Merge pull request #25939 from milljm/25831-clang-container

idaholab · Nov 7, 2023 · f07619a · f07619a
2 parents 445341c + 3f44eb1
commit f07619a
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Showing 33 changed files with 172 additions and 87 deletions.
diff --git a/apptainer/mpich.def b/apptainer/mpich.def
@@ -4,11 +4,15 @@
 {#- Optional jinja arguments                                                                  -#}
 {#- ALTERNATE_FROM: Set an alternate from (currently supported: rocky9)                       -#}
 
+{%- if ALTERNATE_FROM == "clang" %}
+Bootstrap: docker
+{%- else %}
 BootStrap: oras
+{%- endif %}
 {%- if ALTERNATE_FROM == "rocky9" %}
 From: mooseharbor.hpc.inl.gov/moose-hpcbase/rocky9-{{ ARCH }}:9.0-0
 {%- elif ALTERNATE_FROM == "clang" %}
-From: mooseharbor.hpc.inl.gov/moose-hpcbase/rocky8-clang-{{ ARCH }}:8.6-0
+From: rockylinux:8
 {%- elif ALTERNATE_FROM == "cuda" %}
 From: mooseharbor.hpc.inl.gov/moose-hpcbase/rocky8-cuda-{{ ARCH }}:8.6-cuda11.4.0-0
 {%- else %}
@@ -20,8 +24,12 @@ From: harbor.hpc.inl.gov/hpcbase/mpi_03:1.1.0
     export LC_ALL=C
 
 %post
+{%- if ALTERNATE_FROM == "clang" %}
+    export MOOSE_MPICH_DIR=${MOOSE_MPICH_DIR:-"/opt/mpi/mpich-4.1.2"}
+{%- else %}
     export MOOSE_MPICH_DIR=${MOOSE_MPICH_DIR:-"/opt/mpi/mpich-3.4.3"}
     export MOOSE_OPENMPI_DIR=${MOOSE_OPENMPI_DIR:-"/opt/mpi/openmpi-4.1.5"}
+{%- endif %}
 
     # Get the RHEL version
     RHEL_VERSION=$(awk -F'=' '/VERSION_ID/{ gsub(/"/,""); print $2}' /etc/os-release)
@@ -44,6 +52,14 @@ From: harbor.hpc.inl.gov/hpcbase/mpi_03:1.1.0
                    libtirpc libtirpc-devel zlib-devel patch patchutils epel-release file \
                    libpng libpng-devel unzip jq valgrind cppunit doxygen fftw-devel gsl-devel \
                    libtool autoconf automake cppunit-devel
+
+{%- if ALTERNATE_FROM == "clang" %}
+    # Installing Clang, and its dependencies
+    dnf install -y clang.x86_64 clang-devel.x86_64 clang-libs.x86_64 clang-tools-extra.x86_64 \
+                   git-clang-format.x86_64 python3-clang.x86_64 clang-analyzer.noarch \
+                   libomp.x86_64 gcc-toolset-12-gcc-gfortran.x86_64 lldb
+{%- endif %}
+
     # After epel-release
     dnf install -y glpk-devel patchelf lcov
 
