> On 31 Oct 2024, at 2:47 PM, Mark Adams <mfad...@lbl.gov> wrote: > > Interesting. I have seen hypre do fine on elasticity, but do you know if > boomeramg (classical) uses these vectors or is there a smoothed aggregation > solver in hypre?
I’m not sure it is precisely “standard” smoothed aggregation, see bottom paragraph of https://urldefense.us/v3/__https://hypre.readthedocs.io/en/latest/solvers-boomeramg.html*amg-for-systems-of-pdes__;Iw!!G_uCfscf7eWS!fdj4AzKhAcDmM1x_ZQ8gxqWeX6BAKY9urnvATMpT7hC8lw77ak7tqxqXGIX3PMg2wYA5PGu7EzyCW0yzixutBg$ I’ve never made it to work, but I know some do. A while back, Stefano gave me this pointer as well: https://urldefense.us/v3/__https://github.com/mfem/mfem/blob/17955e114020af340e9a06a66ebef43e05012d9c/linalg/hypre.cpp*L5245__;Iw!!G_uCfscf7eWS!fdj4AzKhAcDmM1x_ZQ8gxqWeX6BAKY9urnvATMpT7hC8lw77ak7tqxqXGIX3PMg2wYA5PGu7EzyCW0wVEi33Pw$ Thanks, Pierre > On Thu, Oct 31, 2024 at 8:32 AM Pierre Jolivet <pie...@joliv.et > <mailto:pie...@joliv.et>> wrote: >> >> >>> On 31 Oct 2024, at 12:41 PM, Mark Adams <mfad...@lbl.gov >>> <mailto:mfad...@lbl.gov>> wrote: >>> >>> Just note, GAMG uses these near null space vectors but hypre does not as >>> far as I know. >> >> They do: >> https://urldefense.us/v3/__https://petsc.org/release/src/ksp/pc/impls/hypre/hypre.c.html*line266__;Iw!!G_uCfscf7eWS!fdj4AzKhAcDmM1x_ZQ8gxqWeX6BAKY9urnvATMpT7hC8lw77ak7tqxqXGIX3PMg2wYA5PGu7EzyCW0wJINgbAg$ >> >> <https://urldefense.us/v3/__https://petsc.org/release/src/ksp/pc/impls/hypre/hypre.c.html*line266__;Iw!!G_uCfscf7eWS!fgZ28yXAXjJBIqd4SxJehY7SSaYVe_YNHPW4QnnTewSSOxFsPPcBZFPv6Y2IT8PkI3SDEARmixD85cmswwWL0Vk$> >> >> Thanks, >> Pierre >> >>> Hypre does do elasticity so I would just stick with hypre if you just want >>> to solve your problem (and move on) >>> >>> On Thu, Oct 31, 2024 at 1:01 AM Jed Brown <j...@jedbrown.org >>> <mailto:j...@jedbrown.org>> wrote: >>>> There is MatSetNearNullSpace, which is used to ensure an approximation >>>> property in coarse levels of multigrid. That should always be set when >>>> dealing with problems like this, regardless of boundary conditions. >>>> Separately, there is MatSetNullSpace, which you should only use if you are >>>> solving a singular system with that null space. >>>> >>>> Note that you need at least three non-colinear points to constrain the >>>> null space so if you, for example, have a Dirichlet condition at only one >>>> point or along one straight line, there will still be a null space. >>>> >>>> Amneet Bhalla <mail2amn...@gmail.com <mailto:mail2amn...@gmail.com>> >>>> writes: >>>> >>>> > I think Mark mentioned this earlier, but I want to make sure that the >>>> > rigid >>>> > body null vectors should be specified only when Neumann boundary >>>> > conditions >>>> > are used on all boundaries of the domain, correct? Alternatively, if a >>>> > Dirichlet boundary condition is used (on any part of the domain boundary) >>>> > then there is no null space, i.e., the operator is a full rank matrix? >>>> > >>>> > If the above is true, then I think I do not need to specify the rigid >>>> > body >>>> > null modes because I am using Dirichlet boundary conditions for the >>>> > velocity solver. >>>> > >>>> > On Wed, Oct 30, 2024 at 12:28 PM Jed Brown <j...