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Update moose-mpi & PETSc: default Python packages, pinnings, apptainer exec fix, optimize compiler flags #28656

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@milljm milljm commented Sep 18, 2024

Remove DEBUG and other offending flags from CXXFLAGS/CPPFLAGS.

When installing moose-mpi, supply a default set of python packages necessary to build MOOSE.

Continue to constrain to a Python range. Default Python is latest supported version (3.11 at this commit)

Pin HDF5 to 1.14.2 due to discovered issue: #28350

As requested, incorporating set options we require when launching containers with exec subcommand.

Bump SDK for Mac Intel (PETSc contrib requirement).

Transition to files section for exec fix

Pin several packages, as we are tired of experiencing issues with only small bumps to build versions.

Refs #28427 #28283

Closes #28643

@milljm milljm changed the title Remove flags. Default Python packages moose-mpi Update moose-mpi: default Python packages, pinnings, apptainer exec fix, optimize compiler flags Sep 18, 2024
@milljm milljm changed the title Update moose-mpi: default Python packages, pinnings, apptainer exec fix, optimize compiler flags Update moose-mpi & PETSc: default Python packages, pinnings, apptainer exec fix, optimize compiler flags Sep 18, 2024
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Remove DEBUG and other offending flags from CXXFLAGS/CPPFLAGS.

When installing moose-mpi, supply a default set of python packages
necessary to build MOOSE.

Continue to constrain to a Python range. Default Python is latest
supported version (3.11 at this commit)

Pin HDF5 to 1.14.2 due to discovered issue: idaholab#28350

As requested, incorporating `set` options we require when launching
containers with exec subcommand.

Bump SDK for Mac Intel (PETSc contrib requirement).

Transition to files section for exec fix

Pin several packages, as we are tired of experiencing issues with only small
bumps to build versions.

Refs idaholab#28427 idaholab#28283

Closes idaholab#28643
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Job Precheck on 7de692b wanted to post the following:

The following file(s) are changed:

conda/libmesh/meta.yaml

The libmesh conda configuration has changed; ping @idaholab/moose-dev-ops

GPERFTOOLS_SRC=${ROOT_BUILD_DIR}/gperftools
cd ${GPERFTOOLS_SRC}
./autogen.sh
./configure --prefix={{ GPERF_DIR }} --enable-frame-pointers
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Are people hoping to do a lot of heap profiling? That would be the reason I'd recommend going to the frame-pointer route. Otherwise using libunwind gives more accurate stack traces, particularly in my experience if fortran libraries like mumps are involved

@lindsayad
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I'm confused. Is this meant to replace #28587 ?

@loganharbour
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I'm confused. Is this meant to replace #28587 ?

It combines it into this one. No need to update mpi and up, and then petsc and up in two PRs.

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Job Documentation on 7de692b wanted to post the following:

View the site here

This comment will be updated on new commits.

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Job Coverage on 7de692b wanted to post the following:

Framework coverage

Coverage did not change

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MPI Change: Add influential file. Correct a small permissions issue in mpi.def container
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