Merge pull request idaholab#29104 from milljm/29103-user-override-for…

…reals
aprilnovak · Jan 4, 2025 · 1e17680 · 1e17680
2 parents 44e87a4 + 927f90e
commit 1e17680
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diff --git a/apptainer/app.def b/apptainer/app.def
@@ -36,6 +36,8 @@
 
 BootStrap: {{ APPTAINER_BOOTSTRAP }}
 From: {{ APPTAINER_FROM }}
+# MOOSE-NCRC key
+Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
 
 %setup
     # Load jinja vars

diff --git a/...i/.singularity.d/env/99-user-overrides.sh → ...i/.singularity.d/env/89-user-overrides.sh b/...i/.singularity.d/env/99-user-overrides.sh → ...i/.singularity.d/env/89-user-overrides.sh
diff --git a/apptainer/libmesh.def b/apptainer/libmesh.def
@@ -27,6 +27,8 @@
 
 BootStrap: {{ APPTAINER_BOOTSTRAP }}
 From: {{ APPTAINER_FROM }}
+# MOOSE-NCRC key
+Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
 
 %environment
     # From moose-libmesh

diff --git a/apptainer/moose-dev.def b/apptainer/moose-dev.def
@@ -23,9 +23,6 @@
 {#- Location to install miniforge3                                                            -#}
 {%- set MOOSE_MINIFORGE = '/opt/miniforge3' -%}
 
-{#- Name of the environment to create in conda                                                -#}
-{%- set MOOSE_CONDA_ENV_NAME = 'moose' -%}
-
 {#- The installation location for wasp                                                        -#}
 {%- set WASP_DIR = '/opt/wasp' -%}
 {#- The installation location for gperftools                                                  -#}
@@ -43,10 +40,12 @@
 
 BootStrap: {{ APPTAINER_BOOTSTRAP }}
 From: {{ APPTAINER_FROM }}
+# MOOSE-NCRC key
+Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
 
 %environment
     export PATH={{ MOOSE_MINIFORGE }}/bin:/opt/code-server/bin:$PATH
-    source activate {{ MOOSE_MINIFORGE }}/envs/{{ MOOSE_CONDA_ENV_NAME }}
+    source activate {{ MOOSE_MINIFORGE }}
 
     export WASP_DIR={{ WASP_DIR }}
     export PATH=${WASP_DIR}/bin:$PATH
@@ -153,10 +152,7 @@ From: {{ APPTAINER_FROM }}
     # Create list of Conda Packages to install
     MAMBA_PACKAGES="moose-tools=${MOOSE_TOOLS_VERSION}"
     # Install packages
-    mamba create -yq -n ${MOOSE_CONDA_ENV_NAME} python=${PYTHON_VERSION} ${MAMBA_PACKAGES}
-
-    # Activate the new environment
-    source activate ${MOOSE_MINIFORGE}/envs/${MOOSE_CONDA_ENV_NAME}
+    conda install -yq python=${PYTHON_VERSION} ${MAMBA_PACKAGES}
     # Needed for coverage
     pip3 --no-cache install lcov-cobertura
 

diff --git a/apptainer/mpi.def b/apptainer/mpi.def
@@ -27,14 +27,14 @@
 {#- The files directory for this definition                                                   -#}
 {%- set FILES_DIR = MOOSE_DIR + '/apptainer/files/mpi' -%}
 
+Bootstrap: oras
 {%- if ALTERNATE_FROM == "gcc_min" or ALTERNATE_FROM == "clang" or ALTERNATE_FROM == "clang_min" %}
-Bootstrap: docker
-From: rockylinux:8.9.20231119
+From: mooseharbor.hpc.inl.gov/base/rocky-x86_64:8.10-0
 {%- else %}
-BootStrap: oras
-From: mooseharbor.hpc.inl.gov/moose-hpcbase/rocky-x86_64:8.9-0
+From: mooseharbor.hpc.inl.gov/moose-hpcbase/rocky-x86_64:8.10-0
 {%- endif %}
-
+# Logan Harbour
+Fingerprints: 841AF5A51549CAFFFB474F65207184EA34A4BD48
 %environment
     # Fix locale warnings
     export LC_ALL=C
@@ -102,13 +102,10 @@ EOF
 {%- endif %}
 
     # Additional installs
-    dnf install -y vim tmux emacs wget rsync hostname python3-pyyaml python3-devel python39 \
-                   make cmake bzip2 diffutils bison flex perl-IO-Compress perl-JSON perl-JSON-PP \
-                   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 tar git
-    # After epel-release
-    dnf install -y glpk-devel patchelf lcov
+    dnf install -y tmux emacs make cmake diffutils bison flex perl-IO-Compress perl-JSON \
+        perl-JSON-PP libtirpc libtirpc-devel zlib-devel patch patchutils libpng \
+        libpng-devel valgrind cppunit doxygen fftw-devel gsl-devel libtool autoconf \
+        automake cppunit-devel glpk-devel patchelf lcov
 
