Re: [petsc-users] Profile a matrix-free solver.

Hi Song, I wonder if you have a reference paper on the preconditioning algorithm you are working on, i.e., using the 1st order flux for preconditioning purpose when your 'true' fluxes are evaluated using the 2nd order AUSM scheme. Best, Ling On Fri, Jan 15, 2016 at 1:34 PM, Song Gao

Re: [petsc-users] Profile a matrix-free solver.

_S0021999198960764=BQMFaQ=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00=kuHHom1yjd94zUrBWecnYg=Z6JmjYd7euHq--9l5maVEB6hJHAkMcMNyc8rnVhgDC8=wfmA2PxK68XsQhc1PzBC4HCsxtwNAhBAmxe5VvnLj8Q=> > > It's on page 668 equation 4.6. > > Thanks > > 2016-01-15 15:39 GMT-05:00 Zou (Non-US), Ling <

Re: [petsc-users] How do I know it is steady state?

pley <knep...@gmail.com> wrote: > On Mon, Nov 2, 2015 at 7:29 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > >> >> > On Oct 30, 2015, at 12:23 PM, Zou (Non-US), Ling <ling@inl.gov> >> wrote: >> > >> > Hi All, >> > >>

Re: [petsc-users] How do I know it is steady state?

due to CONVERGED_SNORM_RELATIVE iterations 0 In this case, snes_rtol is ignored. Ling On Mon, Nov 2, 2015 at 6:29 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Oct 30, 2015, at 12:23 PM, Zou (Non-US), Ling <ling@inl.gov> > wrote: > > > > Hi All, &

Re: [petsc-users] How do I know it is steady state?

Barry, thanks for the discussion and help. Ling On Tue, Nov 3, 2015 at 11:55 AM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Nov 3, 2015, at 9:38 AM, Zou (Non-US), Ling <ling@inl.gov> wrote: > > > > > > > > On Tue, Nov 3, 2015 at 8:24 AM

[petsc-users] How do I know it is steady state?

Hi All, >From physics point of view, I know my simulation converges if nothing changes any more. I wonder how normally you do to detect if your simulation reaches steady state from numerical point of view. Is it a good practice to use SNES convergence as a criterion, i.e., SNES converges and it

Re: [petsc-users] A question on finite difference Jacobian

know if anybody did similar things before. Thanks, Ling On Tue, Oct 6, 2015 at 7:09 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Oct 6, 2015, at 4:22 PM, Zou (Non-US), Ling <ling@inl.gov> wrote: > > > > > > > > On Tue, Oct 6, 2015 at 2:

Re: [petsc-users] A question on finite difference Jacobian

well, it has the same risk that Newton direction is not good due to the simplification. However, it worth my trying. On Wed, Oct 7, 2015 at 8:54 AM, Zou (Non-US), Ling <ling@inl.gov> wrote: > Thank you Barry. > > The background I am asking this question is that I want to reduc

Re: [petsc-users] A question on finite difference Jacobian

Thank you Jed. This seems to be hard :) Ling On Wed, Oct 7, 2015 at 9:30 AM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Oct 7, 2015, at 9:54 AM, Zou (Non-US), Ling <ling@inl.gov> wrote: > > > > Thank you Barry. > > > > The background I am

[petsc-users] A question on finite difference Jacobian

Hi All, If the non-zero pattern of a finite difference Jacobian needs 20 colors to color it (20 comes from MatFDColoringView, the non-zero pattern is pre-determined from mesh connectivity), is it true that PETSc needs 40 functions evaluation to get the full Jacobian matrix filled? This is because

Re: [petsc-users] A question on finite difference Jacobian

Ah! That's correct. I forgot that the base vector always keeps the same. Thanks. Ling On Tue, Oct 6, 2015 at 2:33 PM, Jed Brown <j...@jedbrown.org> wrote: > "Zou (Non-US), Ling" <ling@inl.gov> writes: > > > Hi All, > > > > If the non-zero pa

