New PR: Eigen system supports shell matrices #15315

fdkong · 2020-05-19T14:57:46Z

Refs #14406

A new PR is required to use the new libmesh and the new PETSc in the civet. I simply move the old PR #14406 here.

Shell matrices for nonlinear and linear solvers.
Allow users to attach a customized preconditioner (with a matrix-free option for preconditioner). Closes Attach preconditioner for Eigen solver #14297
Support array kernels
Add an option (precond_matrix_includes_eigen) to allow users to add eigen kernels into the preconditioning matrix
getConvergedEigenvalue returns only eigenvalues without touching the eigenvectors. Closes Getting eigenvalue in NonlinearEigenSystem changes solution #14506

Closes #14297

moosebuild · 2020-05-19T16:25:17Z

Job Documentation on 4ae1b39 wanted to post the following:

View the site here

This comment will be updated on new commits.

loganharbour · 2020-05-19T17:00:39Z

test/tests/problems/eigen_problem/eigensolvers/ne.i

@@ -50,7 +50,8 @@

 [Executioner]
  type = Eigenvalue
-  solve_type = MF_MONOLITH_NEWTON
+  matrix_free = true


This is so much better!

lindsayad

looks like some very neat capability!

lindsayad · 2020-05-19T21:22:14Z

framework/include/systems/NonlinearEigenSystem.h

@@ -114,7 +122,17 @@ class NonlinearEigenSystem : public NonlinearSystemBase
   * is the real and the imaginary part of
   * the eigenvalue, respectively.
   */
-  virtual const std::pair<Real, Real> getNthConvergedEigenvalue(dof_id_type n);
+  virtual const std::pair<Real, Real> getConvergedEigenvalue(dof_id_type n);


If you're returning by value, is there a point to making the return value const? Also if returning by value, can you make this method const?

framework/include/systems/NonlinearEigenSystem.h

framework/src/systems/NonlinearEigenSystem.C

framework/src/utils/SlepcSupport.C

Closes idaholab#7398

In order to get the best performance, users should use petsc-3.13 or higher Closes idaholab#7398

We will remove EST_MF_MONOLITH_NEWTON once Rattlesnake is updated

since it is scalable

Closes idaholab#14506

… the preconditioning matrix.

…sEigenKernels

because libmesh could rebuild matrices due to mesh changes or something else.

fdkong · 2020-05-20T00:52:07Z

@lindsayad Hopefully, addressed your comments. Haha

moosebuild · 2020-05-20T03:40:02Z

Job App tests on 4ae1b39 : invalidated by @fdkong

/bin/sh: 1: /opt/civet/build_0/moose/libmesh/installed/contrib/bin/libmesh-config: not found

moosebuild · 2020-05-20T14:26:47Z

Job Modules debug on 4ae1b39 : invalidated by @fdkong

Cancelling job due to step taking longer than the max 21600 seconds

fdkong · 2020-05-20T16:50:19Z

@lindsayad It is ready to review or merge

lindsayad

beautiful code

/opt/civet/build_0/moose/framework/src/utils/SlepcSupport.C:385:40: error: this statement may fall through [-Werror=implicit-fallthrough=] 385 | solver_params._eigen_matrix_free = true; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /opt/civet/build_0/moose/framework/src/utils/SlepcSupport.C:387:5: note: here 387 | case Moose::EST_NEWTON: | ^~~~ cc1plus: all warnings being treated as errors We changed APIs in idaholab#15315, and we need to reserve the old APIs for Griffin for a second. I will go to update Griffin to use new APIs. Once that is done, we could remove the old APIs. Refs idaholab#15315

Refs idaholab#15315

YaqiWang · 2020-08-02T22:59:54Z

@pbalest and @amherm reported an issue to me that an input in Griffin worked before but stopped working. It is not so obvious how that can stop working so I had to spend quite some time on bisection and finally located the trouble some in Griffin, which is a MOOSE submodule update from 22ad65b to 983f0ab. There are bunch of things going on during these two hashes, but this is one is the most susceptible.

fdkong · 2020-08-02T23:21:05Z

@pbalest and @amherm reported an issue to me that an input in Griffin worked before but stopped working. It is not so obvious how that can stop working so I had to spend quite some time on bisection and finally located the trouble some in Griffin, which is a MOOSE submodule update from 22ad65b to 983f0ab. There are bunch of things going on during these two hashes, but this is one is the most susceptible.

