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=OFF
                             -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=OFF
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -123,32 +128,15 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=OFF
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
             build_petsc: -petsc
             on_cron: false
 
-          - name: "Coverage"
-            os: ubuntu-latest
-            cmake_options: "-DBUILD_SHARED_LIBS=ON
-                            -DCMAKE_BUILD_TYPE=Debug
-                            -DCHECK=3
-                            -DENABLE_COVERAGE=ON
-                            -DBOUT_USE_PETSC=ON
-                            -DBOUT_USE_SLEPC=ON
-                            -DBOUT_USE_HDF5=ON
-                            -DBOUT_USE_SUNDIALS=ON
-                            -DBOUT_ENABLE_PYTHON=ON
-                            -DSUNDIALS_ROOT=/home/runner/local"
-            unit_only: YES
-            on_cron: false
         exclude:
-          # Don't run the coverage tests if the branch isn't master or next
-          - is_master_or_next: false
-            config:
-              name: "Coverage"
           - is_cron: true
             config:
               on_cron: false
@@ -178,6 +166,7 @@ jobs:
                  slepc-dev
                  liblapack-dev
                  libparpack2-dev
+                 libhypre-dev
 
       - uses: actions/checkout@v4
         with:
@@ -210,22 +199,6 @@ jobs:
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
-      - name: Capture coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        # Explicitly run the coverage capture target, because
-        # ci_script.sh also does the upload, and we're going to do
-        # that ourselves in the next step
-        run: |
-          # Ensure that there is a corresponding .gcda file for every .gcno file
-          # This is to try and make the coverage report slightly more accurate
-          # It still won't include, e.g. any solvers we don't build with though
-          find . -name "*.gcno" -exec sh -c 'touch -a "${1%.gcno}.gcda"' _ {} \;
-          make -C build code-coverage-capture
-
-      - name: Upload coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        uses: codecov/codecov-action@v4
-
   Fedora:
     # This is its own job as it doesn't use most of the steps of the
     # standard_tests

bout++Config.cmake.in

@@ -91,7 +91,7 @@ elseif(EXISTS "@NCXX4_CONFIG@")
   set(NCXX4_CONFIG "@NCXX4_CONFIG@")
 elseif(EXISTS "@NCXX_BINARY_DIR@")
   # If we downloaded netCDF-cxx4, then we need to add its build directory to our search paths
-  list(APPEND CMAKE_PREFIX_PATH "@NCXX_BINARY_DIR@")  
+  list(APPEND CMAKE_PREFIX_PATH "@NCXX_BINARY_DIR@")
 endif()
 if(EXISTS "@PVODE_ROOT@")
   set(PVODE_ROOT "@PVODE_ROOT@")
@@ -103,6 +103,12 @@ endif()
 if(EXISTS "@Libuuid_ROOT@")
   set(Libuuid_ROOT "@Libuuid_ROOT@")
 endif()
+if(EXISTS "@ADIOS2_ROOT@")
+  set(ADIOS2_ROOT "@ADIOS2_ROOT@")
+elseif(EXISTS "@ADIOS2_BINARY_DIR@")
+  # If we downloaded ADIOS2, then we need to add its build directory to our search paths
+  list(APPEND CMAKE_PREFIX_PATH "@ADIOS2_BINARY_DIR@")
+endif()
 
 if(@BOUT_USE_SYSTEM_MPARK_VARIANT@)
   set(mpark_variant_ROOT "@mpark_variant_ROOT@")
@@ -117,6 +123,11 @@ endif()
 
 set(MPIEXEC_EXECUTABLE @MPIEXEC_EXECUTABLE@)
 find_dependency(MPI @MPI_CXX_VERSION@ EXACT)
+if (BOUT_HAS_ADIOS2 OR BOUT_HAS_HYPRE OR BOUT_HAS_SUNDIALS)
+  # These libraries may also require MPI_C
+  enable_language(C)
+  find_dependency(MPI COMPONENTS C)
+endif()
 
 if (BOUT_USE_OPENMP)
   find_dependency(OpenMP)
@@ -158,5 +169,8 @@ endif()
 if (BOUT_USE_UUID_SYSTEM_GENERATOR)
  find_dependency(Libuuid)
 endif()
+if (BOUT_HAS_ADIOS2)
+  find_dependency(ADIOS2 @ADIOS2_VERSION@ EXACT)
+endif()
 
 include("${CMAKE_CURRENT_LIST_DIR}/bout++Targets.cmake")