Re: [petsc-users] A question on finite difference Jacobian

On Tue, Oct 6, 2015 at 2:38 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Oct 6, 2015, at 3:29 PM, Zou (Non-US), Ling <ling@inl.gov> wrote: > > > > Hi All, > > > > If the non-zero pattern of a finite difference Jacobian needs 20 colors &

Re: [petsc-users] SNES stuck with small residual

I would suggest try '-snes_mffd_type ds' if you are using Jacobian free. It is a magic word that always helps me out of trouble. Ling On Thu, Sep 24, 2015 at 4:44 PM, Barry Smith wrote: > > I completely disagree with Matt, looking at the numbers one sees very > typical

Re: [petsc-users] Weird behavior for log_summary

On Wed, Jul 1, 2015 at 3:52 PM, Michele Rosso mro...@uci.edu wrote: Hi Barry, I accidentally found out what triggers the problem with log_summary. If I specify log_summary from command line, it works as expected. If instead I open and load an options file with -log_summary in it, the

[petsc-users] Two questions on PETSc installation

Hi All, Following the instructions, I installed PETSc 3.5.2 on my Mac and everything works great. Two questions: 1, I suppose the name, PETSC_ARCH=arch-darwin-c-debug, suggests the installation is a debug version? 2, How can I install a faster (optimized?) version of PETSc ? Best, Ling

Re: [petsc-users] Two questions on PETSc installation

Thank you Jed. Ling On Tue, Mar 31, 2015 at 12:59 PM, Jed Brown j...@jedbrown.org wrote: Zou (Non-US), Ling ling@inl.gov writes: Hi All, Following the instructions, I installed PETSc 3.5.2 on my Mac and everything works great. Two questions: 1, I suppose the name, PETSC_ARCH

[petsc-users] A question on -pc_factor_mat_ordering_type

Hi All, I found many available options for PCILU on this webpage: http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCILU.html There is an option named -pc_factor_mat_ordering_type, with possible values such as natural,nd,1wd,rcm,qmd. I wonder if anyone has brief descriptions for

Re: [petsc-users] A question on -pc_factor_mat_ordering_type

Thank you Matt for the link. Ling On Fri, Jan 16, 2015 at 2:30 PM, Matthew Knepley knep...@gmail.com wrote: On Fri, Jan 16, 2015 at 2:36 PM, Zou (Non-US), Ling ling@inl.gov wrote: Hi All, I found many available options for PCILU on this webpage: http://www.mcs.anl.gov/petsc/petsc

Re: [petsc-users] snes + matrix free + coloring

Hi Jed, I was searching a topic on preconditioning in the mail list and found this email. On Wed, Oct 10, 2012 at 2:55 PM, Jed Brown jedbr...@mcs.anl.gov wrote: Then you aren't using a matrix-free method at all. In case of using SNESDefaultComputeJacobianColor to compute Jacobian matrix and

Re: [petsc-users] snes + matrix free + coloring

On Fri, Mar 7, 2014 at 4:56 PM, Jed Brown j...@jedbrown.org wrote: Zou (Non-US), Ling ling@inl.gov writes: Hi Jed, I was searching a topic on preconditioning in the mail list and found this email. On Wed, Oct 10, 2012 at 2:55 PM, Jed Brown jedbr...@mcs.anl.gov wrote

Re: [petsc-users] Modify RHS values at each iteration

Hi Jed. I have a similar situation here. I am intentionally testing an iterative method. It requires me to do some handling (for example copying the current solution vector out) right after a nonlinear iteration is finished, but before anything happening of the next nonlinear iteration. Is there

Re: [petsc-users] Modify RHS values at each iteration

Thanks a lot. On Thu, Jan 2, 2014 at 3:20 PM, Jed Brown jedbr...@mcs.anl.gov wrote: Zou (Non-US), Ling ling@inl.gov writes: Hi Jed. I have a similar situation here. I am intentionally testing an iterative method. It requires me to do some handling (for example copying the current

[petsc-users] understanding the eigenvalues of my system

Dear All, I just explored the user manual v3.4 and I noticed the option -ksp_compute_eigenvalues I test it with my problem with ~1000 number of dofs, and it printed out Iteratively computed eigenvalues 0.840692 + 0i 0.857247 - 0.235747i 0.857247 + 0.235747i 0.93 + 0i 1.03457 + 0i 2.69763 +

