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MPI Change: Add influential file. Correct a small permissions issue in mpi.def container #28643

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milljm opened this issue Sep 17, 2024 · 5 comments · Fixed by #28656
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MPI Change: Add influential file. Correct a small permissions issue in mpi.def container #28643

milljm opened this issue Sep 17, 2024 · 5 comments · Fixed by #28656
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@milljm
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C: Apptainer Tickets pertaining to Singularity/Apptainer T: task An enhancement to the software.

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@milljm
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milljm commented Sep 17, 2024 •
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Motivation

There was a new file added to apptainer/mpi.def that was mistakenly not added to the influential files.

There is a sourced file that has incorrect permissions. While they work at present, they should be world-readable.

Edit:
Using this PR to include changes from a reverted PR #28283 (with fixes). Otherwise, this would be too many rapid changes in such a low lever Conda package.

Design

Track the 01-fix-exec.sh influential file.
Fix permissions on said file during %post.

Impact

The versioner.yaml file will correctly track all related Apptainer files.
The source file will have correct permissions.
@milljm milljm added T: task An enhancement to the software. C: Apptainer Tickets pertaining to Singularity/Apptainer labels Sep 17, 2024
@milljm milljm self-assigned this Sep 17, 2024
@milljm milljm changed the title Add influential file. Correct a small permissions issue in mpi.exe container Add influential file. Correct a small permissions issue in mpi.dev container Sep 17, 2024
@milljm milljm changed the title Add influential file. Correct a small permissions issue in mpi.dev container Add influential file. Correct a small permissions issue in mpi.def container Sep 17, 2024
@milljm milljm changed the title Add influential file. Correct a small permissions issue in mpi.def container MPI Change: Add influential file. Correct a small permissions issue in mpi.def container Sep 17, 2024
@milljm
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milljm commented Sep 17, 2024 •
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When #28587 is ready, incorporate that into this (for a more worth while reason to bump petsc).

@lindsayad
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So for Mac, we will want to add this to LDFLAGS: -Wl,-ld_classic -Wl,-commons,use_dylibs. Additionally on Mac, when configuring mpich we will want to pass --with-device=ch4:ofi. Refs https://gitlab.com/petsc/petsc/-/issues/1569

@milljm
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milljm commented Sep 18, 2024 •
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Due to the setback and reverting of #28399, I'll be making another attempt getting everything rolled into this PR...

Edit:
I am tired of running into small bumps in the underlying stack causing our issues. So for this next moose-mpi 'bump', I'll be adding many more pins.

@loganharbour
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Additionally on Mac, when configuring mpich we will want to pass --with-device=ch4:ofi

We take what we can get with conda mpich:

./configure --prefix=$PREFIX \
            --disable-dependency-tracking \
            --enable-cxx \
            --enable-fortran \
            --enable-f08 \
            --with-wrapper-dl-type=none \
            --disable-opencl \
            --with-device=ch4 \
            || cat config.log

from https://github.com/conda-forge/mpich-feedstock/blob/d187d6d38143e3f03d0eb8a9cb0b16d23175594e/recipe/build-mpi.sh#L94C1-L102C30

milljm added a commit to milljm/moose that referenced this issue Sep 18, 2024
@milljm
Remove flags. Default Python packages moose-mpi
0a2a55f 
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
@milljm milljm mentioned this issue Sep 18, 2024
Merged
milljm added a commit to milljm/moose that referenced this issue Sep 18, 2024
@milljm
Remove flags. Default Python packages moose-mpi
838116c 
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
milljm added a commit to milljm/moose that referenced this issue Sep 18, 2024
@milljm
Remove flags. Default Python packages moose-mpi
bff14fc 
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
milljm added a commit to milljm/moose that referenced this issue Sep 18, 2024
@milljm
Remove flags. Default Python packages moose-mpi
9fb16da 
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
milljm added a commit to milljm/moose that referenced this issue Sep 18, 2024
@milljm
Remove flags. Default Python packages moose-mpi
a63ec30 
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
@lindsayad
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Well if the modification to $LDFLAGS alone is not sufficient to resolve the MUMPS failure that @GiudGiud ran into in BlueCRAB then we might need to talk to mpich-feedstock about allowing control of the device

milljm added a commit to milljm/moose that referenced this issue Oct 1, 2024
@milljm
Remove flags. Default Python packages moose-mpi
38dc8b9 
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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