Noble testing

.github/workflows/ubuntu.yml

@@ -17,18 +17,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        name: [ "Build Jammy", "Build Jammy OMP", "Build Noble" ]
+        name: [ "Build Noble", "Build Noble OMP", "Build Jammy" ]
         include:
 
-          - name: "Build Jammy"
-            release: jammy
-
-          - name: "Build Jammy OMP"
-            release: jammy-omp
-
           - name: "Build Noble"
             release: noble
 
+          - name: "Build Noble OMP"
+            release: noble-omp
+
+          - name: "Build Jammy"
+            release: jammy
+
     steps:
 
       - name: Check Out Repo
@@ -59,28 +59,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        name: [ "Unit Jammy", "Short Jammy", "Medium Jammy", "Unit Noble" ]
+        name: [ "Unit Noble", "Short Noble", "Medium Noble", "Short Jammy" ]
         include:
 
-          - name: "Unit Jammy"
-            release: jammy
+          - name: "Unit Noble"
+            release: noble
             command: "make unittest"
             output: "test_results_unittests.xml"
 
-          - name: "Short Jammy"
-            release: jammy
+          - name: "Short Noble"
+            release: noble
             command: "make THREADS=2 test"
             output: "test_results.xml"
 
-          - name: "Medium Jammy"
-            release: jammy
+          - name: "Medium Noble"
+            release: noble
             command: "make THREADS=2 mediumtest"
             output: "test_results_medium.xml"
 
-          - name: "Unit Noble"
-            release: noble
-            command: "make unittest"
-            output: "test_results_unittests.xml"
+          - name: "Short Jammy"
+            release: jammy
+            command: "make THREADS=2 test"
+            output: "test_results.xml"
 
     steps:
 
@@ -220,8 +220,8 @@ jobs:
       - name: ${{ matrix.name }} Longtesting
         run: |
          chmod 777 .
-         docker pull fluidity/actions:jammy-${{ github.sha }}
-         docker run -v $PWD:/host fluidity/actions:jammy-${{ github.sha }} /bin/bash -c "git clone https://github.com/fluidityproject/longtests && bin/testharness -x test_results_${{ matrix.name }}.xml -f ${{ matrix.name }}.xml && cp -v test_results_${{ matrix.name }}.xml /host"
+         docker pull fluidity/actions:noble-${{ github.sha }}
+         docker run -v $PWD:/host fluidity/actions:noble-${{ github.sha }} /bin/bash -c "git clone https://github.com/fluidityproject/longtests && bin/testharness -x test_results_${{ matrix.name }}.xml -f ${{ matrix.name }}.xml && cp -v test_results_${{ matrix.name }}.xml /host"
 
       - uses: actions/upload-artifact@v4
         with:

assemble/Full_Projection.F90

@@ -432,7 +432,7 @@ subroutine petsc_solve_setup_full_projection(y,A,b,ksp,petsc_numbering_p,name,so
 
       ! Set up RHS and Solution vectors (note these are loaded later):
       b = PetscNumberingCreateVec(petsc_numbering_p)
-      call VecDuplicate(b,y,ierr) ! Duplicate vector b and form vector y
+      call FixedVecDuplicate(b,y,ierr) ! Duplicate vector b and form vector y
 
       ! Schur complement objects now fully set up. The next stage is to setup
       ! KSP and PC for the solution of Ay = b, where A = G_t*M^-1*G.

assemble/tests/test_matrix_free.F90

@@ -298,7 +298,7 @@ subroutine petsc_solve_matrix_free(x, matrix, rhs)
 
   call VecCreateSeq(MPI_COMM_SELF,size(rhs%val), b, ierr)
 
-  call VecDuplicate(b, y, ierr)
+  call FixedVecDuplicate(b, y, ierr)
 
   ! copy array into PETSc vecs
   call VecSetValues(b, size(rhs%val), &

docker/Dockerfile.noble

@@ -19,14 +19,18 @@ RUN apt-get update && \
      apt-get update && \
      echo "Europe/London" > /etc/timezone && \
      apt-get -y install fluidity-dev texlive-pstricks texlive texlive-latex-extra texlive-science python3-pip python3-junit.xml && \
+     apt-get -y install sudo flex bison && \
      apt-get clean
 
+# Use old version of gmsh in CI to avoid mesh-sensitive tests failing
 WORKDIR /usr/local
-RUN curl -fsL https://gmsh.info/bin/Linux/gmsh-4.14.0-Linux64.tgz | tar --strip-components=1 -zxf -
+RUN curl -fsL https://gmsh.info/bin/Linux/gmsh-2.16.0-Linux64.tgz | tar --strip-components=1 -zxf -
 
 ENV OMPI_MCA_btl_vader_single_copy_mechanism=none
 ENV OMPI_MCA_rmaps_base_oversubscribe=1
 