@jedbrown.org >>>> > <mailto:j...@jedbrown.org>> wrote: >>>> > >>>> >> Yes to 6 null vectors in 3D, 3 null vectors in 2D. The center of mass >>>> >> does >>>> >> not need to be identified because you can algebraically orthogonalize >>>> >> (lines 411-420 here). >>>> >> >>>> >> >>>> >> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/plexfem.c?ref_type=heads*L377-425__;Iw!!G_uCfscf7eWS!fdj4AzKhAcDmM1x_ZQ8gxqWeX6BAKY9urnvATMpT7hC8lw77ak7tqxqXGIX3PMg2wYA5PGu7EzyCW0wNnvPLMA$ >>>> >> >>>> >> <https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/plexfem.c?ref_type=heads*L377-425__;Iw!!G_uCfscf7eWS!b0T54ExhpyMjL9O-B63FmKcfUHpYoH0-ixjUnroOoB0PZPSEVH2-LEMb_Yw57sybhA0rknBisFM2erfwfjN2syg$> >>>> >> >>>> >> See also this implementation with raw coordinates. GAMG orthogonalizes >>>> >> within each aggregate (in a later phase of the algorithm) so global >>>> >> orthogonalization is not necessary. >>>> >> >>>> >> >>>> >> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/pc/impls/gamg/agg.c?ref_type=heads*L387__;Iw!!G_uCfscf7eWS!fdj4AzKhAcDmM1x_ZQ8gxqWeX6BAKY9urnvATMpT7hC8lw77ak7tqxqXGIX3PMg2wYA5PGu7EzyCW0yNqXfRKQ$ >>>> >> >>>> >> <https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/pc/impls/gamg/agg.c?ref_type=heads*L387__;Iw!!G_uCfscf7eWS!b0T54ExhpyMjL9O-B63FmKcfUHpYoH0-ixjUnroOoB0PZPSEVH2-LEMb_Yw57sybhA0rknBisFM2erfw3-yhJ68$> >>>> >> >>>> >> Amneet Bhalla <mail2amn...@gmail.com <mailto:mail2amn...@gmail.com>> >>>> >> writes: >>>> >> >>>> >> > I think the nullspace for the velocity operator is of the form >>>> >> > >>>> >> > vnull = U + ω × r >>>> >> > in which U is a rigid body velocity and ω is the rigid body rotational >>>> >> > velocity, and r is the radius vector from the center of mass. I >>>> >> > believe I >>>> >> > need to construct 6 nullspace vectors in 3D and 3 nullspace vectors in >>>> >> 2D. >>>> >> > Sounds correct? Also does the center of mass coordinates matter when >>>> >> > defining r? >>>> >> > >>>> >> > On Wed, Oct 30, 2024 at 7:53 AM Amneet Bhalla <mail2amn...@gmail.com >>>> >> > <mailto:mail2amn...@gmail.com>> >>>> >> wrote: >>>> >> > >>>> >> >> @Mark: Is there some document/paper that I can follow to check the >>>> >> algebra >>>> >> >> of these zero eigenvectors/null space modes? >>>> >> >> >>>> >> >> @Jed : We use a projection method preconditioner to solve the coupled >>>> >> >> velocity pressure system as described here ( >>>> >> >> https://urldefense.us/v3/__https://www.sciencedirect.com/science/article/pii/S0021999123004205__;!!G_uCfscf7eWS!fdj4AzKhAcDmM1x_ZQ8gxqWeX6BAKY9urnvATMpT7hC8lw77ak7tqxqXGIX3PMg2wYA5PGu7EzyCW0xFZnni7g$ >>>> >> >> >>>> >> >> <https://urldefense.us/v3/__https://www.sciencedirect.com/science/article/pii/S0021999123004205__;!!G_uCfscf7eWS!b0T54ExhpyMjL9O-B63FmKcfUHpYoH0-ixjUnroOoB0PZPSEVH2-LEMb_Yw57sybhA0rknBisFM2erfwvAPghoI$>). >>>> >> It >>>> >> >> is an approximation of the Schur complement. As a part of projection >>>> >> >> preconditioner, we need to solve just the momentum equation >>>> >> >> separately >>>> >> >> without considering the pressure part. >>>> >> >> >>>> >> >> On Tue, Oct 29, 2024 at 8:03 PM Jed Brown <j...