I checked PR a while ago and did not see anything wrong. Do you have a moose-only input file?

YaqiWang · 2020-08-02T23:24:30Z

No. It is a complicated Griffin input. An eigenvalue problem with flux coupled with delayed neutron precursor drift. The capability is tested in Griffin but the test works fine. I have no idea how this can break that input. I can send you the input to you. The hash in Griffin from working to non-working is 47473250 -> 26589755.

YaqiWang · 2020-08-02T23:30:23Z

I am checking out moose hash 8e8e1dc, the merge commit of this PR to make sure it is indeed this one causing trouble.

fdkong · 2020-08-02T23:32:29Z

Could you add a griffin branch or PR? So I could just grab your branch.

YaqiWang · 2020-08-02T23:33:12Z

Ok, let me add that input into a branch.

YaqiWang · 2020-08-02T23:37:38Z

Please grab my msr_problemtic_input branch. The top commit is the input (examples/msr/diff.i). It is based on the first not-working hash 265889755 in Griffin.

YaqiWang · 2020-08-02T23:40:37Z

Wait, this hash (8e8e1dc) seems working ok. Could be something else breaking the input. Or maybe I need to do a make clobberall...

YaqiWang · 2020-09-17T02:46:44Z

framework/src/preconditioners/PhysicsBasedPreconditioner.C

@@ -137,7 +137,7 @@ PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(const InputParameters & p
  for (unsigned int var = 0; var < n_vars; var++)
    addSystem(var, off_diag[var], _pre_type[var]);

-  _nl.nonlinearSolver()->attach_preconditioner(this);
+  _nl.attachPreconditioner(this);


@fdkong there are several places in Griffin that need to be patched like this here.

OK, I will take a look

GiudGiud · 2022-06-11T03:49:48Z

@amherm could you please get in touch with me or Alex.
We'd like to have your name for the acknowledgements in a paper and it's not listed on Github
thank you!

amherm · 2022-06-14T19:38:49Z

Hi Guillaume, Is there anything you need from me regarding this? Thanks, Andrew

On Fri, Jun 10, 2022 at 11:50 PM Guillaume Giudicelli < ***@***.***> wrote: @amherm could you please get in touch with me or Alex. We'd like to have your name for the acknowledgements in a paper and it's not listed on Github thank you! — Reply to this email directly, view it on GitHub, or unsubscribe ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd @amherm <https://urldefense.com/v3/__https://github.com/amherm__;!!KwNVnqRv!GvsviNJt0kL0RNCMpUagHPWV4vtDo6tCU0oQ9VVUXiLysJwjNY1Dms7L9CYiEhEnUIX1vJ6iyfi5889sZYE9fho$> could you please get in touch with me or Alex. We'd like to have your name for the acknowledgements in a paper and it's not listed on Github thank you! — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/idaholab/moose/pull/15315*issuecomment-1152848211__;Iw!!KwNVnqRv!GvsviNJt0kL0RNCMpUagHPWV4vtDo6tCU0oQ9VVUXiLysJwjNY1Dms7L9CYiEhEnUIX1vJ6iyfi5889sSDenRI4$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AHTKD4V6NPL3YUBDJ4EP6UTVOQEGNANCNFSM4NFCR3UQ__;!!KwNVnqRv!GvsviNJt0kL0RNCMpUagHPWV4vtDo6tCU0oQ9VVUXiLysJwjNY1Dms7L9CYiEhEnUIX1vJ6iyfi5889sopflITA$> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Respectfully, Andrew Hermosillo Graduate Student Texas A&M University Nuclear Engineering

GiudGiud · 2022-06-14T20:07:21Z

Ok got your name, that's all I wanted. I should have guessed. Thanks Andrew!