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

@@ -190,9 +190,12 @@ 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)
+  enable_language(C)
+  find_package(MPI REQUIRED COMPONENTS C)
+
   if (BOUT_DOWNLOAD_ADIOS2)
     message(STATUS "Downloading and configuring ADIOS2")
     include(FetchContent)
@@ -211,18 +214,11 @@ if (BOUT_USE_ADIOS2)
     # Note: SST requires <rdma/fabric.h> but doesn't check at configure time
     set(ADIOS2_USE_SST OFF CACHE BOOL "" FORCE)
     FetchContent_MakeAvailable(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)
   endif()
+  target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
 endif()
 message(STATUS "ADIOS2 support: ${BOUT_USE_ADIOS2}")
 set(BOUT_HAS_ADIOS2 ${BOUT_USE_ADIOS2})

examples/elm-pb/data-hypre/BOUT.inp

@@ -1,26 +1,18 @@
-wall_limit = 1.55  # wall time limit (in hours)
-
 zperiod = 15        # Fraction of a torus to simulate
 MZ = 16             # Number of points in Z
 
-dump_format = "nc"      # Dump file format. "nc" = NetCDF, "pdb" = PDB
-restart_format = "nc"   # Restart file format
-
 [mesh]
-
 staggergrids = false    # Use staggered grids
 
 file = "cbm18_dens8.grid_nx68ny64.nc"  # Grid file
 
 [mesh:paralleltransform]
-
-type = shifted # Use shifted metric method
+type = shiftedinterp
 
 ##################################################
 # derivative methods
 
 [mesh:ddx]
-
 first = C4  # order of first x derivatives
 second = C4 # order of second x derivatives
 upwind = W3 # order of upwinding method W3 = Weno3
@@ -36,20 +28,6 @@ first = C4  # Z derivatives can be done using FFT
 second = C4
 upwind = W3
 
-[output]
-shiftoutput = true  # Put the output into field-aligned coordinates
-
-##################################################
-# Laplacian inversion routines
-
-[laplace]
-type = hypre3d
-
-flags = 0   # Flags for Laplacian inversion
-
-rtol = 1e-09
-atol = 1e-14
-
 ##################################################
 # FFTs
 
@@ -63,23 +41,12 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 [solver]
 
 # mudq, mldq, mukeep, mlkeep preconditioner options
-atol = 1e-08 # absolute tolerance
-rtol = 1e-05  # relative tolerance
+atol = 1.0e-8 # absolute tolerance
+rtol = 1.0e-5  # relative tolerance
 
 use_precon = false    # Use preconditioner: User-supplied or BBD
-use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs
-adams_moulton = false # Use Adams-Moulton method (default is BDF)
-func_iter = false     # Functional iteration (default is Newton)
-output_step = 1       # time between outputs
-# settings file for BOUT++
-# High-Beta reduced MHD case
-
-##################################################
-# Global settings used by the core code
-
-nout = 40          # number of time-steps
 
 ##################################################
 # settings for high-beta reduced MHD
@@ -116,7 +83,7 @@ diamag_phi0 = true    # Balance ExB against Vd for stationary equilibrium
 bm_exb_flag = 0
 bm_mag_flag = 0
 ##################################################################
-withflow = false     # With flow or not
+withflow = false    # With flow or not
 D_0 = 1.3e5         # differential potential
 D_s = 20            # shear parameter
 K_H_term = false    # Contain K-H term
@@ -125,8 +92,8 @@ x0 = 0.855          # peak location
 D_min = 3000        # constant
 ##################################################################
 