@jedbrown.org >>>> >> >> <mailto:j...@jedbrown.org>> wrote: >>>> >> >> >>>> >> >>> And to be clear, we recommend using fieldsplit Schur to separate the >>>> >> >>> pressure and velocity part (there are many examples). Applying AMG >>>> >> directly >>>> >> >>> to the saddle point problem will not be a good solver because the >>>> >> >>> heuristics assume positivity and do not preserve inf-sup stability >>>> >> (nor do >>>> >> >>> standard smoothers). >>>> >> >>> >>>> >> >>> Mark Adams <mfad...@lbl.gov <mailto:mfad...@lbl.gov>> writes: >>>> >> >>> >>>> >> >>> > This is linear elasticity and there are 6 "null" vectors (if you >>>> >> removed >>>> >> >>> > Dirichlet boundary conditions these are eigenvectors with zero >>>> >> >>> eigenvalue): >>>> >> >>> > 3 translations, x, y, z, and three rotatiions xx, yy ,zz. >>>> >> >>> > x = (1,0,0,1,0,0,1,0 ...) >>>> >> >>> > and xx is something like (0, z_1, -y_1, 0, z_2, -y_2, ...) where >>>> >> >>> > z_1 >>>> >> is >>>> >> >>> the >>>> >> >>> > z coordinate of the first vertex, etc. >>>> >> >>> > >>>> >> >>> > Mark >>>> >> >>> > >>>> >> >>> > On Tue, Oct 29, 2024 at 3:47 PM Amneet Bhalla >>>> >> >>> > <mail2amn...@gmail.com <mailto:mail2amn...@gmail.com> >>>> >> > >>>> >> >>> wrote: >>>> >> >>> > >>>> >> >>> >> Hi Mark, >>>> >> >>> >> >>>> >> >>> >> Thanks! I am not sure how to construct null space and zero energy >>>> >> modes >>>> >> >>> >> manually for this operator. Is there some theory or >>>> >> >>> >> documentation I >>>> >> can >>>> >> >>> >> follow to figure out what the null space and zero energy modes >>>> >> >>> >> look >>>> >> >>> like >>>> >> >>> >> for this operator? Once I know what these are in symbolic form, I >>>> >> >>> think I >>>> >> >>> >> should be able to construct them manually. >>>> >> >>> >> >>>> >> >>> >> Best, >>>> >> >>> >> --Amneet >>>> >> >>> >> >>>> >> >>> >> On Tue, Oct 29, 2024 at 7:35 AM Mark Adams <mfad...@lbl.gov >>>> >> >>> >> <mailto:mfad...@lbl.gov>> wrote: >>>> >> >>> >> >>>> >> >>> >>> Oh my mistake. You are using staggered grids. So you don't have >>>> >> >>> >>> a >>>> >> >>> block >>>> >> >>> >>> size that hypre would use for the "nodal" methods. >>>> >> >>> >>> I'm not sure what you are doing exactly, but try hypre and you >>>> >> could >>>> >> >>> >>> create the null space, zero energy modes, manually, attach to >>>> >> >>> >>> the >>>> >> >>> matrix >>>> >> >>> >>> and try GAMG. >>>> >> >>> >>> You can run with '-info :pc' and grep on GAMG to see if GAMG is >>>> >> >>> picking >>>> >> >>> >>> the null space up (send this output if you can't figure it out). >>>> >> >>> >>> >>>> >> >>> >>> Thanks, >>>> >> >>> >>> Mark >>>> >> >>> >>> >>>> >> >>> >>> On Tue, Oct 29, 2024 at 9:28 AM Mark Adams <mfad...@lbl.gov >>>> >> >>> >>> <mailto:mfad...