Merge pull request #27605 from cticenhour/petsc-3211

Update PETSc to 3.21.4 and fixup breaking tests
idaholab · Aug 13, 2024 · a062c21 · a062c21
2 parents bdbf31a + 076c686
commit a062c21
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diff --git a/apptainer/petsc.def b/apptainer/petsc.def
@@ -90,6 +90,7 @@ From: {{ APPTAINER_FROM }}
 %files
     {{ MOOSE_DIR }}/scripts/configure_petsc.sh {{ ROOT_BUILD_DIR }}/scripts/configure_petsc.sh
     {{ MOOSE_DIR }}/scripts/update_and_rebuild_petsc.sh {{ ROOT_BUILD_DIR }}/scripts/update_and_rebuild_petsc.sh
+    {{ MOOSE_DIR }}/scripts/tao_restore_viewer.patch {{ ROOT_BUILD_DIR }}/scripts/tao_restore_viewer.patch
 {%- if PETSC_ALT is defined %}
     {{ MOOSE_DIR }}/scripts/update_and_rebuild_petsc_alt.sh {{ ROOT_BUILD_DIR }}/scripts/update_and_rebuild_petsc_alt.sh
 {%- endif %}
diff --git a/conda/libmesh-vtk/conda_build_config.yaml b/conda/libmesh-vtk/conda_build_config.yaml
@@ -3,7 +3,7 @@ mpi:
   - openmpi
 
 moose_mpi:
-  - moose-mpi 2024.07.10
+  - moose-mpi 2024.08.05
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/libmesh-vtk/meta.yaml b/conda/libmesh-vtk/meta.yaml
@@ -3,7 +3,7 @@
 #   libmesh/*
 #
 # As well as any directions pertaining to modifying those files.
-{% set build = 0 %}
+{% set build = 1 %}
 {% set vtk_version = "9.3.0" %}
 {% set vtk_friendly_version = "9.3" %}
 {% set sha256 = "fdc7b9295225b34e4fdddc49cd06e66e94260cb00efee456e0f66568c9681be9" %}

diff --git a/conda/libmesh/conda_build_config.yaml b/conda/libmesh/conda_build_config.yaml
@@ -3,12 +3,12 @@ mpi:
   - openmpi
 
 moose_petsc:
-  - moose-petsc 3.20.3 mpich_1
-  - moose-petsc 3.20.3 openmpi_1
+  - moose-petsc 3.21.4 mpich_0
+  - moose-petsc 3.21.4 openmpi_0
 
 moose_libmesh_vtk:
-  - moose-libmesh-vtk 9.3.0 mpich_0
-  - moose-libmesh-vtk 9.3.0 openmpi_0
+  - moose-libmesh-vtk 9.3.0 mpich_1
+  - moose-libmesh-vtk 9.3.0 openmpi_1
 
 zip_keys:
   - mpi

diff --git a/conda/libmesh/meta.yaml b/conda/libmesh/meta.yaml
@@ -4,7 +4,7 @@
 #
 # As well as any directions pertaining to modifying those files.
 # ALSO: Follow the directions in scripts/tests/versioner_hashes.yaml
-{% set build = 0 %}
+{% set build = 1 %}
 {% set version = "2024.07.27" %}
 
 package:

diff --git a/conda/moose-dev/conda_build_config.yaml b/conda/moose-dev/conda_build_config.yaml
@@ -3,8 +3,8 @@ mpi:
   - openmpi
 
 moose_libmesh:
-  - moose-libmesh 2024.07.27 mpich_0
-  - moose-libmesh 2024.07.27 openmpi_0
+  - moose-libmesh 2024.07.27 mpich_1
+  - moose-libmesh 2024.07.27 openmpi_1
 
 moose_wasp:
   - moose-wasp 2024.05.08
@@ -13,7 +13,7 @@ moose_tools:
   - moose-tools 2024.07.19
 
