Update packages by nmnobre · Pull Request #32757 · idaholab/moose

nmnobre · 2026-04-13T14:38:42Z

libMesh update libMesh/libmesh@`0185b8b...870e4eb`

...

Conda packages

`moose-petsc 3.25.1 [mpich,openmpi]_0`

Update petsc v3.24.6..v3.25.1

`moose-libmesh 2026.05.01_870e4eb [mpich,openmpi]_0`

Use updated PETSc from moose-petsc 3.25.1_0
Update libmesh libMesh/libmesh@0185b8b...870e4eb

`moose-dev 2026.05.01 [mpich,openmpi]`

Use updated PETSc from moose-petsc 3.25.1 [mpich,openmpi]_0
Use updated libMesh from moose-libmesh 2026.05.01_870e4eb [mpich,openmpi]_0

Apptainer containers

`moose-petsc:3.25.1_0`

Update petsc v3.24.6..v3.25.1
Workaround missing libnvidia-ml.so.1 by passing -DCMAKE_EXE_LINKER_FLAGS=-Wl,--as-needed to SLATE's CMake command to drop that library dependency
Override OpenBLAS build settings if using the oneAPI compilers by passing DYNAMIC_ARCH=1 NOFORTRAN=0 F_COMPILER=INTEL FEXTRALIB= to its make command

`moose-libmesh:2026.05.01_870e4eb_0`

Use updated moose-petsc:3.25.1_0 container as base
Update libmesh libMesh/libmesh@0185b8b...870e4eb
Workaround missing libnvidia-ml.so.1 by passing -Wl,--as-needed to netCDF's configure command to drop that library dependency

`moose-dev:2026.05.01`

Use updated moose-libmesh:2026.05.01_870e4eb_0 container as base
Update mfem mfem/mfem@64ef39b...e52948f
Update conduit llnl/conduit@8543892...4ae5a69
Workaround missing libnvidia-ml.so.1 by passing -DPETSC_EXECUTABLE_RUNS=YES to MFEM's CMake command to ignore failing PETSc tests

moosebuild · 2026-04-13T17:19:39Z

Job Documentation, step Docs: sync website on cd9634f wanted to post the following:

View the site here

This comment will be updated on new commits.

NamjaeChoi · 2026-04-13T23:28:33Z

@lindsayad Can we make sure your MetaPhysicL fix will be in with this update?

lindsayad · 2026-04-14T21:58:35Z

@lindsayad Can we make sure your MetaPhysicL fix will be in with this update?

sounds good

lindsayad · 2026-04-28T22:37:53Z

warning that I force pushed

moosebuild · 2026-04-28T22:45:30Z

@@ -1 +1 @@
-Subproject commit 0185b8b2a7e31300bdf020b323342c49030b8da0
+Subproject commit 6998008117e29a3d139d0b417185ac21b0863eff


Caution! This contains a submodule update

nmnobre · 2026-04-28T22:47:39Z

Just before Alex pushed, the cheese graters actually behaved Logan! Besides rebooting, limiting the number of concurrent CIVET runs might help (like how many events are allowed to concurrently use them), in case the machines really are struggling for memory...?

moosebuild · 2026-04-29T03:28:35Z

Job Coverage, step Verify coverage on 4d21ed1 wanted to post the following:

The following coverage requirement(s) failed:

Failed to generate framework coverage rate (required: 81.0%)
Failed to generate chemical_reactions coverage rate (required: 92.0%)
Failed to generate combined coverage rate (required: 37.0%)
Failed to generate contact coverage rate (required: 87.0%)
Failed to generate electromagnetics coverage rate (required: 94.0%)
Failed to generate external_petsc_solver coverage rate (required: 84.0%)
Failed to generate fluid_properties coverage rate (required: 84.0%)
Failed to generate fsi coverage rate (required: 85.0%)
Failed to generate functional_expansion_tools coverage rate (required: 81.0%)
Failed to generate geochemistry coverage rate (required: 96.0%)
Failed to generate heat_transfer coverage rate (required: 87.0%)
Failed to generate level_set coverage rate (required: 85.0%)
Failed to generate misc coverage rate (required: 32.0%)
Failed to generate navier_stokes coverage rate (required: 77.0%)
Failed to generate optimization coverage rate (required: 86.0%)
Failed to generate peridynamics coverage rate (required: 77.0%)
Failed to generate phase_field coverage rate (required: 85.0%)
Failed to generate porous_flow coverage rate (required: 95.0%)
Failed to generate ray_tracing coverage rate (required: 93.0%)
Failed to generate rdg coverage rate (required: 63.0%)
Failed to generate reactor coverage rate (required: 90.0%)
Failed to generate scalar_transport coverage rate (required: 81.0%)
Failed to generate solid_mechanics coverage rate (required: 84.0%)
Failed to generate solid_properties coverage rate (required: 83.0%)
Failed to generate stochastic_tools coverage rate (required: 88.0%)
Failed to generate subchannel coverage rate (required: 87.0%)
Failed to generate thermal_hydraulics coverage rate (required: 88.0%)
Failed to generate xfem coverage rate (required: 80.0%)

lindsayad · 2026-04-29T19:08:18Z

valgrind failure is unrelated to this PR

NamjaeChoi · 2026-04-30T02:48:54Z

Do we want to turn on GPU vector ghosting? We will need a small patch in libMesh to remove ghost PETSc vector prefix.

This reverts commit d908ec3.