Refs idaholab#15315

fdkong changed the base branch from devel to next May 19, 2020 14:59

moosebuild added the PR: Failed but allowed label May 19, 2020

loganharbour reviewed May 19, 2020

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moosebuild removed the PR: Failed but allowed label May 19, 2020

fdkong requested a review from lindsayad May 19, 2020 19:10

moosebuild added the PR: Failed but allowed label May 19, 2020

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fdkong force-pushed the matrix_free_eigenvalue branch from 51aebaa to ddb7174 Compare May 20, 2020 00:40

moosebuild removed the PR: Failed but allowed label May 20, 2020

fdkong added 17 commits May 19, 2020 18:47

Support matrix-free for eigenvalue solvers from SLEPc

239d945

Closes idaholab#7398

Eigenvalue Solver: Support shell matrices

a9af0b8

Closes idaholab#7398

Eigenvalue solver (matrix-free) works with old petsc

fda4aed

In order to get the best performance, users should use petsc-3.13 or higher Closes idaholab#7398

Make it back-compatible with Rattlesnake

b24e75d

We will remove EST_MF_MONOLITH_NEWTON once Rattlesnake is updated

Eigenvalue solver: rename dir so that we can add more tests

038b31c

Eigen solvers work with MoosePreconditioner

43d4ef0

Using sys.update instead of localize

8e29961

mooseSlepcEigenFormFunctionAB: Use system update to update solution

0a071d7

since it is scalable

Support array kernels in eigenvalue system

0fe7ce3

Fixed "getting eigenvalue in NonlinearEigenSystem changes solution"

4e041ca

Closes idaholab#14506

Support shell preconditioning matrix

526687d

Eigenvalue system: Optionally allow users to include eigen kernels in…

0e1e0e2

… the preconditioning matrix.

Use tagging system to support eigen kernels in the precond matrix

22349c0

Fixed several tests with PETSc-3.12.5

79ab9c4

Safe guard NonlinearEigenSystem member function: precondMatrixInclude…

4131552

…sEigenKernels

Added doc for EigenArrayDirichletBC

c54bc49

Delay the attachment of callbacks to SLEPc as much as possible

fc4e369

because libmesh could rebuild matrices due to mesh changes or something else.

fdkong force-pushed the matrix_free_eigenvalue branch from ddb7174 to b9d4ec4 Compare May 20, 2020 00:50

fdkong force-pushed the matrix_free_eigenvalue branch from b9d4ec4 to 1328b95 Compare May 20, 2020 01:44

Address reviewer's comments

4ae1b39

fdkong force-pushed the matrix_free_eigenvalue branch from 1328b95 to 4ae1b39 Compare May 20, 2020 03:07

moosebuild added the PR: Failed but allowed label May 20, 2020

fdkong added the PR: Ready for review/merge label May 20, 2020

lindsayad approved these changes May 20, 2020

View reviewed changes

lindsayad merged commit 8e8e1dc into idaholab:next May 20, 2020

fdkong mentioned this pull request May 20, 2020

Fixed "fall through" for PR "New PR: Eigen system supports shell matrices" #15324

Merged

fdkong added a commit to fdkong/moose that referenced this pull request Jun 8, 2020

Eigenvalue solver: clean up legacy code

2a75638

Refs idaholab#15315

fdkong mentioned this pull request Jun 8, 2020

Remove the legacy code of eigenvalue solver #15432

Merged

fdkong added a commit to fdkong/moose that referenced this pull request Jun 8, 2020

Eigenvalue solver: clean up legacy code

c62e77c

Refs idaholab#15315

YaqiWang reviewed Sep 17, 2020

View reviewed changes

lindsayad added a commit to lindsayad/moose that referenced this pull request Jun 21, 2023

Clarifying comment about relationship between eigen/solution vector

e601000

Refs idaholab#15315

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New PR: Eigen system supports shell matrices #15315

New PR: Eigen system supports shell matrices #15315

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New PR: Eigen system supports shell matrices #15315

New PR: Eigen system supports shell matrices #15315

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