Merge branch 'next' into PR_same_app

idaholab · Mar 28, 2022 · 04da9bf · 04da9bf
2 parents abf344c + c90b1f0
commit 04da9bf
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diff --git a/CODEOWNERS b/CODEOWNERS
@@ -1,6 +1,5 @@
 /conda @loganharbour @milljm @cticenhour
 /docker_ci @loganharbour
-/hooks @loganharbour
 /m4 @lindsayad
 
 /COPYING @permcody

diff --git a/conda/libmesh-vtk/build.sh b/conda/libmesh-vtk/build.sh
@@ -30,15 +30,14 @@ cmake .. -G "Ninja" \
     -DVTK_GROUP_ENABLE_Web:STRING=NO \
     -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT}
 
-CORES=$(echo "${CPU_COUNT:-2} / 2" | bc)
-ninja install -v -j $CORES
+ninja install -v -j ${MOOSE_JOBS:-2}
 
 # VTK 9.1 now places libs in lib64 when installed on linux, linking to the "expected" location of lib
 if [[ $(uname) == Linux ]]; then
     ln -s ${VTK_PREFIX}/lib64 ${VTK_PREFIX}/lib
 fi
 
-# Set LIBMESH_DIR environment variable for those that need it
+# Set VTK environment variables for those that need it
 mkdir -p "${PREFIX}/etc/conda/activate.d" "${PREFIX}/etc/conda/deactivate.d"
 cat <<EOF > "${PREFIX}/etc/conda/activate.d/activate_${PKG_NAME}.sh"
 export VTKLIB_DIR=${VTK_PREFIX}/lib

diff --git a/conda/libmesh-vtk/meta.yaml b/conda/libmesh-vtk/meta.yaml
@@ -1,5 +1,5 @@
 # Do not use jinja templating (A physical change to this file is required to trigger a build)
-{% set build = 4 %}
+{% set build = 5 %}
 {% set strbuild = "build_" + build|string %}
 {% set vtk_version = "9.1.0" %}
 {% set friendly_version = "9.1" %}
@@ -17,6 +17,8 @@ build:
   number: {{ build }}
   string: {{ strbuild }}
   skip: true  # [win]
+  script_env:
+    - MOOSE_JOBS
 
 requirements:
   build:

diff --git a/conda/libmesh/build.sh b/conda/libmesh/build.sh
@@ -79,7 +79,7 @@ LIBMESH_DIR=${PREFIX}/libmesh \
                     --with-vtk-include=${BUILD_PREFIX}/libmesh-vtk/include/vtk-${SHORT_VTK_NAME} \
                     $*
 
-CORES=$(echo "${CPU_COUNT:-2} / 2" | bc)
+CORES=${MOOSE_JOBS:-2}
 make -j $CORES
 make install
 sed_replace

diff --git a/conda/libmesh/meta.yaml b/conda/libmesh/meta.yaml
@@ -1,7 +1,7 @@
 # Do not use jinja templating (A physical change to this file is required to trigger a build)
 {% set build = 0 %}
 {% set strbuild = "build_" + build|string %}
-{% set version = "2022.03.02" %}
+{% set version = "2022.03.18" %}
 
 package:
   name: moose-libmesh
@@ -15,6 +15,8 @@ build:
   number: {{ build }}
   string: {{ strbuild }}
   skip: true                                            # [win]
+  script_env:
+    - MOOSE_JOBS
 
 requirements:
   build:
@@ -24,7 +26,6 @@ requirements:
     - make                                              # [arm64]
     - m4                                                # [arm64]
     - pkg-config
-    - {{ moose_ld64 }}                                  # [osx]
     - {{ moose_libmesh_vtk }}
     - {{ moose_petsc }}
 

diff --git a/conda/mpich/build.sh b/conda/mpich/build.sh
@@ -1,99 +1,14 @@
 #!/bin/bash
 set -eu
-export PATH=/bin:$PATH
 