@@ -99,10 +115,46 @@ EOF
     cd git-lfs-3.2.0
     ./install.sh
 
+{%- if ALTERNATE_FROM == "clang" %}
+    # Build and Install MPICH Clang
+    mkdir ${TEMP_LOC}/mpich
+    cd ${TEMP_LOC}/mpich
+    curl -L -O http://www.mpich.org/static/downloads/4.1.2/mpich-4.1.2.tar.gz
+    tar -xf mpich-4.1.2.tar.gz
+    mkdir mpich-4.1.2/build
+    cd mpich-4.1.2/build
+    export PATH=/opt/rh/gcc-toolset-12/root/bin:${PATH}
+    export LD_LIBRARY_PATH=/opt/rh/gcc-toolset-12/root/lib:/opt/rh/gcc-toolset-12/root/lib64:${LD_LIBRARY_PATH}
+    ../configure --prefix=${MOOSE_MPICH_DIR} \
+      --enable-shared \
+      --enable-sharedlibs=clang \
+      --enable-fast=O2 \
+      --enable-debuginfo \
+      --enable-totalview \
+      --enable-two-level-namespace \
+      CC=clang \
+      CXX=clang++ \
+      FC=gfortran \
+      F77=gfortran \
+      F90='' \
+      CFLAGS='' \
+      CXXFLAGS='' \
+      FFLAGS='-fallow-argument-mismatch' \
+      FCFLAGS='-fallow-argument-mismatch' \
+      F90FLAGS='' \
+      F77FLAGS=''
+    make -j ${MOOSE_JOBS:-6}
+    make install
+{%- endif %}
+
     # Basic script for setting mpich environment
     USE_MPI_SCRIPT='export LD_LIBRARY_PATH=${MOOSE_MPI_DIR}/lib:${LD_LIBRARY_PATH}
 export MANPATH=${MOOSE_MPI_DIR}/share/man:${MANPATH}
 export PATH=${MOOSE_MPI_DIR}/bin:${PATH}
+{%- if ALTERNATE_FROM == "clang" %}
+export PATH=/opt/rh/gcc-toolset-12/root/bin:${PATH}
+export LD_LIBRARY_PATH=/opt/rh/gcc-toolset-12/root/lib:/opt/rh/gcc-toolset-12/root/lib64:${LD_LIBRARY_PATH}
+{%- endif %}
 export CC=mpicc CXX=mpicxx FC=mpif90 F90=mpif90 F77=mpif77'
 
     # Add script for loading mpich environment

diff --git a/conda/libmesh-vtk/conda_build_config.yaml b/conda/libmesh-vtk/conda_build_config.yaml
@@ -1,5 +1,5 @@
 moose_mpich:
-  - moose-mpich 4.0.2 build_12
+  - moose-mpich 4.0.2 build_13
 
 #### 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 = 5 %}
+{% set build = 6 %}
 {% set vtk_version = "9.2.6" %}
 {% set vtk_friendly_version = "9.2" %}
 {% set sha256 = "06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12" %}

diff --git a/conda/libmesh/conda_build_config.yaml b/conda/libmesh/conda_build_config.yaml
@@ -1,8 +1,8 @@
 moose_petsc:
-  - moose-petsc 3.20.0 build_0
+  - moose-petsc 3.20.0 build_1
 
 moose_libmesh_vtk:
-  - moose-libmesh-vtk 9.2.6 build_5
+  - moose-libmesh-vtk 9.2.6 build_6
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/libmesh/meta.yaml b/conda/libmesh/meta.yaml
@@ -4,8 +4,8 @@
 #
 # As well as any directions pertaining to modifying those files.
 # ALSO: Follow the directions in scripts/tests/versioner_hashes.yaml
-{% set build = 4 %}
-{% set version = "2023.09.06" %}
+{% set build = 0 %}
+{% set version = "2023.11.06" %}
 {% set vtk_friendly_version = "9.2" %}
 
 # permanent

diff --git a/conda/moose-dev/conda_build_config.yaml b/conda/moose-dev/conda_build_config.yaml
@@ -1,11 +1,11 @@
 moose_libmesh:
-  - moose-libmesh 2023.09.06 build_4
+  - moose-libmesh 2023.11.06 build_0
 
 moose_wasp:
-  - moose-wasp 2023.10.24
+  - moose-wasp 2023.11.06
 
 moose_tools:
   - moose-tools 2023.10.27
 
 moose_peacock:
-  - moose-peacock 2023.10.23
+  - moose-peacock 2023.11.06
diff --git a/conda/moose-dev/meta.yaml b/conda/moose-dev/meta.yaml
@@ -3,8 +3,11 @@
 #   moose/conda_build_config.yaml
 #   template/conda_build_config.yaml
 #
+#   And documentation:
+#   framework/doc/packages_config.yml
+#
 # As well as any directions pertaining to modifying those files.
-{% set version = "2023.10.27" %}
+{% set version = "2023.11.06" %}
 
 package:
   name: moose-dev

diff --git a/conda/moose/conda_build_config.yaml b/conda/moose/conda_build_config.yaml
@@ -1,5 +1,5 @@
 moose_dev:
-  - moose-dev 2023.10.27
+  - moose-dev 2023.11.06
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/mpich/meta.yaml b/conda/mpich/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 build = 12 %}
+{% set build = 13 %}
 {% set version = "4.0.2" %}
 
 # permanent

diff --git a/conda/peacock/conda_build_config.yaml b/conda/peacock/conda_build_config.yaml
@@ -1,5 +1,5 @@
 moose_mpich:
-  - moose-mpich 4.0.2 build_12
+  - moose-mpich 4.0.2 build_13
 
