Fix minor HYPRE and ADIOS2 compilation issues

.github/workflows/tests.yml

@@ -47,9 +47,10 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DBOUT_USE_ADIOS2=ON
                             -DBOUT_ENABLE_PYTHON=ON
-                            -DADIOS2_ROOT=/home/runner/local/adios2
+                            -DADIOS2_ROOT=/home/runner/local
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
@@ -74,6 +75,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
@@ -86,6 +88,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
@@ -97,6 +100,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DBOUT_BUILD_DOCS=OFF
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -110,6 +114,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -123,6 +128,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
@@ -178,6 +184,7 @@ jobs:
                  slepc-dev
                  liblapack-dev
                  libparpack2-dev
+                 libhypre-dev
 
       - uses: actions/checkout@v4
         with:

cmake/FindHYPRE.cmake

@@ -7,14 +7,15 @@ include(FindPackageHandleStandardArgs)
 
 find_package(HYPRE CONFIG QUIET)
 if (HYPRE_FOUND)
+  message(STATUS "Found HYPRE: ${HYPRE_VERSION}")
   return()
 endif()
 
 find_path(HYPRE_INCLUDE_DIR
   NAMES HYPRE.h
   DOC "HYPRE include directories"
   REQUIRED
-  PATH_SUFFIXES include
+  PATH_SUFFIXES include include/hypre
 )
 
 find_library(HYPRE_LIBRARY

cmake/SetupBOUTThirdParty.cmake

@@ -190,7 +190,7 @@ endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
 
-option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" ON)
+option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" OFF)
 option(BOUT_DOWNLOAD_ADIOS2 "Download and build ADIOS2" OFF)
 if (BOUT_USE_ADIOS2)
   if (BOUT_DOWNLOAD_ADIOS2)
@@ -214,14 +214,10 @@ if (BOUT_USE_ADIOS2)
     target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi)
     message(STATUS "ADIOS2 done configuring")
   else()
-    find_package(ADIOS2)
-    if (ADIOS2_FOUND)
-      ENABLE_LANGUAGE(C)
-      find_package(MPI REQUIRED COMPONENTS C)
-      target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
-    else()
-      set(BOUT_USE_ADIOS2 OFF)
-    endif()
+    find_package(ADIOS2 REQUIRED)
+    enable_language(C)
+    find_package(MPI REQUIRED COMPONENTS C)
+    target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
   endif()
 endif()
 message(STATUS "ADIOS2 support: ${BOUT_USE_ADIOS2}")

include/bout/field3d.hxx

@@ -569,7 +569,7 @@ void checkData(const Field3D& f, const std::string& region = "RGN_NOBNDRY");
 /// Ignored with disabled CHECK; Throw an exception if \p f is not
 /// allocated or if any elements are non-finite (for CHECK > 2)
 inline void checkData(const Field3D& UNUSED(f),
-                      const std::string& UNUSED(region) = "RGN_NOBNDRY") {};
+                      const std::string& UNUSED(region) = "RGN_NOBNDRY"){};
 #endif
 
 /// Fourier filtering, removes all except one mode

include/bout/utils.hxx

@@ -45,8 +45,8 @@
 #include <list>
 #include <memory>
 #include <set>
-#include <string>
 #include <sstream>
+#include <string>
 
 #ifdef _MSC_VER
 // finite is not actually standard C++, it's a BSD extention for C
@@ -544,7 +544,7 @@ inline void checkData(BoutReal f) {
 }
 #else
 /// Ignored with disabled CHECK; Throw an exception if \p f is not finite
-inline void checkData(BoutReal UNUSED(f)) {};
+inline void checkData(BoutReal UNUSED(f)){};
 #endif
 
 /*!

