Update MFEM and PETSc #31906
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Update MFEM and PETSc #31906
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nmnobre
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cticenhour,
lindsayad and
recuero
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PR: Updates packages
moosebuild
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Nov 13, 2025
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Job Documentation, step Docs: sync website on 06fbdc0 wanted to post the following: View the site here This comment will be updated on new commits. |
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Job Coverage, step Generate coverage on 2dec510 wanted to post the following: Framework coverageCoverage did not change Modules coverageCoverage did not change Full coverage reportsReports
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@roystgnr need any updates from libmesh? |
loganharbour
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- Please edit the PR comment to include context about the updates, and reference the PR number in the commit that bumps the packages. See #31650 (comment) for an example of the PR comment and fe70eed of the package bump comment
- Include a summary of the bumps in the comment in versioner_hashes.yaml
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Another aside - on package updates, we add all recipes from next and devel |
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For https://civet.inl.gov/job/3382174/ and https://civet.inl.gov/job/3382157/: if additional submodules are needed, they must be cloned in the fetch and branch step. internet is not available outside of that step. |
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@loganharbour - We could definitely use updates from libMesh. Probably won't have a hash ready for you until late tonight, though. We need to get libMesh/libmesh#4324 in first (one of the most useful updates broke one of our devel->master tests). |
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Summary of changes:
- A long-deprecated behavior has been removed: code initializing data
using an `FE` object now *must* prerequest all data it will later
access; it can no longer prerequest nothing and rely on libMesh to
interpret that as a potential need for everything.
- A large number of long-deprecated APIs have been removed:
- The `DofObject::set_unique_id()` overload that returns a reference
is gone; use the overload that takes an argument instead.
- `Elem::centroid()` is gone. Code that requires an accurate
approximation of ths should be using `Elem::true_centroid()`
instead; code that requires a non-centroidal but
quick-to-calculate internal point should be using
`Elem::vertex_average()` instead.
- `Elem::which_node_am_i()` is gone. Use `Elem::local_side_node()`
instead.
- The `BoundaryInfo::build_*_list()` overloads that fill vector
arguments are gone. Use the overloads that return vectors
instead, or use the `multimap` getters.
- `CondensedEigenSystem` no longer supports direct access to raw
`condensed_matrix_A` and `condensed_matrix_B` pointers; use e.g.
`get_condensed_matrix_A()` instead.
- The `MeshFunction::init()` overload taking a tree build type is
gone. Use the other `init()` overload instead.
- The poorly named `EquationSystems::get_solution()` is gone. Use
`EquationSystems::build_elemental_solution_vector() for elemental
data instead.
- `System::read_legacy_data()` is gone. Use libMesh .xda files that
postdate 2007, and show your pre-2007 libMesh .xda files to Roy to
amuse and delight him.
- The old `libmesh/mesh_inserter_iterator.h` header is gone. Rely
on `Node` and `Elem` unpacking specializations to insert
communicated objects into a target `UnstructuredMesh`.
- The `libmesh_make_unique` macro is gone. Use `std::make_unique`
directly.
- The old `libmesh/auto_ptr.h` header and macro is gone. Use
`std::unique_ptr`.
- `Utility::iota()` and `Utility::is_sorted()` are gone. Use
`std::iota()` and `std::is_sorted()`
- `DynaIO::clear_spline_nodes()` is gone. Use
`MeshTools::clear_spline_nodes()` instead.
- `DifferentiableSystem::swap_physics()` is gone. Use `push_physics()` and
`pop_physics()` instead.
- `DifferentiableSystem::init_qoi()` is gone. Override
`DifferentiableQoI::init_qoi_count()` in `DifferentiableQoI`
subclasses instead.
- `RBParameterized::get_parameter_names()` and an
`RBEvaluation::eval_output_dual_norm()` overload have been
removed. Use `get_parameters_map()` or the remaining
`eval_output_dual_norm()` overload.
- libMesh now throws `DegenerateMap` exceptions when encountering
singularities while evaluating geometric element mappings or
factoring dense matrices, not `LogicError` exceptions, which are
reserved for errors in logic. Code catching these exceptions should
use the new type, or for compatibility with old libMesh can catch
`std::exception & e` and examine `e.what()` to determine the exception
details.
- MetaPhysicL code can now run on accelerator/GPU devices, using Kokkos
- `VariationalSmoother` now supports meshes with tetrahedral elements.
- `VariationalSmoother` now supports fine-grained user-controlled
verbosity, and emits better error messages in cases where a smoother
optimization solve fails.
- Added `SparseMatrix::print_coreform_hdf5`, to create CSR-structured
matrix data in HDF5 files in the Coreform format.
- `LaplaceMeshSmoother` now has API signatures to match
`VariationalSmoother`.
- `Elem::size_vertex_average_normal()` now supports `Edge3` (and in
theory `Edge4`) elements
- Added `ExodusII_IO::set_unique_ids_from_maps()` to set `unique_id()`
rather than `id()` from Exodus file numbering. This can be useful
for efficiency when loading very sparse numberings into a
`ReplicatedMesh`.
- Added `libmesh_assert_valid_point_locator()` method to verify
`PointLocator` consistency when debugging with potentially-changed
meshes
- Bug fixes:
- The VariationalSmoother is now calculating target elements
properly; this gives better-smoothed results for meshes with
triangle, prism, and pyramid elements.
- libMesh no longer triggers deprecation warnings with PETSc 3.24
and newer versions
- libMesh no longer triggers compiler warnings from NVidia HPC SDK
compilers
- Add ExodusII::set_max_name_length() to reduce truncation of long
identifier strings in ExodusII files
refs idaholab#31906
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| @@ -1 +1 @@ | |||
| Subproject commit 910736a3a20aded528c3ba99371ce65980dc8e2c | |||
| Subproject commit 001b6e1ae8f06b37ea005c3ce763f3fe2da4ead7 | |||
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Caution! This contains a submodule update
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Job Precheck, step Versioner verify on 06fbdc0 wanted to post the following: Versioner templatesFound 14 templates, 0 failed Versioner influential filesFound 58 influential files, 9 changed, 0 added, 0 removed
Versioner versionsFound 9 packages, 3 changed, 0 failed
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Job Test, step Results summary on 06fbdc0 wanted to post the following: Framework test summaryCompared against aea74f0 in job civet.inl.gov/job/3385248. No change Modules test summaryCompared against aea74f0 in job civet.inl.gov/job/3385248. No change |
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Reason/Impact
Unblocks #31250 and #31525. Fixes memory deallocation bug in GPU builds of SuperLU_DIST.
Design
Update MFEM submodule, and PETSc submodule to version 3.24.1, to include fixes contributed upstream.