+# Build vtk 9.4 instead of noble's vtk 9.2 as we need the fix for https://gitlab.kitware.com/vtk/vtk/-/issues/19258
+# (failing reading of vtk files with newer versions of expat)
 WORKDIR /root
 RUN curl -fsL https://vtk.org/files/release/9.4/VTK-9.4.0.tar.gz | tar -xzf - && \
     cd VTK-9.4.0 && \
@@ -38,6 +42,22 @@ RUN curl -fsL https://vtk.org/files/release/9.4/VTK-9.4.0.tar.gz | tar -xzf - &&
     cd ../.. && \
     rm -rf VTK-9.4.0
 
+# Build petsc 3.24 because noble's petsc version has an intermediate gamg with known issues
+WORKDIR /tmp
+RUN curl -O https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.24.2.tar.gz
+RUN tar -xzf petsc-3.24.2.tar.gz && mv petsc-3.24.2 /opt/petsc && rm petsc-3.24.2.tar.gz
+
+WORKDIR /opt/petsc
+RUN ./configure --with-debugging=1 --with-fortran-bindings=1 --with-shared-libraries=1 --with-strict-petscerrorcode --with-bison --with-fftw --with-hdf5 --with-hwloc --with-metis --with-mumps --download-netcdf --download-pnetcdf --download-ptscotch --with-scalapack-lib=-lscalapack-openmpi --with-suitesparse --download-superlu_dist --with-zlib --download-hypre -download-hdf5
+RUN make PETSC_DIR=/opt/petsc PETSC_ARCH=arch-linux-c-debug all
+
+# Environment for building fluidity with this vtk and petsc
+ENV VTK_INSTALL_PREFIX=/opt/vtk-9.4.0
+ENV PETSC_DIR=/opt/petsc
+ENV PETSC_ARCH=arch-linux-c-debug
+ENV PATH="$PETSC_DIR/$PETSC_ARCH/bin:$PATH"
+ENV PYTHONPATH="/opt/vtk-9.4.0/lib/python3.12/site-packages"
+
 # Add a Fluidity user who will be the default user for this container
 # Make sure the user has a userid matching the host system
 # -- pass this as an argument at build time

docker/actions/Dockerfile.actions.noble

@@ -4,7 +4,6 @@ USER root
 
 RUN apt-get -y update && \
       apt-get -y dist-upgrade && \
-      apt-get -y install sudo && \
       rm -rf /var/cache/apt/archives && \
       rm -rf /var/lib/apt/lists
 
@@ -15,11 +14,21 @@ COPY . /home/fluidity
 RUN chown -R fluidity /home/fluidity
 
 USER fluidity
+WORKDIR /home/fluidity
 
-ENV VTK_INSTALL_PREFIX=/opt/vtk-9.4.0
 RUN ./configure --enable-2d-adaptivity
+# NOTE: running "make makefiles" is only needed for
+# developers that have changed any of the module use statements
+# For all other users, this step is NOT needed.
+# "make makefiles" regenerates the */Makefile.dependencies
+# which should already be committed to the repo. We do this here
+# only to check whether the regenerated files have changed from
+# the committed version, in which case the "test -z" and thus the
+# build fails. If that happens, developers should run "make makefiles"
+# locally and commit the changes.
 RUN make makefiles
 RUN test -z "$(git status --porcelain */Makefile.dependencies)"
+
 RUN make
 RUN make fltools
 RUN make manual

docker/actions/Dockerfile.actions.noble-omp

@@ -0,0 +1,37 @@
+FROM fluidity/baseimages:noble
+
+USER root
+
+RUN apt-get -y update && \
+      apt-get -y dist-upgrade && \
+      rm -rf /var/cache/apt/archives && \
+      rm -rf /var/lib/apt/lists
+
+RUN adduser fluidity sudo
+RUN echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+
+COPY . /home/fluidity
+RUN chown -R fluidity /home/fluidity
+
+USER fluidity
+WORKDIR /home/fluidity
+
+RUN ./configure --enable-2d-adaptivity --enable-omp
+# NOTE: running "make makefiles" is only needed for
+# developers that have changed any of the module use statements
+# For all other users, this step is NOT needed.
+# "make makefiles" regenerates the */Makefile.dependencies
+# which should already be committed to the repo. We do this here
+# only to check whether the regenerated files have changed from
+# the committed version, in which case the "test -z" and thus the
+# build fails. If that happens, developers should run "make makefiles"
+# locally and commit the changes.
+RUN make makefiles
+RUN test -z "$(git status --porcelain */Makefile.dependencies)"
+
+RUN make
+RUN make fltools
+RUN make manual
+
+# Python module 'assess' is required for some longtests
+RUN python3 -m pip install --break-system-packages assess