 # 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 = "2023.10.23" %}
+{% set version = "2023.11.06" %}
 
 package:
   name: moose-peacock

diff --git a/conda/petsc/conda_build_config.yaml b/conda/petsc/conda_build_config.yaml
@@ -1,5 +1,5 @@
 moose_mpich:
-  - moose-mpich 4.0.2 build_12
+  - moose-mpich 4.0.2 build_13
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/petsc/meta.yaml b/conda/petsc/meta.yaml
@@ -2,9 +2,12 @@
 # REMEMBER TO UPDATE the .yaml files for the following packages:
 #   libmesh/*
 #
+#   And documentation:
+#   framework/doc/packages_config.yml
+#
 # 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 = "3.20.0" %}
 
 # permanent

diff --git a/conda/pyhit/conda_build_config.yaml b/conda/pyhit/conda_build_config.yaml
@@ -1,5 +1,5 @@
 moose_wasp:
-  moose-wasp 2023.10.24
+  moose-wasp 2023.11.06
 
 moose_python:
   - python 3.10

diff --git a/conda/pyhit/meta.yaml b/conda/pyhit/meta.yaml
@@ -1,5 +1,4 @@
-{% set build = 0 %}
-{% set version = "2023.10.24" %}
+{% set version = "2023.11.06" %}
 
 package:
   name: moose-pyhit
@@ -9,7 +8,8 @@ source:
   git_url: https://github.com/milljm/moose-pyhit.git
 
 build:
-  number:              # [linux,osx]
+  number: 0
+  string: build_0
   skip: true           # [win]
   pin_depends: record
 

diff --git a/conda/template/conda_build_config.yaml b/conda/template/conda_build_config.yaml
@@ -1,5 +1,5 @@
 moose_dev:
-  - moose-dev 2023.10.27
+  - moose-dev 2023.11.06
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/wasp/meta.yaml b/conda/wasp/meta.yaml
@@ -5,9 +5,7 @@
 #
 # As well as any directions pertaining to modifying those files.
 # ALSO: Follow the directions in scripts/tests/versioner_hashes.yaml
-{% set build = 0 %}
-{% set strbuild = "build_" + build|string %}
-{% set version = "2023.10.24" %}
+{% set version = "2023.11.06" %}
 
 package:
   name: moose-wasp
@@ -18,8 +16,8 @@ source:
   - path: ../../scripts/configure_wasp.sh
 
 build:
-  number: {{ build }}
-  string: {{ strbuild }}
+  number: 0
+  string: build_0
   skip: true  # [win]
   script_env:
     - MOOSE_JOBS

diff --git a/docker_ci/Dockerfile b/docker_ci/Dockerfile
@@ -114,7 +114,7 @@ if [ ! -d $PETSC_DIR/lib/petsc ]; then exit 1; fi
 #-----------------------------------------------------------------------------#
 # Install Libmesh to system path
 #-----------------------------------------------------------------------------#
-ARG LIBMESH_REV=ceff84386bdc83d87e9eb98ac3a9b745711e415a
+ARG LIBMESH_REV=b2248b506847fd72d37cff56b6f4d8432f6c7e92
 ARG LIBMESH_OPTIONS
 ARG LIBMESH_METHODS="opt dbg"
 ENV LIBMESH_DIR=/usr/local \

diff --git a/framework/doc/packages_config.yml b/framework/doc/packages_config.yml
@@ -5,4 +5,5 @@ minimum_clang: 10.0.1
 minimum_python: 3.7
 mpich: 4.0.2
 petsc_alt: 3.11.4
-petsc: 3.16.6
+petsc: 3.20.0
+moose_dev: 2023.11.06
diff --git a/framework/include/utils_nonunity/SymmetricRankTwoTensor.h b/framework/include/utils_nonunity/SymmetricRankTwoTensor.h
@@ -143,9 +143,6 @@ class SymmetricRankTwoTensorTempl
       const T & S11, const T & S22, const T & S33, const T & S23, const T & S13, const T & S12);
 
 public:
-  /// Copy assignment operator must be defined if used
-  SymmetricRankTwoTensorTempl(const SymmetricRankTwoTensorTempl<T> & a) = default;
-
   /// Copy constructor from TensorValue<T>
   explicit SymmetricRankTwoTensorTempl(const TensorValue<T> & a);
 

diff --git a/framework/src/meshgenerators/XYDelaunayGenerator.C b/framework/src/meshgenerators/XYDelaunayGenerator.C
@@ -363,7 +363,9 @@ XYDelaunayGenerator::generate()
         next_hole_boundary_point[mh.point(pi - 1)] = mh.point(pi);
       next_hole_boundary_point[mh.point(np - 1)] = mh.point(0);
 