-export FCFLAGS="$FFLAGS"
-export CC=$(basename "$CC")
-export CXX=$(basename "$CXX")
-export FC=$(basename "$FC")
-
-if [[ $HOST == arm64-apple-darwin20.0.0 ]]; then
-    # use Conda-Forge's Arm64 config.guess and config.sub, see
-    # https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/
-    list_config_to_patch=$(find ./ -name config.guess | sed -E 's/config.guess//')
-    for config_folder in $list_config_to_patch; do
-        echo "copying config to $config_folder ...\n"
-        cp -v $BUILD_PREFIX/share/gnuconfig/config.* $config_folder
-    done
-    ./autogen.sh
-fi
-
-# In order to set a CXXFLAGS during moose-mpich activation with the proper C++
-# standard (as clang and gcc from conda-forge still default to C++14), we extract
-# what moose_cxx gives us here, before we unset it. The  "-fdebug-prefix-map"
-# flags are also removed, as they are specific to the conda build process.
-TEMP_CXXFLAGS=${CXXFLAGS%%-fdebug-prefix-map*}
-# Finally, swap "-std=c++14" with "-std=c++17" to set our basic standard requirement.
-ACTIVATION_CXXFLAGS=${TEMP_CXXFLAGS/-std=c++14/-std=c++17}
-
-unset LDFLAGS CPPFLAGS CFLAGS CXXFLAGS FFLAGS FCFLAGS F90 F77
-export LDFLAGS="-L$PREFIX/lib -Wl,-rpath,$PREFIX/lib"
-export LIBRARY_PATH="$PREFIX/lib"
-
-if [[ $(uname) == Darwin ]]; then
-    if [[ $target_platform == osx-arm64 ]]; then
-        CTUNING="-mcpu=apple-a12 -I$PREFIX/include"
-        FTUNING="-march=armv8.3-a -I$PREFIX/include"
-        OPTIONS="--disable-opencl --enable-cxx --enable-fortran"
-        export pac_cv_f77_accepts_F=yes
-        export pac_cv_f77_flibs_valid=unknown
-        export pac_cv_f77_sizeof_double_precision=8
-        export pac_cv_f77_sizeof_integer=4
-        export pac_cv_f77_sizeof_real=4
-        export pac_cv_fc_accepts_F90=yes
-        export pac_cv_fc_and_f77=yes
-        export pac_cv_fc_module_case=lower
-        export pac_cv_fc_module_ext=mod
-        export pac_cv_fc_module_incflag=-I
-        export pac_cv_fc_module_outflag=-J
-        export pac_cv_fort90_real8=yes
-        export pac_cv_fort_integer16=yes
-        export pac_cv_fort_integer1=yes
-        export pac_cv_fort_integer2=yes
-        export pac_cv_fort_integer4=yes
-        export pac_cv_fort_integer8=yes
-        export pac_cv_fort_real16=no
-        export pac_cv_fort_real4=yes
-        export pac_cv_fort_real8=yes
-        export pac_cv_prog_f77_and_c_stdio_libs=none
-        export pac_cv_prog_f77_exclaim_comments=yes
-        export pac_cv_prog_f77_has_incdir=-I
-        export pac_cv_prog_f77_library_dir_flag=-L
-        export pac_cv_prog_f77_mismatched_args=yes
-        export pac_cv_prog_f77_mismatched_args_parm=
-        export pac_cv_prog_f77_name_mangle='lower uscore'
-        export pac_cv_prog_fc_and_c_stdio_libs=none
-        export pac_cv_prog_fc_int_kind_16=8
-        export pac_cv_prog_fc_int_kind_8=4
-        export pac_cv_prog_fc_works=yes
-        export pac_MOD='mod'
-    else
-        CTUNING="-march=core2 -mtune=haswell -I$PREFIX/include"
-        FTUNING="-march=core2 -mtune=haswell -I$PREFIX/include"
-        OPTIONS=""
-    fi
-    SHARED="clang"
-else
-    SHARED="gcc"
-    CTUNING="-march=nocona -mtune=haswell -I$PREFIX/include"
-    FTUNING="-march=nocona -mtune=haswell -I$PREFIX/include"
-    OPTIONS=""
-fi
-
-./configure --prefix="${PREFIX}" \
-            --enable-shared \
-            --enable-sharedlibs="${SHARED}" \
-            --enable-fast=O2 \
-            --enable-debuginfo \
-            --enable-two-level-namespace \
-            --with-device=ch3 \
-            CC="${CC}" CXX="${CXX}" FC="${FC}" F77="${FC}" F90="" \
-            CFLAGS="${CTUNING}" CXXFLAGS="${CTUNING}" FFLAGS="${FTUNING}" LDFLAGS="${LDFLAGS}" \
-            FCFLAGS="${FTUNING}" F90FLAGS="" F77FLAGS="" \
-            ${OPTIONS}
-CORES=$(echo "${CPU_COUNT:-2} / 2" | bc)
-make -j $CORES
-make install
+# In order to set CXXFLAGS during moose-mpich activation with the proper C++
+# standard, we first extract what mpich-mpicxx gives us during build. Just in case
+# the clang or gcc conda-forge packages set a standard, remove any occurence of
+# "-std=c++XX"
+TEMP_CXXFLAGS=${CXXFLAGS//-std=c++[0-9][0-9]}
+# The  "-fdebug-prefix-map" flags then need to be removed, as they are specific
+# to the conda build process. Finally, `-std=c++17` can be appended to the end.
+ACTIVATION_CXXFLAGS=${TEMP_CXXFLAGS%%-fdebug-prefix-map*}-std=c++17
 
