETSc CMake targets to be INTERFACE IMPORTED instead of UNKNOWN IMPORTED.
Deprecation Notice
Deprecated the following functions, it is recommended to use the
SUNLogger API instead.
ARKStepSetDiagnosticsERKStepSetDiagnosticsMRIStepSetDiagnosticsKINSetInfoFileSUNNonlinSolSetPrintLevel_NewtonSUNNonlinSolSetInfoFile_NewtonSUNNonlinSolSetPrintLevel_FixedPointSUNNonlinSolSetInfoFile_FixedPointSUNLinSolSetInfoFile_PCGSUNLinSolSetPrintLevel_PCGSUNLinSolSetInfoFile_SPGMRSUNLinSolSetPrintLevel_SPGMRSUNLinSolSetInfoFile_SPFGMRSUNLinSolSetPrintLevel_SPFGMRSUNLinSolSetInfoFile_SPTFQMSUNLinSolSetPrintLevel_SPTFQMRSUNLinSolSetInfoFile_SPBCGSSUNLinSolSetPrintLevel_SPBCGS
The SUNLinSolSetInfoFile_* and SUNNonlinSolSetInfoFile_* family of
functions are now enabled by setting the CMake option
SUNDIALS_LOGGING_LEVEL to a value >= 3.
15.15. Changes to SUNDIALS in release 6.1.1
New Feature
Added new Fortran example program,
examples/arkode/F2003_serial/ark_kpr_mri_f2003.f90 demonstrating MRI
capabilities.
Bug Fixes
Fixed exported SUNDIALSConfig.cmake.
Fixed Fortran interface to MRIStepInnerStepper and
MRIStepCoupling structures and functions.
15.16. Changes to SUNDIALS in release 6.1.0
New Features
Added new reduction implementations for the CUDA and HIP vectors that use
shared memory (local data storage) instead of atomics. These new implementations
are recommended when the target hardware does not provide atomic support for the
floating point precision that SUNDIALS is being built with. The HIP vector uses
these by default, but the N_VSetKernelExecPolicy_Cuda() and
N_VSetKernelExecPolicy_Hip() functions can be used to choose between
different reduction implementations.
SUNDIALS::<lib> targets with no static/shared suffix have been added for use
within the build directory (this mirrors the targets exported on installation).
CMAKE_C_STANDARD is now set to 99 by default.
Bug Fixes
Fixed exported SUNDIALSConfig.cmake when profiling is enabled without
Caliper.
Fixed sundials_export.h include in sundials_config.h.
Fixed memory leaks in the SuperLU_MT linear solver interface.
15.17. Changes to SUNDIALS in release 6.0.0
Breaking Changes
SUNContext Object Added
SUNDIALS v6.0.0 introduces a new SUNContext object on which all other
SUNDIALS objects depend. As such, the constructors for all SUNDIALS packages,
vectors, matrices, linear solvers, nonlinear solvers, and memory helpers have
been updated to accept a context as the last input. Users upgrading to SUNDIALS
v6.0.0 will need to call SUNContext_Create() to create a context object
with before calling any other SUNDIALS library function, and then provide this
object to other SUNDIALS constructors. The context object has been introduced to
allow SUNDIALS to provide new features, such as the profiling/instrumentation
also introduced in this release, while maintaining thread-safety. See the
§1.4 for more details.
The script scripts/upgrade-to-sundials-6-from-5.sh has been provided with
this release (and obtainable from the GitHub release page) to help ease the
transition to SUNDIALS v6.0.0. The script will add a SUNCTX_PLACEHOLDER
argument to all of the calls to SUNDIALS constructors that now require a
SUNContext object. It can also update deprecated SUNDIALS
constants/types to the new names. It can be run like this:
./upgrade-to-sundials-6-from-5.sh <files to update>
Updated SUNMemoryHelper Function Signatures
The SUNMemoryHelper functions SUNMemoryHelper_Alloc(),
SUNMemoryHelper_Dealloc(), and SUNMemoryHelper_Copy() have been
updated to accept an opaque handle as the last input. At a minimum, user-defined
SUNMemoryHelper implementations will need to update these functions to
accept the additional argument. Typically, this handle is the execution stream
(e.g., a CUDA/HIP stream or SYCL queue) for the operation. The CUDA, HIP, and
SYCL implementations have been updated accordingly. Additionally, the
constructor SUNMemoryHelper_Sycl() has been updated to remove the SYCL
queue as an input.
Deprecated Functions Removed
The previously deprecated constructor N_VMakeWithManagedAllocator_Cuda and
the function N_VSetCudaStream_Cuda have been removed and replaced with
N_VNewWithMemHelp_Cuda() and N_VSetKernelExecPolicy_Cuda()
respectively.
The previously deprecated macros PVEC_REAL_MPI_TYPE and
PVEC_INTEGER_MPI_TYPE have been removed and replaced with
MPI_SUNREALTYPE and MPI_SUNINDEXTYPE respectively.
The following previously deprecated SUNLinearSolver functions have
been removed:
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The deprecated functions MRIStepGetCurrentButcherTables and
MRIStepWriteButcher and the utility functions MRIStepSetTable and
MRIStepSetTableNum have been removed. Users wishing to create an MRI-GARK
method from a Butcher table should use MRIStepCoupling_MIStoMRI() to
create the corresponding MRI coupling table and attach it with
MRIStepSetCoupling().
The previously deprecated functions ARKStepSetMaxStepsBetweenLSet and
ARKStepSetMaxStepsBetweenJac have been removed and replaced with
ARKStepSetLSetupFrequency() and ARKStepSetJacEvalFrequency()
respectively.
The previously deprecated function CVodeSetMaxStepsBetweenJac has been
removed and replaced with CVodeSetJacEvalFrequency().
The ARKODE, CVODE, IDA, and KINSOL Fortran 77 interfaces has been removed. See §1.9 and the F2003 example programs for more details using the SUNDIALS Fortran 2003 module interfaces.
Namespace Changes
The CUDA, HIP, and SYCL execution policies have been moved from the sundials
namespace to the sundials::cuda, sundials::hip, and sundials::sycl
namespaces respectively. Accordingly, the prefixes “Cuda”, “Hip”, and “Sycl”
have been removed from the execution policy classes and methods.
The Sundials namespace used by the Trilinos Tpetra N_Vector
implementation has been replaced with the sundials::trilinos::nvector_tpetra
namespace.
Major Features
Profiling Capability
A capability to profile/instrument SUNDIALS library code has been added. This
can be enabled with the CMake option SUNDIALS_BUILD_WITH_PROFILING. A
built-in profiler will be used by default, but the Caliper library can also be used instead with the
CMake option ENABLE_CALIPER. See the documentation section on
profiling for more details.
Warning
Profiling will impact performance, and should be enabled judiciously.
IMEX MRI Methods and MRIStepInnerStepper Object
The MRIStep module has been extended to support implicit-explicit (ImEx)
multirate infinitesimal generalized additive Runge–Kutta (MRI-GARK) methods. As
such, MRIStepCreate() has been updated to include arguments for the slow
explicit and slow implicit ODE right-hand side functions.
MRIStepCreate() has also been updated to require attaching an
MRIStepInnerStepper for evolving the fast time scale. MRIStepReInit()
has been similarly updated to take explicit and implicit right-hand side
functions as input. Codes using explicit or implicit MRI methods will need to
update MRIStepCreate() and MRIStepReInit() calls to pass
NULL for either the explicit or implicit right-hand side function as
appropriate. If ARKStep is used as the fast time scale integrator, codes will
need to call ARKStepCreateMRIStepInnerStepper() to wrap the ARKStep
memory as an MRIStepInnerStepper object. Additionally,
MRIStepGetNumRhsEvals() has been updated to return the number of slow
implicit and explicit function evaluations. The coupling table,
MRIStepCoupling, and the functions MRIStepCoupling_Alloc()
and MRIStepCoupling_Create() have also been updated to support
IMEX-MRI-GARK methods.
New Features
Two new optional vector operations, N_VDotProdMultiLocal() and
N_VDotProdMultiAllReduce(), have been added to support
low-synchronization methods for Anderson acceleration.
The implementation of solve-decoupled implicit MRI-GARK methods has been updated to remove extraneous slow implicit function calls and reduce the memory requirements.
Added a new function CVodeGetLinSolveStats() to get the CVODES linear
solver statistics as a group.
Added a new function, CVodeSetMonitorFn(), that takes a user-function
to be called by CVODES after every nst successfully completed time-steps.
This is intended to provide a way of monitoring the CVODES statistics
throughout the simulation.
New orthogonalization methods were added for use within the KINSOL Anderson
acceleration routine. See Anderson Acceleration QR Factorization and KINSetOrthAA()
for more details.
Deprecation Notice
The serial, PThreads, PETSc, hypre, Parallel, OpenMP_DEV, and OpenMP vector
functions N_VCloneVectorArray_* and N_VDestroyVectorArray_* have been
deprecated. The generic N_VCloneVectorArray() and
N_VDestroyVectorArray() functions should be used instead.
Many constants, types, and functions have been renamed so that they are properly namespaced. The old names have been deprecated and will be removed in SUNDIALS v7.0.0.
The following constants, macros, and typedefs are now deprecated:
Deprecated Name |
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In addition, the following functions are now deprecated (compile-time warnings will be printed if supported by the compiler):
Deprecated Name |
New Name |
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In addition, the entire sundials_lapack.h header file is now deprecated for
removal in SUNDIALS v7.0.0. Note, this header file is not needed to use the
SUNDIALS LAPACK linear solvers.
Deprecated “bootstrap” and “minimum correction” predictors in ARKStep (options 4
and 5 to ARKStepSetPredictorMethod()) and the “bootstrap” predictor in
MRIStep (option 4 to MRIStepSetPredictorMethod()). These functions will
output a deprecation warning message and will be removed in a future release.
15.18. Changes to SUNDIALS in release 5.8.0
New Features
The RAJA vector implementation has been updated to
support the SYCL backend in addition to the CUDA and HIP backend. Users can
choose the backend when configuring SUNDIALS by using the
SUNDIALS_RAJA_BACKENDS CMake variable. This vector remains
experimental and is subject to change from version to version.