 {%- if ALTERNATE_FROM == "clang" %}
     # Installing system Clang, and its GCC GNU dependencies
@@ -131,18 +128,6 @@ EOF
     source /opt/rh/gcc-toolset-${CLANG_GCC_VERSION}/enable
 {%- endif %}
 
-    # Make python default to python3.9
-    alternatives --set python /usr/bin/python3.9
-    alternatives --set python3 /usr/bin/python3.9
-
-    # We need git lfs
-    mkdir ${ROOT_BUILD_DIR}/gitlfs
-    cd ${ROOT_BUILD_DIR}/gitlfs
-    curl -L -O https://github.com/git-lfs/git-lfs/releases/download/v3.2.0/git-lfs-linux-amd64-v3.2.0.tar.gz
-    tar -xf git-lfs-linux-amd64-v3.2.0.tar.gz
-    cd git-lfs-3.2.0
-    ./install.sh
-
 {%- if ALTERNATE_FROM == "clang_min" %}
     # Build minimum Clang {{ MIN_CLANG_VERSION }} from source
     cd ${ROOT_BUILD_DIR}
@@ -229,4 +214,4 @@ EOF
 %files
     {{ MOOSE_DIR }}/apptainer/set_prompt.bash {{ SET_PROMPT_SCRIPT }}
     {{ FILES_DIR }}/.singularity.d/env/01-fix-exec.sh /.singularity.d/env/01-fix-exec.sh
-    {{ FILES_DIR }}/.singularity.d/env/99-user-overrides.sh /.singularity.d/env/99-user-overrides.sh
+    {{ FILES_DIR }}/.singularity.d/env/89-user-overrides.sh /.singularity.d/env/89-user-overrides.sh
diff --git a/apptainer/petsc.def b/apptainer/petsc.def
@@ -22,6 +22,8 @@
 
 BootStrap: {{ APPTAINER_BOOTSTRAP }}
 From: {{ APPTAINER_FROM }}
+# MOOSE-NCRC key
+Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
 
 %environment
     # Set the MPI environment

diff --git a/apptainer/remove_channels.def b/apptainer/remove_channels.def
@@ -5,6 +5,8 @@
 
 BootStrap: {{ APPTAINER_BOOTSTRAP }}
 From: {{ APPTAINER_FROM }}
+# MOOSE-NCRC key
+Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
 
 %post
     readarray -t channels <<< "$(conda config --show channels)"

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 2024.11.13
+  - moose-mpi 2024.12.23
 
 #### 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 = 4 %}
+{% set build = 5 %}
 {% 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 3.22.1.193.g72c1e49ee3d mpich_0
-  - moose-petsc 3.22.1.193.g72c1e49ee3d openmpi_0
+  - moose-petsc 3.22.1.193.g72c1e49ee3d mpich_1
+  - moose-petsc 3.22.1.193.g72c1e49ee3d openmpi_1
 
 moose_libmesh_vtk:
-  - moose-libmesh-vtk 9.3.0 mpich_4
-  - moose-libmesh-vtk 9.3.0 openmpi_4
+  - moose-libmesh-vtk 9.3.0 mpich_5
+  - moose-libmesh-vtk 9.3.0 openmpi_5
 
 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 = "2024.12.02" %}
 
 package:

diff --git a/conda/moose-dev/conda_build_config.yaml b/conda/moose-dev/conda_build_config.yaml
@@ -3,17 +3,17 @@ mpi:
   - openmpi
 
 moose_libmesh:
-  - moose-libmesh 2024.12.02 mpich_0
-  - moose-libmesh 2024.12.02 openmpi_0
+  - moose-libmesh 2024.12.02 mpich_1
+  - moose-libmesh 2024.12.02 openmpi_1
 
 moose_wasp:
-  - moose-wasp 2024.11.13
+  - moose-wasp 2024.12.23
 
 moose_tools:
-  - moose-tools 2024.11.13
+  - moose-tools 2024.12.23
 
 moose_peacock:
-  - moose-peacock 2024.11.13
+  - moose-peacock 2024.12.23
 
 zip_keys:
   - mpi

diff --git a/conda/moose-dev/meta.yaml b/conda/moose-dev/meta.yaml
@@ -2,7 +2,7 @@
 # REMEMBER TO UPDATE the .yaml files for the following packages:
 #   moose/conda_build_config.yaml
 # As well as any directions pertaining to modifying those files.
-{% set version = "2024.12.02" %}
+{% set version = "2024.12.23" %}
 
 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 2024.12.02
+  - moose-dev 2024.12.23
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

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 = "2024.11.13" %}
+{% set version = "2024.12.23" %}
 
 # HDF5 Version
 {% set hdf5_version = "1.14.2" %}

diff --git a/conda/peacock/conda_build_config.yaml b/conda/peacock/conda_build_config.yaml
@@ -3,4 +3,4 @@ mpi:
   - openmpi
 
 moose_mpi:
-  - moose-mpi 2024.11.13
+  - moose-mpi 2024.12.23
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 = "2024.11.13" %}
+{% set version = "2024.12.23" %}
 
 package:
   name: moose-peacock
@@ -25,6 +25,7 @@ requirements:
     - pandas
     - pyqt
     - matplotlib !=3.9.0
+    - libgl                           # [linux]
     - vtk
   run_constrained:
     # Python max constraints

