Merge pull request #390 from FluidityProject/fix-petsc-makefile

Updates for VTK9 and PETSC 3.15-24:
* (most of) https://github.com/dsroberts/fluidity/tree/dsroberts/noble including fixes for petsc v3.19 and support for configuring with vtk 9 from autoconf. Except the manual changes (which break on Jammy). Keeping the gmsh version at 2.6 in the Docker container for now (to be fixed later).
* drop Bionic and Focal builds
* fixes for petsc 3.23/3.24. One open issue is that with a debug petsc build it spews a lot of warnings, which I attempted to fix but that seemed to change answers for reasons I don't understand. See bbe7ea0 for the reversal of that "attempted fix". Again I will leave that for now as without the fix, everything seems to work.

Now builds succesfully in CI on Noble. Still some failing short and medium tests that need sorting out later.

Author: stephankramer

.github/workflows/ubuntu.yml

@@ -17,21 +17,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        name: [ "Build Bionic", "Build Focal", "Build Jammy", "Build Jammy OMP" ]
+        name: [ "Build Jammy", "Build Jammy OMP", "Build Noble" ]
         include:
 
-          - name: "Build Bionic"
-            release: bionic
-
-          - name: "Build Focal"
-            release: focal
-
           - name: "Build Jammy"
             release: jammy
 
           - name: "Build Jammy OMP"
             release: jammy-omp
 
+          - name: "Build Noble"
+            release: noble
+
     steps:
 
       - name: Check Out Repo
@@ -62,29 +59,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        name: [ "Short Bionic", "Unit Focal", "Short Focal", "Medium Focal", "Unit Jammy", "Short Jammy", "Medium Jammy" ]
+        name: [ "Unit Jammy", "Short Jammy", "Medium Jammy", "Unit Noble" ]
         include:
 
-          - name: "Short Bionic"
-            release: bionic
-            command: "make THREADS=2 test"
-            output: "test_results.xml"
-
-          - name: "Unit Focal"
-            release: focal
-            command: "make unittest"
-            output: "test_results_unittests.xml"
-
-          - name: "Short Focal"
-            release: focal
-            command: "make THREADS=2 test"
-            output: "test_results.xml"
-
-          - name: "Medium Focal"
-            release: focal
-            command: "make THREADS=2 mediumtest"
-            output: "test_results_medium.xml"
-
           - name: "Unit Jammy"
             release: jammy
             command: "make unittest"
@@ -100,6 +77,11 @@ jobs:
             command: "make THREADS=2 mediumtest"
             output: "test_results_medium.xml"
 
+          - name: "Unit Noble"
+            release: noble
+            command: "make unittest"
+            output: "test_results_unittests.xml"
+
     steps:
 
       - name: ${{ matrix.name }} Testing

aclocal.m4

@@ -419,11 +419,11 @@ if test "x$PETSC_DIR" == "x"; then
 fi
 AC_MSG_NOTICE([Using PETSC_DIR=$PETSC_DIR])
 
-PETSC_LINK_LIBS=`make -s -f petsc_makefile_old getlinklibs 2> /dev/null || make -s -f petsc_makefile getlinklibs`
+PETSC_LINK_LIBS=`make -s -f petsc_makefile getlinklibs`
 LIBS="$PETSC_LINK_LIBS $LIBS"
 
 # need to add -I$PWD/include/ to what we get from petsc, so we can use our own petsc_legacy.h wrapper
-PETSC_INCLUDE_FLAGS=`make -s -f petsc_makefile_old getincludedirs 2> /dev/null || make -s -f petsc_makefile getincludedirs`
+PETSC_INCLUDE_FLAGS=`make -s -f petsc_makefile getincludedirs`
 CPPFLAGS="$CPPFLAGS $PETSC_INCLUDE_FLAGS -I$PWD/include/"
 FCFLAGS="$FCFLAGS $PETSC_INCLUDE_FLAGS -I$PWD/include/"
 
@@ -562,6 +562,9 @@ AC_LANG_RESTORE
 
 
 AC_DEFINE(HAVE_PETSC,1,[Define if you have the PETSc library.])
+if test "0$PETSC_VERSION_MAJOR" -ge 3 -a "0$PETSC_VERSION_MINOR" -lt 19; then
+       AC_DEFINE(PETSC_NULLPTR,PETSC_NULL,[Name of PETSc's null pointer type])
+fi
 
 ])dnl ACX_PETSc
 

assemble/tests/test_main.cpp

@@ -65,7 +65,7 @@ int main(int argc, char **argv)
   }
 #endif
 #ifdef HAVE_PETSC
-  PetscInitialize(&argc, &argv, NULL, PETSC_NULL);
+  PetscInitialize(&argc, &argv, NULL, PETSC_NULLPTR);
   PetscInitializeFortran();
 #endif
 

climatology/Makefile.in

@@ -32,7 +32,7 @@ LINKER = $(CXX)
 CXXFLAGS = -I../include @CXXFLAGS@ @CPPFLAGS@
 
 LFLAGS   = @LDFLAGS@
-LIBS = -L../lib/ @LIBS@ @FLIBS@
+LIBS = -L../lib/ @LIBS@ @FLIBS@ @LAPACK_LIBS@
 
 .SUFFIXES: .cpp .o