New SUNMatrix and SUNLinearSolver implementation were added
to interface with the Intel oneAPI Math Kernel Library (oneMKL). Both the matrix
and the linear solver support general dense linear systems as well as block
diagonal linear systems. See §10.14 for more
details. This matrix is experimental and is subject to change from version to
version.
Added a new optional function to the SUNLinearSolver API,
SUNLinSolSetZeroGuess(), to indicate that the next call to
SUNLinSolSolve() will be made with a zero initial guess. SUNLinearSolver
implementations that do not use the SUNLinSolNewEmpty() constructor
will, at a minimum, need set the setzeroguess function pointer in the linear
solver ops structure to NULL. The SUNDIALS iterative linear solver
implementations have been updated to leverage this new set function to remove
one dot product per solve.
The time integrator packages (ARKODE, CVODE(S), and IDA(S)) all now support a
new “matrix-embedded” SUNLinearSolver type. This type supports
user-supplied SUNLinearSolver implementations that set up and solve the
specified linear system at each linear solve call. Any matrix-related data
structures are held internally to the linear solver itself, and are not provided
by the SUNDIALS package.
Added functions to ARKODE and CVODE(S) for supplying an alternative right-hand side function and to IDA(S) for supplying an alternative residual for use within nonlinear system function evaluations:
Support for user-defined inner (fast) integrators has been to the MRIStep module. See MRIStep Custom Inner Steppers for more information on providing a user-defined integration method.
Added specialized fused HIP kernels to CVODE which may offer better performance
on smaller problems when using CVODE with the HIP vector. See the optional input
function CVodeSetUseIntegratorFusedKernels() for more information. As
with other SUNDIALS HIP features, this capability is considered experimental and
may change from version to version.
New KINSOL options have been added to apply a constant damping factor in the
fixed point and Picard iterations (see KINSetDamping()), to delay the
start of Anderson acceleration with the fixed point and Picard iterations (see
KINSetDelayAA()), and to return the newest solution with the fixed point
iteration (see KINSetReturnNewest()).
The installed SUNDIALSConfig.cmake file now supports the COMPONENTS
option to find_package. The exported targets no longer have IMPORTED_GLOBAL
set.
Bug Fixes
A bug was fixed in SUNMatCopyOps() where the matrix-vector product setup
function pointer was not copied.
A bug was fixed in the SPBCGS and SPTFQMR solvers for the case where a non-zero initial guess and a solution scaling vector are provided. This fix only impacts codes using SPBCGS or SPTFQMR as standalone solvers as all SUNDIALS packages utilize a zero initial guess.
A bug was fixed in the ARKODE stepper modules where the stop time may be passed after resetting the integrator.
A bug was fixed in IDASetJacTimesResFn() in IDAS where the supplied
function was used in the dense finite difference Jacobian computation rather
than the finite difference Jacobian-vector product approximation.
A bug was fixed in the KINSOL Picard iteration where the value of
KINSetMaxSetupCalls() would be ignored.
15.19. Changes to SUNDIALS in release 5.7.0
A new N_Vector implementation based on the SYCL abstraction layer has
been added targeting Intel GPUs. At present the only SYCL compiler supported is
the DPC++ (Intel oneAPI) compiler. See §8.17 for more
details. This vector is considered experimental and is subject to major changes
even in minor releases.
A new SUNMatrix and SUNLinearSolver implementation were
added to interface with the MAGMA linear algebra library. Both the matrix and
the linear solver support general dense linear systems as well as block diagonal
linear systems, and both are targeted at GPUs (AMD or NVIDIA). See
§10.13 for more details.
15.20. Changes to SUNDIALS in release 5.6.1
Fixed a CMake bug which caused an error if the CMAKE_CXX_STANDARD and
SUNDIALS_RAJA_BACKENDS options were not provided.
Fixed some compiler warnings when using the IBM XL compilers.
15.21. Changes to SUNDIALS in release 5.6.0
A new N_Vector implementation based on the AMD ROCm HIP platform has
been added. This vector can target NVIDIA or AMD GPUs. See
§8.16 for more details. This vector is considered experimental
and is subject to change from version to version.
The RAJA vector implementation has been updated to
support the HIP backend in addition to the CUDA backend. Users can choose the
backend when configuring SUNDIALS by using the SUNDIALS_RAJA_BACKENDS
CMake variable. This vector remains experimental and is subject to change from
version to version.
A new optional operation, N_VGetDeviceArrayPointer(), was added to the
N_Vector API. This operation is useful for vectors that utilize dual memory
spaces, e.g. the native SUNDIALS CUDA N_Vector.
The SUNDIALS matrix and linear solver interfaces to the cuSparse matrix and cuSolver batched QR solver no longer require using the CUDA
N_Vector. Instead, they require that the vector utilized provides the
N_VGetDeviceArrayPointer() operation, and that the pointer returned by
N_VGetDeviceArrayPointer() is a valid CUDA device pointer.
15.22. Changes to SUNDIALS in release 5.5.0
Refactored the SUNDIALS build system. CMake 3.12.0 or newer is now required.
Users will likely see deprecation warnings, but otherwise the changes
should be fully backwards compatible for almost all users. SUNDIALS
now exports CMake targets and installs a SUNDIALSConfig.cmake file.
Added support for SuperLU DIST 6.3.0 or newer.
15.23. Changes to SUNDIALS in release 5.4.0
Major Features
A new class, SUNMemoryHelper, was added to support GPU users who
have complex memory management needs such as using memory pools. This is paired
with new constructors for the CUDA and RAJA vectors that accept a
SUNMemoryHelper object. Refer to §1.10,
§13, §8.15 and §8.18 for
more information.
Added full support for time-dependent mass matrices in ARKStep, and expanded existing non-identity mass matrix infrastructure to support use of the fixed point nonlinear solver.
An interface between ARKStep and the XBraid multigrid reduction in time (MGRIT)
library [1] has been added to enable parallel-in-time integration. See the
Multigrid Reduction in Time with XBraid section for more information and the example
codes in examples/arkode/CXX_xbraid. This interface required the addition of
three new N_Vector operations to exchange vector data between computational
nodes, see N_VBufSize(), N_VBufPack(), and
N_VBufUnpack(). These N_Vector operations are only used within the
XBraid interface and need not be implemented for any other context.
New Features
The RAJA vector has been updated to mirror the CUDA
vector. Notably, the update adds managed memory support to the RAJA vector.
Users of the vector will need to update any calls to the N_VMake_Raja()
function because that signature was changed. This vector remains experimental
and is subject to change from version to version.
The expected behavior of SUNNonlinSolGetNumIters() and
SUNNonlinSolGetNumConvFails() in the SUNNonlinearSolver API
have been updated to specify that they should return the number of nonlinear
solver iterations and convergence failures in the most recent solve respectively
rather than the cumulative number of iterations and failures across all solves
respectively. The API documentation and SUNDIALS provided
SUNNonlinearSolver implementations have been updated accordingly. As
before, the cumulative number of nonlinear iterations and failures may be
retrieved with the following functions:
Added the following the following functions that advanced users might find
useful when providing a custom SUNNonlinSolSysFn():
Added new functions to CVODE(S), ARKODE, and IDA(S) to to specify the factor for
converting between integrator tolerances (WRMS norm) and linear solver tolerances
(L2 norm) i.e., tol_L2 = nrmfac * tol_WRMS:
Added new reset functions ARKStepReset(), ERKStepReset(),
and MRIStepReset() to reset the stepper time and state vector to
user-provided values for continuing the integration from that point while
retaining the integration history. These function complement the
reinitialization functions ARKStepReInit(), ERKStepReInit(),
and MRIStepReInit() which reinitialize the stepper so that the problem
integration should resume as if started from scratch.
Updated the MRIStep time-stepping module in ARKODE to support higher-order MRI-GARK methods [108], including methods that involve solve-decoupled, diagonally-implicit treatment of the slow time scale.
The function CVodeSetLSetupFrequency() has been added to CVODE(S) to set
the frequency of calls to the linear solver setup function.
The Trilinos Tpetra N_Vector interface has been updated to work with
Trilinos 12.18+. This update changes the local ordinal type to always be an
int.
Added support for CUDA 11.
Bug Fixes
A minor inconsistency in CVODE(S) and a bug ARKODE when checking the Jacobian
evaluation frequency has been fixed. As a result codes using using a non-default
Jacobian update frequency through a call to CVodeSetMaxStepsBetweenJac
or ARKStepSetMaxStepsBetweenJac will need to increase the provided
value by 1 to achieve the same behavior as before.
In IDAS and CVODES, the functions for forward integration with checkpointing
(IDASolveF(), CVodeF()) are now subject to a restriction on the
number of time steps allowed to reach the output time. This is the same
restriction applied to IDASolve() and CVode(). The default
maximum number of steps is 500, but this may be changed using the
CVodeSetMaxNumSteps() and IDASetMaxNumSteps() function. This
change fixes a bug that could cause an infinite loop in IDASolveF() and
CVodeF(). This change may cause a runtime error in existing user
code.
Fixed bug in using ERK method integration with static mass matrices.
Deprecation Notice
For greater clarity the following functions have been deprecated:
CVodeSetMaxStepsBetweenJacARKStepSetMaxStepsBetweenJacARKStepSetMaxStepsBetweenLSet
The following functions should be used instead:
15.24. Changes to SUNDIALS in release 5.3.0
Major Feature
Added support to CVODE for integrating IVPs with constraints using BDF methods
and projecting the solution onto the constraint manifold with a user defined
projection function. This implementation is accompanied by additions to user
documentation and CVODE examples. See CVodeSetProjFn() for more
information.
New Features
Added the ability to control the CUDA kernel launch parameters for the CUDA vector and spare matrix implementations. These implementations remain experimental and are subject to change from version to version. In addition, the CUDA vector kernels were rewritten to be more flexible. Most users should see equivalent performance or some improvement, but a select few may observe minor performance degradation with the default settings. Users are encouraged to contact the SUNDIALS team about any performance changes that they notice.
