End-to-end CUDA container, remove peacock, bump python to 3.13

apptainer/app.def

@@ -6,14 +6,15 @@
 {#- BINARY_NAME: Name of the application binary                                               -#}
 
 {#- Optional jinja arguments                                                                  -#}
+{#- EXTRA_MAMBA_PACKAGES: Extra mamba packages to install                                     -#}
+{#- EXTRA_BINARIES: Colon separated list of extra binaries that this application installs     -#}
 {#- MOOSE_JOBS: Number of jobs to pass to the build                                           -#}
 {#- MOOSE_OPTIONS: Options to pass to the MOOSE configure                                     -#}
 {#- MOOSE_SKIP_DOCS: Set to anything to skip the docs build                                   -#}
 {#- MOOSE_DOCS_FLAGS: Doc options to pass during the make install                             -#}
 {#- METHOD: The method to build; defaults to "opt"                                            -#}
+{#- SKIP_FINGERPRINTS: Set to skip fingerprint verification                                   -#}
 {#- TEST_DIRS: Directories to test in the %test section; defaults to just "tests"             -#}
-{#- EXTRA_MAMBA_PACKAGES: Extra mamba packages to install                                     -#}
-{#- EXTRA_BINARIES: Colon separated list of extra binaries that this application installs     -#}
 
 {#- Civet Specific jinja arguments                                                            -#}
 {#- CIVET_STEP_ALLOWED_TO_FAIL: BOOL, specific to Civet. Available in %post, %test section    -#}
@@ -36,8 +37,10 @@
 
 BootStrap: {{ APPTAINER_BOOTSTRAP }}
 From: {{ APPTAINER_FROM }}
+{%- if SKIP_FINGERPRINTS is not defined %}
 # MOOSE-NCRC key
 Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
+{%- endif %}
 
 %setup
     # Load jinja vars

apptainer/files/moose-dev/pytorch_clang.patch

@@ -0,0 +1,13 @@
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 1813f4418a..73c1c28cb6 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -1151,7 +1151,7 @@ if(USE_DISTRIBUTED AND USE_TENSORPIPE)
+     # Tensorpipe uses cuda_add_library
+     torch_update_find_cuda_flags()
+     add_subdirectory(${PROJECT_SOURCE_DIR}/third_party/tensorpipe)
+-
++    target_compile_options_if_supported(tensorpipe -Wno-missing-template-arg-list-after-template-kw)
+     list(APPEND Caffe2_DEPENDENCY_LIBS tensorpipe)
+     list(APPEND Caffe2_DEPENDENCY_LIBS nlohmann)
+     if(USE_CUDA)

apptainer/libmesh.def

@@ -12,6 +12,7 @@
 {#- LIBMESH_OPTIONS: Options to pass to the libMesh build script                              -#}
 {#- MOOSE_JOBS: Number of jobs to pass to the libMesh build script                            -#}
 {#- METHODS: Methods to build (defaults to all methods)                                       -#}
+{#- SKIP_FINGERPRINTS: Set to skip fingerprint verification                                   -#}
 
 {#- The within-container build directory to use                                               -#}
 {%- set ROOT_BUILD_DIR = '/root/build' -%}
@@ -27,8 +28,10 @@
 
 BootStrap: {{ APPTAINER_BOOTSTRAP }}
 From: {{ APPTAINER_FROM }}
+{%- if SKIP_FINGERPRINTS is not defined %}
 # MOOSE-NCRC key
 Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
+{%- endif %}
 
 %environment
     # From moose-libmesh
@@ -61,8 +64,8 @@ Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
         tar -xf $(basename ${VTK_URL})
 
         # Build VTK
+        mkdir -p ${VTK_DIR}/logs
         cd ${ROOT_BUILD_DIR}/$(basename ${VTK_URL} .tar.gz)
-
         mkdir -p build; cd build
         cmake .. \
             -Wno-dev \
@@ -76,11 +79,12 @@ Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
             -DVTK_BUILD_EXAMPLES:BOOL=OFF \
             -DBUILD_SHARED_LIBS:BOOL=ON \
             -DVTK_USE_MPI:BOOL=ON \
+            -DVTK_USE_CUDA:BOOL=OFF \
             -DVTK_GROUP_ENABLE_Rendering:STRING=DONT_WANT \
             -DVTK_GROUP_ENABLE_Qt::STRING=NO \
             -DVTK_GROUP_ENABLE_Views:STRING=NO \
-            -DVTK_GROUP_ENABLE_Web:STRING=NO
-        make install -j ${MOOSE_JOBS}
+            -DVTK_GROUP_ENABLE_Web:STRING=NO 2>&1 | tee ${VTK_DIR}/logs/cmake.log
+        make install -j ${MOOSE_JOBS} 2>&1 | tee ${VTK_DIR}/logs/install.log
         export VTKINCLUDE_DIR
         export VTKLIB_DIR
     fi
@@ -95,8 +99,10 @@ Fingerprints: 0CFFCAB55E806363601C442D211817B01E0911DB
     # Build libMesh
     umask 022
     cd ${ROOT_BUILD_DIR}
+    mkdir -p ${LIBMESH_DIR}/logs
     METHODS="{{ METHODS or "opt dbg oprof devel" }}"
-    LIBMESH_SRC_DIR=${LIBMESH_SRC_DIR} LIBMESH_DIR=${LIBMESH_DIR} MOOSE_JOBS=${MOOSE_JOBS} METHODS=${METHODS} ./scripts/{{ LIBMESH_BUILD_SCRIPT }} {{ LIBMESH_OPTIONS }} --skip-submodule-update
+    LIBMESH_SRC_DIR=${LIBMESH_SRC_DIR} LIBMESH_DIR=${LIBMESH_DIR} MOOSE_JOBS=${MOOSE_JOBS} METHODS=${METHODS} ./scripts/{{ LIBMESH_BUILD_SCRIPT }} \
+        {{ LIBMESH_OPTIONS }} --skip-submodule-update 2>&1 | tee ${LIBMESH_DIR}/logs/build.log
 
     # Fix possibly bad permissions
     chmod -R o=u-w,g=u-w ${LIBMESH_DIR}