 # Set MPICH environment variables for those that need it, and set CXXFLAGS using our ACTIVATION_CXXFLAGS variable
 mkdir -p "${PREFIX}/etc/conda/activate.d" "${PREFIX}/etc/conda/deactivate.d"

diff --git a/conda/mpich/conda_build_config.yaml b/conda/mpich/conda_build_config.yaml
@@ -2,7 +2,7 @@
 ## Any changes made will require additional changes to any item above that.
 
 moose_libmesh:
-  - moose-libmesh 2022.03.02 build_0
+  - moose-libmesh 2022.03.18 build_0
 
 SHORT_VTK_NAME:
   - 9.1
@@ -11,13 +11,13 @@ vtk_version:
   - 9.1.0
 
 moose_libmesh_vtk:
-  - moose-libmesh-vtk 9.1.0 build_4
+  - moose-libmesh-vtk 9.1.0 build_5
 
 moose_petsc:
-  - moose-petsc 3.15.1 build_7
+  - moose-petsc 3.16.5 build_0
 
 moose_mpich:
-  - moose-mpich 3.4.2 build_3
+  - moose-mpich 4.0.1 build_0
 
 #### MOOSE_TOOLS stuff (order is important, must match python version order)
 moose_python:
@@ -194,55 +194,25 @@ zip_keys:
   - moose_sympy
 
 #### Compilers
-moose_cc:                                                   # [unix]
-  - gcc_linux-64 9.3.0 h7247604_29                          # [linux]
-  - clang_osx-64 12.0.1 h633439f_6                          # [not arm64 and osx]
-  - clang_osx-arm64 12.0.1 h54d7cd3_0                       # [arm64]
-
-moose_cxx:                                                  # [unix]
-  - gxx_linux-64 9.3.0 h0d07fa4_29                          # [linux]
-  - clangxx_osx-64 12.0.1 hdb584c0_6                        # [not arm64 and osx]
-  - clangxx_osx-arm64 12.0.1 hb84c830_0                     # [arm64]
-
-moose_fortran:                                              # [unix]
-  - gfortran_linux-64 9.3.0 ha1c937c_29                     # [linux]
-  - gfortran_osx-64 9.3.0 h18f7dce_15                       # [not arm64 and osx]
-  - gfortran_osx-arm64 11.0.1.dev0 h57527a5_14              # [arm64]
-
-moose_impl:                                                 # [linux]
-  - gcc_impl_linux-64 9.3.0 h70c0ae5_19                     # [linux]
-
-moose_impl_xx:                                              # [linux]
-  - gxx_impl_linux-64 9.3.0 hd87eabc_19                     # [linux]
-
-moose_libgcc:                                               # [linux]
-  - libgcc-devel_linux-64 9.3.0 h7864c58_19                 # [linux]
-
-moose_libstd:                                               # [linux]
-  - libstdcxx-devel_linux-64 9.3.0 hb016644_19              # [linux]
-
-moose_sysroot:                                              # [linux]
-  - sysroot_linux-64 2.17 h4a8ded7_13                       # [linux]
-
-moose_libcxx:                                               # [osx]
-  - libcxx 12.0.1 habf9029_1                                # [not arm64 and osx]
-  - libcxx 12.0.1 h168391b_0                                # [arm64]
-
-moose_libclang:                                             # [osx]
-  - libclang 13.0.0 default_he082bbe_0                      # [not arm64 and osx]
-  - libclang 12.0.1 default_h2cfa9b4_4                      # [arm64]
-
-moose_openmp:                                               # [osx]
-  - llvm-openmp 12.0.1 hda6cdc1_1                           # [not arm64 and osx]
-  - llvm-openmp 12.0.1 hf3c4609_1                           # [arm64]
-
-moose_llvm_tools:                                           # [osx]
-  - llvm-tools 12.0.1 hd011deb_2                            # [not arm64 and osx]
-  - llvm-tools 12.0.1 h93073aa_2                            # [arm64]
-
-moose_ld64:                                                 # [osx]
-  - ld64 609 hd2e7500_4                                     # [not arm64 and osx]
-  - ld64_osx-arm64 530 ha291f0b_23                          # [arm64]
+base_mpich:
+  - mpich 4.0.1 h846660c_100                               # [linux]
+  - mpich 4.0.1 hd33e60e_100                               # [not arm64 and osx]
+  - mpich 4.0.1 hd4b5bf3_100                               # [arm64]
+
+base_mpicc:
+  - mpich-mpicc 4.0.1 hb600da9_100                         # [linux]
+  - mpich-mpicc 4.0.1 h4fd26ce_100                         # [not arm64 and osx]
+  - mpich-mpicc 4.0.1 haad7f49_100                         # [arm64]
+
+base_mpicxx:
+  - mpich-mpicxx 4.0.1 h166bdaf_100                        # [linux]
+  - mpich-mpicxx 4.0.1 h5eb16cf_100                        # [not arm64 and osx]
+  - mpich-mpicxx 4.0.1 h1c322ee_100                        # [arm64]
+
+base_mpifort:
+  - mpich-mpifort 4.0.1 h924138e_100                       # [linux]
+  - mpich-mpifort 4.0.1 hbb4e6a2_100                       # [not arm64 and osx]
+  - mpich-mpifort 4.0.1 h3e96240_100                       # [arm64]
 
