boutproject · bendudson · Feb 17, 2023 · Feb 17, 2023 · Feb 17, 2023 · Feb 17, 2023
diff --git a/.build_petsc_for_ci.sh b/.build_petsc_for_ci.sh
@@ -0,0 +1,60 @@
+#!/bin/bash
+
+set -e
+
+if test $BUILD_PETSC ; then
+    if [[ ! -d $HOME/local/petsc/include/petsc ]]; then
+	echo "****************************************"
+	echo "Building PETSc"
+	echo "****************************************"
+
+	git clone -b release https://gitlab.com/petsc/petsc.git petsc --depth=1
+
+	unset PETSC_DIR
+	unset PETSC_ARCH
+
+	pushd petsc
+	./configure \
+	    --with-mpi=yes \
+	    --with-precision=double \
+	    --with-scalar-type=real \
+	    --with-shared-libraries=1 \
+	    --with-debugging=0 \
+	    {C,CXX,F}OPTFLAGS="-O3 -march=native" \
+	    --prefix=$HOME/local/petsc
+
+	make && make install
+	popd
+
+	echo "****************************************"
+	echo " Finished building PETSc"
+	echo "****************************************"
+
+	echo "****************************************"
+	echo "Building SLEPc"
+	echo "****************************************"
+
+    git clone -b release https://gitlab.com/slepc/slepc.git slepc --depth=1
+
+    pushd slepc
+	unset SLEPC_DIR
+	unset SLEPC_ARCH
+    PETSC_DIR=$HOME/local/petsc ./configure --prefix=$HOME/local/slepc
+
+    make SLEPC_DIR=$(pwd) PETSC_DIR=$HOME/local/petsc
+    make SLEPC_DIR=$(pwd) PETSC_DIR=$HOME/local/petsc install
+    popd
+
+	echo "****************************************"
+	echo " Finished building SLEPc"
+	echo "****************************************"
+    else
+	echo "****************************************"
+	echo " PETSc already installed"
+	echo "****************************************"
+    fi
+else
+    echo "****************************************"
+    echo " PETSc not requested"
+    echo "****************************************"
+fi
diff --git a/.ci_fedora.sh b/.ci_fedora.sh
@@ -49,7 +49,7 @@ then
     sudo -u test ${0/\/tmp/\/home\/test} $mpi
 ## If we are called as normal user, run test
 else
-    pip install --user zoidberg
+    pip install --user zoidberg natsort
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
     export OMPI_MCA_rmaps_base_oversubscribe=yes

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -83,6 +83,21 @@ jobs:
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
 
+          - name: "CMake, new PETSc"
+            os: ubuntu-20.04
+            cmake_options: "-DBUILD_SHARED_LIBS=ON
+                            -DBOUT_ENABLE_METRIC_3D=ON
+                            -DBOUT_ENABLE_OPENMP=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_ENABLE_PYTHON=ON
+                            -DSUNDIALS_ROOT=/home/runner/local
+                            -DPETSC_DIR=/home/runner/local/petsc
+                            -DSLEPC_DIR=/home/runner/local/slepc"
+
+            build_petsc: -petsc
+
           - name: "Coverage"
             os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
@@ -142,12 +157,15 @@ jobs:
         uses: actions/cache@v2
         with:
           path: /home/runner/local
-          key: bout-sundials-${{ matrix.config.os }}
+          key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
 
       - name: Build SUNDIALS
         run: ./.build_sundials_for_ci.sh
 
-      - name: Build (CMake)
+      - name: Build PETSc
+        run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh
+
+      - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
       - name: Capture coverage
@@ -176,7 +194,7 @@ jobs:
         with:
           submodules: true
       - name: Build Fedora rawhide
-        run: ./.ci_fedora.sh setup mpich rawhide
+        run: ./.ci_fedora.sh setup openmpi rawhide
         shell: bash
         env:
           TRAVIS_BUILD_DIR: ${{ github.workspace }}
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -15,6 +15,13 @@ if(${CMAKE_VERSION} VERSION_GREATER_EQUAL 3.22)
   cmake_policy(SET CMP0127 NEW)
 endif()
 
+if ("${CMAKE_CURRENT_BINARY_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}")
+  option(BOUT_ALLOW_INSOURCE_BUILD "Whether BOUT++ should really allow to build in source." OFF)
+  if (NOT ${BOUT_ALLOW_INSOURCE_BUILD})
+    message(FATAL_ERROR "BOUT++ does not recommend in source builds. Try building out of source, e.g. with `cmake -S . -B build` or set -DBOUT_ALLOW_INSOURCE_BUILD=ON - but things may break!")
+  endif()
+endif()
+
 # CMake currently doesn't support proper semver
 # Set the version here, strip any extra tags to use in `project`
 # We try to use git to get a full description, inspired by setuptools_scm

diff --git a/cmake/FindPETSc.cmake b/cmake/FindPETSc.cmake
@@ -264,7 +264,7 @@ show :
 
   include(Check${PETSC_LANGUAGE_BINDINGS}SourceRuns)
 