 moose_peacock:
-  - moose-peacock 2024.07.10
+  - moose-peacock 2024.08.05
 
 zip_keys:
   - mpi

diff --git a/conda/moose-dev/meta.yaml b/conda/moose-dev/meta.yaml
@@ -6,7 +6,7 @@
 #   framework/doc/packages_config.yml
 #
 # As well as any directions pertaining to modifying those files.
-{% set version = "2024.07.27" %}
+{% set version = "2024.08.05" %}
 
 package:
   name: moose-dev

diff --git a/conda/moose/conda_build_config.yaml b/conda/moose/conda_build_config.yaml
@@ -3,7 +3,7 @@ mpi:
   - openmpi
 
 moose_dev:
-  - moose-dev 2024.07.27
+  - moose-dev 2024.08.05
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/mpi/build.sh b/conda/mpi/build.sh
@@ -15,9 +15,23 @@ ACTIVATION_CXXFLAGS=${TEMP_CXXFLAGS%%-fdebug-prefix-map*}-std=c++17
 mkdir -p "${PREFIX}/etc/conda/activate.d" "${PREFIX}/etc/conda/deactivate.d"
 cat <<EOF > "${PREFIX}/etc/conda/activate.d/activate_${PKG_NAME}.sh"
 export CC=mpicc CXX=mpicxx FC=mpif90 F90=mpif90 F77=mpif77 C_INCLUDE_PATH=${PREFIX}/include \
- MOOSE_NO_CODESIGN=true MPIHOME=${PREFIX} CXXFLAGS="$ACTIVATION_CXXFLAGS" HDF5_DIR=${PREFIX} \
- FI_PROVIDER=tcp
+ MOOSE_NO_CODESIGN=true MPIHOME=${PREFIX} CXXFLAGS="$ACTIVATION_CXXFLAGS" HDF5_DIR=${PREFIX}
 EOF
 cat <<EOF > "${PREFIX}/etc/conda/deactivate.d/deactivate_${PKG_NAME}.sh"
-unset CC CXX FC F90 F77 C_INCLUDE_PATH MOOSE_NO_CODESIGN MPIHOME CXXFLAGS HDF5_DIR FI_PROVIDER
+unset CC CXX FC F90 F77 C_INCLUDE_PATH MOOSE_NO_CODESIGN MPIHOME CXXFLAGS HDF5_DIR
 EOF
+if [[ "${mpi}" == 'mpich' ]]; then
+    cat <<EOF >> "${PREFIX}/etc/conda/activate.d/activate_${PKG_NAME}.sh"
+export FI_PROVIDER=tcp
+EOF
+    cat <<EOF >> "${PREFIX}/etc/conda/deactivate.d/deactivate_${PKG_NAME}.sh"
+unset FI_PROVIDER
+EOF
+elif [[ "${mpi}" == 'openmpi' ]]; then
+    cat <<EOF >> "${PREFIX}/etc/conda/activate.d/activate_${PKG_NAME}.sh"
+export OMPI_MCA_mca_base_component_show_load_errors=0
+EOF
+    cat <<EOF >> "${PREFIX}/etc/conda/deactivate.d/deactivate_${PKG_NAME}.sh"
+unset OMPI_MCA_mca_base_component_show_load_errors
+EOF
+fi
diff --git a/conda/mpi/meta.yaml b/conda/mpi/meta.yaml
@@ -6,7 +6,7 @@
 #
 # As well as any directions pertaining to modifying those files.
 # ALSO: Follow the directions in scripts/tests/versioner_hashes.yaml
-{% set version = "2024.07.10" %}
+{% set version = "2024.08.05" %}
 
