Merge branch 'develop' into maintenance/copyright

.github/workflows/check-swig.yml

@@ -15,6 +15,10 @@ jobs:
     if: ${{ github.event_name != 'issue_comment' || (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
     runs-on: ubuntu-latest
     steps:
+      - name: Install pcre
+        run: |
+          sudo apt install libpcre3-dev
+
       - name: Install swig
         run: |
           git clone https://github.com/sundials-codes/swig

.github/workflows/ubuntu-clang-latest.yml

@@ -26,11 +26,6 @@ jobs:
         logging_level: [0, 1, 2, 3, 4, 5]
 
     steps:
-    - name: Install LLVM and Clang
-      uses: KyleMayes/install-llvm-action@v2
-      with:
-        version: "14.0"
-
     - uses: actions/checkout@v4
 
     - name: Configure CMake
@@ -70,11 +65,6 @@ jobs:
         profiling: ['OFF', 'ON']
 
     steps:
-    - name: Install LLVM and Clang
-      uses: KyleMayes/install-llvm-action@v2
-      with:
-        version: "14.0"
-
     - uses: actions/checkout@v4
 
     - name: Configure CMake

CHANGELOG.md

@@ -8,13 +8,17 @@
 
 ### Bug Fixes
 
+Fixed bug in the ARKODE SPRKStep `SPRKStepReInit` function and `ARKodeReset` function
+with SPRKStep that could cause a segmentation fault when compensated summation is not
+used.
+
 ### Deprecation Notices
 
 ## Changes to SUNDIALS in release 7.2.1
 
 ### New Features and Enhancements
 
-Unit tests were separated from examples. To that end, the following directories 
+Unit tests were separated from examples. To that end, the following directories
 were moved out of the `examples/` directory to the `test/unit_tests` directory:
 `nvector`, `sunmatrix`, `sunlinsol`, and `sunnonlinsol`.
 

doc/arkode/guide/source/Mathematics.rst

@@ -978,7 +978,7 @@ arise from the **separable** Hamiltonian system
 where
 
 .. math::
-   f_1(t, q) \equiv \frac{\partial V(t, q)}{\partial q}, \qquad
+   f_1(t, q) \equiv -\frac{\partial V(t, q)}{\partial q}, \qquad
    f_2(t, p) \equiv \frac{\partial T(t, p)}{\partial p}.
 
 When *H* is autonomous, then *H* is a conserved quantity. Often this corresponds

doc/arkode/guide/source/Usage/SPRKStep/User_callable.rst

@@ -48,7 +48,7 @@ SPRKStep initialization and deallocation functions
    This function allocates and initializes memory for a problem to
    be solved using the SPRKStep time-stepping module in ARKODE.
 
-   :param f1: the name of the C function (of type :c:func:`ARKRhsFn()`) defining :math:`f_1(t,q) = \frac{\partial V(t,q)}{\partial q}`
+   :param f1: the name of the C function (of type :c:func:`ARKRhsFn()`) defining :math:`f_1(t,q) = -\frac{\partial V(t,q)}{\partial q}`
    :param f2: the name of the C function (of type :c:func:`ARKRhsFn()`) defining :math:`f_2(t,p) = \frac{\partial T(t,p)}{\partial p}`
    :param t0: the initial value of :math:`t`
    :param y0: the initial condition vector :math:`y(t_0)`

doc/shared/RecentChanges.rst

@@ -4,4 +4,8 @@
 
 **Bug Fixes**
 
+Fixed bug in the ARKODE SPRKStep :c:func:`SPRKStepReInit` function and
+:c:func:`ARKodeReset` function with SPRKStep that could cause a segmentation
+fault when compensated summation is not used.
+
 **Deprecation Notices**

src/arkode/arkode_sprkstep.c

@@ -232,7 +232,7 @@ int SPRKStepReInit(void* arkode_mem, ARKRhsFn f1, ARKRhsFn f2, sunrealtype t0,
   step_mem->istage = 0;
 
   /* Zero yerr for compensated summation */
-  N_VConst(ZERO, step_mem->yerr);
+  if (ark_mem->use_compensated_sums) { N_VConst(ZERO, step_mem->yerr); }
 
   return (ARK_SUCCESS);
 }
@@ -309,7 +309,10 @@ int sprkStep_Reset(ARKodeMem ark_mem, SUNDIALS_MAYBE_UNUSED sunrealtype tR,
   retval = sprkStep_AccessStepMem(ark_mem, __func__, &step_mem);
   if (retval != ARK_SUCCESS) { return (retval); }
 
-  N_VConst(SUN_RCONST(0.0), step_mem->yerr);
+  if (ark_mem->use_compensated_sums)
+  {
+    N_VConst(SUN_RCONST(0.0), step_mem->yerr);
+  }
   return (ARK_SUCCESS);
 }
 

test/unit_tests/arkode/C_serial/ark_test_forcingstep.c

@@ -41,9 +41,9 @@ static int f_forward_2(sunrealtype t, N_Vector y, N_Vector ydot, void* user_data
 }
 
 /* Integrates the ODE
- * 
+ *
  * y' = [t / y] + [1 / y]
- * 
+ *
  * with initial condition y(0) = 1 and partitioning specified by the square
  * brackets. We integrate to t = 1 and check the error against the exact
  * solution y(t) = |t + 1|.
@@ -121,10 +121,10 @@ static int f_mixed_direction_2(sunrealtype t, N_Vector z, N_Vector zdot,
 }
 
 /* Integrates the ODE
- * 
+ *
  * y_1' = y_2 - t
  * y_2' = t - y_1
- * 
+ *
  * with initial condition y(0) = [1, 1]^T backward in time to t = -1, then
  * forward to t = 0.4, and backward to t = 0. We apply a splitting method using
  * a component partitioning and check that the numerical solution is close to
@@ -198,9 +198,9 @@ static int test_mixed_directions(SUNContext ctx)
 }
 
 /* Integrates the ODE
- * 
+ *
  * y' = [t / y] + [1 / y]
- * 
+ *
  * with initial condition y(0) = 1 and partitioning specified by the square
  * brackets. We integrate to t = 1 then reinitialize the forcing method by
  * swapping the SUNSteppers and updating the initial condition to y(1) = -1.
@@ -269,7 +269,7 @@ static int test_reinit(SUNContext ctx)
   return fail;
 }
 
-int main()
+int main(void)
 {
   SUNContext ctx = NULL;
   SUNErrCode err = SUNContext_Create(SUN_COMM_NULL, &ctx);