June 2016 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] WTF
by Barry Smith 29 Jun '16

29 Jun '16

Who are these people and why to they have this webpage? Almost for sure they are doing no process binding and no proper assignment of processes to memory domains. In addition they are likely filling up all the cores on the first node before adding processes to the second core etc. If the studies had been done properly there should be very little fail off on the strong scaling in going from 1 to 2 to 4 processes and even beyond. Similarly the huge fail off in going from 4 to 8 to 16 would not occur for weak scaling. Barry > On Jun 29, 2016, at 7:47 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > http://guest.ams.sunysb.edu/~zgao/work/airfoil/scaling.html > > Can we rerun this on something at ANL since I think this cannot be true. > > Matt > > -- > 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

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Re: [petsc-dev] WTF
by Paul T. Bauman 29 Jun '16

29 Jun '16

On Wed, Jun 29, 2016 at 8:47 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > Why the hell does BoomerAMG have such shitty scaling on the Laplace > equation: > > http://guest.ams.sunysb.edu/~zgao/work/airfoil/scaling.html > > Can we rerun this on something at ANL since I think this cannot be true. > Why are they using GMRES for a symmetric problem?

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WTF
by Matthew Knepley 29 Jun '16

29 Jun '16

Why the hell does BoomerAMG have such shitty scaling on the Laplace equation: http://guest.ams.sunysb.edu/~zgao/work/airfoil/scaling.html Can we rerun this on something at ANL since I think this cannot be true. Matt -- 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

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Re: [petsc-dev] MatMFFDSetType
by Adrian Croucher 28 Jun '16

28 Jun '16

hi On 28/06/16 10:39, Barry Smith wrote: > I have added MatFDColoringSetType() in the branch barry/add-missing-apis/maint and merged the branch into next for testing. If it builds and runs everywhere I will put it into the maint branch (and master) and it will be in the next patch release. Thanks, that appears to work fine for me. - Adrian -- Dr Adrian Croucher Senior Research Fellow Department of Engineering Science University of Auckland, New Zealand email: a.croucher(a)auckland.ac.nz tel: +64 (0)9 923 84611

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Re: [petsc-dev] asm / gasm
by Barry Smith 28 Jun '16

28 Jun '16

Mark When I run with exactly the options in this file on either 1 or 8 process and MatView() the matrix you pass to KSP the matrix has ALL zeros. So of course the GAMG solver is not happy. Is the matrix suppose to have all zeros? When I run the command line options in the make file for runex56 the matrix has nonzero values in it and GAMG runs fine. Barry > On Jun 27, 2016, at 6:56 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > > Barry, > > I am having problems with your branch on ksp/ex56. First I was getting an error with the increase of the overlap that you added (I don't want that to be the default). So I set this back to 0 in gamg.c. > > Next, I get the same error with the vec out of range because ex56 has BCs in the matrix. I created a branch mark/fix-gamg-asm-aggs from your branch and added the dummy ASM block. But I am getting all kinds of errors. I get errors in get MatSubMatrix and a funny error when it tries to free a prefix string. > > I've attached the valgrind output of one process, of 8. There is a lot of noise with string operations but it looks like the first non-string thing is in MatGetSubMatrices. ex56 is elasticity. Maybe there is a block size problem? > > > <out_val_1>

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Re: [petsc-dev] TSComputeRHSJacobianConstant issue
by Jed Brown 28 Jun '16

28 Jun '16

Barry Smith <bsmith(a)mcs.anl.gov> writes: >> On Jun 28, 2016, at 9:30 AM, Jed Brown <jed(a)jedbrown.org> wrote: >> >> Thanks, Barry. My blunder with the tests. Should we still try to do the optimization? > > I don't know, but it is creating a whole bunch of matrices which I didn't understand since with only RHS Jacobian it should be able to just use the one matrix. > > So is it ending up with 3 matrices in memory requiring 3 times the memory needs? Definitely a bad thing! > > Perhaps you can debug why my optimization broke the reuse ability and fix the reuse issue (if it is fixable) with my optimization? I don't have time to do it now. I'm not confident enough to do it now and I'm about to go offline in India for a few weeks. Hopefully this will help me get back to it. https://bitbucket.org/petsc/petsc/issues/135/memory-optimization-for-ts

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Re: [petsc-dev] Problem with assembly of Jacobian in ex12 & ex77
by Matthew Knepley 28 Jun '16