+#ifndef NDEBUG
       int found_hole_sides = 0;
+#endif
       for (auto elem : hole_mesh.element_ptr_range())
       {
         if (elem->dim() != 2)
@@ -377,14 +379,18 @@ XYDelaunayGenerator::generate()
             if (it_s->second == elem->point((s + 1) % ns))
             {
               hole_boundary_info.add_side(elem, s, new_hole_bcid);
+#ifndef NDEBUG
               ++found_hole_sides;
+#endif
             }
         }
       }
       mooseAssert(found_hole_sides == np, "Failed to find full outer boundary of meshed hole");
 
       auto & mesh_boundary_info = mesh->get_boundary_info();
+#ifndef NDEBUG
       int found_inner_sides = 0;
+#endif
       for (auto elem : mesh->element_ptr_range())
       {
         auto ns = elem->n_sides();
@@ -395,7 +401,9 @@ XYDelaunayGenerator::generate()
             if (it_s->second == elem->point(s))
             {
               mesh_boundary_info.add_side(elem, s, inner_bcid);
+#ifndef NDEBUG
               ++found_inner_sides;
+#endif
             }
         }
       }

diff --git a/framework/src/utils/FillBetweenPointVectorsTools.C b/framework/src/utils/FillBetweenPointVectorsTools.C
@@ -508,13 +508,11 @@ isBoundarySimpleClosedLoop(MeshBase & mesh,
   max_node_radius = 0.0;
   BoundaryInfo & boundary_info = mesh.get_boundary_info();
   auto side_list_tmp = boundary_info.build_side_list();
-  unsigned int elem_counter = 0;
   std::vector<std::pair<dof_id_type, dof_id_type>> boundary_node_assm;
   for (unsigned int i = 0; i < side_list_tmp.size(); i++)
   {
     if (std::get<2>(side_list_tmp[i]) == bid)
     {
-      elem_counter++;
       // store two nodes of each side
       boundary_node_assm.push_back(std::make_pair(mesh.elem_ptr(std::get<0>(side_list_tmp[i]))
                                                       ->side_ptr(std::get<1>(side_list_tmp[i]))

diff --git a/libmesh b/libmesh
diff --git a/modules/doc/content/getting_started/installation/install_conda_moose.md b/modules/doc/content/getting_started/installation/install_conda_moose.md
@@ -5,9 +5,9 @@ Create a unique conda environment for [!ac](MOOSE), named `moose`, and install t
 packages:
 !style-end!
 
-```bash
-mamba create -n moose moose-dev
-```
+!package! code
+mamba create -n moose moose-dev=__MOOSE_DEV__
+!package-end!
 
 After the installation completes, activate the new environment:
 

diff --git a/modules/doc/content/getting_started/installation/true_update_conda.md b/modules/doc/content/getting_started/installation/true_update_conda.md
@@ -1,9 +1,11 @@
 Update Conda:
 
-```bash
+!package! code
+mamba activate base
+mamba env remove -n moose
+mamba create moose moose-dev=__MOOSE_DEV__
 mamba activate moose
-mamba update moose-dev
-```
+!package-end!
 
 !alert note title=Always Update MOOSE and the Conda/Mamba packages together
 There is a tight dependency between libraries being provided by Conda, and what libraries MOOSE

diff --git a/modules/doc/content/help/faq/build_issues.md b/modules/doc/content/help/faq/build_issues.md
@@ -7,10 +7,12 @@ date.
 - Verify the Conda Environment is active and up to date, with the latest version of our moose
   packages:
 
-  ```bash
+  !package! code
+  mamba activate base
+  mamba env remove -n moose
+  mamba create -n moose moose-dev=__MOOSE_DEV__
   mamba activate moose
-  mamba update moose-dev
-  ```
+  !package-end!
 
   if `mamba activate moose` failed, see [Conda Issues](help/troubleshooting.md#condaissues) above.