Merge branch 'develop' into feature/remove-deprecated-code

LLNL · Nov 6, 2023 · 7f6f328 · 7f6f328
2 parents 2b39a12 + 9b01e93
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diff --git a/.github/workflows/double-precision.yml b/.github/workflows/double-precision.yml
@@ -4,6 +4,12 @@ name: double precision build and test with GCC+TPLs (no GPUs)
 on:
   push:
   pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build_and_test:
@@ -26,17 +32,17 @@ jobs:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
       - name: Archive build files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
             !${{ github.workspace }}/test/build_*/Testing/output
       - name: Archive output files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: output_files
           path: |
-            ${{ github.workspace }}/test/build_*/Testing/output
+            ${{ github.workspace }}/test/build_*/Testing/
diff --git a/.github/workflows/extended-precision.yml b/.github/workflows/extended-precision.yml
@@ -3,6 +3,12 @@ name: extended precision build and test with GCC+TPLs (no GPUs)
 
 on:
   pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build_and_test:
@@ -25,17 +31,17 @@ jobs:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
       - name: Archive build files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
             !${{ github.workspace }}/test/build_*/Testing/output
       - name: Archive output files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: output_files
           path: |
-            ${{ github.workspace }}/test/build_*/Testing/output
+            ${{ github.workspace }}/test/build_*/Testing/
diff --git a/.github/workflows/macos-latest.yml b/.github/workflows/macos-latest.yml
@@ -2,6 +2,12 @@ name: MacOS short test
 
 on:
   pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)

diff --git a/.github/workflows/single-precision.yml b/.github/workflows/single-precision.yml
@@ -3,6 +3,12 @@ name: single precision build and test with GCC+TPLs (no GPUs)
 
 on:
   pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build_and_test:
@@ -25,17 +31,17 @@ jobs:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
       - name: Archive build files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
             !${{ github.workspace }}/test/build_*/Testing/output
       - name: Archive output files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: output_files
           path: |
-            ${{ github.workspace }}/test/build_*/Testing/output
+            ${{ github.workspace }}/test/build_*/Testing/
diff --git a/.github/workflows/spack-develop.yml b/.github/workflows/spack-develop.yml
@@ -3,10 +3,15 @@ name: spack@develop build and test with GCC+TPLs (no GPUs)
 
 on:
   pull_request:
+  merge_group:
   workflow_dispatch:
   schedule:
   - cron: '00 22 * * *'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build_and_test:
     runs-on: ubuntu-latest
@@ -28,17 +33,17 @@ jobs:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
       - name: Archive build files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
             !${{ github.workspace }}/test/build_*/Testing/output
       - name: Archive output files from failed build
-        uses: actions/upload-artifact@v2.2.4
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: output_files
           path: |
-            ${{ github.workspace }}/test/build_*/Testing/output
+            ${{ github.workspace }}/test/build_*/Testing/
diff --git a/.github/workflows/ubuntu-clang-latest.yml b/.github/workflows/ubuntu-clang-latest.yml
@@ -2,6 +2,12 @@ name: Ubuntu (clang) short test
 
 on:
   pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)

diff --git a/.github/workflows/windows-latest-mingw.yml b/.github/workflows/windows-latest-mingw.yml
@@ -2,6 +2,12 @@ name: Windows (mingw) short test
 
 on:
   pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)

diff --git a/.github/workflows/windows-latest.yml b/.github/workflows/windows-latest.yml
@@ -2,6 +2,12 @@ name: Windows short test
 
 on:
   pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)

diff --git a/doc/arkode/examples/source/index.rst b/doc/arkode/examples/source/index.rst
@@ -45,7 +45,7 @@ B598130 from `Lawrence Livermore National Laboratory
 
 Along with the ARKode solver, we have created a suite of example
 problems demonstrating its usage on applications written in C, C++ and
-Fortran 77 and Fortran 90.  These examples demonstrate a large variety
+Fortran.  These examples demonstrate a large variety
 of ARKode solver options, including explicit, implicit and ImEx
 solvers, root-finding, Newton and fixed-point nonlinear solvers,
 direct and iterative linear solvers, adaptive resize capabilities, and
@@ -60,8 +60,7 @@ The following tables summarize the salient features of each of the
 example problems in this document.  Each example is designed to be
 relatively self-contained, so that you need only study and/or emulate
 the problem that is most closely related to your own.  We group these
-examples according to programming language (C, C++, Fortran 77,
-Fortran 90). 
+examples according to programming language (C, C++, Fortran).
 
 
 ARKode example problems written in C are summarized in the table
@@ -106,35 +105,36 @@ Problem                  Integrator  Nonlinear    Linear  Size           Extras
 =======================  ==========  ===========  ======  =============  =================================
 
 
-ARKode example problems written in Fortran 77 are summarized in the table
-below, and are further described in the chapters :ref:`serial_f77` and
-:ref:`parallel_f77`. 
+..
+   ARKode example problems written in Fortran 77 are summarized in the table
+   below, and are further described in the chapters :ref:`serial_f77` and
+   :ref:`parallel_f77`.
 
