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GA features update - Having multi-objective optimization (NSGA-II ) #2326

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@JunyungKim JunyungKim commented May 23, 2024


Pull Request Description

What issue does this change request address? (Use "#" before the issue to link it, i.e., #42.)

Closes #2069
Closes #2386

What are the significant changes in functionality due to this change request?

For Change Control Board: Change Request Review

The following review must be completed by an authorized member of the Change Control Board.

  • 1. Review all computer code.
  • 2. If any changes occur to the input syntax, there must be an accompanying change to the user manual and xsd schema. If the input syntax change deprecates existing input files, a conversion script needs to be added (see Conversion Scripts).
  • 3. Make sure the Python code and commenting standards are respected (camelBack, etc.) - See on the wiki for details.
  • 4. Automated Tests should pass, including run_tests, pylint, manual building and xsd tests. If there are changes to Simulation.py or JobHandler.py the qsub tests must pass.
  • 5. If significant functionality is added, there must be tests added to check this. Tests should cover all possible options. Multiple short tests are preferred over one large test. If new development on the internal JobHandler parallel system is performed, a cluster test must be added setting, in XML block, the node <internalParallel> to True.
  • 6. If the change modifies or adds a requirement or a requirement based test case, the Change Control Board's Chair or designee also needs to approve the change. The requirements and the requirements test shall be in sync.
  • 7. The merge request must reference an issue. If the issue is closed, the issue close checklist shall be done.
  • 8. If an analytic test is changed/added is the the analytic documentation updated/added?
  • 9. If any test used as a basis for documentation examples (currently found in raven/tests/framework/user_guide and raven/docs/workshop) have been changed, the associated documentation must be reviewed and assured the text matches the example.

JunyungKim and others added 30 commits February 24, 2023 12:14
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Job Test slurm bitterroot on 8943fef : invalidated by @joshua-cogliati-inl

failed in build_raven remove directories.

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Job Test slurm bitterroot on 1b1d6e7 : invalidated by @joshua-cogliati-inl

failed in build_raven remove directories.

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Job Test slurm bitterroot on 1b1d6e7 : invalidated by @joshua-cogliati-inl

failed in build_raven remove directories.

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Job Mingw Test on dfaf577 : invalidated by @joshua-cogliati-inl

failed in fetch

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Job Test qsubs sawtooth legacy on fb4c93d : invalidated by @joshua-cogliati-inl

failed in fetch

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Job Test qsubs sawtooth on fb4c93d : invalidated by @joshua-cogliati-inl

failed in fetch

@joshua-cogliati-inl joshua-cogliati-inl mentioned this pull request Mar 5, 2025
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Job Test slurm bitterroot on fb4c93d : invalidated by @joshua-cogliati-inl

failed in build_raven remove directories.

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Job Test slurm bitterroot on fb4c93d : invalidated by @joshua-cogliati-inl

failed in build_raven remove directories.

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@Jimmy-INL , @wangcj05, FYI, the tests passed for the current version of NSGA-II.

@Jimmy-INL Jimmy-INL dismissed their stale review March 6, 2025 21:15

Josh has addressed most of my requests. The rest might be followups in future PRs.

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alfoa commented Mar 7, 2025

@joshua-cogliati-inl @Jimmy-INL @wangcj05 can anybody from INL make sure that the GA works with Raven Running Raven? I am getting crashes also for a single objective optimization.

I opened few issues on this in the past but it seems that this MR does not fix them (since there are no tests associated with them)

(No need to fix it in this PR but maybe a "priority_critical" issue in case it does not work on your side would be nice to capture this)

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Jimmy-INL commented Mar 8, 2025 via email

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alfoa commented Mar 10, 2025

GA only on the inner? Best, Mohammad G. Abdo, Ph.D. Modeling and Simulation Scientist | Digital Reactor Technology and Development (C160) Reactor Systems Design and Analysis | NS&T @.@.> | REC EROB IF-654 3EL103 | Phone: 208-526-4640 Idaho National Laboratory | 2525 Fremont Ave. | Idaho Falls, ID | 83415 [6GC4jc7QCCEAAAAASUVORK5CYII=]https://www.linkedin.com/in/mohammad-abdo-a7625082/. [PXly9OZ1PK9LcRv4PSG3pAb9jevQAAAAASUVORK5CYII=] https://www.researchgate.net/profile/Mohammad_Abdo/research [RPr5ytnPx9Cc691m9I+4T+nIo7v4HxgxndxMwKP8AAAAASUVORK5CYII=] https://github.com/Jimmy-INL

On both (inner and outer)

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alfoa commented Mar 10, 2025

GA only on the inner? Best, Mohammad G. Abdo, Ph.D. Modeling and Simulation Scientist | Digital Reactor Technology and Development (C160) Reactor Systems Design and Analysis | NS&T @.**@.**> | REC EROB IF-654 3EL103 | Phone: 208-526-4640 Idaho National Laboratory | 2525 Fremont Ave. | Idaho Falls, ID | 83415 [6GC4jc7QCCEAAAAASUVORK5CYII=]https://www.linkedin.com/in/mohammad-abdo-a7625082/. [PXly9OZ1PK9LcRv4PSG3pAb9jevQAAAAASUVORK5CYII=] https://www.researchgate.net/profile/Mohammad_Abdo/research [RPr5ytnPx9Cc691m9I+4T+nIo7v4HxgxndxMwKP8AAAAASUVORK5CYII=] https://github.com/Jimmy-INL

On both (inner and outer)
inner_test.xml.txt
outer_test.xml.txt

@Jimmy-INL I attach 2 example inputs that show the structure of what I am talking about (2 GA, 1 outer, 1 inner)

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@joshua-cogliati-inl Could you try to clean up this PR based on my comments. Right now, the web view is very slow. Once you have done that, please let me know, I will continue my review.

Comment on lines 265 to 276
minimalGeneticAlgorithmMultiObjective = r"""
\hspace{24pt}
Genetic Algorithm Example:
\begin{lstlisting}[style=XML]
<Optimizers>
<GeneticAlgorithm name="GAopt">
<samplerInit>
<limit>15</limit>
<initialSeed>42</initialSeed>
<writeSteps>every</writeSteps>
<type>min,min</type>
</samplerInit>
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It seems this example is repeating the example above it.

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Fixed.

@@ -11122,7 +11122,7 @@ \subsubsection{DMDBase}
performed.
\default{0}

\item \xmlNode{normalize\_y}: \xmlDesc{[True, Yes, 1, False, No, 0, t, y, 1, f, n, 0]},
\item \xmlNode{normalize\_y}: \xmlDesc{[True, Yes, 1, False, No, 0, t, y, 1, f, n, 0]},
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I do not see any obvious changes except added extra space at the end of the line. Please try to clean the end line spaces, and see if there is any changes that you want to change. It seems to me you do not need to change this file "internalRom.tex" for this PR.

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@joshua-cogliati-inl joshua-cogliati-inl Mar 11, 2025

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I removed all trailing whitespace in internalRom.tex, sklRom.tex and optimizer.tex.

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If you would like the whitespace removal as a separate pull request, let me know. Thanks.

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Here is the branch with just a whitespace cleanup: https://github.com/joshua-cogliati-inl/raven/tree/whitespace_cleanup

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Fixed with the merge of #2453

Note that generateOptimizerDoc uses the Optimizers.factory.knownTypes(),
so only examples with the name in there will get used.
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