…CMakeLists.txt

…ders where necessary.

example_utilities.hpp requires `stoi` and similar methods. These are
declared in `<string>`, but `<string>` is not included. This means this
file will break any TU it's included in.

Resolves LLNL#330

Co-authored-by: Cody Balos <[email protected]>

Fixes LLNL#335

Co-authored-by: David Gardner <[email protected]>

…NL#337)

Fixes LLNL#333. Some other typedefs already had specialized (towards idas or
cvodes) prefixed names, it won't harm to generalize this.

---------

Co-authored-by: Cody Balos <[email protected]>

Add scripts for comparing benchmark and example timings against release timings and a notebook using Thicket to visualize data

---------

Co-authored-by: David J. Gardner <[email protected]>
Co-authored-by: Cody J. Balos <[email protected]>

Fixes part of LLNL#253 by avoiding nested loops that take `O(M*N)` operations.

Also fixes LLNL#256.

---------

Signed-off-by: phannebohm <[email protected]>
Co-authored-by: Cody Balos <[email protected]>

Fix missing soversion on some SUNLinSol and SUNNonlinSol targets

---------

Signed-off-by: Julien Schueller <[email protected]>
Co-authored-by: Cody Balos <[email protected]>

1. Adds missing implicit tables to the ARKODE constants docs
2. Makes formatting of constants consistent in ARKODE docs
3. Groups implicit tables by order

---------

Co-authored-by: David Gardner <[email protected]>

Update ARKStepSetTableNum to recognize ARK2-3-1-2 as a valid ARK pair.

Fixes LLNL#339: A regression was introduced by the stop time bug fix in
v6.6.1 causing integrators to 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.

Also fixes a missing check in ARKODE to interpolate (or not) the
solution at the stop time.

Fix CVodeQuadSStolerances docs, add CVodeQuadSVtolerances docs (Fixes LLNL#340)

Only adding the `Sofroniou-Spaletta-5-3-4` method but not changing the
defaults like LLNL#345

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>
Co-authored-by: David Gardner <[email protected]>

This PR adds the ginkgo dpcpp support in the examples: sunmatrix,
sunlinsol, and cvode/cv_heat2D

I currently only know `queue->wait_and_throw()` to synchronize which
requires queue unlike `cudaDeviceSynchronize` or `hipDeviceSynchronize`
In sunlinsol and cv_heat2D, some function signatures are also used in
other files such that I can not pass an additional parameter.
I use global variable to store ginkgo executor and then get the queue
when SYCL needs sync or submit the kernel in those functions.

---------

Signed-off-by: Yu-Hsiang M. Tsai <[email protected]>
Co-authored-by: Cody Balos <[email protected]>

Always append hipblas and hipsparse CMake targets with HIP backend as these
libraries are not reliably included in the pkgconfig file.

Replace cublas and cusparse with the CMake targets because the library path in
the pkgconfig file is not reliable. Specifically, the path is wrong on systems
using the NVIDIA HPC SDK.

---------

Co-authored-by: David Gardner <[email protected]>

Added Fortran support for the LAPACK dense SUNLinearSolver implementation.

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>

 Additional embedded explicit Runge--Kutta
methods to ARKODE.

---------

Co-authored-by: Steven Roberts <[email protected]>
Co-authored-by: David J. Gardner <[email protected]>

Updated `SUNProfiler` to note rely on `MPI_WTime`. Fixes LLNL#312 

---------

Co-authored-by: David Gardner <[email protected]>

Fix the description of `ONE_STEP` mode in ARKODE. The solution at the
end of the step is always returned and interpolation is not performed.

Upload artifact with just output files so the artifact is smaller

---------

Co-authored-by: David Gardner <[email protected]>

Remove unused files from the repo

* Cancel existing workflow on new push
* Add dispatch trigger for all actions
* Upload all outputs from testing directory

---------

Co-authored-by: Cody Balos <[email protected]>

Remove F77 interface examples from `develop` branch. Once this PR is
merged, a new `archive` branch can be created for easy reference until
LLNL#302 is merged and the `archive` branch can be deleted.

---------

Co-authored-by: Cody Balos <[email protected]>

Simplify tarscript to include directories rather than individual files

---------

Co-authored-by: Cody Balos <[email protected]>

Fixed a bug in ERKStep where methods with `c[s-1] = 1` but `a[s-1,j] !=
b[j]` were incorrectly treated as having the first same as last (FSAL)
property.

Fixed a bug in `MRIStepCoupling_Write` where explicit coupling tables
were not written to the output file pointer.

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.

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>
Co-authored-by: Cody Balos <[email protected]>

New object-oriented infrastructure for time step adaptivity controllers.

---------

Co-authored-by: David J. Gardner <[email protected]>
Co-authored-by: Balos, Cody, J <[email protected]>
Co-authored-by: Cody Balos <[email protected]>

Add developer docs to RTD superbuild
Add instructions for updating answers in the developer docs.

---------

Co-authored-by: David Gardner <[email protected]>

Remove deprecated functions

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>

Remove `realtype`, `booleantype`, and related deprecated macros.

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>
Co-authored-by: Steven Roberts <[email protected]>
Co-authored-by: David J. Gardner <[email protected]>

Fix table name for the implicit part of 5th order IMEX-ARK methods

Add graphviz to Read the Docs config to display graphviz figures

… same example with different arguments

Addresses LLNL#275. Requires MPI to be linked to SUNDIALS core if it is enabled thus all-in-one MPI and non-MPI builds are no longer supported. Instead user will have to separately build and install with and without MPI.

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>
Co-authored-by: Steven Roberts <[email protected]>
Co-authored-by: David J. Gardner <[email protected]>

…ns build)

…r arrays

…f2003-examples into feature/f2003-examples

…ed CMakeLists.txt accordingly

Add core error handling functions and macros 

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>
Co-authored-by: David J. Gardner <[email protected]>

Apply clang-format and clang-tidy. There are changes/additions
in the following files:

- .clang-format
- .clang-tidy
- .github/actions/free-space-ubuntu/action.yml
- .github/workflows/build-llvm-container.yml
- .github/workflows/check-clang-format.yml
- cmake/SundialsSetupCompilers.cmake
- scripts/format.sh
- scripts/tidy_and_format.sh

---------

Co-authored-by: Daniel R. Reynolds <[email protected]>
Co-authored-by: David J. Gardner <[email protected]>

…e the new F2003 examples

…f2003-examples into feature/f2003-examples