-.. cssclass:: table-bordered
+   .. cssclass:: table-bordered
 
-==========================   ==========  ===========  ======  =============  =================================
-Problem                      Integrator  Nonlinear    Linear  Size           Extras
-==========================   ==========  ===========  ======  =============  =================================
-:ref:`fark_diurnal_kry_bp`   DIRK        Newton       SPGMR   10             banded preconditioner
-:ref:`fark_roberts_dnsL`     DIRK        Newton       Dense   3              LAPACK dense solver, rootfinding
-:ref:`fark_diag_kry_bbd_p`   DIRK        Newton       SPGMR   10*NProcs      parallel BBD preconditioner
-:ref:`fark_diag_non_p`       ERK         N.A.         N.A.    10*NProcs      parallel
-==========================   ==========  ===========  ======  =============  =================================
+   ==========================   ==========  ===========  ======  =============  =================================
+   Problem                      Integrator  Nonlinear    Linear  Size           Extras
+   ==========================   ==========  ===========  ======  =============  =================================
+   :ref:`fark_diurnal_kry_bp`   DIRK        Newton       SPGMR   10             banded preconditioner
+   :ref:`fark_roberts_dnsL`     DIRK        Newton       Dense   3              LAPACK dense solver, rootfinding
+   :ref:`fark_diag_kry_bbd_p`   DIRK        Newton       SPGMR   10*NProcs      parallel BBD preconditioner
+   :ref:`fark_diag_non_p`       ERK         N.A.         N.A.    10*NProcs      parallel
+   ==========================   ==========  ===========  ======  =============  =================================
 
 
-ARKode example problems written in Fortran 90 are summarized in the table
-below, and are further described in the chapters :ref:`serial_f90` and
-:ref:`parallel_f90`. 
+   ARKode example problems written in Fortran 90 are summarized in the table
+   below, and are further described in the chapters :ref:`serial_f90` and
+   :ref:`parallel_f90`.
 
-.. cssclass:: table-bordered
+   .. cssclass:: table-bordered
 
-==========================  ==========  =========  ======  =============  ===============================================
-Problem                     Integrator  Nonlinear  Linear  Size           Extras
-==========================  ==========  =========  ======  =============  ===============================================
-:ref:`ark_bruss`            ARK         Newton     Dense   3              
-:ref:`ark_bruss1D_FEM_klu`  DIRK        Newton     KLU     3N             finite-element, :math:`M\ne I`, sparse matrices
-:ref:`fark_heat2D`          DIRK        Newton     PCG     :math:`nx*ny`  parallel
-==========================  ==========  =========  ======  =============  ===============================================
+   ==========================  ==========  =========  ======  =============  ===============================================
+   Problem                     Integrator  Nonlinear  Linear  Size           Extras
+   ==========================  ==========  =========  ======  =============  ===============================================
+   :ref:`ark_bruss`            ARK         Newton     Dense   3
+   :ref:`ark_bruss1D_FEM_klu`  DIRK        Newton     KLU     3N             finite-element, :math:`M\ne I`, sparse matrices
+   :ref:`fark_heat2D`          DIRK        Newton     PCG     :math:`nx*ny`  parallel
+   ==========================  ==========  =========  ======  =============  ===============================================
 
 
 
@@ -154,14 +154,14 @@ Problem                     Integrator  Nonlinear  Linear  Size           Extras
    c_parhyp
    cpp_serial
    cpp_parallel
-   f77_serial
-   f77_parallel
-   f90_serial
-   f90_parallel
-   References           
-
+   References
+..
+  Remove F77 interface examples
+  f77_serial
+  f77_parallel
+  f90_serial
+  f90_parallel
+
 .. only:: html
 
    * :ref:`search`
-
-
diff --git a/doc/cvode/Makefile b/doc/cvode/Makefile
@@ -22,7 +22,9 @@ cv_ex_intro.tex \
 cv_ex_serial.tex \
 cv_ex_parallel.tex \
 cv_ex_parhyp.tex \
-cv_ex_fortran.tex \
 cv_ex_tests.tex
 
+# Remove F77 example text
+# cv_ex_fortran.tex \
+
 include ../Makefile.in
diff --git a/doc/cvode/cv_ex_codes.tex b/doc/cvode/cv_ex_codes.tex
@@ -30,14 +30,12 @@ \section{Listing of cvDiurnal\_kry\_bbd\_p.c}\label{s:cvDiurnal_bbd_p_c}
 
 %% Fortran examples
 
-\lstset{language=[77]Fortran}
-
-\newpage
-\section{Listing of fcvDiurnal\_kry.f}\label{s:fcvDiurnal_f}
-\includeCode{../../examples/cvode/fcmix_serial/fcvDiurnal_kry.f}
-
-\newpage
-\section{Listing of fcvDiag\_kry\_bbd\_p.f}\label{s:fcvDiag_bbd_p_f}
-\includeCode{../../examples/cvode/fcmix_parallel/fcvDiag_kry_bbd_p.f}
+%% \lstset{language=[77]Fortran}
 
+%% \newpage
+%% \section{Listing of fcvDiurnal\_kry.f}\label{s:fcvDiurnal_f}
+%% \includeCode{../../examples/cvode/fcmix_serial/fcvDiurnal_kry.f}
 
+%% \newpage
+%% \section{Listing of fcvDiag\_kry\_bbd\_p.f}\label{s:fcvDiag_bbd_p_f}
+%% \includeCode{../../examples/cvode/fcmix_parallel/fcvDiag_kry_bbd_p.f}
diff --git a/doc/cvode/cv_ex_intro.tex b/doc/cvode/cv_ex_intro.tex
@@ -7,9 +7,9 @@ \section{Introduction}\label{s:ex_intro}
 listings, on the example programs supplied with the {\cvode} distribution
 package.
 