 # HDF5 Version
 {% set hdf5_version = "1.14.3" %}

diff --git a/conda/peacock/conda_build_config.yaml b/conda/peacock/conda_build_config.yaml
@@ -3,7 +3,7 @@ mpi:
   - openmpi
 
 moose_mpi:
-  - moose-mpi 2024.07.10
+  - moose-mpi 2024.08.05
 
 # Pesky packages that break internal CI
 # Note: Modifying/Updating this will require changes to conda/mpich!

diff --git a/conda/peacock/meta.yaml b/conda/peacock/meta.yaml
@@ -3,7 +3,7 @@
 #   moose-dev/*
 #
 # As well as any directions pertaining to modifying those files.
-{% set version = "2024.07.10" %}
+{% set version = "2024.08.05" %}
 
 package:
   name: moose-peacock

diff --git a/conda/petsc/build.sh b/conda/petsc/build.sh
@@ -6,6 +6,10 @@ export PETSC_ARCH=arch-conda-c-opt
 # Remove std=C++17 from CXXFLAGS as we specify the C++ dialect for PETSc as C++17 in configure_petsc.
 # Specifying both causes an error as of PETSc 3.17.
 CXXFLAGS=${CXXFLAGS//-std=c++[0-9][0-9]}
+# This linker argument leads to segmentation faults when testing MUMPS during PETSc make check. We
+# are not the only ones who have had problems with this option. See
+# https://gitlab.c3s.unito.it/enocera/nnpdf/-/issues/307
+LDFLAGS=${LDFLAGS//-Wl,-dead_strip_dylibs}
 
 ## TODO: the following is a partial requirement for the day we introduce pytorch
 # Handle switches created by Conda variants
@@ -54,9 +58,7 @@ function build_petsc() {
   make PETSC_DIR="$SRC_DIR" PETSC_ARCH=$PETSC_ARCH install
   # set forth by MPI conda-forge package
   # shellcheck disable=SC2154
-  if [[ "${mpi}" == 'mpich' ]]; then
-      make PETSC_DIR="$SRC_DIR" PETSC_ARCH=$PETSC_ARCH check
-  fi
+  make SLEPC_DIR="$PREFIX"/petsc PETSC_DIR="$PREFIX"/petsc PETSC_ARCH="" check
 }
 
 function no_exit_failure(){

diff --git a/conda/petsc/conda_build_config.yaml b/conda/petsc/conda_build_config.yaml
@@ -3,7 +3,7 @@ mpi:
   - openmpi
 
 moose_mpi:
-  - moose-mpi 2024.07.10
+  - moose-mpi 2024.08.05
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/petsc/meta.yaml b/conda/petsc/meta.yaml
@@ -7,8 +7,8 @@
 #
 # As well as any directions pertaining to modifying those files.
 # ALSO: Follow the directions in scripts/tests/versioner_hashes.yaml
-{% set build = 1 %}
-{% set version = "3.20.3" %}
+{% set build = 0 %}
+{% set version = "3.21.4" %}
 
 package:
   name: moose-petsc
@@ -19,6 +19,7 @@ source:
   - path: ../../scripts/configure_petsc.sh
   - patches:
       - no-cppflags-in-pkgconfig-cflags.patch
+      - ../../scripts/tao_restore_viewer.patch
 
 build:
   number: {{ build }}

diff --git a/docker_ci/Dockerfile b/docker_ci/Dockerfile
@@ -99,7 +99,7 @@ WORKDIR ${MOOSE_DIR}
 #-----------------------------------------------------------------------------#
 # Install PETSc to system path
 #-----------------------------------------------------------------------------#
-ARG PETSC_REV=9a61b8cbbacd10b14c2a18c9bc314b0ecb8ec018
+ARG PETSC_REV=0d6defa7a01093b0f9cf3ff983d2b19d1f01a13e
 ARG PETSC_OPTIONS
 ENV PETSC_DIR=/usr/local
 COPY scripts/update_and_rebuild_petsc.sh ${MOOSE_DIR}/scripts/update_and_rebuild_petsc.sh