-  macro (PETSC_TEST_RUNS includes libraries runs)
+  macro (petsc_test_compiles includes libraries runs)
     message(STATUS "PETSc test with : ${includes} ${libraries}" )
     if (PETSC_VERSION VERSION_GREATER 3.1)
       set (_PETSC_TSDestroy "TSDestroy(&ts)")
@@ -287,12 +287,12 @@ int main(int argc,char *argv[]) {
   return 0;
 }
 ")
-    multipass_source_runs ("${includes}" "${libraries}" "${_PETSC_TEST_SOURCE}" ${runs} "${PETSC_LANGUAGE_BINDINGS}")
+    multipass_source_compiles ("${includes}" "${libraries}" "${_PETSC_TEST_SOURCE}" ${runs} "${PETSC_LANGUAGE_BINDINGS}")
     if (${${runs}})
-      set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
+      set (PETSC_EXECUTABLE_COMPILES "YES" CACHE BOOL
         "Can the system successfully run a PETSc executable?  This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build.  If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
     endif (${${runs}})
-  endmacro (PETSC_TEST_RUNS)
+  endmacro ()
 
 
   find_path (PETSC_INCLUDE_DIR petscts.h
@@ -314,14 +314,14 @@ int main(int argc,char *argv[]) {
   set (petsc_mpi_include_dirs "${MPI_${PETSC_LANGUAGE_BINDINGS}_INCLUDE_DIRS}")
   #set (petsc_additional_libraries "MPI::MPI_${PETSC_LANGUAGE_BINDINGS}${petsc_openmp_library}")
 
-  petsc_test_runs ("${petsc_includes_minimal};${petsc_mpi_include_dirs}"
+  petsc_test_compiles ("${petsc_includes_minimal};${petsc_mpi_include_dirs}"
     "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
     petsc_works_minimal)
   if (petsc_works_minimal)
     message (STATUS "Minimal PETSc includes and libraries work.  This probably means we are building with shared libs.")
     set (petsc_includes_needed "${petsc_includes_minimal}")
   else (petsc_works_minimal)     # Minimal includes fail, see if just adding full includes fixes it
-    petsc_test_runs ("${petsc_includes_all};${petsc_mpi_include_dirs}"
+    petsc_test_compiles ("${petsc_includes_all};${petsc_mpi_include_dirs}"
       "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
       petsc_works_allincludes)
     if (petsc_works_allincludes) # It does, we just need all the includes (
@@ -332,7 +332,7 @@ int main(int argc,char *argv[]) {
       foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
         list (APPEND PETSC_LIBRARIES_${pkg}  ${petsc_libraries_external})
       endforeach (pkg)
-      petsc_test_runs ("${petsc_includes_minimal};${petsc_mpi_include_dirs}"
+      petsc_test_compiles ("${petsc_includes_minimal};${petsc_mpi_include_dirs}"
         "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
         petsc_works_alllibraries)
       if (petsc_works_alllibraries)
@@ -341,7 +341,7 @@ int main(int argc,char *argv[]) {
       else (petsc_works_alllibraries)
         # It looks like we really need everything, should have listened to Matt
         set (petsc_includes_needed ${petsc_includes_all})
-        petsc_test_runs ("${petsc_includes_all};${petsc_mpi_include_dirs}"
+        petsc_test_compiles ("${petsc_includes_all};${petsc_mpi_include_dirs}"
           "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
           petsc_works_all)
         if (petsc_works_all) # We fail anyways
@@ -372,15 +372,15 @@ if (NOT PETSC_INCLUDES AND NOT TARGET PETSc::PETSc)
     pkg_search_module(PkgPETSC PETSc>3.4.0 petsc>3.4.0)
     set (PETSC_LIBRARIES ${PkgPETSC_LINK_LIBRARIES} CACHE STRING "PETSc libraries" FORCE)
     set (PETSC_INCLUDES ${PkgPETSC_INCLUDE_DIRS} CACHE STRING "PETSc include path" FORCE)
-    set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
+    set (PETSC_EXECUTABLE_COMPILES "YES" CACHE BOOL
         "Can the system successfully run a PETSc executable?  This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build.  If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
   endif()
 endif()
 
 # Note that we have forced values for all these choices.  If you
 # change these, you are telling the system to trust you that they
 # work.  It is likely that you will end up with a broken build.
-mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_RUNS)
+mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_COMPILES)
 
 include (FindPackageHandleStandardArgs)
 find_package_handle_standard_args (PETSc

diff --git a/cmake/FindPackageMultipass.cmake b/cmake/FindPackageMultipass.cmake
@@ -32,6 +32,8 @@
 #  Always runs the given test, use this when you need to re-run tests
 #  because parent variables have made old cache entries stale.
 