[petsc-users] SNES and TS

Dear All, I've been playing with TS with my transient problem. It so far works fine and I was able to deal with forward Euler and backward Euler time integration scheme very easy pretty much without changing anything in my code. I understand that TS works fine when the non-linear equations look

Re: [petsc-users] Getting Different Solution from KSP with different resolution

I suppose you need at least one Dirichlet boundary condition for your problem? i.e., you could not do this: 2T(1) - T(2) = 0 and -T(N-1) + 2T(N) = 0 at the same time. On Thu, Jul 18, 2013 at 11:09 AM, Armelius Cameron armeli...@gmail.com wrote: Hello, I am trying to work on getting to know

Re: [petsc-users] example on manually setup matrix coloring for finite difference Jacobian?

, but use keyword SNESDefaultComputeJacobian, which is very slow 3, using matrix free operation to avoid the Jacobian calculation Any suggestion? On Wed, Jul 17, 2013 at 5:06 PM, Matthew Knepley knep...@gmail.com wrote: On Wed, Jul 17, 2013 at 6:02 PM, Zou (Non-US), Ling ling@inl.gov wrote: Hi

Re: [petsc-users] Segmentation fault in PetscInitialize()

I have petsc 3.3p5 on my Mac. PetscInitialize(NULL, NULL, NULL, NULL); It seems working fine here. Ling On Tue, Jun 25, 2013 at 4:54 PM, Longxiang Chen suifen...@gmail.com wrote: Dear all, I try to use ksp to solve Ax=b. ALL programs are in fortran, except petscsolve() in c.

Re: [petsc-users] Segmentation fault in PetscInitialize()

Hmmm... I guess you cannot do PetscInitialize multiple times. Ling On Tue, Jun 25, 2013 at 5:47 PM, Zou (Non-US), Ling ling@inl.govwrote: I have petsc 3.3p5 on my Mac. PetscInitialize(NULL, NULL, NULL, NULL); It seems working fine here. Ling On Tue, Jun 25, 2013 at 4:54 PM

[petsc-users] snes/examples/tutorials/ex3 x-window plot issue

Hi, All I tried snes/examples/tutorials/ex3 on my Mac OS 10.7.5, with X11 (XQuartz 2.6.5 (xorg-server 1.10.6)) installed. Everything seems fine, as I got output from the terminal as: == atol=1e-50, rtol=1e-08, stol=1e-08, maxit=50, maxf=1 iter = 0,SNES Function norm

[petsc-users] working with cmake

Hi All, I am trying to use PETSc working with cmake, following the instructions found on: http://www.mcs.anl.gov/petsc/documentation/faq.html#cmake Can I use CMake to build my own project that depends on PETSc?Use the

[petsc-users] compare snes_mf_operator and snes_fd

Thank you Matt and Barry. I didn't get a chance to reply you yesterday. Here are the new output files with -snes_view on. Ling On Wed, Jan 30, 2013 at 6:40 PM, Matthew Knepley knepley at gmail.com wrote: On Wed, Jan 30, 2013 at 6:30 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Hi, All

[petsc-users] compare snes_mf_operator and snes_fd

On Thu, Jan 31, 2013 at 11:28 AM, Matthew Knepley knepley at gmail.com wrote: On Thu, Jan 31, 2013 at 1:16 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Thank you Matt and Barry. I didn't get a chance to reply you yesterday. Here are the new output files with -snes_view on. It seems

[petsc-users] compare snes_mf_operator and snes_fd

jedbrown at mcs.anl.gov wrote: On Thu, Jan 31, 2013 at 1:29 PM, Matthew Knepley knepley at gmail.comwrote: On Thu, Jan 31, 2013 at 2:25 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: On Thu, Jan 31, 2013 at 11:28 AM, Matthew Knepley knepley at gmail.comwrote: On Thu, Jan 31, 2013 at 1