28 Jun '16

On Tue, Jun 28, 2016 at 6:47 PM, Sander Arens <Sander.Arens(a)ugent.be> wrote: > Please reply to all, so that other people can also read this discussion on > the mailing list. > > I do currently have problems understanding the inner workings of PetscFE. >> For example how the element matrix is assembled. As far as I could deduce >> from your example, g3_uu_3d is the fourth-order elasticity tensor which >> means that we should form the double-dot product of it with the strain for >> it to be the integrand of the gradient of the basis functions ( int_omega >> [g3:epsilon]•grad(v) d omega). So for a linear elastic problem, according >> to my understanding, g3 *should* be the elasticity tensor and g0,g1,g2 = >> NULL if there is no volumetric force. And the residual should be f0 = 0 ; >> f1= the cauchy stress tensor. >> >> Yes, that seems correct. > > I also have troubles understanding how to apply boundary conditions. There >> seems to be the concept of DMAddBoundary() and the PetscDSSetBdJacobian() >> and PetscDSSetBdResidual(). I struggle to understand what sets them apart >> from each other. My impression is that DMAddBoundary() is for Dirichlet and >> Neumann conditions and that PetscDSSetBdJacobian() and >> PetscDSSetBdResidual() are for BC types that do not fall in those >> categories? > > Note that you can also use PetscDSAddBoundary now (if you use the master > branch). DMAddBoundary is basically used to tell which boundary region to > apply which bc. If it's a Dirichlet bc you have to provide a function to > prescribe the values on the boundary, if it's a Neumann bc you just give it > NULL. PetscDSSetBdJacobian() and PetscDSSetBdResidual() are for Neumann > bcs. > The reason why there's this difference for Dirichlet and Neumann bcs is > because for finite elements you need to assemble stuff for non-zero Neumann > bcs while for Dirichlet you set some dofs to some prescribed value. > > ex77 works with the options you provided me with. However the solver does >> not seem to converge. >> > What do you mean that it works but it doesn't converge? Did you use all > the options I provided you? In case not, you should send the output of > -snes_view. > The output of -ksp_view -ksp_monitor_true_residual -ksp_converged_reason > The problem I have with the documentation online so far is that I fail to >> fully understand how to apply petscFE. I did for example not know that you >> had to set the order of the finite element space and I have the feeling >> that there is much more I am missing. >> > > I don't really understand what you mean with "applying PetscFE". > I think the simplest way to learn how to use it is to start from one of > the examples and if you don't understand what a function does you look it > up in the documentation. If you want to see what kind of options there are > for some object, for example petscspace, you add "-help|grep petscspace" to > the command line. > PetscFE is a Ciarlet triple (P, P', K) meaning a PetscSpace for the primal space P, PetscDualSpace for the dual space P', and reference cell K which is a DM. The main function of PetscFE is to tabulate the basis at quadrature points, and to act with dual space basis vectors on functions. Thanks, Matt > Thanks, > Sander > > On 28 June 2016 at 17:47, <rickcha(a)googlemail.com> wrote: > >> Yes, that was vague, I should have formulated that better. >> What I’m trying to accomplish is writing a FEM code to calculate >> deformation and stress of structure. As a first step analysing a linear >> elastic and static problem in 2D, which I plan to extend to a >> elastic-plastic transient analysis for a 3D case. >> >> I do currently have problems understanding the inner workings of PetscFE. >> For example how the element matrix is assembled. As far as I could deduce >> from your example, g3_uu_3d is the fourth-order elasticity tensor which >> means that we should form the double-dot product of it with the strain for >> it to be the integrand of the gradient of the basis functions ( int_omega >> [g3:epsilon]•grad(v) d omega). So for a linear elastic problem, according >> to my understanding, g3 *should* be the elasticity tensor and g0,g1,g2 = >> NULL if there is no volumetric force. And the residual should be f0 = 0 ; >> f1= the cauchy stress tensor. >> >> I also have troubles understanding how to apply boundary conditions. >> There seems to be the concept of DMAddBoundary() and the >> PetscDSSetBdJacobian() and PetscDSSetBdResidual(). I struggle to understand >> what sets them apart from each other. My impression is that DMAddBoundary() >> is for Dirichlet and Neumann conditions and that PetscDSSetBdJacobian() and >> PetscDSSetBdResidual() are for BC types that do not fall in those >> categories? >> >> ex77 works with the options you provided me with. However the solver does >> not seem to converge. >> >> The problem I have with the documentation online so far is that I fail to >> fully understand how to apply petscFE. I did for example not know that you >> had to set the order of the finite element space and I have the feeling >> that there is much more I am missing. >> >> Thank you for your precious time, >> >> M. Hartig >> >> >> On 28 Jun 2016, at 14:30, Sander Arens <Sander.Arens(a)ugent.be> wrote: >> >> What are you trying to do with it? I don't think there's more >> documentation on how to use PetscFE than what's already in the online >> documentation and in the examples. >> What do you mean with "grasp the concept"? >> >> Thanks, >> Sander >> >> On 27 June 2016 at 17:41, <rickcha(a)googlemail.com> wrote: >> >>> That did do the trick with the examples, thank you. I am still >>> struggling with my own simple example however. Is there any documentation >>> available on how to use petscFE? I could not find anything besides the >>> three examples. And I yet have to grasp the concept. >>> >>> >>> Thanks in advance, >>> M. Hartig >>> >>> On 27 Jun 2016, at 15:49, Sander Arens <Sander.Arens(a)ugent.be> wrote: >>> >>> I think you forgot to set the order of the finite element spaces, which >>> default to 0. Does it work if you try for example ex77 with the following >>> options found here? >>> <https://bitbucket.org/petsc/petsc/src/8bc5349a152c81f25b59a9592e1e5936c0186…> >>> >>> Thanks, >>> Sander >>> >>> On 27 June 2016 at 15:28, <rickcha(a)googlemail.com> wrote: >>> >>>> Dear Petsc developer team, >>>> >>>> while learning the ways of the petscFE I came across a curiosity I’d >>>> like to point out to you. The Jacobians that are created from the petscFE >>>> object seem to have only 0-entries (apart from the obviously empty regions) >>>> in examples 12 and 77. That might be due to a limited understanding from my >>>> side on how exactly petscFE and the mentioned examples work, but it struck >>>> me as unusual. >>>> >>>> Thanks in advance, >>>> >>>> M. Hartig >>> >>> >>> >>> >> >> > -- 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

