Increase val-2f/val-2c reproducibility by lindsayad · Pull Request #385 · idaholab/tmap8

lindsayad · 2026-03-13T18:32:26Z

This has failed thus far as CI will show

EDIT:
(Ref. #380)
(Ref. #382)

(Ref. idaholab#380)

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

…issue

refs #0

moosebuild · 2026-03-23T21:06:00Z

Job Documentation, step Sync to remote on d6906cb wanted to post the following:

View the site here

This comment will be updated on new commits.

A working case for all three phases of the simulation Probably all four of these are important components - Nondimensionalization with different reference concentrations for all species so that active set numerics are decent for all - nl_rel_tol = 1e-9 with no nl_abs_tol - Reduce growth factor to 1.05 (1.1 was too high ... led to diffs) - Refine the light case twice (once refined was still not refined enough, it led to diffs) Sometimes you need a sufficient amount of accuracy in order for the test to be robust, especially in problems like this where for most of the simulation only like 1/20th of the simulation domain has non-trivial concentrations Refs idaholab#200

…in code

moosebuild · 2026-04-06T23:04:38Z

Job Precheck, step Format Check Clang on e28b7c8 wanted to post the following:

Your code requires style changes.

A patch was auto generated and copied here
You can directly apply the patch by running, in the top level of your repository:

curl -s https://mooseframework.inl.gov/tmap8/docs/PRs/385/clang_format/style.patch | git apply -v

Alternatively, with your repository up to date and in the top level of your repository:

git clang-format 7d1a0b5b28a8af593cadf654a8165c44ffd14bc6

simopier

I understand this is still a work in progress @lin-yang-ly, but here are some minor comments.

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

lin-yang-ly · 2026-04-07T23:03:19Z

@simopier, this PR is ready for your review. For val-2c and heavy tests of val-2f, we have two versions in gold folder: one using scheme = 'implicit-euler' for test checks across different environments, and another using scheme = 'bdf2' retained as a gold file for plotting in the documentation.

In the corresponding tests, I also include two versions, one use CSVDiff and ExoDiff for the tests with scheme = 'implicit-euler', another one use RunApp for tests with scheme = 'bdf2' since we only need to ensure these simulations can still run under current parameters.

simopier

@lin-yang-ly, let's have a discussion about the requirements for the tests for (1) stability, (2) making sure the gold files used in the documentation remain up to date.

Also, investigate the possibility of having csv of outputs at regular, specific sync times to avoid some of the issues we've seen with bdf2 across environments and number of cores.

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

lin-yang-ly · 2026-04-10T00:25:24Z

@simopier The PR is ready for your review. It currently includes both schemes to ensure each gold file is covered by a corresponding test.

In addition, the abs_zero values in val-2f_heavy_csv_bdf2 and val-2f_heavy_csv_inf_recombination_bdf2 may appear large, but they are reasonable when compared to the typical magnitudes observed during the simulations. The variation of each parameter in these cases are shown below:

simopier

Thank you @lin-yang-ly for finalizing this!

I have very minor comments left. Could you address those and update the moose submodule, as discussed. This will be good to go after that.

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

lin-yang-ly · 2026-04-10T04:25:58Z

Thank you @lin-yang-ly for finalizing this!

I have very minor comments left. Could you address those and update the moose submodule, as discussed. This will be good to go after that.

@simopier Thank you for these comments! I have updated the MOOSE submodule already, currently, the MOOSE version is "76a12d39d8", which is the latest MOOSE version in master branch.

moosebuild · 2026-04-10T04:32:57Z

Job Build test summary, step Build test summary on d6906cb wanted to post the following:

Test summary

Compared against c94cbdd in job civet.inl.gov/job/3717731.

Removed tests

Test	Time (s)	Memory (MB)
`test:val-2c.val-2c_immediate_injection_csv`	12.73	218.51
`test:val-2c.val-2c_delay_csv`	3.15	93.18
`test:val-2c.val-2c_delay_calibrated_csv`	2.90	67.47
`test:val-2f.val-2f_heavy_csv_inf_recombination`	SKIP	0.00
`test:val-2f.val-2f_heavy_exodus`	SKIP	0.00
`test:val-2f.val-2f_heavy_csv`	SKIP	0.00
`test:val-2c.val-2c_immediate_injection_exodus`		0.00
`test:val-2c.val-2c_delay_exodus`		0.00

Added tests

Test	Time (s)	Memory (MB)
`test:val-2c.val-2c_immediate_injection_csv_implicit-euler`	13.26	212.38
`test:val-2c.val-2c_delay_csv_implicit-euler`	3.43	94.02
`test:val-2c.val-2c_delay_csv_bdf2`	3.23	101.00
`test:val-2c.val-2c_immediate_injection_csv_bdf2`	3.22	117.77
`test:val-2c.val-2c_delay_calibrated_csv_implicit-euler`	3.15	75.58
`test:val-2c.val-2c_delay_calibrated_csv_bdf2`	3.10	115.13
`test:physics/more_species_on_component.trapping_dimensionless_other_trap`	0.62	41.83
`test:val-2f.val-2f_heavy_csv_inf_recombination_bdf2`	SKIP	0.00
`test:val-2f.val-2f_heavy_csv_bdf2`	SKIP	0.00
`test:val-2f.val-2f_heavy_csv_inf_recombination_implicit-euler`	SKIP	0.00
`test:val-2f.val-2f_heavy_exodus_implicit-euler`	SKIP	0.00
`test:val-2f.val-2f_heavy_csv_implicit-euler`	SKIP	0.00
`test:val-2c.val-2c_immediate_injection_exodus_implicit-euler`		0.00
`test:val-2c.val-2c_delay_exodus_implicit-euler`		0.00

simopier

Thank you @lindsayad, @loganharbour, and @lin-yang-ly!
A follow up PR will re-organize the tests/verification/validation/examples to help select the tests to run on MOOSE's CI, and which ones to run only on TMAP8's.