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 2024.11.13
+  - moose-mpi 2024.12.23
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

diff --git a/conda/petsc/meta.yaml b/conda/petsc/meta.yaml
@@ -7,7 +7,7 @@
 #
 # 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 = "3.22.1.193.g72c1e49ee3d" %}
 
 package:

diff --git a/conda/pprof/meta.yaml b/conda/pprof/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2024.11.13" %}
+{% set version = "2024.12.23" %}
 {% set build = 0 %}
 {% set strbuild = "build_" + build|string %}
 

diff --git a/conda/seacas/meta.yaml b/conda/seacas/meta.yaml
@@ -1,5 +1,5 @@
 # MAKE SURE THAT seacas_version and seacas_git_rev match if performing a version update!
-{% set build = "1" %}
+{% set build = "2" %}
 {% set seacas_version = "2024.08.15" %}
 {% set seacas_git_rev = "v2024-08-15" %}
 {% set strbuild = "build_" + build|string %}
@@ -26,7 +26,7 @@ requirements:
     - {{ moose_gfortran }}
     - {{ moose_ccompiler }}
     - {{ moose_cxxcompiler }}
-    - xorg-libx11
+    - xorg-libx11 1.8.9
     - cmake
     - make
     - automake

diff --git a/conda/tools/meta.yaml b/conda/tools/meta.yaml
@@ -3,7 +3,7 @@
 #   moose-dev/*
 #
 # As well as any directions pertaining to modifying those files.
-{% set version = "2024.11.13" %}
+{% set version = "2024.12.23" %}
 
 package:
   name: moose-tools
@@ -45,6 +45,7 @@ requirements:
     - packaging
     - pandas
     - paramiko
+    - psutil
     - psycopg2
     - pyarrow
     - pybtex

diff --git a/conda/wasp/build_pyhit.sh b/conda/wasp/build_pyhit.sh
@@ -5,6 +5,7 @@ do_build(){
     rm -rf "${SP_DIR:?}/pyhit/"
     cp -R pyhit "${SP_DIR:?}/"
     cd "${SRC_DIR:?}/src"
+    make clean
     make bindings
     install hit.so "${SP_DIR:?}/pyhit/" || return 1
     cat > "${SP_DIR:?}/pyhit-${PKG_VERSION:?}.egg-info" <<FAKE_EGG || exit 1

diff --git a/conda/wasp/message.patch b/conda/wasp/message.patch
@@ -0,0 +1,13 @@
+diff --git a/pyhit/mooseutils/message.py b/pyhit/mooseutils/message.py
+index 98cfc029c7..fc89230e74 100644
+--- a/pyhit/mooseutils/message.py
++++ b/pyhit/mooseutils/message.py
+@@ -8,7 +8,7 @@
+ #* https://www.gnu.org/licenses/lgpl-2.1.html
+ import os
+ import traceback
+-from mooseutils import colorText
++from . import colorText
+
+ try:
+     from PyQt5 import QtWidgets, QtCore
diff --git a/conda/wasp/meta.yaml b/conda/wasp/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 version = "2024.11.13" %}
+{% set version = "2024.12.23" %}
 
 package:
   name: moose-wasp
@@ -25,8 +25,13 @@ source:
   - path: ../../python/pyhit/pyhit.py
     folder: pyhit
   - path: ../functions/retry_build.sh
+  - path: pyhit/__init__.py
+    folder: pyhit
+  - path: pyhit/mooseutils/__init__.py
+    folder: pyhit/mooseutils
   - patches:
       - pyhit.patch
+      - message.patch
 
 build:
   number: 0
@@ -72,14 +77,13 @@ outputs:
         - make
         - cython
         - setuptools
-      host:
-        - {{ moose_python }}
       run:
         - {{ moose_python }}
         - {{ pin_subpackage("moose-wasp-base", exact=True) }}
     test:
       imports:
         - pyhit
+      script: test_pyhit.py
 
   - name: moose-wasp
     requirements:

diff --git a/conda/wasp/test_pyhit.py b/conda/wasp/test_pyhit.py
@@ -0,0 +1,9 @@
+#!/usr/bin/env python3
+""" Test pyhit """
+import sys
+
+if __name__ == '__main__':
+    print('\n\n\nTEST loading hit library\n')
+    from pyhit import hit
+    print(f'Successs: {hit.__file__}')
+    sys.exit()
diff --git a/scripts/tests/versioner_hashes.yaml b/scripts/tests/versioner_hashes.yaml
@@ -390,3 +390,10 @@ cece3f711bd9c235af31c9d5a4c54e292400ecc1: #29074
   libmesh: d060615
   wasp: 0b6b0db
   moose-dev: a1e01c7
+2d96c03b18667fc623198e73e1ad1f2a8727232a: #29103 #29090
+  tools: 5abb5f2
+  mpi: 82bbd28
+  petsc: e78a9a4
+  libmesh: b8b3d69
+  wasp: 2fbcef5
+  moose-dev: 5e9be02