Added new capabilities for monitoring the solve phase in the Newton and
fixed-point SUNNonlinearSolver, and the SUNDIALS iterative linear
solvers. SUNDIALS must be built with the CMake option
SUNDIALS_BUILD_WITH_MONITORING to use these capabilities.
Added specialized fused CUDA kernels to CVODE which may offer better performance
on smaller problems when using CVODE with the CUDA vector. See the optional
input function CVodeSetUseIntegratorFusedKernels() for more
information. As with other SUNDIALS CUDA features, this is feature is
experimental and may change from version to version.
Added a new function, CVodeSetMonitorFn(), that takes a user-function
to be called by CVODE after every nst successfully completed time-steps.
This is intended to provide a way of monitoring the CVODE statistics
throughout the simulation.
Added a new function CVodeGetLinSolveStats() to get the CVODE linear solver
statistics as a group.
Added the following optional functions to provide an alternative ODE right-hand side function (ARKODE and CVODE(S)), DAE residual function (IDA(S)), or nonlinear system function (KINSOL) for use when computing Jacobian-vector products with the internal difference quotient approximation:
Bug Fixes
Fixed a bug in the iterative linear solvers where an error is not returned if
the Atimes function is NULL or, if preconditioning is enabled, the
PSolve function is NULL.
Fixed a bug in ARKODE where the prototypes for ERKStepSetMinReduction()
and ARKStepSetMinReduction() were not included in arkode_erkstep.h
and arkode_arkstep.h respectively.
Fixed a bug in ARKODE where inequality constraint checking would need to be
disabled and then re-enabled to update the inequality constraint values after
resizing a problem. Resizing a problem will now disable constraints and a call
to ARKStepSetConstraints() or ERKStepSetConstraints() is
required to re-enable constraint checking for the new problem size.
15.25. Changes to SUNDIALS in release 5.2.0
New Features
The following functions were added to each of the time integration packages to enable or disable the scaling applied to linear system solutions with matrix-based linear solvers to account for lagged matrix information:
When using a matrix-based linear solver with ARKODE, IDA(S), or BDF methods in CVODE(S) scaling is enabled by default.
Added a new SUNMatrix implementation that interfaces to the sparse
matrix implementation from the NVIDIA cuSPARSE library, see
§9.13 for more details. In addition, the CUDA Sparse
linear solver has been updated to use the new matrix, as such, users of this
matrix will need to update their code. This implementations are still considered
to be experimental, thus they are subject to breaking changes even in minor
releases.
Added a new “stiff” interpolation module to ARKODE, based on Lagrange polynomial
interpolation, that is accessible to each of the ARKStep, ERKStep and MRIStep
time-stepping modules. This module is designed to provide increased
interpolation accuracy when integrating stiff problems, as opposed to the
ARKODE-standard Hermite interpolation module that can suffer when the IVP
right-hand side has large Lipschitz constant. While the Hermite module remains
the default, the new Lagrange module may be enabled using one of the routines
ARKStepSetInterpolantType(), ERKStepSetInterpolantType(), or
MRIStepSetInterpolantType(). The serial example problem
ark_brusselator.c has been converted to use this Lagrange interpolation
module. Created accompanying routines ARKStepSetInterpolantDegree(),
ARKStepSetInterpolantDegree() and ARKStepSetInterpolantDegree()
to provide user control over these interpolating polynomials.
Added two new functions, ARKStepSetMinReduction() and
ERKStepSetMinReduction(), to change the minimum allowed step size
reduction factor after an error test failure.
Bug Fixes
Fixed a build system bug related to the Fortran 2003 interfaces when using the
IBM XL compiler. When building the Fortran 2003 interfaces with an XL compiler
it is recommended to set CMAKE_Fortran_COMPILER to f2003,
xlf2003, or xlf2003_r.
Fixed a bug in how ARKODE interfaces with a user-supplied, iterative, unscaled
linear solver. In this case, ARKODE adjusts the linear solver tolerance in an
attempt to account for the lack of support for left/right scaling matrices.
Previously, ARKODE computed this scaling factor using the error weight vector,
ewt; this fix changes that to the residual weight vector, rwt, that can
differ from ewt when solving problems with non-identity mass matrix.
Fixed a linkage bug affecting Windows users that stemmed from dllimport/dllexport attribute missing on some SUNDIALS API functions.
Fixed a memory leak in CVODES and IDAS from not deallocating the atolSmin0
and atolQSmin0 arrays.
Fixed a bug where a non-default value for the maximum allowed growth factor after the first step would be ignored.
Deprecation Notice
The routines ARKStepSetDenseOrder(), ARKStepSetDenseOrder() and
ARKStepSetDenseOrder() have been deprecated and will be removed in a
future release. The new functions ARKStepSetInterpolantDegree(),
ARKStepSetInterpolantDegree(), and ARKStepSetInterpolantDegree()
should be used instead.
15.26. Changes to SUNDIALS in release 5.1.0
New Features
Added support for a user-supplied function to update the prediction for each
implicit stage solution in ARKStep. If supplied, this routine will be called
after any existing ARKStep predictor algorithm completes, so that the
predictor may be modified by the user as desired. The new user-supplied routine
has type ARKStagePredictFn, and may be set by calling
ARKStepSetStagePredictFn().
The MRIStep module has been updated to support attaching different user data
pointers to the inner and outer integrators. If applicable, user codes will need
to add a call to ARKStepSetUserData() to attach their user data pointer
to the inner integrator memory as MRIStepSetUserData() will not set the
pointer for both the inner and outer integrators. The MRIStep examples have been
updated to reflect this change.
Added support for damping when using Anderson acceleration in KINSOL. See the
Mathematical Considerations and the description of the
KINSetDampingAA() function for more details.
Added support for constant damping to the fixed-point
SUNNonlinearSolver when using Anderson acceleration. See
SUNNonlinSol_FixedPoint description and the
SUNNonlinSolSetDamping_FixedPoint() for more details.
Added two utility functions, SUNDIALSFileOpen() and
SUNDIALSFileClose() for creating/destroying file pointers. These are
useful when using the Fortran 2003 interfaces.
Added a new build system option, CUDA_ARCH, to specify the CUDA
architecture to target.
Bug Fixes
Fixed a build system bug related to finding LAPACK/BLAS.
Fixed a build system bug related to checking if the KLU library works.
Fixed a build system bug related to finding PETSc when using the CMake
variables PETSC_INCLUDES and PETSC_LIBRARIES instead of
PETSC_DIR.
Fixed a bug in the Fortran 2003 interfaces to the ARKODE Butcher table routines
and structure. This includes changing the ARKodeButcherTable type to
be a type(c_ptr) in Fortran.
15.27. Changes to SUNDIALS in release 5.0.0
Build System
Increased the minimum required CMake version to 3.5 for most SUNDIALS configurations, and 3.10 when CUDA or OpenMP with device offloading are enabled.
The CMake option BLAS_ENABLE and the variable BLAS_LIBRARIES have been
removed to simplify builds as SUNDIALS packages do not use BLAS directly. For
third party libraries that require linking to BLAS, the path to the BLAS library
should be included in the _LIBRARIES variable for the third party library
e.g., SUPERLUDIST_LIBRARIES when enabling SuperLU_DIST.
NVector
Two new functions were added to aid in creating custom N_Vector
objects. The constructor N_VNewEmpty() allocates an “empty” generic
N_Vector with the object’s content pointer and the function pointers
in the operations structure initialized to NULL. When used in the
constructor for custom objects this function will ease the introduction of any
new optional operations to the N_Vector API by ensuring only required
operations need to be set. Additionally, the function N_VCopyOps() has
been added to copy the operation function pointers between vector objects. When
used in clone routines for custom vector objects these functions also will ease
the introduction of any new optional operations to the N_Vector API by
ensuring all operations are copied when cloning objects.
Added new N_Vector implementations, ManyVector and MPIManyVector, to
support flexible partitioning of solution data among different processing
elements (e.g., CPU + GPU) or for multi-physics problems that couple distinct
MPI-based simulations together (see the §8.22 and
§8.23 for more details). This implementation is
accompanied by additions to user documentation and SUNDIALS examples.
Additionally, an MPIPlusX vector implementation has been created to support the MPI+X paradigm where X is a type of on-node parallelism (e.g., OpenMP, CUDA, etc.). The implementation is accompanied by additions to user documentation and SUNDIALS examples.
One new required vector operation and ten new optional vector operations have
been added to the N_Vector API. The new required operation,
N_VGetLength(), returns the global vector length. The optional
operations have been added to support the new MPIManyVector implementation. The
operation N_VGetCommunicator() must be implemented by subvectors that
are combined to create an MPIManyVector, but is not used outside of this
context. The remaining nine operations are optional local reduction operations
intended to eliminate unnecessary latency when performing vector reduction
operations (norms, etc.) on distributed memory systems. The optional local
reduction vector operations are N_VDotProdLocal,
N_VMaxNormLocal, N_VMinLocal, N_VL1NormLocal,
N_VWSqrSumLocal, N_VWSqrSumMaskLocal,
N_VInvTestLocal, N_VConstrMaskLocal, and
N_VMinQuotientLocal. If an N_Vector implementation defines
any of the local operations as NULL, then the MPIManyVector will call
standard N_Vector operations to complete the computation.
The *_MPICuda and *_MPIRaja functions have been removed from the CUDA
and RAJA vector implementations respectively. Accordingly, the
nvector_mpicuda.h, nvector_mpiraja.h, libsundials_nvecmpicuda.lib,
and libsundials_nvecmpicudaraja.lib files have been removed. Users should
use the MPI+X vector in conjunction with the CUDA and RAJA vectors to replace
the functionality. The necessary changes are minimal and should require few code
modifications. See the example programs in examples/ida/mpicuda and
examples/ida/mpiraja for examples of how to use the MPI+X vector with the
CUDA and RAJA vectors, respectively.
Made performance improvements to the CUDA vector. Users who utilize a non-default stream should no longer see default stream synchronizations after memory transfers.
Added a new constructor to the CUDA vector that allows a user to provide custom allocate and free functions for the vector data array and internal reduction buffer.
Added three new N_Vector utility functions,
N_VGetVecAtIndexVectorArray(), N_VSetVecAtIndexVectorArray(),
and N_VNewVectorArray(), for working with N_Vector arrays when
using the Fortran 2003 interfaces.