-eHall = false         # Include electron pressue effects in Ohm's law?
-AA = 2.0          # ion mass in units of proton mass
+eHall = false         # Include electron pressure effects in Ohm's law?
+AA = 2.0              # ion mass in units of proton mass
 
 noshear = false        # zero all shear
 
@@ -174,14 +141,14 @@ damp_t_const = 0.01  # Damping time constant
 
 ## Parallel pressure diffusion
 
-diffusion_par = -1.0   # Parallel pressure diffusion (< 0 = none)
+diffusion_par = -1.0    # Parallel pressure diffusion (< 0 = none)
 diffusion_p4 = -1e-05   # parallel hyper-viscous diffusion for pressure (< 0 = none)
-diffusion_u4 = 1e-05    # parallel hyper-viscous diffusion for vorticity (< 0 = none)
+diffusion_u4 = -1e-05   # parallel hyper-viscous diffusion for vorticity (< 0 = none)
 diffusion_a4 = -1e-05   # parallel hyper-viscous diffusion for vector potential (< 0 = none)
 
 ## heat source in pressure in watts
 
-heating_P = -1   #   heat power in watts (< 0 = none)
+heating_P = -1     #   heat power in watts (< 0 = none)
 hp_width = 0.1     #   heat width, in percentage of nx (< 0 = none)
 hp_length = 0.3    #   heat length in percentage of nx (< 0 = none)
 
@@ -205,22 +172,19 @@ su_lengthr = 0.1     #   right edge sink length in percentage of nx (< 0 = none)
 ## Viscosity and Hyper-viscosity
 
 viscos_par = -0.1   # Parallel viscosity (< 0 = none)
-viscos_perp = -1.0  # Perpendicular
+viscos_perp = -1.0  # Perpendicular viscosity (< 0 = none)
 hyperviscos = -1.0  # Radial hyper viscosity
 
 ## Compressional terms (only when compress = true)
 phi_curv = true    # Include curvature*Grad(phi) in P equation
 # gamma = 1.6666
 
 [phiSolver]
-#inner_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
-#outer_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
-inner_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
-outer_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
+type = hypre3d
+inner_boundary_flags = 0 # Dirichlet
+outer_boundary_flags = 0 # Dirichlet
 
 [aparSolver]
-#inner_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
-#outer_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
 inner_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
 outer_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
 
@@ -271,12 +235,9 @@ bndry_ydown = free_o3
 # Zero gradient in the core
 bndry_core = neumann
 
-[Vpar]
-
-bndry_core = neumann
-
 [phi]
 
 bndry_xin = none
 bndry_xout = none
-bndry_target = neumann
+#bndry_target = neumann
+

examples/elm-pb/data/BOUT.inp

@@ -94,7 +94,7 @@ diamag_phi0 = true    # Balance ExB against Vd for stationary equilibrium
 bm_exb_flag = 0
 bm_mag_flag = 0
 ##################################################################
-withflow = false     # With flow or not
+withflow = false    # With flow or not
 D_0 = 1.3e5         # differential potential
 D_s = 20            # shear parameter
 K_H_term = false    # Contain K-H term
@@ -104,7 +104,7 @@ D_min = 3000        # constant
 ##################################################################
 
 eHall = false         # Include electron pressure effects in Ohm's law?
-AA = 2.0          # ion mass in units of proton mass
+AA = 2.0              # ion mass in units of proton mass
 
 noshear = false        # zero all shear
 
@@ -152,14 +152,14 @@ damp_t_const = 0.01  # Damping time constant
 
 ## Parallel pressure diffusion
 
-diffusion_par = -1.0   # Parallel pressure diffusion (< 0 = none)
+diffusion_par = -1.0    # Parallel pressure diffusion (< 0 = none)
 diffusion_p4 = -1e-05   # parallel hyper-viscous diffusion for pressure (< 0 = none)
-diffusion_u4 = -1e-05    # parallel hyper-viscous diffusion for vorticity (< 0 = none)
+diffusion_u4 = -1e-05   # parallel hyper-viscous diffusion for vorticity (< 0 = none)
 diffusion_a4 = -1e-05   # parallel hyper-viscous diffusion for vector potential (< 0 = none)
 
 ## heat source in pressure in watts
 
-heating_P = -1   #   heat power in watts (< 0 = none)
+heating_P = -1     #   heat power in watts (< 0 = none)
 hp_width = 0.1     #   heat width, in percentage of nx (< 0 = none)
 hp_length = 0.3    #   heat length in percentage of nx (< 0 = none)