Remove using namespace libMesh #28842

GiudGiud · 2024-10-14T00:01:07Z

patches:

SAM https://git-nse.egs.anl.gov/SAM/SAM/-/merge_requests/971
falcon Use libmesh namespace in code that uses it implicitly falcon#148
pronghorn merged
griffin https://github.inl.gov/ncrc/griffin/pull/2147

I used the techniques below to make this a little painful. Some of these are not "best practices" so I can avoid these shortcuts, but at the cost of a lot more work most likely.

For source files:

added libMesh:: in a lot of source files initially. This was taking forever so I...
added using namespace libMesh at the top of source files. This is probably the cleaner way to do this. Unfortunately this quick and easy solution should not be done in headers. And because of unity build I probably have to do this again a few times to get every single source file that actually needs it

For headers:

I did add libMesh:: in a lot of headers as well. This was also taking forever, it would be needed in thousands of places
so I started adding using libMesh::Real/ .../ in common headers. Namely MooseTypes.h, MooseMesh.h, AuxiliarySystem.h .... This is not a recommended practice but I don't really see us having libMesh::Real (or using libMesh::Real;) in every header?? But maybe we should. Since too many files were needed, I ended up centralizing in libMeshReduceNamespace.h
for the nested namespaces, I added something like namespace Threads = libMesh::Threads which effectively nullifies the effect of removing using namespace libMesh. So we keep the same degree of contamination with regards to these nested namespaces of libMesh (e.g. you can't use a Threads namespace with overlapping symbols from another library)
then to pass CI of the other apps I basically had to add a couple other using libMesh:: at the end of the libMeshReducedNamespace.h. The alternative is to patch every single app, which is not very reasonable at this point. Unfortunately most apps do not have a XYZnameoftheapp.h header they include everywhere.

In any case, even if we don't like any of these practices, we can fix these gradually, unlike the removal of using namespace libMesh which can only be brutal

I think I can improve what I did in libMeshReducedNamespace.h by using forward declarations. I ll try that
EDIT: done

@grmnptr

GiudGiud · 2024-10-14T00:09:00Z

@dschwen @lindsayad

GiudGiud · 2024-10-15T22:20:03Z

framework/include/base/Moose.h

 #include "libmesh/perf_log.h"
 #include "libmesh/libmesh_common.h"
 #include "XTermConstants.h"
+#include "libmesh/utility.h" // to declare namespace


self-note to remove this

You want it just for the namespace declaration? You can just put namespace libMesh {} in MOOSE code to get that.

yup! I ended up figuring this out later on

moosebuild · 2024-10-15T23:42:39Z

Job Documentation, step Docs: sync website on 340196c wanted to post the following:

View the site here

This comment will be updated on new commits.

moosebuild · 2024-10-15T23:53:54Z

Job Coverage, step Generate coverage on 340196c wanted to post the following:

Framework coverage

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	85.05%	85.04%	-0.00%	70.10%
Hits	106298	106311	+13	340
Misses	18691	18696	+5	145

Diff coverage report

Full coverage report

Modules coverage

Heat transfer

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	88.71%	88.71%	+0.00%	100.00%
Hits	4351	4352	+1	5
Misses	554	554	-	0

Diff coverage report

Full coverage report

Level set

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	85.45%	85.49%	+0.04%	100.00%
Hits	323	324	+1	2
Misses	55	55	-	0

Diff coverage report

Full coverage report

Navier stokes

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	84.48%	84.48%	-	100.00%
Hits	17002	17002	-	2
Misses	3123	3123	-	0

Diff coverage report

Full coverage report

Phase field

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	86.01%	86.01%	+0.00%	75.00%
Hits	13673	13675	+2	6
Misses	2224	2224	-	2

Diff coverage report

Full coverage report

Porous flow

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	95.30%	95.30%	-	100.00%
Hits	11336	11336	-	4
Misses	559	559	-	0

Diff coverage report

Full coverage report

Ray tracing

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	95.33%	95.33%	-	100.00%
Hits	4364	4364	-	7
Misses	214	214	-	0

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Reactor

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	93.65%	93.65%	-	100.00%
Hits	7613	7613	-	1
Misses	516	516	-	0

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Richards

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	93.11%	93.11%	-	100.00%
Hits	3324	3324	-	2
Misses	246	246	-	0

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Full coverage report

Solid mechanics

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	84.91%	84.91%	-	100.00%
Hits	28158	28158	-	3
Misses	5006	5006	-	0