SUNMatrix
Two new functions were added to aid in creating custom SUNMatrix
objects. The constructor SUNMatNewEmpty() allocates an “empty” generic
SUNMatrix with the object’s content pointer and the function pointers
in the operations structure initialized to NULL. When used in the
constructor for custom objects this function will ease the introduction of any
new optional operations to the SUNMatrix API by ensuring only required
operations need to be set. Additionally, the function SUNMatCopyOps()
has been added to copy the operation function pointers between matrix
objects. When used in clone routines for custom matrix objects these functions
also will ease the introduction of any new optional operations to the
SUNMatrix API by ensuring all operations are copied when cloning
objects.
A new operation, SUNMatMatvecSetup(), was added to the
SUNMatrix API to perform any setup necessary for computing a
matrix-vector product. This operation is useful for SUNMatrix
implementations which need to prepare the matrix itself, or communication
structures before performing the matrix-vector product. Users who have
implemented a custom SUNMatrix will need to at least update their code
to set the corresponding ops structure member, matvecsetup, to NULL.
The generic SUNMatrix API now defines error codes to be returned by
matrix operations. Operations which return an integer flag indicating
success/failure may return different values than previously.
A new SUNMatrix (and SUNLinearSolver) implementation was
added to facilitate the use of the SuperLU_DIST library with SUNDIALS.
SUNLinearSolver
A new function was added to aid in creating custom SUNLinearSolver
objects. The constructor SUNLinSolNewEmpty() allocates an “empty”
generic SUNLinearSolver with the object’s content pointer and the
function pointers in the operations structure initialized to NULL. When used
in the constructor for custom objects this function will ease the introduction
of any new optional operations to the SUNLinearSolver API by ensuring
only required operations need to be set.
The return type of the SUNLinSolLastFlag in the
SUNLinearSolver has changed from long int to
sunindextype to be consistent with the type used to store row indices
in dense and banded linear solver modules.
Added a new optional operation to the SUNLinearSolver API,
SUNLinSolGetID(), that returns a SUNLinearSolver_ID for
identifying the linear solver module.
The SUNLinearSolver API has been updated to make the initialize and
setup functions optional.
A new SUNLinearSolver (and SUNMatrix) implementation was
added to facilitate the use of the SuperLU_DIST library with SUNDIALS.
Added a new SUNLinearSolver implementation, cuSolverSp_batchQR, which leverages the NVIDIA cuSOLVER sparse batched QR
method for efficiently solving block diagonal linear systems on NVIDIA GPUs.
Added three new accessor functions to the KLU linear solver to provide user
access to the underlying KLU solver structures:
SUNLinSol_KLUGetSymbolic(), SUNLinSol_KLUGetNumeric(), and
SUNLinSol_KLUGetCommon().
SUNNonlinearSolver
A new function was added to aid in creating custom SUNNonlinearSolver
objects. The constructor SUNNonlinSolNewEmpty() allocates an “empty”
generic SUNNonlinearSolver with the object’s content pointer and the
function pointers in the operations structure initialized to NULL. When used
in the constructor for custom objects this function will ease the introduction
of any new optional operations to the SUNNonlinearSolver API by
ensuring only required operations need to be set.
To facilitate the use of user supplied nonlinear solver convergence test
functions the SUNNonlinSolSetConvTestFn() function in the
SUNNonlinearSolver API has been updated to take a void* data
pointer as input. The supplied data pointer will be passed to the nonlinear
solver convergence test function on each call.
The inputs values passed to the first two inputs of the SUNNonlinSolSolve()
function in the SUNNonlinearSolver have been changed to be the predicted
state and the initial guess for the correction to that state. Additionally,
the definitions of SUNNonlinSolLSetupFn() and SUNNonlinSolLSolveFn() in the
SUNNonlinearSolver API have been updated to remove unused input parameters.
For more information on the nonlinear system formulation and the API functions
see Nonlinear Algebraic Solvers.
Added a new SUNNonlinearSolver implementation for interfacing with the
PETSc SNES nonlinear solver.
New Features
A new linear solver interface functions, ARKLsLinSysFn and
CVLsLinSysFn, as added as an alternative method for evaluating the
linear systems \(M - \gamma J\) or \(I - \gamma J\).
Added the following functions to get the current state and gamma value to ARKStep, CVODE and CVODES that may be useful to users who choose to provide their own nonlinear solver implementation:
Removed extraneous calls to N_VMin() for simulations where the scalar
valued absolute tolerance, or all entries of the vector-valued absolute
tolerance array, are strictly positive. In this scenario ARKODE, CVODE(S), and
IDA(S) steppers will remove at least one global reduction per time step.
The ARKODE, CVODE(S), IDA(S), and KINSOL linear solver interfaces have been
updated to only zero the Jacobian matrix before calling a user-supplied Jacobian
evaluation function when the attached linear solver has type
SUNLINEARSOLVER_DIRECT.
Added new Fortran 2003 interfaces to all of the SUNDIALS packages (ARKODE,
CVODE(S), IDA(S), and KINSOL as well as most of the N_Vector,
SUNMatrix, SUNLinearSolver, and SUNNonlinearSolver
implementations. See §1.9 section for more details.
These new interfaces were generated with SWIG-Fortran and provide a user an
idiomatic Fortran 2003 interface to most of the SUNDIALS C API.
The MRIStep module has been updated to support explicit, implicit, or IMEX
methods as the fast integrator using the ARKStep module. As a result some
function signatures have been changed including MRIStepCreate() which
now takes an ARKStep memory structure for the fast integration as an input.
The reinitialization functions ERKStepReInit(), ARKStepReInit(),
and MRIStepReInit() have been updated to retain the minimum and maximum
step size values from before reinitialization rather than resetting them to the
default values.
Added two new embedded ARK methods of orders 4 and 5 to ARKODE (from [85]).
Support for optional inequality constraints on individual components of the
solution vector has been added the ARKODE ERKStep and ARKStep modules. See the
descriptions of ERKStepSetConstraints() and
ARKStepSetConstraints() for more details. Note that enabling constraint
handling requires the N_Vector operations N_VMinQuotient(),
N_VConstrMask(), and N_VCompare() that were not previously
required by ARKODE.
Add two new ‘Set’ functions to MRIStep, MRIStepSetPreInnerFn() and
MRIStepSetPostInnerFn(), for performing communication or memory transfers
needed before or after the inner integration.
Bug Fixes
Fixed a bug in the build system that prevented the PThreads NVECTOR module from being built.
Fixed a memory leak in the PETSc N_Vector clone function.
Fixed a memory leak in the ARKODE, CVODE, and IDA F77 interfaces when not using the default nonlinear solver.
Fixed a bug in the ARKStep time-stepping module in ARKODE that would result in an infinite loop if the nonlinear solver failed to converge more than the maximum allowed times during a single step.
Fixed a bug in ARKODE that would result in a “too much accuracy requested” error when using fixed time step sizes with explicit methods in some cases.
Fixed a bug in ARKStep where the mass matrix linear solver setup function was not called in the Matrix-free case.
Fixed a minor bug in ARKStep where an incorrect flag is reported when an error occurs in the mass matrix setup or Jacobian-vector product setup functions.
Fixed a bug in the CVODE and CVODES constraint handling where the step size could be set below the minimum step size.
Fixed a bug in the CVODE and CVODES nonlinear solver interfaces where the norm of the accumulated correction was not updated when using a non-default convergence test function.
Fixed a bug in the CVODES cvRescale function where the loops to compute the
array of scalars for the fused vector scale operation stopped one iteration
early.
Fixed a bug in CVODES and IDAS where CVodeF() and IDASolveF()
would return the wrong flag under certain circumstances.
Fixed a bug in CVODES and IDAS where CVodeF() and IDASolveF()
would not return a root in NORMAL_STEP mode if the root occurred after the
desired output time.
Fixed a bug in the IDA and IDAS linear solver interfaces where an incorrect Jacobian-vector product increment was used with iterative solvers other than SPGMR and SPFGMR.
Fixed a bug the IDAS IDAQuadReInitB() function where an incorrect memory
structure was passed to IDAQuadReInit().
Fixed a bug in the KINSOL linear solver interface where the auxiliary scalar
sJpnorm was not computed when necessary with the Picard iteration and the
auxiliary scalar sFdotJp was unnecessarily computed in some cases.
15.28. Changes to SUNDIALS in release 4.1.0
Removed Implementation Headers
The implementation header files (*_impl.h) are no longer installed. This
means users who are directly accessing or manipulating package memory structures
will need to update their code to use the package’s public API.
New Features
An additional N_Vector implementation was added for interfacing with
the Tpetra vector from Trilinos library to facilitate interoperability between
SUNDIALS and Trilinos. This implementation is accompanied by additions to user
documentation and SUNDIALS examples.
Bug Fixes
The EXAMPLES_ENABLE_RAJA CMake option has been removed. The option
EXAMPLES_ENABLE_CUDA enables all examples that use CUDA including the
RAJA examples with a CUDA back end (if RAJA is enabled).
Python is no longer required to run make test and make test_install.
A bug was fixed where a nonlinear solver object could be freed twice in some use cases.
Fixed a bug in ARKodeButcherTable_Write() when printing a Butcher table
without an embedding.
15.29. Changes to SUNDIALS in release 4.0.2
Added information on how to contribute to SUNDIALS and a contributing agreement.
Moved the definitions of backwards compatibility functions for the prior direct
linear solver (DLS) and scaled preconditioned iterarive linear solvers (SPILS)
to a source file. The symbols are now included in the appropriate package
library, e.g. libsundials_cvode.lib.
15.30. Changes to SUNDIALS in release 4.0.1
A bug in ARKODE where single precision builds would fail to compile has been fixed.
15.31. Changes to SUNDIALS in release 4.0.0
The direct and iterative linear solver interfaces in all SUNDIALS packages have
been merged into a single unified linear solver interface to support any valid
SUNLinearSolver. This includes the DIRECT and ITERATIVE types
as well as the new MATRIX_ITERATIVE type. Details regarding how SUNDIALS
packages utilize linear solvers of each type as well as a discussion regarding
the intended use cases for user-supplied linear solver implementations are
included in §10. All example programs have been updated to use
the new unified linear solver interfaces.