lindsayad · 2026-04-10T15:58:20Z

Thanks for finishing up the work @lin-yang-ly !

lindsayad · 2026-04-10T16:00:41Z

Doesn't this close #200?

simopier · 2026-04-10T22:04:56Z

Doesn't this close #200?

You are absolutely right! Thank you for catching this! I just closed it.

Increase val-2f/val-2c reproducibility

lin-yang-ly and others added 18 commits March 20, 2026 16:38

Fix light tests

9141968

(Ref. idaholab#380)

update val-2f HPC and local MacOS mismatch

54f0f4a

update petsc hyperparameters to solve the multi-cores mismatch

01adb18

update for multi-cores runs on HPC

745ddf4

avoid recover issue in this PR

562d5c3

update val-2c_immediate_injection_exodus for failure with 2 threads

3ad6b55

solve the multi-core issue for yttrium_hydrogen_system

303045c

keep multi-core issue of val-2f for future

8780a32

MacOS faulure of heavy tests will be solved in another PR

a1b7fee

move val-2f parameters to test file

9151669

leave the recover issue and val-2f multi-core issue for now

5cbba6d

Apply suggestions from code review

7d0c2f3

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

update test checks for solved recover and multi-core issue

150c67d

update documentation

3a765b6

solve one recover failure for yttrium_hydrogen_system

484f9a9

ignore recover issue due to current PR focusing on OS and multi-core …

9dae4e6

…issue

Update moose submodule

b0bf4d0

refs #0

solve failure for val-2c_delay_csv with moose update

0f0c001

lindsayad force-pushed the try-some-regularization branch from 13317be to 4b7c29c Compare March 23, 2026 20:21

lindsayad changed the title ~~Try some regularization in reaction kernels to increase val-2f reproducibility~~ Increase val-2f reproducibility Mar 23, 2026

lindsayad force-pushed the try-some-regularization branch 2 times, most recently from fe6789b to 1f52004 Compare March 23, 2026 20:46

lindsayad mentioned this pull request Mar 23, 2026

Fix the light tests failure on MacOS #382

Merged

lindsayad added 6 commits March 23, 2026 16:45

Remove nondimensionalization doc

bf6bf19

Simplify dimensionless physics/kernel logic

b45e478

Clarify trapping_prefactor

a1c5994

Robustify physics exception testing after parameter check reordering …

f01815d

…in code

Ignore temporary testharness_time files

2d7ecdb

lin-yang-ly added 2 commits April 6, 2026 17:08

quick test only for val-2c: update formats

45fa6e0

fix physics test case

ab9e876

simopier requested changes Apr 7, 2026

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Comment thread test/tests/val-2c/val-2c_base.i Outdated

Comment thread test/tests/val-2c/val-2c_base.i Outdated

Comment thread test/tests/val-2c/val-2c_base.i Outdated

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lin-yang-ly and others added 7 commits April 6, 2026 20:47

Apply suggestions from code review

4ef6a28

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

revert YHx tests

3fdbb02

quick test for val-2f:light case

25d0d83

quick tests for val-2f:heavy

fa79738

update YHx failure tests

400bbb3

update val-2f-heavy tests

df7679f

Add the two versions of accuracy for val-2c and val-2f

9a3a2f5

simopier requested changes Apr 8, 2026

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Comment thread doc/content/verification_and_validation/val-2c.md Outdated

Comment thread test/tests/val-2c/tests Outdated

Comment thread test/tests/val-2c/tests Outdated

Comment thread test/tests/val-2f/tests

Comment thread test/tests/val-2f/tests Outdated

lin-yang-ly and others added 5 commits April 7, 2026 22:15

Apply suggestions from code review

6699bcf

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

Add val-2c bdf2 tests: quick test

991b650

val-2f heavy tests: including both schemes quick test

28fa0d7

update submodule

06b6e92

update heavy tests rel_err

4a7917a

simopier requested changes Apr 10, 2026

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Comment thread doc/content/verification_and_validation/val-2c.md Outdated

Comment thread doc/content/verification_and_validation/val-2f.md Outdated

Comment thread test/tests/val-2c/tests Outdated

Apply suggestions from code review

d6906cb

Co-authored-by: Pierre-Clement Simon <pierreclement.simon@gmail.com>

simopier approved these changes Apr 10, 2026

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simopier merged commit 5ce6c4f into idaholab:devel Apr 10, 2026
11 checks passed

simopier mentioned this pull request Apr 10, 2026

Val-2c/val-2f should perform consistently with 1 or 2 processors. #200

Closed

simopier added a commit to simopier/TMAP8 that referenced this pull request May 4, 2026

Merge pull request idaholab#385 from lindsayad/try-some-regularization

49eeb7e

Increase val-2f/val-2c reproducibility

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Test summary

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lindsayad commented Mar 13, 2026 •

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