examples/rotating_channel/channel.flml

@@ -207,9 +207,7 @@
               <integer_value rank="0">40</integer_value>
             </restart>
           </iterative_method>
-          <preconditioner name="hypre">
-            <hypre_type name="euclid"/>
-          </preconditioner>
+          <preconditioner name="sor"/>
           <relative_error>
             <real_value rank="0">1.0e-10</real_value>
           </relative_error>

examples/water_collapse/water_collapse.xml

@@ -31,7 +31,7 @@ nodesend= stat("water_collapse.stat")["CoordinateMesh"]["nodes"][-1]</variable>
   <pass_tests>
     <test name="finish_time" language="python">assert finishtime &gt; 2.4</test>
     <test name="water_conservation" language="python">print('mass loss = ', abs(vfracintend-vfracintstart)/vfracintstart)
-assert abs(vfracintend-vfracintstart)/vfracintstart &lt; 1.e-5
+assert abs(vfracintend-vfracintstart)/vfracintstart &lt; 5.e-5
 </test>
     <test name="divergence" language="python">print('divergence = ', max(maxdivergence, mindivergence))
 assert max(maxdivergence, mindivergence) &lt; 1.E-5

femtools/Diagnostic_variables.F90

@@ -1184,10 +1184,11 @@ subroutine initialise_constant_diagnostics(unit, binary_format)
 
     call get_environment_variable(name="HOSTNAME", value=value_buffer, status=stat)
     if (stat /= 0) then
-      ewrite(-1, *) "GET_ENVIRONMENT_VARIABLE('HOSTNAME') returned no-zero status: ", stat
+      ewrite(0, *) "GET_ENVIRONMENT_VARIABLE('HOSTNAME') returned no-zero status: ", stat
+    else
+      buffer=constant_tag(name="HostName", type="string", value=trim(value_buffer))
+      write(unit, '(a)') trim(buffer)
     end if
-    buffer=constant_tag(name="HostName", type="string", value=trim(value_buffer))
-    write(unit, '(a)') trim(buffer)
 
     ! Constant values
     if(present_and_true(binary_format)) then

femtools/Multigrid.F90

@@ -746,7 +746,7 @@ function Prolongator(A, epsilon, omega, maxclustersize, cluster) result (P)
   call VecCopy(diag, sqrt_diag, ierr)
   call VecSqrtAbs(sqrt_diag, ierr)
   !
-  call VecDuplicate(sqrt_diag, inv_sqrt_diag, ierr)
+  call FixedVecDuplicate(sqrt_diag, inv_sqrt_diag, ierr)
   call VecCopy(sqrt_diag, inv_sqrt_diag, ierr)
   call VecReciprocal(inv_sqrt_diag, ierr)
   call MatDiagonalScale(A, inv_sqrt_diag, inv_sqrt_diag, ierr)
@@ -802,7 +802,7 @@ function Prolongator(A, epsilon, omega, maxclustersize, cluster) result (P)
   ! now restore the original matrix
   ! unfortunately MatDiagonalScale is broken for one-sided scaling, i.e.
   ! supplying PETSC_NULL(_OBJECT) for one the vectors
-  call VecDuplicate(diag, one, ierr)
+  call FixedVecDuplicate(diag, one, ierr)
   call VecSet(one, 1.0_PetscReal_kind, ierr)
   call MatDiagonalScale(A, diag, one, ierr)
 

femtools/Petsc_Tools.F90

@@ -118,6 +118,7 @@ module Petsc_Tools
   logical, public, save :: petsc_test_error_handler_called = .false.
   public petsc_test_error_handler
   public IsNullMatNullSpace
+  public FixedVecDuplicate
 
 contains
 
@@ -1030,6 +1031,7 @@ function block_csr2petsc(A, petsc_numbering, column_petsc_numbering, &
                if (A%diagonal .and. bh/=bv) cycle
                ! row number in PETSc land:
                rows(1)=row_numbering%gnn2unn(i, bv)
+               if (rows(1)<0) cycle
                vals => row_val_ptr(A, bv, bh, i)
 #ifdef DOUBLEP
                call MatSetValues(M, 1, rows, len, colidx(1:len), vals, &
@@ -1539,5 +1541,18 @@ function IsNullMatNullSpace(nullsp)
 
 end function IsNullMatNullSpace
 
+subroutine FixedVecDuplicate(v, newv, ierr)
+  ! It appears that for VecSeq, petsc does not copy the options
+  ! of the duplicated vector. Ensure it does.
+  Vec, intent(in) :: v
+  Vec, intent(out) :: newv
+  PetscErrorCode :: ierr
+
+    call VecDuplicate(v, newv, ierr)
+    call VecSetOption(newv, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE, ierr)
+    call VecSetOption(newv, VEC_IGNORE_OFF_PROC_ENTRIES, PETSC_TRUE, ierr)
+
+end subroutine FixedVecDuplicate
+
 #include "Reference_count_petsc_numbering_type.F90"
 end module Petsc_Tools