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Stochastic tools

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	90.68%	90.68%	-	100.00%
Hits	8093	8093	-	1
Misses	832	832	-	0

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Full coverage report

Thermal hydraulics

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	88.35%	88.35%	+0.00%	100.00%
Hits	13910	13911	+1	15
Misses	1834	1834	-	0

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Full coverage report

Xfem

	b3924e	#28842 340196
	Total	Total	+/-	New
Rate	82.38%	82.38%	-	100.00%
Hits	6907	6907	-	1
Misses	1477	1477	-	0

Diff coverage report

Full coverage report

Full coverage reports

Reports

Warnings

framework new line coverage rate 70.10% is less than the suggested 90.0%
phase_field new line coverage rate 75.00% is less than the suggested 90.0%

This comment will be updated on new commits.

GiudGiud · 2024-10-17T14:19:10Z

All (needed with the huge concessions on the namespace) patches are merged this should be good to go.

This will collect merge conflicts and unexpected failures (from new uses of objects that are not in the namespace) like no other PR so it'd be great to process it fast

loganharbour

At the very least needs a newsletter entry. this is pretty significant

Added more testing for nonstandard configurations. I suspect we might break a few apps with nonstandard configs (that aren't tested in on-moose app tests), but we can deal with that on app devels as they pop up

- declare sub-namespaces of libMesh as their own namespaces - add libMesh:: in front of many objects - add using libMesh::many_common_ones refs idaholab#28499

- heavily rely on using namespace libMesh - for some files, add libMesh:: everywhere refs idaholab#28499

refs idaholab#28499

rfs idaholab#28499

…bal scope

lindsayad

seems like a great start

GiudGiud · 2024-10-23T23:36:46Z

Thanks thanks
Looks like the jit stuff fails on Mac I ll try to figure it out

GiudGiud self-assigned this Oct 14, 2024

GiudGiud force-pushed the PR_delibmeshisize branch from 1eb640f to 8018a7f Compare October 14, 2024 00:11

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GiudGiud marked this pull request as ready for review October 15, 2024 22:09

GiudGiud requested review from lindsayad and bwspenc as code owners October 15, 2024 22:09

GiudGiud requested review from jiangwen84, joshuahansel, dschwen, sapitts, zachmprince, grmnptr, loganharbour, roystgnr and cpgr as code owners October 15, 2024 22:09

GiudGiud commented Oct 15, 2024

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GiudGiud added the PR: Ready for review/merge label Oct 16, 2024

loganharbour requested changes Oct 18, 2024

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GiudGiud added 7 commits October 18, 2024 22:52

Remove libMesh namespace from framework: mostly headers

7e6286d

- declare sub-namespaces of libMesh as their own namespaces - add libMesh:: in front of many objects - add using libMesh::many_common_ones refs idaholab#28499

Remove libMesh namespace from framework source:

8faebe0

- heavily rely on using namespace libMesh - for some files, add libMesh:: everywhere refs idaholab#28499

Adapt framework test objects to libMesh namespace removal

e5ffd5f

refs idaholab#28499

Adapt modules to removal of libMesh namespace

78ca384

rfs idaholab#28499

Adapt MOOSE unit tests to removal of 'using namespace libMesh' in glo…

c35aaec

…bal scope

Misc change to pass precheck

22e82f7

Add more of libMesh namespace to pass downstream app tests

25206b0

GiudGiud force-pushed the PR_delibmeshisize branch from cc51284 to 340196c Compare October 18, 2024 20:53

GiudGiud requested a review from cticenhour as a code owner October 18, 2024 20:53

lindsayad reviewed Oct 23, 2024

View reviewed changes

Add newsletter entry for libMesh namespace inclusion removal

8966c74

GiudGiud force-pushed the PR_delibmeshisize branch from 340196c to 8966c74 Compare October 23, 2024 23:49

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Remove using namespace libMesh #28842

Remove using namespace libMesh #28842

GiudGiud commented Oct 14, 2024 •

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GiudGiud commented Oct 23, 2024

Remove using namespace libMesh #28842

Are you sure you want to change the base?

Remove using namespace libMesh #28842

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Framework coverage

Modules coverage

Heat transfer

Level set

Navier stokes

Phase field

Porous flow

Ray tracing

Reactor

Richards

Solid mechanics

Stochastic tools

Thermal hydraulics

Xfem

Full coverage reports

Warnings

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