 #### Support Libraries (libMesh and VTK)
 moose_libglu:                                               # [linux]

diff --git a/conda/mpich/meta.yaml b/conda/mpich/meta.yaml
@@ -1,15 +1,13 @@
-{% set build = 3 %}
+{% set build = 0 %}
 {% set strbuild = "build_" + build|string %}
-{% set version = "3.4.2" %}
+{% set version = "4.0.1" %}
 
 package:
   name: moose-mpich
   version: {{ version }}
 
 source:
-  fn: mpich-{{ version }}.tar.gz
-  url: https://www.mpich.org/static/downloads/{{ version }}/mpich-{{ version }}.tar.gz
-  sha256: 5c19bea8b84e8d74cca5f047e82b147ff3fba096144270e3911ad623d6c587bf
+  - path: .
 
 build:
   number: {{ build }}
@@ -20,57 +18,35 @@ build:
 
 requirements:
   build:
-    - {{ moose_cc }}
-    - {{ moose_cxx }}
-    - {{ moose_fortran }}
-    - {{ moose_impl }}          # [linux]
-    - {{ moose_impl_xx }}       # [linux]
-    - {{ moose_libgcc }}        # [linux]
-    - {{ moose_libstd }}        # [linux]
-    - {{ moose_sysroot }}       # [linux]
-    - {{ moose_libcxx }}        # [osx]
-    - {{ moose_libclang }}      # [osx]
-    - {{ moose_openmp }}        # [osx]
-    - {{ moose_llvm_tools }}    # [osx]
-    - {{ moose_ld64 }}          # [osx]
+    - {{ base_mpich }}
+    - {{ base_mpicc }}
+    - {{ base_mpicxx }}
+    - {{ base_mpifort }}
     - autoconf                  # [unix]
     - automake                  # [unix]
     - libtool                   # [unix]
     - make                      # [unix]
     - gnuconfig                 # [arm64]
   host: []
   run:
-    - {{ moose_cc }}
-    - {{ moose_cxx }}
-    - {{ moose_fortran }}
-    - {{ moose_impl }}          # [linux]
-    - {{ moose_impl_xx }}       # [linux]
-    - {{ moose_libgcc }}        # [linux]
-    - {{ moose_libstd }}        # [linux]
-    - {{ moose_sysroot }}       # [linux]
-    - {{ moose_libcxx }}        # [osx]
-    - {{ moose_libclang }}      # [osx]
-    - {{ moose_openmp }}        # [osx]
-    - {{ moose_llvm_tools }}    # [osx]
-    - {{ moose_ld64 }}          # [osx]
+    - {{ base_mpich }}
+    - {{ base_mpicc }}
+    - {{ base_mpicxx }}
+    - {{ base_mpifort }}
     - autoconf                  # [osx]
     - automake                  # [osx]
     - libtool                   # [osx]
     - make                      # [osx]
     - {{ pin_compatible('setuptools', lower_bound='58', upper_bound='60') }}
     - mpi 1.0 mpich
 test:
-  script: run_test.sh
-  files:
-    - mpiexec.sh
-    - tests/helloworld.sh
+  commands:
+    - test -f $PREFIX/etc/conda/activate.d/activate_moose-mpich.sh
 
 about:
-  home: http://www.mpich.org/
-  license: MPICH
-  license_file: COPYRIGHT
-  license_family: Other
-  summary: 'A high performance widely portable implementation of the MPI standard.'
+  home: https://mooseframework.org/
+  license: LGPL 2.1
+  summary: 'A top-level package designed to control environment variables related to conda-forge provided MPICH'
   description: |
     MPICH is a high performance and widely portable implementation of the
     Message Passing Interface (MPI) standard.

diff --git a/conda/mpich/mpiexec.sh b/conda/mpich/mpiexec.sh