src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx

@@ -71,23 +71,23 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
 
   // Checking flags are set to something which is not implemented
   // This is done binary (which is possible as each flag is a power of 2)
-  if (global_flags & ~implemented_flags) {
+  if (isGlobalFlagSet(~implemented_flags)) {
     throw BoutException("Attempted to set Laplacian inversion flag that is not "
                         "implemented in LaplaceHypre3d");
   }
-  if (inner_boundary_flags & ~implemented_boundary_flags) {
+  if (isInnerBoundaryFlagSet(~implemented_boundary_flags)) {
     throw BoutException("Attempted to set Laplacian inversion boundary flag that is not "
                         "implemented in LaplaceHypre3d");
   }
-  if (outer_boundary_flags & ~implemented_boundary_flags) {
+  if (isOuterBoundaryFlagSet(~implemented_boundary_flags)) {
     throw BoutException("Attempted to set Laplacian inversion boundary flag that is not "
                         "implemented in LaplaceHypre3d");
   }
-  if (lower_boundary_flags & ~implemented_boundary_flags) {
+  if ((lower_boundary_flags & ~implemented_boundary_flags) != 0) {
     throw BoutException("Attempted to set Laplacian inversion boundary flag that is not "
                         "implemented in LaplaceHypre3d");
   }
-  if (upper_boundary_flags & ~implemented_boundary_flags) {
+  if ((upper_boundary_flags & ~implemented_boundary_flags) != 0) {
     throw BoutException("Attempted to set Laplacian inversion boundary flag that is not "
                         "implemented in LaplaceHypre3d");
   }
@@ -123,7 +123,7 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   }
 
   BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) {
-    if (lower_boundary_flags & INVERT_AC_GRAD) {
+    if ((lower_boundary_flags & INVERT_AC_GRAD) != 0) {
       // Neumann on lower Y boundary
       operator3D(i, i) = -1. / coords->dy[i] / sqrt(coords->g_22[i]);
       operator3D(i, i.yp()) = 1. / coords->dy[i] / sqrt(coords->g_22[i]);
@@ -135,7 +135,7 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   }
 
   BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) {
-    if (upper_boundary_flags & INVERT_AC_GRAD) {
+    if ((upper_boundary_flags & INVERT_AC_GRAD) != 0) {
       // Neumann on upper Y boundary
       operator3D(i, i) = 1. / coords->dy[i] / sqrt(coords->g_22[i]);
       operator3D(i, i.ym()) = -1. / coords->dy[i] / sqrt(coords->g_22[i]);
@@ -200,19 +200,19 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) {
   }
 
   BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) {
-    const BoutReal val = (lower_boundary_flags & INVERT_SET) ? x0[i] : 0.;
+    const BoutReal val = ((lower_boundary_flags & INVERT_SET) != 0) ? x0[i] : 0.;
     ASSERT1(std::isfinite(val));
-    if (!(lower_boundary_flags & INVERT_RHS)) {
+    if ((lower_boundary_flags & INVERT_RHS) == 0) {
       b[i] = val;
     } else {
       ASSERT1(std::isfinite(b[i]));
     }
   }
 
   BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) {
-    const BoutReal val = (upper_boundary_flags & INVERT_SET) ? x0[i] : 0.;
+    const BoutReal val = ((upper_boundary_flags & INVERT_SET) != 0) ? x0[i] : 0.;
     ASSERT1(std::isfinite(val));
-    if (!(upper_boundary_flags & INVERT_RHS)) {
+    if ((upper_boundary_flags & INVERT_RHS) == 0) {
       b[i] = val;
     } else {
       ASSERT1(std::isfinite(b[i]));
@@ -277,7 +277,7 @@ void LaplaceHypre3d::updateMatrix3D() {
   const Field3D dc_dx = issetC ? DDX(C2) : Field3D();
   const Field3D dc_dy = issetC ? DDY(C2) : Field3D();
   const Field3D dc_dz = issetC ? DDZ(C2) : Field3D();
-  const Field2D dJ_dy = DDY(coords->J / coords->g_22);
+  const auto dJ_dy = DDY(coords->J / coords->g_22);
 
   // Set up the matrix for the internal points on the grid.
   // Boundary conditions were set in the constructor.
@@ -286,7 +286,8 @@ void LaplaceHypre3d::updateMatrix3D() {
     // avoid confusing it with the x-index.
 