+include(CheckCXXSourceCompiles)
+
 macro (FIND_PACKAGE_MULTIPASS _name _current)
   string (TOUPPER ${_name} _NAME)
   set (_args ${ARGV})
@@ -104,3 +106,27 @@ endmacro (MULTIPASS_SOURCE_RUNS)
 macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
   multipass_source_runs("${includes}" "${libraries}" "${source}" ${runs} "C")
 endmacro (MULTIPASS_C_SOURCE_RUNS)
+
+macro (MULTIPASS_SOURCE_COMPILES includes libraries source runs language)
+  include (Check${language}SourceRuns)
+  # This is a ridiculous hack.  CHECK_${language}_SOURCE_* thinks that if the
+  # *name* of the return variable doesn't change, then the test does
+  # not need to be re-run.  We keep an internal count which we
+  # increment to guarantee that every test name is unique.  If we've
+  # gotten here, then the configuration has changed enough that the
+  # test *needs* to be rerun.
+  if (NOT MULTIPASS_TEST_COUNT)
+    set (MULTIPASS_TEST_COUNT 00)
+  endif (NOT MULTIPASS_TEST_COUNT)
+  math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
+  set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
+  set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+  set (CMAKE_REQUIRED_INCLUDES ${includes})
+  set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+  if(${language} STREQUAL "C")
+    check_c_source_compiles ("${source}" ${testname})
+  elseif(${language} STREQUAL "CXX")
+    check_cxx_source_compiles ("${source}" ${testname})
+  endif()
+  set (${runs} "${${testname}}")
+endmacro ()
diff --git a/cmake/FindSLEPc.cmake b/cmake/FindSLEPc.cmake
@@ -137,10 +137,9 @@ show :
 endif()
 
 if (SLEPC_SKIP_BUILD_TESTS)
-  set(SLEPC_TEST_RUNS TRUE)
   set(SLEPC_VERSION "UNKNOWN")
   set(SLEPC_VERSION_OK TRUE)
-elseif (SLEPC_LIBRARIES AND SLEPC_INCLUDE_DIRS AND NOT SLEPC_TEST_RUNS)
+elseif (SLEPC_LIBRARIES AND SLEPC_INCLUDE_DIRS)
 
   # Set flags for building test program
   set(CMAKE_REQUIRED_INCLUDES ${SLEPC_INCLUDE_DIRS})
@@ -192,72 +191,6 @@ int main() {
     set(SLEPC_VERSION_OK TRUE CACHE BOOL "")
   endif()
   mark_as_advanced(SLEPC_VERSION_OK)
-
-  # Run SLEPc test program
-  set(SLEPC_TEST_LIB_CPP
-    "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/slepc_test_lib.cpp")
-  file(WRITE ${SLEPC_TEST_LIB_CPP} "
-#include \"petsc.h\"
-#include \"slepceps.h\"
-int main()
-{
-  PetscErrorCode ierr;
-  int argc = 0;
-  char** argv = NULL;
-  ierr = SlepcInitialize(&argc, &argv, PETSC_NULL, PETSC_NULL);
-  EPS eps;
-  ierr = EPSCreate(PETSC_COMM_SELF, &eps); CHKERRQ(ierr);
-  //ierr = EPSSetFromOptions(eps); CHKERRQ(ierr);
-#if PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR <= 1
-  ierr = EPSDestroy(eps); CHKERRQ(ierr);
-#else
-  ierr = EPSDestroy(&eps); CHKERRQ(ierr);
-#endif
-  ierr = SlepcFinalize(); CHKERRQ(ierr);
-  return 0;
-}
-")
-
-  try_run(
-    SLEPC_TEST_LIB_EXITCODE
-    SLEPC_TEST_LIB_COMPILED
-    ${CMAKE_CURRENT_BINARY_DIR}
-    ${SLEPC_TEST_LIB_CPP}
-    CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:STRING=${CMAKE_REQUIRED_INCLUDES}"
-    LINK_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES}
-    COMPILE_OUTPUT_VARIABLE SLEPC_TEST_LIB_COMPILE_OUTPUT
-    RUN_OUTPUT_VARIABLE SLEPC_TEST_LIB_OUTPUT
-    )
-
-  if (SLEPC_TEST_LIB_COMPILED AND SLEPC_TEST_LIB_EXITCODE EQUAL 0)
-    message(STATUS "Performing test SLEPC_TEST_RUNS - Success")
-    set(SLEPC_TEST_RUNS TRUE CACHE BOOL "SLEPc test program can run")
-  else()
-    message(STATUS "Performing test SLEPC_TEST_RUNS - Failed")
-
-    # Test program does not run - try adding SLEPc 3rd party libs and test again
-    list(APPEND CMAKE_REQUIRED_LIBRARIES ${SLEPC_EXTERNAL_LIBRARIES})
-
-    try_run(
-      SLEPC_TEST_3RD_PARTY_LIBS_EXITCODE
-      SLEPC_TEST_3RD_PARTY_LIBS_COMPILED
-      ${CMAKE_CURRENT_BINARY_DIR}
-      ${SLEPC_TEST_LIB_CPP}
-      CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:STRING=${CMAKE_REQUIRED_INCLUDES}"
-      LINK_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES}
-      COMPILE_OUTPUT_VARIABLE SLEPC_TEST_3RD_PARTY_LIBS_COMPILE_OUTPUT
-      RUN_OUTPUT_VARIABLE SLEPC_TEST_3RD_PARTY_LIBS_OUTPUT
-      )
-
-    if (SLEPC_TEST_3RD_PARTY_LIBS_COMPILED AND SLEPC_TEST_3RD_PARTY_LIBS_EXITCODE EQUAL 0)
-      message(STATUS "Performing test SLEPC_TEST_3RD_PARTY_LIBS_RUNS - Success")
-      set(SLEPC_LIBRARIES ${SLEPC_LIBRARIES} ${SLEPC_EXTERNAL_LIBRARIES}
-        CACHE STRING "SLEPc libraries." FORCE)
-      set(SLEPC_TEST_RUNS TRUE CACHE BOOL "SLEPc test program can run")
-    else()
-      message(STATUS "Performing test SLEPC_TEST_3RD_PARTY_LIBS_RUNS - Failed")
-    endif()
-  endif()
 endif()
 