[petsc-users] PETSc 3.3 p5 installation newbie question

Hi, all I downloaded the PETSc 3.3 p5 version and installed it. Everything seems to be working fine as I followed those instructions and eventually I did the test like: make PETSC_DIR=/opt/packages/petsc/petsc-3.3-p5 PETSC_ARCH=arch-darwin-c-debug test and I got: Running test examples to

[petsc-users] PETSc 3.3 p5 installation newbie question

for export PETSC_DIR=/opt/packages/petsc/petsc-3.3-p5 PETSC_ARCH=arch-darwin-c-debug (or include in make command) followed by make ex1 make runex1 You can also make alltests but this is overkill. On Mon, Jan 21, 2013 at 6:41 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Hi, all I

[petsc-users] PETSc 3.3 p5 installation newbie question

Jed, thanks again for your reply. Have a good night. Ling On Mon, Jan 21, 2013 at 6:05 PM, Jed Brown jedbrown at mcs.anl.gov wrote: On Mon, Jan 21, 2013 at 7:03 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Thank you Jed. After 'export PETSC_DIR=/opt/packages/petsc/petsc-3.3-p5

[petsc-users] how to control snes_mf_operator

Dear All, I have recently had an issue using snes_mf_operator. I've tried to figure it out from PETSc manual and PETSc website but didn't get any luck, so I submit my question here and hope some one could help me out. (1) = A little

[petsc-users] how to control snes_mf_operator

at 1:34 PM, Zou (Non-US), Ling ling.zou at inl.gov wrote: Dear All, I have recently had an issue using snes_mf_operator. I've tried to figure it out from PETSc manual and PETSc website but didn't get any luck, so I submit my question here and hope some one could help me out. (1

[petsc-users] how to control snes_mf_operator

Matt, one more question. Can I combine the options -snes_type test and -mat_mffd_err 1.e-10 to see the effect? Best, Ling On Tue, Dec 11, 2012 at 2:47 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: thank you Matt. I will try to figure it out. Non-dimensionalization is certainly

[petsc-users] how to control snes_mf_operator

: On Tue, Dec 11, 2012 at 2:19 PM, Zou (Non-US), Ling ling.zou at inl.gov wrote: Matt, one more question. Can I combine the options -snes_type test and -mat_mffd_err 1.e-10 to see the effect? I do not understand your question. test does compare the analytic and FD Jacobian

[petsc-users] how to control snes_mf_operator

PM, Matthew Knepley knepley at gmail.com wrote: On Tue, Dec 11, 2012 at 2:40 PM, Zou (Non-US), Ling ling.zou at inl.gov wrote: Hmm... I have an 'approximated' analytical Jacobian to compare. And I did this: ./my-moose-project -i input.i -snes_type test -snes_test_display out I

[petsc-users] how to control snes_mf_operator

Thank you Matt. Ling On Tue, Dec 11, 2012 at 4:02 PM, Matthew Knepley knepley at gmail.com wrote: On Tue, Dec 11, 2012 at 2:59 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: ok. I tried. Seems there is no effect. ./my-moose-project -i input.i -snes_type test -mat_mffd_umin 1.e-10

[petsc-users] PETSc Execution Error

Well, I am not PETSc expert, but the 'Floating point exception!' error message seems to me that you are trying to do a divide zero operation (or something else). I had this kind of error message before when I assemble my Jacobian matrix and I made a mistake trying to do this, like, return a/b;

[petsc-users] question on PETSc option '-snes_mf_operator'

Dear all, I have a question on the PETSc option '-snes_mf_operator'. I am reading thePETSc Users Manual Revision 3.3. On page 100, 2nd paragraph, it says: == However, it allows us to check the analytic Jacobian we

[petsc-users] question on PETSc option '-snes_mf_operator'

: On Thu, Sep 27, 2012 at 2:01 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Dear all, I have a question on the PETSc option '-snes_mf_operator'. I am reading thePETSc Users Manual Revision 3.3. On page 100, 2nd paragraph, it says

[petsc-users] question on PETSc option '-snes_mf_operator'