     // Calculate coefficients for the terms in the differential operator
-    BoutReal C_df_dx = coords->G1[l], C_df_dz = coords->G3[l];
+    BoutReal C_df_dx = coords->G1[l];
+    BoutReal C_df_dz = coords->G3[l];
     if (issetD) {
       C_df_dx *= D[l];
       C_df_dz *= D[l];
@@ -304,9 +305,9 @@ void LaplaceHypre3d::updateMatrix3D() {
       C_df_dz += Ez[l];
     }
 
-    BoutReal C_d2f_dx2 = coords->g11[l],
-             C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]),
-             C_d2f_dz2 = coords->g33[l];
+    BoutReal C_d2f_dx2 = coords->g11[l];
+    BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]);
+    BoutReal C_d2f_dz2 = coords->g33[l];
     if (issetD) {
       C_d2f_dx2 *= D[l];
       C_d2f_dy2 *= D[l];
@@ -343,8 +344,8 @@ void LaplaceHypre3d::updateMatrix3D() {
     // The values stored in the y-boundary are already interpolated
     // up/down, so we don't want the matrix to do any such
     // interpolation there.
-    const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0,
-              ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0;
+    const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0;
+    const int ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0;
     operator3D.yup(yup)(l, l.yp()) = 0.0;
     operator3D.ydown(ydown)(l, l.ym()) = 0.0;
     operator3D.yup(yup)(l, l.xp().yp()) = 0.0;
@@ -376,7 +377,8 @@ void LaplaceHypre3d::updateMatrix3D() {
       C_d2f_dy2 *= D[l];
     }
 
-    BoutReal C_d2f_dxdy = 2 * coords->g12[l], C_d2f_dydz = 2 * coords->g23[l];
+    BoutReal C_d2f_dxdy = 2 * coords->g12[l];
+    BoutReal C_d2f_dydz = 2 * coords->g23[l];
     if (issetD) {
       C_d2f_dxdy *= D[l];
       C_d2f_dydz *= D[l];
@@ -396,8 +398,8 @@ void LaplaceHypre3d::updateMatrix3D() {
     // The values stored in the y-boundary are already interpolated
     // up/down, so we don't want the matrix to do any such
     // interpolation there.
-    const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0,
-              ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0;
+    const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0;
+    const int ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0;
 
     operator3D.yup(yup)(l, l.yp()) += C_df_dy + C_d2f_dy2;
     operator3D.ydown(ydown)(l, l.ym()) += -C_df_dy + C_d2f_dy2;
@@ -437,19 +439,15 @@ OperatorStencil<Ind3D> LaplaceHypre3d::getStencil(Mesh* localmesh,
   OffsetInd3D zero;
 
   // Add interior cells
-  const std::vector<OffsetInd3D> interpolatedUpElements = {zero.yp(), zero.xp().yp(),
-                                                           zero.xm().yp(), zero.yp().zp(),
-                                                           zero.yp().zm()},
-                                 interpolatedDownElements = {
-                                     zero.ym(), zero.xp().ym(), zero.xm().ym(),
-                                     zero.ym().zp(), zero.ym().zm()};
-  std::set<OffsetInd3D> interiorStencil = {zero,           zero.xp(),
-                                           zero.xm(),      zero.zp(),
-                                           zero.zm(),      zero.xp().zp(),
-                                           zero.xp().zm(), zero.xm().zp(),
-                                           zero.xm().zm()},
-                        lowerEdgeStencil = interiorStencil,
-                        upperEdgeStencil = interiorStencil;
+  const std::vector<OffsetInd3D> interpolatedUpElements = {
+      zero.yp(), zero.xp().yp(), zero.xm().yp(), zero.yp().zp(), zero.yp().zm()};
+  const std::vector<OffsetInd3D> interpolatedDownElements = {
+      zero.ym(), zero.xp().ym(), zero.xm().ym(), zero.ym().zp(), zero.ym().zm()};
+  std::set<OffsetInd3D> interiorStencil = {
+      zero,           zero.xp(),      zero.xm(),      zero.zp(),     zero.zm(),
+      zero.xp().zp(), zero.xp().zm(), zero.xm().zp(), zero.xm().zm()};
+  std::set<OffsetInd3D> lowerEdgeStencil = interiorStencil;
+  std::set<OffsetInd3D> upperEdgeStencil = interiorStencil;
 