 # Standard package handling
@@ -266,8 +199,7 @@ find_package_handle_standard_args(SLEPc
   FOUND_VAR SLEPC_FOUND
   FAIL_MESSAGE "SLEPc could not be found. Be sure to set SLEPC_DIR, PETSC_DIR, and PETSC_ARCH."
   VERSION_VAR SLEPC_VERSION
-  REQUIRED_VARS SLEPC_LIBRARIES SLEPC_DIR SLEPC_INCLUDE_DIRS SLEPC_TEST_RUNS
-                SLEPC_VERSION_OK)
+  REQUIRED_VARS SLEPC_LIBRARIES SLEPC_DIR SLEPC_INCLUDE_DIRS SLEPC_VERSION_OK)
 
 if (SLEPC_FOUND)
   if (NOT TARGET SLEPc::SLEPc)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
@@ -167,16 +167,20 @@ if (BOUT_USE_NETCDF)
     # Use our own FindnetCDF module which uses nc-config
     find_package(netCDF REQUIRED)
     FetchContent_MakeAvailable(netcdf-cxx4)
+    target_link_libraries(bout++ PUBLIC netCDF::netcdf-cxx4)
   else()
-    find_package(netCDFCxx REQUIRED)
-    foreach(FLAG ${netCDF_CXX_LIBRARY} ${netCDF_LIBRARIES})
-      if("${FLAG}" STREQUAL "netcdf")
-	    set(FLAG -lnetcdf)
-      endif()
-      set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${FLAG}")
-    endforeach()
+    find_package(netCDFCxx)
+    if (netCDFCxx_FOUND)
+      set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${netCDF_CXX_LIBRARY} ${netCDF_LIBRARIES}")
+      target_link_libraries(bout++ PUBLIC netCDF::netcdf-cxx4)
+    else()
+      find_package(PkgConfig REQUIRED)
+      pkg_check_modules(NETCDF REQUIRED IMPORTED_TARGET netcdf-cxx4)
+      target_link_libraries(bout++ PUBLIC PkgConfig::NETCDF)
+      list(JOIN NETCDF_LDFLAGS " " NETCDF_LDFLAGS_STRING)
+      set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${NETCDF_LDFLAGS_STRING}")
+    endif()
   endif()
-  target_link_libraries(bout++ PUBLIC netCDF::netcdf-cxx4)
 endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})

diff --git a/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx b/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx
@@ -13,12 +13,14 @@ int main(int argc, char** argv) {
                                                 bout::globals::mesh);
 
     /// Solution
-    Field2D x = 0.0;
+    Field2D solution = 0.0;
 
-    x = laplacexy.solve(rhs, x);
+    solution = laplacexy.solve(rhs, solution);
 
-    SAVE_ONCE2(rhs, x);
-    bout::globals::dump.write(); // Save output file
+    Options dump;
+    dump["rhs"] = rhs;
+    dump["x"] = solution;
+    bout::writeDefaultOutputFile(dump);
   }
   BoutFinalise();
 #if BOUT_HAS_CUDA