Thanks again, Matt. Your answers are really helpful to me. Best, Ling On Thu, Sep 27, 2012 at 12:22 PM, Matthew Knepley knepley at gmail.com wrote: On Thu, Sep 27, 2012 at 2:13 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Thank you Matt. I've noticed that there is a different

[petsc-users] question on PETSc option '-snes_mf_operator'

are those default options. Appreciate your answer. Ling On Thu, Sep 27, 2012 at 12:30 PM, Dmitry Karpeev karpeev at mcs.anl.govwrote: On Thu, Sep 27, 2012 at 1:22 PM, Matthew Knepley knepley at gmail.comwrote: On Thu, Sep 27, 2012 at 2:13 PM, Zou (Non-US), Ling ling.zou at inl.govwrote

[petsc-users] using '-snes_type test' to test my coded Jacobian

] as the base solution vector when using the '-snes_type test' option to test my hand-coded Jacobian. Best Regards, Ling Ling On Wed, Sep 5, 2012 at 11:35 AM, Matthew Knepley knepley at gmail.com wrote: On Wed, Sep 5, 2012 at 12:24 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Dear

[petsc-users] using '-snes_type test' to test my coded Jacobian

On Wed, Sep 19, 2012 at 1:03 PM, Jed Brown jedbrown at mcs.anl.gov wrote: On Wed, Sep 19, 2012 at 1:54 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Dear Matt, Thanks again for helping me on the '-snes_type test' issue. This is a great tool which helped us make really good progress

[petsc-users] using '-snes_type test' to test my coded Jacobian

No Jacobian output showed when I did this, ./my-project-opt -i input.i -snes_compare_explicit Any suggestion? Ling On Wed, Sep 19, 2012 at 1:12 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: On Wed, Sep 19, 2012 at 1:03 PM, Jed Brown jedbrown at mcs.anl.gov wrote: On Wed, Sep 19

[petsc-users] using '-snes_type test' to test my coded Jacobian

my version is 3.1.0. Ling On Wed, Sep 19, 2012 at 2:31 PM, Jed Brown jedbrown at mcs.anl.gov wrote: Are you using an older version of PETSc? On Wed, Sep 19, 2012 at 2:56 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: No Jacobian output showed when I did this, ./my-project-opt -i

[petsc-users] using '-snes_type test' to test my coded Jacobian

Thank you Matt. I am working under MOOSE framework, so I am afraid I am not able to do it alone. I will seek help from them. Thanks Ling On Wed, Sep 19, 2012 at 2:35 PM, Matthew Knepley knepley at gmail.com wrote: On Wed, Sep 19, 2012 at 3:34 PM, Zou (Non-US), Ling ling.zou at inl.govwrote

[petsc-users] using '-snes_type test' to test my coded Jacobian

Thanks Jed. Ling On Wed, Sep 19, 2012 at 2:37 PM, Jed Brown jedbrown at mcs.anl.gov wrote: Upgrade to petsc-3.3 On Wed, Sep 19, 2012 at 3:34 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: == Framework Information: SVN Revision

[petsc-users] using '-snes_type test' to test my coded Jacobian

good to know, I will try it. Ling On Wed, Sep 19, 2012 at 2:42 PM, Jed Brown jedbrown at mcs.anl.gov wrote: On Wed, Sep 19, 2012 at 3:40 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Thank you Matt. I am working under MOOSE framework, so I am afraid I am not able to do it alone. I

[petsc-users] using '-snes_type test' to test my coded Jacobian

Dear All, I am trying to use the option '-snes_type test' to test my coded Jacobian. I tested with different snes options and it gives me different answers. I wonder if someone could give me a hint what is wrong with my settings. The command line looks like this: ./my-code-opt -i test.i

[petsc-users] using '-snes_type test' to test my coded Jacobian

Thanks Matt. This is really helpful. Best, Ling On 9/5/12, Matthew Knepley knepley at gmail.com wrote: On Wed, Sep 5, 2012 at 12:24 PM, Zou (Non-US), Ling ling.zou at inl.govwrote: Dear All, I am trying to use the option '-snes_type test' to test my coded Jacobian. I tested