…cks missing libnvidia-ml.so.1 For SLATE and netCDF we leverage the fact that the simple programs that CMake and autotools use to test the compilers do not actually need libnvidia-ml.so, they are just linked against it because that is an inherited dependency from PETSc (as of 5268dc8a, !8817). We use -Wl,--as-needed to drop that dependency at compile time, so the dynamic linker does not complain at runtime. For MFEM, the check is on the PETSc library itself, which we know must be working correctly since, by the time we build MFEM, we have already compiled libMesh against PETSc. As PETSc does require libnvidia-ml.so.1, we bypass the test altogether with -DPETSC_EXECUTABLE_RUNS=YES.

OpenBLAS uses a script, f_check, to determine what the Fortran compiler is. Problem is, with FC=mpif90, even though mpif90 wraps ifx, OpenBLAS makes a mess and assigns NOFORTRAN=1 and other flags relative to gfortran instead. The net effect is that PETSc's post-install checks hang.

… petsc recipe The conda scalapack package's scalapack-targets.cmake embeds absolute CI build-machine paths (/opt/civet0/...) and GCC emulated-TLS libs (-lemutls_w, -lheapt_w) in INTERFACE_LINK_LIBRARIES. These propagate through MUMPS into MFEM's link libraries, causing fatal link errors on macOS Apple Silicon. Extend the existing Darwin GCC-stripping block to also cover scalapack-targets.cmake: add it to the existing sed for -lemutls_w/-lheapt_w/ -lgcc_s.1, and add a second sed to strip the -Wl,-rpath and -L flags pointing at /opt/civet0 (which don't appear in the PETSc files and so weren't handled before). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

moosebuild · 2026-05-01T21:50:25Z

@@ -1 +1 @@
-Subproject commit 0185b8b2a7e31300bdf020b323342c49030b8da0
+Subproject commit 870e4eb6b27ba407762776931d2c2a4dd1b63ff0


Caution! This contains a submodule update

moosebuild · 2026-05-01T21:50:27Z

Job Precheck, step Versioner verify on cd9634f wanted to post the following:

Versioner templates

Found 11 templates, 0 failed

Versioner influential files

Found 53 influential files, 13 changed, 0 added, 0 removed

package	status	file
petsc	CHANGE	apptainer/petsc.def
petsc	CHANGE	conda/petsc
petsc	CHANGE	conda/petsc/meta.yaml
petsc	CHANGE	petsc
petsc	CHANGE	scripts/configure_petsc.sh
libmesh	CHANGE	apptainer/libmesh.def
libmesh	CHANGE	conda/libmesh
libmesh	CHANGE	conda/libmesh/meta.yaml
libmesh	CHANGE	libmesh
moose-dev	CHANGE	apptainer/moose-dev.def
moose-dev	CHANGE	conda/moose-dev/meta.yaml
moose-dev	CHANGE	framework/contrib/conduit
moose-dev	CHANGE	framework/contrib/mfem

Versioner versions

Found 10 packages, 3 changed, 0 failed

package	status	hash	to hash	version	to version
petsc	CHANGE	2fee174	b035b4c	3.24.6 build 0	3.25.1 build 0
libmesh	CHANGE	b73472f	583f3ed	2026.04.13_0185b8b build 0	2026.05.01_870e4eb build 0
moose-dev	CHANGE	0bf4d15	cc067d7	2026.04.21	2026.05.01

moosebuild · 2026-05-02T00:17:17Z

Job Test, step Results summary on cd9634f wanted to post the following:

Framework test summary

Compared against dd5a896 in job civet.inl.gov/job/3793511.

No change

Modules test summary

Compared against dd5a896 in job civet.inl.gov/job/3793511.

No change

moosebuild · 2026-05-02T02:37:36Z

Job Coverage, step Verify coverage on cd9634f wanted to post the following:

The following coverage requirement(s) failed:

Failed to generate framework coverage rate (required: 81.0%)
Failed to generate chemical_reactions coverage rate (required: 92.0%)
Failed to generate combined coverage rate (required: 37.0%)
Failed to generate contact coverage rate (required: 87.0%)
Failed to generate electromagnetics coverage rate (required: 94.0%)
Failed to generate external_petsc_solver coverage rate (required: 84.0%)
Failed to generate fluid_properties coverage rate (required: 84.0%)
Failed to generate fsi coverage rate (required: 85.0%)
Failed to generate functional_expansion_tools coverage rate (required: 81.0%)
Failed to generate geochemistry coverage rate (required: 96.0%)
Failed to generate heat_transfer coverage rate (required: 87.0%)
Failed to generate level_set coverage rate (required: 85.0%)
Failed to generate misc coverage rate (required: 32.0%)
Failed to generate navier_stokes coverage rate (required: 77.0%)
Failed to generate optimization coverage rate (required: 86.0%)
Failed to generate peridynamics coverage rate (required: 77.0%)
Failed to generate phase_field coverage rate (required: 85.0%)
Failed to generate porous_flow coverage rate (required: 95.0%)
Failed to generate ray_tracing coverage rate (required: 93.0%)
Failed to generate rdg coverage rate (required: 63.0%)
Failed to generate reactor coverage rate (required: 90.0%)
Failed to generate scalar_transport coverage rate (required: 81.0%)
Failed to generate solid_mechanics coverage rate (required: 84.0%)
Failed to generate solid_properties coverage rate (required: 83.0%)
Failed to generate stochastic_tools coverage rate (required: 88.0%)
Failed to generate subchannel coverage rate (required: 87.0%)
Failed to generate thermal_hydraulics coverage rate (required: 88.0%)
Failed to generate xfem coverage rate (required: 80.0%)

nmnobre added C: libMesh C: PETSc/SLEPc Tickets pertaining to PETSc/SLEPc PR: Updates packages Pull requests that update versioner packages C: MFEM Tickets pertaining to MFEM Backend integration labels Apr 13, 2026

moosebuild reviewed Apr 13, 2026

View reviewed changes