diff --git a/framework/doc/packages_config.yml b/framework/doc/packages_config.yml
@@ -10,8 +10,8 @@ maximum_python: 3.11
 mpich: 4.2.1
 openmpi: 4.1.6
 petsc_alt: 3.11.4
-petsc: 3.20.3
-moose_dev: 2024.07.27
+petsc: 3.21.4
+moose_dev: 2024.08.05
 moose_tools: 2024.07.19
 apptainer_rockylinux: 8.8.20230518
 apptainer_mpich: 3.4.3

diff --git a/modules/contact/test/tests/mortar_tm/2d/frictionless_second/small.i b/modules/contact/test/tests/mortar_tm/2d/frictionless_second/small.i
@@ -86,7 +86,7 @@ name = 'small'
     primary = plank_right
     secondary = block_left
     formulation = mortar
-    c_normal = 1e0
+    c_normal = 1e3
   []
 []
 
@@ -147,13 +147,13 @@ name = 'small'
   type = Transient
   solve_type = 'PJFNK'
   petsc_options = '-snes_converged_reason -ksp_converged_reason'
-  petsc_options_iname = '-pc_type -mat_mffd_err -pc_factor_shift_type -pc_factor_shift_amount'
-  petsc_options_value = 'lu       1e-5          NONZERO               1e-15'
+  petsc_options_iname = '-pc_type -mat_mffd_err -pc_factor_shift_type -pc_factor_shift_amount -pc_factor_mat_solver_type'
+  petsc_options_value = 'lu       1e-5          NONZERO               1e-15                   mumps'
   end_time = 5.0
   dt = 0.1
   dtmin = 0.1
   timestep_tolerance = 1e-6
-  line_search = 'contact'
+  line_search = 'none'
 []
 
 [Postprocessors]

diff --git a/modules/heat_transfer/test/tests/heat_source_bar/tests b/modules/heat_transfer/test/tests/heat_source_bar/tests
@@ -22,7 +22,7 @@
     type = 'PetscJacobianTester'
     input = 'ad_heat_source_bar.i'
     ratio_tol = 2e-7
-    difference_tol = 1e-2
+    difference_tol = 2e-2
     run_sim = True
     requirement = 'The system shall produce correct Jacobians for the AD heat conduction and heat source kernel objects.'
     design = "ADMatHeatSource.md"

diff --git a/modules/optimization/test/tests/executioners/basic_optimize/debug_gradient.i b/modules/optimization/test/tests/executioners/basic_optimize/debug_gradient.i
@@ -15,8 +15,8 @@
 [Executioner]
   type = Optimize
   tao_solver = taobncg
-  petsc_options_iname='-tao_fd_test -tao_test_gradient -tao_fd_gradient -tao_fd_delta'
-  petsc_options_value='true true false 1e-8'
+  petsc_options_iname='-tao_fd_test -tao_test_gradient -tao_fd_gradient -tao_fd_delta -tao_ls_type'
+  petsc_options_value='true true false 1e-8 unit'
   petsc_options = '-tao_test_gradient_view'
   verbose = true
 []
diff --git a/modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialStrictMassConservation.cmp b/modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialStrictMassConservation.cmp
@@ -0,0 +1,15 @@
+COORDINATES absolute 1.e-6    # min separation not calculated
+
+TIME STEPS relative 5.5e-6 floor 1e-10     # min:               0 @ t1 max:          0.0003 @ t4
+
+
+# No GLOBAL VARIABLES
+
+NODAL VARIABLES relative 5.5e-6 floor 1e-10
+	w relative 6e-06    # min:               0 @ t1,n1	max:       8.1220764 @ t2,n609
+
+ELEMENT VARIABLES relative 5.5e-6 floor 1e-10
+
+# No NODESET VARIABLES
+
+# No SIDESET VARIABLES
diff --git a/modules/phase_field/test/tests/GrandPotentialPFM/tests b/modules/phase_field/test/tests/GrandPotentialPFM/tests
@@ -31,6 +31,7 @@
     type = 'Exodiff'
     input = 'GrandPotentialStrictMassConservation.i'
     exodiff = 'GrandPotentialStrictMassConservation_out.e'
+    custom_cmp = GrandPotentialStrictMassConservation.cmp
     issues = '#23329'
     design = '/GrandPotentialKernelAction.md'
     requirement = 'The system shall provide classes to implement a Grand Potential phase field '