-The {\cvode} distribution contains examples of six types: serial
-{\CC} examples, parallel {\CC} examples, serial and parallel {\F}
-examples, an OpenMP example, and a {\hypre} example.
+The {\cvode} distribution contains examples of the following types: serial
+{\CC} examples, parallel {\CC} examples, an OpenMP example, and a {\hypre}
+example.
 %%
 With the exception of ''demo''-type example files, the names of all the examples
 distributed with {\sundials} are of the form \verb![slv][PbName]_[ls]_[prec]_[p]!,
@@ -159,28 +159,28 @@ \section{Introduction}\label{s:ex_intro}
 \id{cvAdvDiff\_non\_p} but with {\hypre} vectors instead of
 {\sundials} parallel vectors.
 
-\vspace{0.2in}\noindent
-As part of the {\fcvode} module, in the directories
-{\em srcdir}\id{/examples/cvode/fcmix\_serial} and
-{\em srcdir}\id{/examples/cvode/fcmix\_parallel}, are the following examples for
-the {\F}-{\CC} interface.  The first five of these are serial, while
-the last three are parallel.
-\begin{itemize}
-\item \id{fcvRoberts\_dns} is a serial chemical kinetics example (\id{BDF}/{\sunlinsoldense})
-  with rootfinding.
-\item \id{fcvRoberts\_dns\_constraints} is the same as \id{fcvRoberts\_dns} but
-  but imposes the constraint $u \geq 0.0$ for all components.
-\item \id{fcvRoberts\_dnsL} is the same as \id{fcvRoberts\_dns} but uses the Lapack
-  implementation of {\sunlinsollapdense}.
-\item \id{fcvAdvDiff\_bnd} is a serial advection-diffusion example (\id{BDF}/{\sunlinsolband}).
-\item \id{fcvDiurnal\_kry} is a serial kinetics-transport example (\id{BDF}/{\sunlinsolspgmr}).
-\item \id{fcvDiurnal\_kry\_bp} is the \id{fcvDiurnal\_kry} example with {\fcvbp}.
-\item \id{fcvDiag\_non\_p} is a nonstiff parallel diagonal ODE example
-  (\id{ADAMS}/\id{FIXEDPOINT}).
-\item \id{fcvDiag\_kry\_p} is a stiff parallel diagonal ODE example (\id{BDF}/{\sunlinsolspgmr}).
-\item \id{fcvDiag\_kry\_bbd\_p} is the same as the \id{fcvDiag\_kry\_p} example
-       but using the {\fcvbbd} module.
-\end{itemize}
+%% \vspace{0.2in}\noindent
+%% As part of the {\fcvode} module, in the directories
+%% {\em srcdir}\id{/examples/cvode/fcmix\_serial} and
+%% {\em srcdir}\id{/examples/cvode/fcmix\_parallel}, are the following examples for
+%% the {\F}-{\CC} interface.  The first five of these are serial, while
+%% the last three are parallel.
+%% \begin{itemize}
+%% \item \id{fcvRoberts\_dns} is a serial chemical kinetics example (\id{BDF}/{\sunlinsoldense})
+%%   with rootfinding.
+%% \item \id{fcvRoberts\_dns\_constraints} is the same as \id{fcvRoberts\_dns} but
+%%   but imposes the constraint $u \geq 0.0$ for all components.
+%% \item \id{fcvRoberts\_dnsL} is the same as \id{fcvRoberts\_dns} but uses the Lapack
+%%   implementation of {\sunlinsollapdense}.
+%% \item \id{fcvAdvDiff\_bnd} is a serial advection-diffusion example (\id{BDF}/{\sunlinsolband}).
+%% \item \id{fcvDiurnal\_kry} is a serial kinetics-transport example (\id{BDF}/{\sunlinsolspgmr}).
+%% \item \id{fcvDiurnal\_kry\_bp} is the \id{fcvDiurnal\_kry} example with {\fcvbp}.
+%% \item \id{fcvDiag\_non\_p} is a nonstiff parallel diagonal ODE example
+%%   (\id{ADAMS}/\id{FIXEDPOINT}).
+%% \item \id{fcvDiag\_kry\_p} is a stiff parallel diagonal ODE example (\id{BDF}/{\sunlinsolspgmr}).
+%% \item \id{fcvDiag\_kry\_bbd\_p} is the same as the \id{fcvDiag\_kry\_p} example
+%%        but using the {\fcvbbd} module.
+%% \end{itemize}
 
 \vspace{0.2in}\noindent
 In the following sections, we give detailed descriptions of some (but