The unified linear solver interface is very similar to the previous DLS (direct linear solver) and SPILS (scaled preconditioned iterative linear solver) interface in each package. To minimize challenges in user migration to the unified linear solver interfaces, the previous DLS and SPILS functions may still be used however, these are now deprecated and will be removed in a future release. Additionally, that Fortran users will need to enlarge their array of optional integer outputs, and update the indices that they query for certain linear solver related statistics.
The names of all SUNDIALS-provided SUNLinearSolver constructors have
have been updated to follow the naming convention SUNLinSol_* where * is
the name of the linear solver. The new constructor names are:
Linear solver-specific “set” routine names have been similarly standardized. To minimize challenges in user migration to the new names, the previous function names may still be used however, these are now deprecated and will be removed in a future release. All example programs and the standalone linear solver examples have been updated to use the new naming convention.
The SUNLinSol_Band() constructor has been simplified to remove the
storage upper bandwidth argument.
SUNDIALS integrators (ARKODE, CVODE(S), and IDA(S)) have been updated to utilize
generic nonlinear solvers defined by the SUNNonlinearSolver API. This
enables the addition of new nonlinear solver options and allows for external or
user-supplied nonlinear solvers. The nonlinear solver API and SUNDIALS provided
implementations are described in Nonlinear Algebraic Solvers and follow the same
object oriented design used by the N_Vector, SUNMatrix, and
SUNLinearSolver classes. Currently two nonlinear solver
implementations are provided, Newton and
fixed-point. These replicate the previous
integrator-specific implementations of Newton’s method and a fixed-point
iteration (previously referred to as a functional iteration), respectively. Note
the new fixed-point implementation can
optionally utilize Anderson’s method to accelerate convergence. Example programs
using each of these nonlinear solvers in a standalone manner have been added and
all example programs have been updated accordingly.
The SUNDIALS integrators (ARKODE, CVODE(S), and IDA(S)) all now use the
Newton SUNNonlinearSolver by default.
Users that wish to use the fixed-point
SUNNonlinearSolver will need to create the corresponding nonlinear
solver object and attach it to the integrator with the appropriate set function:
Functions for setting the nonlinear solver options or getting nonlinear solver
statistics remain unchanged and internally call generic SUNNonlinearSolver
functions as needed.
With the introduction of the SUNNonlinearSolver class, the input
parameter iter to CVodeCreate() has been removed along with the
function CVodeSetIterType and the constants CV_NEWTON and
CV_FUNCTIONAL. While SUNDIALS includes a fixed-point nonlinear solver, it is
not currently supported in IDA.
Three fused vector operations and seven vector array operations have been added
to the N_Vector API. These optional operations are disabled by
default and may be activated by calling vector specific routines after creating
a vector (see §8.1 for more details). The new
operations are intended to increase data reuse in vector operations, reduce
parallel communication on distributed memory systems, and lower the number of
kernel launches on systems with accelerators. The fused operations are:
and the vector array operations are:
If an N_Vector implementation defines the implementation any of these
operations as NULL, then standard vector operations will automatically be
called as necessary to complete the computation.
A new N_Vector implementation, OpenMPDEV,
leveraging OpenMP device offloading has been added.
Multiple updates to the CUDA vector were made:
Changed the
N_VMake_Cuda()function to take a host data pointer and a device data pointer instead of anN_VectorContent_Cudaobject.Changed
N_VGetLength_Cudato return the global vector length instead of the local vector length.Added
N_VGetLocalLength_Cudato return the local vector length.Added
N_VGetMPIComm_Cudato return the MPI communicator used.Removed the accessor functions in the
suncudavecnamespace.Added the ability to set the
cudaStream_tused for execution of the CUDA kernels. See the functionN_VSetCudaStreams_Cuda.Added
N_VNewManaged_Cuda(),N_VMakeManaged_Cuda(), andN_VIsManagedMemory_Cuda()functions to accommodate using managed memory with the CUDA vector.
Multiple updates to the RAJA vector were made:
Changed
N_VGetLength_Rajato return the global vector length instead of the local vector length.Added
N_VGetLocalLength_Rajato return the local vector length.Added
N_VGetMPIComm_Rajato return the MPI communicator used.Removed the accessor functions in the
sunrajavecnamespace.
Two changes were made in the ARKODE and CVODE(S) initial step size algorithm:
Fixed an efficiency bug where an extra call to the RHS function was made.
Changed the behavior of the algorithm if the max-iterations case is hit. Before the algorithm would exit with the step size calculated on the penultimate iteration. Now it will exit with the step size calculated on the final iteration.
Fortran 2003 interfaces to CVODE, the fixed-point and Newton nonlinear solvers, the dense, band, KLU, PCG, SPBCGS, SPFGMR, SPGMR, and SPTFQMR linear solvers, and the serial, PThreads, and OpenMP vectors have been added.
The ARKODE library has been entirely rewritten to support a modular approach to
one-step methods, which should allow rapid research and development of novel
integration methods without affecting existing solver functionality. To support
this, the existing ARK-based methods have been encapsulated inside the new
ARKStep time-stepping module. Two new time-stepping modules have been added:
The
ERKStepmodule provides an optimized implementation for explicit Runge–Kutta methods with reduced storage and number of calls to the ODE right-hand side function.The
MRIStepmodule implements two-rate explicit-explicit multirate infinitesimal step methods utilizing different step sizes for slow and fast processes in an additive splitting.
This restructure has resulted in numerous small changes to the user interface,
particularly the suite of “Set” routines for user-provided solver parameters and
“Get” routines to access solver statistics, that are now prefixed with the name
of time-stepping module (e.g., ARKStep or ERKStep) instead of
ARKODE. Aside from affecting the names of these routines, user-level changes
have been kept to a minimum. However, we recommend that users consult both this
documentation and the ARKODE example programs for further details on the updated
infrastructure.
As part of the ARKODE restructuring an ARKodeButcherTable structure
has been added for storing Butcher tables. Functions for creating new Butcher
tables and checking their analytic order are provided along with other utility
routines. For more details see the Butcher Table Data Structure section.
ARKODE’s dense output infrastructure has been improved to support higher-degree Hermite polynomial interpolants (up to degree 5) over the last successful time step.
15.32. Changes to SUNDIALS in release 3.2.1
Fixed a bug in the CUDA vector where the
N_VInvTest() operation could write beyond the allocated vector data.
Fixed the library installation path for multiarch systems. This fix changes the
default library installation path from CMAKE_INSTALL_PREFIX/lib to
CMAKE_INSTALL_PREFIX/CMAKE_INSTALL_LIBDIR. The default value library
directory name is automatically set to lib, lib64, or
lib/<multiarch-tuple> depending on the system, but maybe be overridden by
setting CMAKE_INSTALL_LIBDIR.
15.33. Changes to SUNDIALS in release 3.2.0
Library Name Change
Changed the name of the RAJA nvector library from libsundials_nvecraja.lib
to libsundials_nveccudaraja.lib to better reflect that the RAJA vector only
support the CUDA backend currently.
New Features
Added hybrid MPI+CUDA and MPI+RAJA vectors to allow use of more than one MPI rank when using a GPU system. The vectors assume one GPU device per MPI rank.
Support for optional inequality constraints on individual components of the
solution vector has been added to CVODE and CVODES. For more details see the
Mathematical Considerations and Optional input functions sections. Use
of CVodeSetConstraints() requires the N_Vector operations
N_VMinQuotient(), N_VConstrMask(), and N_VCompare() that
were not previously required by CVODE and CVODES.
CMake Updates
CMake 3.1.3 is now the minimum required CMake version.
Deprecated the behavior of the SUNDIALS_INDEX_TYPE CMake option and
added the SUNDIALS_INDEX_SIZE CMake option to select the
sunindextype integer size.
The native CMake FindMPI module is now used to locate an MPI installation.
If MPI is enabled and MPI compiler wrappers are not set, the build system will
check if CMAKE_<language>_COMPILER can compile MPI programs before trying
to locate and use an MPI installation.
The previous options for setting MPI compiler wrappers and the executable for
running MPI programs have been have been deprecated. The new options that align
with those used in native CMake FindMPI module are MPI_C_COMPILER,
MPI_CXX_COMPILER, MPI_Fortran_COMPILER, and
MPIEXEC_EXECUTABLE.
When a Fortran name-mangling scheme is needed (e.g., ENABLE_LAPACK is
ON) the build system will infer the scheme from the Fortran compiler. If a
Fortran compiler is not available or the inferred or default scheme needs to be
overridden, the advanced options SUNDIALS_F77_FUNC_CASE and
SUNDIALS_F77_FUNC_UNDERSCORES can be used to manually set the name-mangling
scheme and bypass trying to infer the scheme.
Parts of the main CMakeLists.txt file were moved to new files in the src
and example directories to make the CMake configuration file structure more
modular.
Bug Fixes
Fixed a problem with setting sunindextype which would occur with some
compilers (e.g. armclang) that do not define __STDC_VERSION__.
Fixed a thread-safety issue in CVODES and IDAS when using adjoint sensitivity analysis.
Fixed a bug in IDAS where the saved residual value used in the nonlinear solve for consistent initial conditions was passed as temporary workspace and could be overwritten.
15.34. Changes to SUNDIALS in release 3.1.2
CMake Updates
Updated the minimum required version of CMake to 2.8.12 and enabled using rpath by default to locate shared libraries on OSX.
New Features
Added the function SUNSparseMatrix_Reallocate() to allow specification
of the matrix nonzero storage.
Added named constants for the two reinitialization types for the KLU SUNLinearSolver.
Updated the SUNMatScaleAdd() and SUNMatScaleAddI()
implementations in the sparse SUNMatrix to more optimally handle the case where
the target matrix contained sufficient storage for the sum, but had the wrong
sparsity pattern. The sum now occurs in-place, by performing the sum backwards
in the existing storage. However, it is still more efficient if the
user-supplied Jacobian routine allocates storage for the sum
\(M + \gamma J\) or \(M + \gamma J\) manually (with zero entries if
needed).