diff --git a/modules/porous_flow/test/tests/actions/tests b/modules/porous_flow/test/tests/actions/tests
@@ -206,5 +206,6 @@
     issues = '#28030'
     design = 'actions/PorousFlowFullySaturated.md actions/PorousFlowBasicTHM.md actions/PorousFlowUnsaturated.md'
     valgrind = 'heavy'
+    method = "!dbg"
   []
 []
diff --git a/modules/porous_flow/test/tests/gravity/fully_saturated_grav01c.i b/modules/porous_flow/test/tests/gravity/fully_saturated_grav01c.i
@@ -132,8 +132,8 @@
   type = Steady
   solve_type = Newton
   nl_rel_tol = 1E-12
-  petsc_options_iname = '-pc_factor_shift_type'
-  petsc_options_value = 'NONZERO'
+  petsc_options_iname = '-pc_factor_shift_type -snes_linesearch_type'
+  petsc_options_value = 'NONZERO               basic'
 []
 
 [Outputs]

diff --git a/modules/richards/test/tests/pressure_pulse/pp22.i b/modules/richards/test/tests/pressure_pulse/pp22.i
@@ -182,7 +182,7 @@
   solve_type = Newton
   dt = 1E3
   dtmin = 1E3
-  nl_rel_tol=1.e-10
+  nl_rel_tol=8.e-8
   nl_max_its=20
   end_time = 1E4
 []

diff --git a/modules/solid_mechanics/test/tests/ad_smeared_cracking/tests b/modules/solid_mechanics/test/tests/ad_smeared_cracking/tests
@@ -39,6 +39,7 @@
     exodiff_opts = '-steps 0:1200:1'
     valgrind = HEAVY
     requirement = 'The MOOSE SolidMechanics module shall simulate exponential stress relase while using the rz coordinate system using AD and match non-AD methods.'
+    method = "!dbg"
   []
   [power]
     type = Exodiff

diff --git a/modules/solid_mechanics/test/tests/crystal_plasticity/twinning/tests b/modules/solid_mechanics/test/tests/crystal_plasticity/twinning/tests
@@ -117,6 +117,7 @@
       detail = 'continue to compute the plastic shear due to twinning after '
                'a simulation restart.'
       prereq = 'constiutive_model/only_twinning_fcc'
+      method = "!dbg"
     []
     [combined_twinning_slip_111tension_restart]
       type = CSVDiff

diff --git a/modules/thermal_hydraulics/tutorials/single_phase_flow/05_secondary_side.cmp b/modules/thermal_hydraulics/tutorials/single_phase_flow/05_secondary_side.cmp
@@ -0,0 +1,4 @@
+TIME STEPS relative 5.5e-06 floor 1e-10
+
+GLOBAL VARIABLES relative 5.5e-06 floor 1e-10
+    core_delta_p relative 3e-05
diff --git a/modules/thermal_hydraulics/tutorials/single_phase_flow/tests b/modules/thermal_hydraulics/tutorials/single_phase_flow/tests
@@ -30,15 +30,16 @@
       csvdiff = '04_loop_out.csv'
       cli_args = 'Outputs/csv=true Executioner/num_steps=10'
       recover = false
-      max_parallel = 1
       detail = 'fourth step,'
       # PR #26848. Clang 16 Apple Si is not compatible.
       machine = X86_64
+      rel_err = 4e-5
     []
     [05]
       type = CSVDiff
       input = '05_secondary_side.i'
       csvdiff = '05_secondary_side_out.csv'
+      comparison_file = 05_secondary_side.cmp
       cli_args = 'Outputs/csv=true Executioner/num_steps=10'
       recover = false
       max_parallel = 1

diff --git a/petsc b/petsc