[petsc-users] Nonzero I-j locations
Matthew Knepley
knepley at gmail.com
Fri May 31 05:44:28 CDT 2019
On Fri, May 31, 2019 at 12:09 AM Manav Bhatia via petsc-users <
petsc-users at mcs.anl.gov> wrote:
> I managed to get this to work.
>
> I defined a larger matrix with the dense blocks appended to the end of the
> matrix on the last processor. Currently, I am only running with one extra
> unknown, so this should not be a significant penalty for load balancing.
>
> Since the larger matrix has the same I-j locations for the FE non-zeros, I
> use it directly in the FE assembly.
>
> I have tested with parallel MUMPS solves and it working smoothly. Also,
> the monolithic system removes the issue with the singularity of J_fe
> at/near the bifurcation point.
>
> Next, I would like to figure out if there are ways to bring in iterative
> solvers to solve this more efficiently. My J_fe comes from a nonlinear
> shell deformation problem with snap through response.
>
> I am not sure if it would make sense to use an AMG solver on this
> monolithic matrix, as opposed to using it as a preconditioner for J_fe in
> the Schur-factorization approach. The LOCA solver in Trillions was able to
> find some success with the latter approach:
> https://www.worldscientific.com/doi/abs/10.1142/S0218127405012508
>
> I would appreciate any general thoughts concerning this.
>
Hi Manav,
If you are using this formulation to uncover sophisticated properties of
the system, I can understand all the work for solving it.
However, if you are just using it to follow solution branches like LOCA, I
think there is a better way.
Look at this algorithm,
https://arxiv.org/abs/1410.5620
https://arxiv.org/abs/1904.13299
It is strikingly simple, and you can compute it only with a modified FEM
matrix, so your
subblock solver will work fine. He uses it on a bunch of examples
https://arxiv.org/abs/1603.00809
https://arxiv.org/abs/1609.08842
https://arxiv.org/abs/1706.04597
There are more if you check arXiv.
Thanks,
Matt
> Regards,
> Manav
>
>
> On May 29, 2019, at 9:11 PM, Manav Bhatia <bhatiamanav at gmail.com> wrote:
>
> Barry,
>
> Thanks for the detailed message.
>
> I checked libMesh’s continuation sovler and it appears to be using the
> same system solver without creating a larger matrix:
> https://github.com/libMesh/libmesh/blob/master/src/systems/continuation_system.C
>
>
> I need to implement this in my code, MAST, for various reasons (mainly,
> it fits inside a bigger workflow). The current implementation
> implementation follows the Schur factorization approach:
> https://mastmultiphysics.github.io/class_m_a_s_t_1_1_continuation_solver_base.html#details
>
>
> I will look into some solutions pertaining to the use of
> MatGetLocalSubMatrix or leverage some existing functionality in libMesh.
>
> Thanks,
> Manav
>
>
> On May 29, 2019, at 7:04 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>
>
> Understood. Where are you putting the "few extra unknowns" in the vector
> and matrix? On the first process, on the last process, some places in the
> middle of the matrix?
>
> We don't have any trivial code for copying a big matrix into a even
> larger matrix directly because we frown on doing that. It is very wasteful
> in time and memory.
>
> The simplest way to do it is call MatGetRow() twice for each row, once
> to get the nonzero locations for each row to determine the numbers needed
> for preallocation and then the second time after the big matrix has been
> preallocated to get the nonzero locations and numerical values for the row
> to call MatSetValues() with to set that row into the bigger matrix. Note of
> course when you call MatSetValues() you will need to shift the rows and
> column locations to take into account the new rows and columns in the
> bigger matrix. If you put the "extra unknowns" at the every end of the
> rows/columns on the last process you won't have to shift.
>
> Note that B being dense really messes up chances for load balancing
> since its rows are dense and take a great deal of space so whatever process
> gets those rows needs to have much less of the mesh.
>
> The correct long term approach is to have libmesh provide the needed
> functionality (for continuation) for the slightly larger matrix directly so
> huge matrices do not need to be copied.
>
> I noticed that libmesh has some functionality related to continuation. I
> do not know if they handle it by creating the larger matrix and vector and
> filling that up directly for finite elements. If they do then you should
> definitely take a look at that and see if it can be extended for your case
> (ignore the continuation algorithm they may be using, that is not relevant,
> the question is if they generate the larger matrices and if you can
> leverage this).
>
>
> The ultimate hack would be to (for example) assign the extra variables to
> the end of the last process and hack lib mesh a little bit so the matrix it
> creates (before it puts in the numerical values) has the extra rows and
> columns, that libmesh will not put the values into but you will. Thus you
> get libmesh to fill up the true final matrix for its finite element problem
> (not realizing the matrix is a little bigger then it needs) directly, no
> copies of the data needed. But this is bit tricky, you'll need to combine
> libmesh's preallocation information with yours for the final columns and
> rows before you have lib mesh put the numerical values in. Double check if
> they have any support for this first.
>
> Barry
>
>
> On May 29, 2019, at 6:29 PM, Manav Bhatia <bhatiamanav at gmail.com> wrote:
>
> Thanks, Barry.
>
> I am working on a FE application (involving bifurcation behavior) with
> libMesh where I need to solve the system of equations along with a few
> extra unknowns that are not directly related to the FE mesh. I am able to
> assemble the n x 1 residual (R_fe) and n x n Jacobian (J_fe ) from my
> code and libMesh provides me with the sparsity pattern for this.
>
> Next, the system of equations that I need to solve is:
>
> [ J_fe A ] { dX } = { R_fe }
> [ B C ] { dV } = {R_ext }
>
> Where, C is a dense matrix of size m x m ( m << n ), A is n x m, B is m x
> n, R_ext is m x 1. A, B and C are dense matrixes. This comes from the
> bordered system for my path continuation solver.
>
> I have implemented a solver using Schur factorization ( this is outside of
> PETSc and does not use the FieldSplit construct ). This works well for most
> cases, except when J_fe is close to singular.
>
> I am now attempting to create a monolithic matrix that solves the complete
> system.
>
> Currently, the approach I am considering is to compute J_fe using my
> libMesh application, so that I don’t have to change that. I am defining a
> new matrix with the extra non-zero locations for A, B, C.
>
> With J_fe computed, I am looking to copy its non-zero entries to this new
> matrix. This is where I am stumbling since I don’t know how best to get the
> non-zero locations in J_fe. Maybe there is a better approach to copy from
> J_fe to the new matrix?
>
> I have looked through the nested matrix construct, but have not given this
> a serious consideration. Maybe I should? Note that I don’t want to solve
> J_fe and C separately (not as separate systems), so the field-split
> approach will not be suitable here.
>
> Also, I am currently using MUMPS for all my parallel solves.
>
> I would appreciate any advice.
>
> Regards,
> Manav
>
>
> On May 29, 2019, at 6:07 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>
>
> Manav,
>
> For parallel sparse matrices using the standard PETSc formats the matrix
> is stored in two parts on each process (see the details in MatCreateAIJ())
> thus there is no inexpensive way to access directly the IJ locations as a
> single local matrix. What are you hoping to use the information for?
> Perhaps we have other suggestions on how to achieve the goal.
>
> Barry
>
>
> On May 29, 2019, at 2:27 PM, Manav Bhatia via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
> Hi,
>
> Once a MPI-AIJ matrix has been assembled, is there a method to get the
> nonzero I-J locations? I see one for sequential matrices here:
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetRowIJ.html
> , but not for parallel matrices.
>
> Regards,
> Manav
>
>
>
>
>
>
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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