The following examples from the usage notes page of the SUNDIALS website, and updated them to work with SUNDIALS 3.x:
cvDisc_dns.cdemonstrates using CVODE with discontinuous solutions or RHS.cvRoberts_dns_negsol.cillustrates the use of the RHS function return value to control unphysical negative concentrations.cvRoberts_FSA_dns_Switch.cdemonstrates switching on/off forward sensitivity computations. This example came from the usage notes page of the SUNDIALS website.
Bug Fixes
Fixed a Windows specific problem where sunindextype was not correctly
defined when using 64-bit integers. On Windows sunindextype is now
defined as the MSVC basic type __int64.
Fixed a bug in the full KLU SUNLinearSolver reinitialization approach where the sparse SUNMatrix pointer would go out of scope on some architectures.
The misnamed function CVSpilsSetJacTimesSetupFnBS has been deprecated and
replaced by CVSpilsSetJacTimesBS. The deprecated function
CVSpilsSetJacTimesSetupFnBS will be removed in the next major release.
Changed LICENSE install path to instdir/include/sundials.
15.35. Changes to SUNDIALS in release 3.1.1
Bug Fixes
Fixed a minor bug in the CVODE and CVODES cvSLdet, where a return was
missing in the error check for three inconsistent roots.
Fixed a potential memory leak in the SPGMR and SPFGMR linear solvers. If “Initialize” was called multiple times then the solver memory was reallocated (without being freed).
Fixed a minor bug in ARKReInit, where a flag was incorrectly set to indicate
that the problem had been resized (instead of just re-initialized).
Fixed C++11 compiler errors/warnings about incompatible use of string literals.
Updated the KLU SUNLinearSolver to use a typedef for the precision-specific solve functions to avoid compiler warnings.
Added missing typecasts for some (void*) pointers to avoid compiler
warnings.
Fixed bug in the sparse SUNMatrix where int was used instead of
sunindextype in one location.
Fixed a minor bug in KINPrintInfo where a case was missing for
KIN_REPTD_SYSFUNC_ERR leading to an undefined info message.
Added missing #include <stdio.h> in N_Vector and
SUNMatrix header files.
Added missing prototypes for ARKSpilsGetNumMTSetups in ARKODE and
IDASpilsGetNumJTSetupEvals in IDA and IDAS.
Fixed an indexing bug in the CUDA vector implementation of
N_VWrmsNormMask() and revised the RAJA vector implementation of
N_VWrmsNormMask() to work with mask arrays using values other than zero
or one. Replaced double with realtype in the RAJA vector test functions.
Fixed compilation issue with GCC 7.3.0 and Fortran programs that do not require
a SUNMatrix or SUNLinearSolver e.g., iterative linear
solvers, explicit methods in ARKODE, functional iteration in CVODE, etc.
15.36. Changes to SUNDIALS in release 3.1.0
Added N_Vector print functions that write vector data to a specified
file (e.g., N_VPrintFile_Serial()).
Added make test and make test_install options to the build system for
testing SUNDIALS after building with make and installing with make
install respectively.
15.37. Changes to SUNDIALS in release 3.0.0
Major Feature
Added new linear solver and matrix interfaces for all SUNDIALS packages and updated the existing linear solver and matrix implementations. The goal of the redesign is to provide greater encapsulation and ease interfacing custom linear solvers with linear solver libraries. Specific changes include:
Added a
SUNMatrixinterface with three provided implementations: dense, banded, and sparse. These replicate previous SUNDIALS direct (Dls) and sparse (Sls) matrix structures.Added example problems demonstrating use of the matrices.
Added a
SUNLinearSolverinterface with eleven provided implementations: dense, banded, LAPACK dense, LAPACK band, KLU, SuperLU_MT, SPGMR, SPBCGS, SPTFQMR, SPFGMR, PCG. These replicate previous SUNDIALS generic linear solvers.Added example problems demonstrating use of the linear solvers.
Expanded package-provided direct linear solver (Dls) interfaces and scaled, preconditioned, iterative linear solver (Spils) interfaces to utilize
SUNMatrixandSUNLinearSolverobjects.Removed package-specific, linear solver-specific, solver modules (e.g., CVDENSE, KINBAND, IDAKLU, ARKSPGMR) since their functionality is entirely replicated by the generic Dls/Spils interfaces and
SUNLinearSolver/SUNMatrixclasses. The exception isCVDIAG, a diagonal approximate Jacobian solver available to CVODE and CVODES.Converted all SUNDIALS example problems to utilize new the new matrix and linear solver objects, along with updated Dls and Spils linear solver interfaces.
Added Spils interface routines to ARKODE, CVODE, CVODES, IDA and IDAS to allow specification of a user-provided
JTSetuproutine. This change supports users who wish to set up data structures for the user-provided Jacobian-times-vector (JTimes) routine, and where the cost of oneJTSetupsetup per Newton iteration can be amortized between multipleJTimescalls.
Corresponding updates were made to all the example programs.
New Features
CUDA and RAJA N_Vector
implementations to support GPU systems. These vectors are supplied to provide
very basic support for running on GPU architectures. Users are advised that
these vectors both move all data to the GPU device upon construction, and
speedup will only be realized if the user also conducts the right-hand-side
function evaluation on the device. In addition, these vectors assume the problem
fits on one GPU. For further information about RAJA, users are referred to the
RAJA web site.
Added the type sunindextype to support using 32-bit or 64-bit integer
types for indexing arrays within all SUNDIALS structures. sunindextype
is defined to int32_t or int64_t when portable types are supported,
otherwise it is defined as int or long int. The Fortran interfaces
continue to use long int for indices, except for the sparse matrix interface
that now uses sunindextype. Interfaces to PETSc, hypre, SuperLU_MT,
and KLU have been updated with 32-bit or 64-bit capabilities depending how the
user configures SUNDIALS.
To avoid potential namespace conflicts, the macros defining
booleantype values TRUE and FALSE have been changed to
SUNTRUE and SUNFALSE respectively.
Temporary vectors were removed from preconditioner setup and solve routines for all packages. It is assumed that all necessary data for user-provided preconditioner operations will be allocated and stored in user-provided data structures.
The file include/sundials_fconfig.h was added. This file contains SUNDIALS
type information for use in Fortran programs.
Added support for many xSDK-compliant build system keys. For more information on on xSDK compliance the xSDK policies. The xSDK is a movement in scientific software to provide a foundation for the rapid and efficient production of high-quality, sustainable extreme-scale scientific applications. For more information visit the xSDK web site.
Added functions SUNDIALSGetVersion() and
SUNDIALSGetVersionNumber() to get SUNDIALS release version information
at runtime.
Added comments to arkode_butcher.c regarding which methods should have
coefficients accurate enough for use in quad precision.
Build System
Renamed CMake options to enable/disable examples for greater clarity and added option to enable/disable Fortran 77 examples:
Changed
EXAMPLES_ENABLEtoEXAMPLES_ENABLE_CChanged
CXX_ENABLEtoEXAMPLES_ENABLE_CXXChanged
F90_ENABLEtoEXAMPLES_ENABLE_F90Added
EXAMPLES_ENABLE_F77option
Added separate BLAS_ENABLE and BLAS_LIBRARIES CMake variables.
Fixed minor CMake bugs and included additional error checking during CMake configuration.
Bug Fixes
ARKODE
Fixed RCONST usage in arkode_butcher.c.
Fixed bug in arkInitialSetup to ensure the mass matrix vector product is
set up before the “msetup” routine is called.
Fixed ARKODE printf-related compiler warnings when building SUNDIALS
with extended precision.
CVODE and CVODES
CVodeFree() now calls lfree unconditionally (if non-NULL).
IDA and IDAS
Added missing prototype for IDASetMaxBacksIC() in ida.h and
idas.h.
KINSOL
Corrected KINSOL Fortran name translation for FKIN_SPFGMR.
Renamed KINLocalFn and KINCommFn to KINBBDLocalFn and
KINBBDCommFn respectively in the BBD preconditioner module for
consistency with other SUNDIALS solvers.
15.38. Changes to SUNDIALS in release 2.7.0
New Features and Enhancements
Two additional N_Vector implementations were added – one for
hypre parallel vectors and one for PETSc
vectors. These additions are accompanied by additions to
various interface functions and to user documentation.
Added a new N_Vector function, N_VGetVectorID(), that returns
an identifier for the vector.
The sparse matrix structure was enhanced to support both CSR and CSC matrix storage formats.
Various additions were made to the KLU and SuperLU_MT sparse linear solver interfaces, including support for the CSR matrix format when using KLU.
In all packages, the linear solver and preconditioner free routines were
updated to return an integer.
In all packages, example codes were updated to use N_VGetArrayPointer_*
rather than the NV_DATA macro when using the native vectors shipped with
SUNDIALS.
Additional example programs were added throughout including new examples utilizing the OpenMP vector.
ARKODE
The ARKODE implicit predictor algorithms were updated: methods 2 and 3 were improved slightly, a new predictor approach was added, and the default choice was modified.
The handling of integer codes for specifying built-in ARKODE Butcher tables was
enhanced. While a global numbering system is still used, methods now have
#defined names to simplify the user interface and to streamline
incorporation of new Butcher tables into ARKODE.
The maximum number of Butcher table stages was increased from 8 to 15 to accommodate very high order methods, and an 8th-order adaptive ERK method was added.
Support was added for the explicit and implicit methods in an additive Runge–Kutta method with different stage times to support new SSP-ARK methods.
The FARKODE interface was extended to include a routine to set scalar/array-valued residual tolerances, to support Fortran applications with non-identity mass-matrices.
IDA and IDAS
The optional input function IDASetMaxBacksIC() was added to set the
maximum number of linesearch backtracks in the initial condition calculation.
Bug Fixes
Various minor fixes to installation-related files.
Fixed some examples with respect to the change to use new macro/function names
e.g., SUNRexp, etc.
In all packages, a memory leak was fixed in the banded preconditioner and banded-block-diagonal preconditioner interfaces.
Corrected name N_VCloneEmptyVectorArray to N_VCloneVectorArrayEmpty in
all documentation files.