@lbl.gov>> >>>> >> wrote: >>>> >> >>> >>> >>>> >> >>> >>>> This coordinate interface is just a shortcut for vertex based >>>> >> >>> >>>> discretizations with 3 dof per vertex, etc. (maybe works in >>>> >> >>> >>>> 2D). >>>> >> >>> >>>> You will need to construct the null space vectors manually and >>>> >> >>> attach it >>>> >> >>> >>>> to the matrix. Used by GAMG. >>>> >> >>> >>>> >>>> >> >>> >>>> Note, for hypre you want to use the "nodal" options and it does >>>> >> not >>>> >> >>> use >>>> >> >>> >>>> these null space vectors. That is probably the way you want to >>>> >> >>> >>>> go. >>>> >> >>> >>>> eg: -pc_hypre_boomeramg_nodal_coarsen >>>> >> >>> >>>> >>>> >> >>> >>>> I would run with hypre boomerang and -help and grep on nodal to >>>> >> see >>>> >> >>> all >>>> >> >>> >>>> the "nodal" options and use them. >>>> >> >>> >>>> >>>> >> >>> >>>> Thanks, >>>> >> >>> >>>> Mark >>>> >> >>> >>>> >>>> >> >>> >>>> >>>> >> >>> >>>> On Mon, Oct 28, 2024 at 8:06 PM Amneet Bhalla < >>>> >> mail2amn...@gmail.com <mailto:mail2amn...@gmail.com> >>>> >> >>> > >>>> >> >>> >>>> wrote: >>>> >> >>> >>>> >>>> >> >>> >>>>> Hi Folks, >>>> >> >>> >>>>> >>>> >> >>> >>>>> I am trying to solve the momentum equation in a projection >>>> >> >>> >>>>> preconditioner using GAMG or Hypre solver. The equation looks >>>> >> like >>>> >> >>> for >>>> >> >>> >>>>> velocity variable *v* looks like: >>>> >> >>> >>>>> >>>> >> >>> >>>>> >>>> >> >>> >>>>> [image: Screenshot 2024-10-28 at 4.15.17 PM.png] >>>> >> >>> >>>>> >>>> >> >>> >>>>> Here, μ is spatially varying dynamic viscosity and λ is >>>> >> >>> >>>>> spatially >>>> >> >>> >>>>> varying bulk viscosity. I understand that I need to specify >>>> >> >>> >>>>> rigid >>>> >> >>> body >>>> >> >>> >>>>> nullspace modes to the multigrid solver in order to accelerate >>>> >> its >>>> >> >>> >>>>> convergence. Looking into this routine >>>> >> >>> MatNullSpaceCreateRigidBody() ( >>>> >> >>> >>>>> >>>> >> >>> >>>> >> https://urldefense.us/v3/__https://petsc.org/release/manualpages/Mat/MatNullSpaceCreateRigidBody/__;!!G_uCfscf7eWS!bVR6duCoDqPhZrWS-sm1c5qxsFPjZMhdT86AqLpPzWgVy5qoRhd4_Jue2LJOIS6LRrtV2cHGrqger1Yvb-Y5f-0$ >>>> >> >>> >>>>> < >>>> >> >>> >>>> >> https://urldefense.us/v3/__https://petsc.org/release/manualpages/Mat/MatNullSpaceCreateRigidBody/__;!!G_uCfscf7eWS!eKqgIJjCdMzIU76f7X65AmGxrU_-lC7W02BMWafJ77DNf_IuQk6O1X3qU1x9Ez8NJ20vZEL-mF6T1yNmDnwv0eWa2w$ >>>> >> >>> >), >>>> >> >>> >>>>> I see that I need to provide the coordinates of each node. I >>>> >> >>> >>>>> am >>>> >> >>> using >>>> >> >>> >>>>> staggered grid discretization. Do I need to provide >>>> >> >>> >>>>> coordinates >>>> >> of >>>> >> >>> >>>>> staggered grid locations? >>>> >> >>> >>>>> >>>> >> >>> >>>>> Thanks, >>>> >> >>> >>>>> -- >>>> >> >>> >>>>> --Amneet >>>> >> >>> >>>>> >>>> >> >>> >>>>> >>>> >> >>> >>>>> >>>> >> >>> >>>>> >>>> >> >>> >> >>>> >> >>> >> -- >>>> >> >>> >> --Amneet >>>> >> >>> >> >>>> >> >>> >> >>>> >> >>> >> >>>> >> >>> >> >>>> >> >>> >>>> >> >> >>>> >> >> >>>> >> >> -- >>>> >> >> --Amneet >>>> >> >> >>>> >> >> >>>> >> >> >>>> >> >> >>>> >> > >>>> >> > -- >>>> >> > --Amneet >>>> >> >>>> > >>>> > >>>> > -- >>>> > --Amneet >>