   for (const auto& i : interpolatedDownElements) {
     for (auto& j : interpPattern) {
@@ -466,9 +464,11 @@ OperatorStencil<Ind3D> LaplaceHypre3d::getStencil(Mesh* localmesh,
     upperEdgeStencil.insert(i);
   }
   const std::vector<OffsetInd3D> interiorStencilVector(interiorStencil.begin(),
-                                                       interiorStencil.end()),
-      lowerEdgeStencilVector(lowerEdgeStencil.begin(), lowerEdgeStencil.end()),
-      upperEdgeStencilVector(upperEdgeStencil.begin(), upperEdgeStencil.end());
+                                                       interiorStencil.end());
+  const std::vector<OffsetInd3D> lowerEdgeStencilVector(lowerEdgeStencil.begin(),
+                                                        lowerEdgeStencil.end());
+  const std::vector<OffsetInd3D> upperEdgeStencilVector(upperEdgeStencil.begin(),
+                                                        upperEdgeStencil.end());
 
   // If there is a lower y-boundary then create a part of the stencil
   // for cells immediately adjacent to it.
@@ -536,7 +536,8 @@ OperatorStencil<Ind3D> LaplaceHypre3d::getStencil(Mesh* localmesh,
   return stencil;
 }
 
-int LaplaceHypre3d::Hypre3dMonitor::call(Solver*, BoutReal, int, int) {
+int LaplaceHypre3d::Hypre3dMonitor::call(Solver* /*solver*/, BoutReal /*time*/,
+                                         int /*iter*/, int /*nout*/) {
   if (laplace.n_solves == 0) {
     laplace.average_iterations = 0.0;
     return 0;

src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx

@@ -209,20 +209,17 @@ public:
   public:
     Hypre3dMonitor(LaplaceHypre3d& laplace_in) : laplace(laplace_in) {}
 
-    int call(Solver*, BoutReal, int, int) override;
+    int call(Solver* /*solver*/, BoutReal /*time*/, int /*iter*/, int /*nout*/) override;
 
   private:
     LaplaceHypre3d& laplace;
   };
   Hypre3dMonitor monitor;
 
-  bool use_precon; // Switch for preconditioning
-  bool rightprec;  // Right preconditioning
-
   // These are the implemented flags
-  static constexpr int implemented_flags = INVERT_START_NEW,
-                       implemented_boundary_flags =
-                           INVERT_AC_GRAD + INVERT_SET + INVERT_RHS;
+  static constexpr int implemented_flags = INVERT_START_NEW;
+  static constexpr int implemented_boundary_flags =
+      INVERT_AC_GRAD + INVERT_SET + INVERT_RHS;
 };
 
 #endif // BOUT_HAS_HYPRE

src/invert/laplacexy2/laplacexy2.cxx

@@ -14,10 +14,12 @@
 
 #include <cmath>
 
+namespace {
 Ind2D index2d(Mesh* mesh, int x, int y) {
   int ny = mesh->LocalNy;
   return Ind2D(x * ny + y, ny, 1);
 }
+} // namespace
 
 LaplaceXY2::LaplaceXY2(Mesh* m, Options* opt, const CELL_LOC loc)
     : localmesh(m == nullptr ? bout::globals::mesh : m),

src/invert/laplacexy2/laplacexy2_hypre.cxx

@@ -25,11 +25,6 @@ inline void gpuAssert(cudaError_t code, const char* file, int line, bool abort =
 }
 #endif
 
-Ind2D index2d(Mesh* mesh, int x, int y) {
-  int ny = mesh->LocalNy;
-  return Ind2D(x * ny + y, ny, 1);
-}
-
 LaplaceXY2Hypre::LaplaceXY2Hypre(Mesh* m, Options* opt, const CELL_LOC loc)
     : localmesh(m == nullptr ? bout::globals::mesh : m),
       indexConverter(std::make_shared<GlobalIndexer<Field2D>>(

src/physics/physicsmodel.cxx

@@ -32,11 +32,11 @@
 #include <bout/physicsmodel.hxx>
 #undef BOUT_NO_USING_NAMESPACE_BOUTGLOBALS
 
+#include "bout/version.hxx"
 #include <bout/mesh.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/vector2d.hxx>
 #include <bout/vector3d.hxx>
-#include "bout/version.hxx"
 
 #include <fmt/core.h>
 

src/sys/options/options_adios.cxx

@@ -245,7 +245,7 @@ bool readAttribute(adios2::IO& io, const std::string& name, const std::string& t
   return false;
 }
 
-Options OptionsADIOS::read() {
+Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
   Timer timer("io");
 
   // Open file