Various corrections were made to the interfaces to the sparse solvers KLU and SuperLU_MT.
For each linear solver, the various solver performance counters are now
initialized to 0 in both the solver specification function and in the solver
linit function. This ensures that these solver counters are initialized upon
linear solver instantiation as well as at the beginning of the problem solution.
ARKODE
The missing ARKSpilsGetNumMtimesEvals function was added – this had been
included in the previous documentation but had not been implemented.
The choice of the method vs embedding the Billington and TRBDF2 explicit Runge–Kutta methods were swapped, since in those the lower-order coefficients result in an A-stable method, while the higher-order coefficients do not. This change results in significantly improved robustness when using those methods.
A bug was fixed for the situation where a user supplies a vector of absolute tolerances, and also uses the vector Resize functionality.
A bug was fixed wherein a user-supplied Butcher table without an embedding is supplied, and the user is running with either fixed time steps (or they do adaptivity manually); previously this had resulted in an error since the embedding order was below 1.
CVODE
Corrections were made to three Fortran interface functions.
In FCVODE, fixed argument order bugs in the FCVKLU and FCVSUPERLUMT
linear solver interfaces.
Added missing Fortran interface routines for supplying a sparse Jacobian routine with sparse direct solvers.
CVODES
A bug was fixed in the interpolation functions used in solving backward problems for adjoint sensitivity analysis.
In the interpolation routines for backward problems, added logic to bypass
sensitivity interpolation if input sensitivity argument is NULL.
Changed each the return type of *FreeB functions to int and added
return(0) to each.
IDA
Corrections were made to three Fortran interface functions.
Corrected the output from the idaFoodWeb_bnd.c example, the wrong component
was printed in PrintOutput.
IDAS
In the interpolation routines for backward problems, added logic to bypass
sensitivity interpolation if input sensitivity argument is NULL.
Changed each the return type of *FreeB functions to int and added
return(0) to each.
Corrections were made to three Fortran interface functions.
Added missing Fortran interface routines for supplying a sparse Jacobian routine with sparse direct solvers.
KINSOL
The Picard iteration return was changed to always return the newest iterate upon success.
A minor bug in the line search was fixed to prevent an infinite loop when the beta condition fails and lambda is below the minimum size.
Corrections were made to three Fortran interface functions.
The functions FKINCREATE and FKININIT were added to split the
FKINMALLOC routine into two pieces. FKINMALLOC remains for backward
compatibility, but documentation for it has been removed.
Added missing Fortran interface routines for supplying a sparse Jacobian routine with sparse direct solvers.
Matlab Interfaces Removed
Removed the Matlab interface from distribution as it has not been updated since 2009.
15.39. Changes to SUNDIALS in release 2.6.2
New Features and Enhancements
Various minor fixes to installation-related files
In KINSOL and ARKODE, updated the Anderson acceleration implementation with QR updating.
In CVODES and IDAS, added ReInit and SetOrdering wrappers for backward
problems.
In IDAS, fixed for-loop bugs in IDAAckpntAllocVectors that could lead to a
memory leak.
Bug Fixes
Updated the BiCGStab linear solver to remove a redundant dot product call.
Fixed potential memory leak in KLU ReInit functions in all solvers.
In ARKODE, fixed a bug in the Cash-Karp Butcher table where the method and embedding coefficient were swapped.
In ARKODE, fixed error in arkDoErrorTest in recovery after failure.
In CVODES, added CVKLUB prototype and corrected CVSuperLUMTB prototype.
In the CVODES and IDAS header files, corrected documentation of backward
integration functions, especially the which argument.
In IDAS, added missing backward problem support functions IDALapackDenseB,
IDALapackDenseFreeB, IDALapackBandB, and IDALapackBandFreeB.
In IDAS, made SuperLUMT call for backward problem consistent with CVODES.
In CVODE, IDA, and ARKODE, fixed Fortran interfaces to enable calls to
GetErrWeights, GetEstLocalErrors, and GetDky within a time step.
15.40. Changes to SUNDIALS in release 2.6.1
Fixed loop limit bug in SlsAddMat function.
In all six solver interfaces to KLU and SuperLUMT, added #include lines, and
removed redundant KLU structure allocations.
Minor bug fixes in ARKODE.
15.41. Changes to SUNDIALS in release 2.6.0
Autotools Build Option Removed
With this version of SUNDIALS, support and documentation of the Autotools mode of installation is being dropped, in favor of the CMake mode, which is considered more widely portable.
New Package: ARKODE
Addition of ARKODE package of explicit, implicit, and additive Runge-Kutta methods for ODEs. This package API is close to CVODE so switching between the two should be straightforward. Thanks go to Daniel Reynolds for the addition of this package.
New Features and Enhancements
Added OpenMP and Pthreads
N_Vector implementations for thread-parallel computing environments.
Two major additions were made to the linear system solvers available in all
packages. First, in the serial case, an interface to the sparse direct solver
KLU was added. Second, an interface to SuperLU_MT, the multi-threaded version
of SuperLU, was added as a thread-parallel sparse direct solver option, to be
used with the serial version of the N_Vector module. As part of these
additions, a sparse matrix (CSC format) structure was added to CVODE.
KINSOL
Two major additions were made to the globalization strategy options (KINSol
argument strategy). One is fixed-point iteration, and the other is Picard
iteration. Both can be accelerated by use of the Anderson acceleration
method. See the relevant paragraphs in Chapter Mathematical Considerations.
An interface to the Flexible GMRES iterative linear solver was added.
Bug Fixes
In order to avoid possible name conflicts, the mathematical macro and function
names MIN, MAX, SQR, RAbs, RSqrt, RExp, RPowerI, and
RPowerR were changed to SUNMIN, SUNMAX, SUNSQR, SUNRabs,
SUNRsqrt, SUNRexp, SRpowerI, and SUNRpowerR, respectively. These
names occur in both the solver and example programs.
In the LAPACK banded linear solver interfaces, the line smu = MIN(N-1,mu+ml)
was changed to smu = mu + ml to correct an illegal input error for to
DGBTRF and DGBTRS.
In all Fortran examples, integer declarations were revised so that those which
must match a C type long int are declared INTEGER*8, and a comment was
added about the type match. All other integer declarations are just
INTEGER. Corresponding minor corrections were made to the user guide.
CVODE and CVODES
In cvRootFind, a minor bug was corrected, where the input array was ignored,
and a line was added to break out of root-search loop if the initial interval
size is below the tolerance ttol.
Two minor bugs were fixed regarding the testing of input on the first call to
CVode – one involving tstop and one involving the initialization of
*tret.
The example program cvAdvDiff_diag_p was added to illustrate the use of in
parallel.
In the FCVODE optional input routines FCVSETIIN and FCVSETRIN, the
optional fourth argument key_length was removed, with hardcoded key string
lengths passed to all tests.
In order to eliminate or minimize the differences between the sources for
private functions in CVODE and CVODES, the names of many private functions were
changed from CV* to cv* and a few other names were also changed.
An option was added in the case of Adjoint Sensitivity Analysis with dense or
banded Jacobian. With a call to CVDlsSetDenseJacFnBS or
CVDlsSetBandJacFnBS, the user can specify a user-supplied Jacobian function
of type CVDls***JacFnBS, for the case where the backward problem depends on
the forward sensitivities.
In CVodeQuadSensInit, the line cv_mem->cv_fQS_data = ... was corrected
(missing Q).
In the CVODES User Guide, a paragraph was added in Section 6.2.1 on
CVodeAdjReInit, and a paragraph was added in Section 6.2.9 on
CVodeGetAdjY. In the example cvsRoberts_ASAi_dns, the output was revised
to include the use of CVodeGetAdjY.
For the Adjoint Sensitivity Analysis case in which the backward problem depends
on the forward sensitivities, options have been added to allow for user-supplied
pset, psolve, and jtimes functions.
In the example cvsHessian_ASA_FSA, an error was corrected in the function
fB2, y2 in place of y3 in the third term of Ith(yBdot,6).
IDA and IDAS
In IDARootfind, a minor bug was corrected, where the input array rootdir
was ignored, and a line was added to break out of root-search loop if the
initial interval size is below the tolerance ttol.
A minor bug was fixed regarding the testing of the input tstop on the first
call to IDASolve().
In the FIDA optional input routines FIDASETIIN, FIDASETRIN, and
FIDASETVIN, the optional fourth argument key_length was removed, with
hardcoded key string lengths passed to all strncmp tests.
An option was added in the case of Adjoint Sensitivity Analysis with dense or
banded Jacobian. With a call to IDADlsSetDenseJacFnBS or
IDADlsSetBandJacFnBS, the user can specify a user-supplied Jacobian function
of type IDADls***JacFnBS, for the case where the backward problem depends on
the forward sensitivities.
KINSOL
In function KINStop, two return values were corrected to make the values of
uu and fval consistent.
A bug involving initialization of mxnewtstep was fixed. The error affects
the case of repeated user calls to KINSol with no intervening call to
KINSetMaxNewtonStep.
A bug in the increments for difference quotient Jacobian approximations was
fixed in function kinDlsBandDQJac.
In the FKINSOL module, an incorrect return value ier in FKINfunc was
fixed.
In the FKINSOL optional input routines FKINSETIIN, FKINSETRIN, and
FKINSETVIN, the optional fourth argument key_length was removed, with
hardcoded key string lengths passed to all strncmp tests.
15.42. Changes to SUNDIALS in release 2.5.0
Integer Type Change
One significant design change was made with this release, the problem size and
its relatives, bandwidth parameters, related internal indices, pivot arrays, and
the optional output lsflag have all been changed from type int to type
long int, except for the problem size and bandwidths in user calls to
routines specifying BLAS/LAPACK routines for the dense/band linear solvers. The
function NewIntArray is replaced by a pair NewIntArray /
NewLintArray, for int and long int arrays, respectively.
Bug Fixes
In the installation files, we modified the treatment of the macro
SUNDIALS_USE_GENERIC_MATH, so that the parameter GENERIC_MATH_LIB is
either defined (with no value) or not defined.
In all packages, after the solver memory is created, it is set to zero before being filled.
