[petsc-users] Coupled system of equations on unstructured mesh
Karthikeyan Chockalingam - STFC UKRI
karthikeyan.chockalingam at stfc.ac.uk
Sat Sep 23 08:32:28 CDT 2023
Sorry, you didn’t answer my first equation.
1)The M and N, in MatCreateBIJ, refer to the actual number of global rows/cols or global blocked rows/cols?
2) The row indexes used in MatZeroRowsColumnsIS, would refer to the actual row or the blocked row?
Below is your response to my previous email:
“You would use the actual row numbers instead of block rows. You can use either.” How can I use either (or switch)?
Thanks,
Karthik,
From: Matthew Knepley <knepley at gmail.com>
Date: Saturday, 23 September 2023 at 14:23
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk>
Cc: petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh
On Sat, Sep 23, 2023 at 6:00 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
I just would like to clarify a couple of things.
1)The M and N, in MatCreateBIJ, refer to the actual number of global rows/cols or global blocked rows/cols?
But d_nz and o_nz only refer to blocked rows.
Yes.
2) In MatZeroRowsColumnsIS, you mentioned I could use the actual row numbers instead of block rows. Is there any option to SWITCH between the two, when using MatZeroRowsColumnsIS?
I do not understand the question. When would switching happen?
Thanks,
Matt
Thank you,
Karthik.
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Sunday, 10 September 2023 at 22:03
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh
On Sun, Sep 10, 2023 at 5:00 PM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
I get it.
Q1) In other words when using MatSetValuesBlocked, for bs = 2, I could pass all 64 entrees of the element matrix row-oriented by setting m = n = 4 (along with the respective idxm and idxn)?
Yes.
Q2) However, at a given node variable u can fixed while v is free. In that case, while using MatZeroRowsColumns I need to know the global index of the variable u (i.e. row/column index in the system matrix A). Here, block size does not come in handy as it did when using MatSetValuesBlocked.
You would use the actual row numbers instead of block rows. You can use either.
Q3) When assembling the system matrix A in this way, would it allow me to use PCFIELDSPLIT for coupled systems?
Yes.
Thanks,
Matt
Kind regards,
Karthik.
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Sunday, 10 September 2023 at 21:23
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh
On Sun, Sep 10, 2023 at 4:16 PM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
Thank you. I almost got it and have a couple of questions.
Let me summarize, I have an element Jacobian matrix of size 8 x 8 for QAUD4 (for variables u and v) ordered such that the degrees of freedom at a node are grouped together i.e. [u1 v1 u2 v2 u3 v3 u4 v4].
Q1) But this ordering of element Jacobian matrix of size 8 x 8, does not have an on-diagonal and off-diagonal block structure? Does it not matter?
It does have block structure in that each entry in your original matrix is now a 2x2 block entry in the matrix for 2 fields.
When assembling the element Jacobian into the system matrix A, I would make use of MatSetValues. For each element, I presume m = 8 and n = 8 along with idxm and idxn, are passed to MatSetValues. Meaning I have to figure out the global index (say idxm) set of size 8 corresponding to the system matrix A.
What you can do is call
https://petsc.org/main/manualpages/Mat/MatSetValuesBlocked/
and give the same indices that you would have given for the original matrix, but instead of a value at each location, we now have a 2x2 block.
Q2) What does setting the block size bs = 2 accomplish? Because the way to assemble the Jacobian into the system matrix A seems to me no different than I did for the single variable scalar problem.
This is answered above.
Thanks,
Matt
Kind regards,
Karthik.
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Sunday, 10 September 2023 at 20:18
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh
On Sun, Sep 10, 2023 at 3:15 PM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
I don’t see an option to give block size.
https://petsc.org/release/manualpages/Mat/MatCreateAIJ/
https://petsc.org/release/manualpages/Mat/MatSetBlockSize/
Thanks,
Matt
Many thanks,
Karthik.
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Sunday, 10 September 2023 at 20:09
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh
On Sun, Sep 10, 2023 at 3:01 PM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
I will solve the coupled problem in a non-linear fashion using SNES, so I will have one residual for each variable R(u1) and R(u2) and the resulting Jacobian matrix
J = [J11 J12
J21 J22] for each element.
For first-order Lagrange elements (in 2D) will have four nodes, then J would be of size 8 x 8. Let's say the variables are u and v. The order would be [u1 u2 u3 u4 v1 v2 v3 v4].
Or should I rearrange the above entrées in the element Jacobian so as to have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will not have block ordering I guess.
This is the correct order to get block matrices.
In my case, the discretization of the u and v are from the same element space.
Can you please elaborate when you say, “Just enlarge the block size of your matrix”?
I have never used block size before and not sure what it accomplishes.
Do you mean to say, I should use MATBAIJ instead of MATAIJ?
You do not need to change the type, just give the AIJ matrix a blocksize of 2.
Thanks,
Matt
Kind regards,
Karthik.
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Sunday, 10 September 2023 at 19:03
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh
On Sun, Sep 10, 2023 at 1:48 PM Karthikeyan Chockalingam - STFC UKRI via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
Hello,
I have so far solved scalar field problems using finite elements on a given (unstructured) mesh. I made use of MATMPIAIJ to create matrixes, MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to set boundary conditions.
Now, I would like to solve a coupled system of equations for the quantities u1 and u2 on the (unstructured) mesh. I.e., the matrix should get the double number of rows and columns,
A = [A00 A01
A10 A11]
This is usually not a good way to think of it. This division means that all variables of one field come before
all those of another. It is much more common to group together all the unknowns at a given point.
You could, if the discretizations of u1 and u2 are the same, just enlarge the blocksize of your matrix. Then you set u1 and u2 for each vec location, or a 2x2 block for each Jacobian location.
Thanks,
Matt
the vectors contain twice the number of entries (e.g. first all u1s and then all u2s). I would like to be sure that the entries of u1 and u2, which are associated with the same element are located on the same processor.
Is a pre-defined structure already available within PETSc to enlarge such a single equation to store the entries of coupled equations?
-\Delta u_1+c_{11} u_1+c_{12} u_2=f_1
-\Delta u_2+c_{21} u_1+c_{22} u_2=f_2
Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b);
I don’t know where to begin. I have so far only been exposed to using MATMPIAIJ and MatSetValues to create and assign values to matrix entries respectively. I would be grateful if you could provide the stepwise guide.
Kind regards,
Karthik.
--
Karthik Chockalingam, Ph.D.
Senior Research Software Engineer
High Performance Systems Engineering Group
Hartree Centre | Science and Technology Facilities Council
karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>
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--
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/>
--
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/>
--
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/>
--
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/>
--
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/>
--
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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