In each linear solver interface function, the linear solver memory is freed on
an error return, and the function now includes a line setting to NULL the
main memory pointer to the linear solver memory.
Rootfinding
In CVODE(S) and IDA(S), in the functions Rcheck1 and Rcheck2, when an
exact zero is found, the array glo of \(g\) values at the left endpoint
is adjusted, instead of shifting the \(t\) location tlo slightly.
CVODE and CVODES
In CVSetTqBDF, the logic was changed to avoid a divide by zero.
In a minor change to the CVODES user interface, the type of the index which
was changed from long int to int.
Errors in the logic for the integration of backward problems in CVODES were identified and fixed.
IDA and IDAS
To be consistent with IDAS, IDA uses the function IDAGetDky for optional
output retrieval.
A memory leak was fixed in two of the IDASp***Free functions.
A missing vector pointer setting was added in IDASensLineSrch.
In IDACompleteStep, conditionals around lines loading a new column of three
auxiliary divided difference arrays, for a possible order increase, were fixed.
KINSOL
Three major logic bugs were fixed - involving updating the solution vector, updating the linesearch parameter, and a missing error return.
Three minor errors were fixed - involving setting etachoice in the
Matlab/KINSOL interface, a missing error case in KINPrintInfo, and avoiding
an exponential overflow in the evaluation of omega.
15.43. Changes to SUNDIALS in release 2.4.0
Added a CMake-based build option in addition to the one based on autotools.
The user interface has been further refined. Some of the API changes involve:
a reorganization of all linear solver modules into two families (besides the existing family of scaled preconditioned iterative linear solvers, the direct solvers, including new LAPACK-based ones, were also organized into a direct family);
maintaining a single pointer to user data, optionally specified through a
Set-type function; anda general streamlining of the preconditioner modules distributed with the solvers.
Added interfaces to LAPACK linear solvers for dense and banded matrices to all packages.
An option was added to specify which direction of zero-crossing is to be monitored while performing rootfinding in CVODE(S) and IDA(S).
CVODES includes several new features related to sensitivity analysis, among which are:
support for integration of quadrature equations depending on both the states and forward sensitivity (and thus support for forward sensitivity analysis of quadrature equations),
support for simultaneous integration of multiple backward problems based on the same underlying ODE (e.g., for use in an forward-over-adjoint method for computing second order derivative information),
support for backward integration of ODEs and quadratures depending on both forward states and sensitivities (e.g., for use in computing second-order derivative information), and
support for reinitialization of the adjoint module.
Moreover, the prototypes of all functions related to integration of backward problems were modified to support the simultaneous integration of multiple problems.
All backward problems defined by the user are internally managed through a linked list and identified in the user interface through a unique identifier.
15.44. Changes to SUNDIALS in release 2.3.0
New Features and Enhancements
The main changes in this release involve a rearrangement of the entire
SUNDIALS source tree. At the user interface level, the main impact is in the
mechanism of including SUNDIALS header files which must now include the relative
path e.g., #include <cvode/cvode.h> as all exported header files are now
installed in separate subdirectories of the installation include directory.
The functions in the generic dense linear solver (sundials_dense and
sundials_smalldense) were modified to work for rectangular \(m \times
n\) matrices (\(m \le n\)), while the factorization and solution functions
were renamed to DenseGETRF / denGETRF and DenseGETRS / denGETRS,
respectively. The factorization and solution functions in the generic band
linear solver were renamed BandGBTRF and BandGBTRS, respectively.
In IDA, the user interface to the consistent initial conditions calculations was
modified. The IDACalcIC() arguments t0, yy0, and yp0 were
removed and a new function, IDAGetConsistentIC() is provided.
Bug Fixes
In the CVODES adjoint solver module, the following two bugs were fixed:
In
CVodeFthe solver was sometimes incorrectly taking an additional step before returning control to the user (inCV_NORMALmode) thus leading to a failure in the interpolated output function.In
CVodeB, while searching for the current check point, the solver was sometimes reaching outside the integration interval resulting in a segmentation fault.
In IDA, a bug was fixed in the internal difference-quotient dense and banded Jacobian approximations, related to the estimation of the perturbation (which could have led to a failure of the linear solver when zero components with sufficiently small absolute tolerances were present).
15.45. Changes to SUNDIALS in release 2.2.0
New Header Files Names
To reduce the possibility of conflicts, the names of all header files have been
changed by adding unique prefixes (e.g., cvode_ and sundials_). When
using the default installation procedure, the header files are exported under
various subdirectories of the target include directory. For more details see
Appendix §1.1.
Build System Changes
Updated configure script and Makefiles for Fortran examples to avoid C++
compiler errors (now use CC and MPICC to link only if necessary).
The shared object files are now linked into each SUNDIALS library rater than
into a separate libsundials_shared library.
New Features and Enhancements
Deallocation functions now take the address of the respective memory block pointer as the input argument.
Interfaces to the Scaled Preconditioned Bi-CGstab (SPBCG) and Scaled Preconditioned Transpose-Free Quasi-Minimal Residual (SPTFQMR) linear solver modules have been added to all packages. At the same time, function type names for Scaled Preconditioned Iterative Linear Solvers were added for the user-supplied Jacobian-times-vector and preconditioner setup and solve functions. Additionally, in KINSOL interfaces have been added to the SUNDIALS DENSE, and BAND linear solvers and include support for nonlinear residual monitoring which can be used to control Jacobian updating.
A new interpolation method was added to the CVODES adjoint module. The function
CVadjMalloc has an additional argument which can be used to select the
desired interpolation scheme.
FIDA, a Fortran-C interface module, was added.
The rootfinding feature was added to IDA, whereby the roots of a set of given functions may be computed during the integration of the DAE system.
In IDA a user-callable routine was added to access the estimated local error vector.
In the KINSOL Fortran interface module, FKINSOL, optional inputs are now set
using FKINSETIIN (integer inputs), FKINSETRIN (real inputs), and
FKINSETVIN (vector inputs). Optional outputs are still obtained from the
IOUT and ROUT arrays which are owned by the user and passed as arguments
to FKINMALLOC.
15.46. Changes to SUNDIALS in release 2.1.1
The function N_VCloneEmpty was added to the global vector operations table.
A minor bug was fixed in the interpolation functions of the adjoint CVODES module.
15.47. Changes to SUNDIALS in release 2.1.0
The user interface has been further refined. Several functions used for setting optional inputs were combined into a single one.
In CVODE(S) and IDA, an optional user-supplied routine for setting the error weight vector was added.
Additionally, to resolve potential variable scope issues, all SUNDIALS solvers release user data right after its use.
The build systems has been further improved to make it more robust.
15.48. Changes to SUNDIALS in release 2.0.2
Fixed autoconf-related bug to allow configuration with the PGI Fortran compiler.
Modified the build system to use customized detection of the Fortran name
mangling scheme (autoconf’s AC_F77_WRAPPERS routine is problematic on some
platforms).
A bug was fixed in the CVode function that was potentially leading to
erroneous behavior of the rootfinding procedure on the integration first step.
A new chapter in the User Guide was added - with constants that appear in the user interface.
15.49. Changes to SUNDIALS in release 2.0.1
Build System
Changed the order of compiler directives in header files to avoid compilation errors when using a C++ compiler.
Changed the method of generating sundials_config.h to avoid potential
warnings of redefinition of preprocessor symbols.
New Features
In CVODES the option of activating and deactivating forward sensitivity calculations on successive runs without memory allocation and deallocation.
Bug Fixes
In CVODES bug fixes related to forward sensitivity computations (possible loss of accuracy on a BDF order increase and incorrect logic in testing user-supplied absolute tolerances) were made.
15.50. Changes to SUNDIALS in release 2.0.0
Installation of all of SUNDIALS packages has been completely redesigned and is now based on configure scripts.
The major changes from the previous version involve a redesign of the user
interface across the entire SUNDIALS suite. We have eliminated the mechanism of
providing optional inputs and extracting optional statistics from the solver
through the iopt and ropt arrays. Instead, packages now provide Set
functions to change the default values for various quantities controlling the
solver and Get functions to extract statistics after return from the main
solver routine.
Additionally, the interfaces to several user-supplied routines (such as those
providing Jacobians and preconditioner information) were simplified by reducing
the number of arguments. The same information that was previously accessible
through such arguments can now be obtained through Get-type functions.
In CVODE and CVODES a rootfinding feature was added, whereby the roots of a set of given functions may be computed during the integration of the ODE system.
Changes to the NVector:
Removed
machEnv, redefined table of vector operations (now contained in theN_Vectorstructure itself).All SUNDIALS functions create new
N_Vectorvariables through cloning, using anN_Vectorpassed by the user as a template.A particular vector implementation is supposed to provide user-callable constructor and destructor functions.
Removed the following functions from the structure of vector operations:
N_VNew,N_VNew_S,N_VFree,N_VFree_S,N_VMake,N_VDispose,N_VGetData,N_VSetData,N_VConstrProdPos, andN_VOneMask.Added the following functions to the structure of vector operations:
N_VClone,N_VDestroy,N_VSpace,N_VGetArrayPointer,N_VSetArrayPointer, andN_VWrmsNormMask.Note that
nvec_serandnvec_parare now separate modules outside the shared SUNDIALS module.
Changes to the linear solvers:
In SPGMR, added a dummy
N_Vectorargument to be used as a template for cloning.In SPGMR, removed
N(problem dimension) from the argument list ofSpgmrMalloc.Replaced
iterativ.{c,h}withiterative.{c,h}.Modified constant names in
iterative.h(preconditioner types are prefixed withPREC_).Changed numerical values for
MODIFIED_GS(from0to1) andCLASSICAL_GS(from1to2).
Changes to sundialsmath submodule:
Replaced the internal routine for estimating unit roundoff with definition of unit roundoff from
float.h.Modified functions to call the appropriate math routines given the precision level specified by the user.
Changes to sundialstypes submodule:
Removed
integertype.Added definitions for
BIG_REAL,SMALL_REAL, andUNIT_ROUNDOFFusing values fromfloat.hbased on the precision.Changed definition of macro
RCONSTto depend on the precision level specified by the user.