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Re: [petsc-dev] TSComputeRHSJacobianConstant issue
by Barry Smith 28 Jun '16

28 Jun '16

> On Jun 28, 2016, at 9:30 AM, Jed Brown <jed(a)jedbrown.org> wrote: > > Thanks, Barry. My blunder with the tests. Should we still try to do the optimization? I don't know, but it is creating a whole bunch of matrices which I didn't understand since with only RHS Jacobian it should be able to just use the one matrix. So is it ending up with 3 matrices in memory requiring 3 times the memory needs? Definitely a bad thing! Perhaps you can debug why my optimization broke the reuse ability and fix the reuse issue (if it is fixable) with my optimization? I don't have time to do it now. Barry > > Barry Smith <bsmith(a)mcs.anl.gov> writes: > >> Fixed in barry/fix-tscomputerhsjacobianconstant/maint merged to next for nightly testing >> >> Had I any brains at all I would have had Dominic use git bisect to determine the cause (which was Barry who added an optimization that broke Jed's cool trick for constant Jacobians) and this would have been resolved long ago. Curse on Jed for not adding his test cases, that he did write at least, to the automatic testing list in the makefile. >> >> Barry >> >> >>> On Mar 23, 2016, at 5:54 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: >>> >>> >>> This problem still exists. What do we do? Broken code that a beginner could easily start with is not a good thing. >>> >>> Barry >>> >>>> On Feb 27, 2016, at 5:21 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: >>>> >>>> >>>> Jed and Emil, >>>> >>>> Yes, this is a terrible mess. The TSComputeRHSJacobianConstant() will only work for methods that do not change entries in the Jacobian matrix. And for some reason the runex3_4 and _5 which do not work are turned off in the makefile ! It looks like Rosw does work because it does not change the matrix? And yet it is still turned off? >>>> >>>> I don't know what a good fix is. If we want to keep this capability then the TSComputeRHSJacobianConstant() interface has to keep a copy of the original user provided matrix and copy it into the matrices used by the method each time. This may lead to ugly special case code. >>>> >>>> Something has to be done about (simplest thing is just tossing the entire concept) because now there is a very broken API in TS that beginning users are likely to try and get upset with. >>>> >>>> Barry >>>> >>>> >>>>> On Feb 26, 2016, at 11:04 AM, Dominic Meiser <dmeiser(a)txcorp.com> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> I'm running into problems with TS with a time independent, linear >>>>> rhs. Following the user's manual, I use >>>>> >>>>> ierr=TSSetProblemType(ts, TS_LINEAR);CHKERRQ(ierr); >>>>> ierr=TSSetRHSFunction(ts, 0, TSComputeRHSFunctionLinear, 0);CHKERRQ(ierr); >>>>> ierr=TSSetRHSJacobian(ts, mat, mat, TSComputeRHSJacobianConstant, 0);CHKERRQ(ierr); >>>>> >>>>> But running the code I get: >>>>> >>>>> [dmeiser@ivyamd src]$ ./sd -ts_monitor -snes_monitor -ksp_monitor_true_residual -snes_converged_reason -ts_type beuler -ts_max_steps 20 TS dt 0.01 time 0. >>>>> 0 SNES Function norm 1.433485640883e+00 >>>>> 0 KSP preconditioned resid norm 1.433485640883e-02 true resid norm 1.433485640883e+00 ||r(i)||/||b|| 1.000000000000e+00 >>>>> 1 KSP preconditioned resid norm 6.528150237447e-18 true resid norm 6.122666587510e-16 ||r(i)||/||b|| 4.271173992185e-16 >>>>> 1 SNES Function norm 1.419007435910e+02 >>>>> Nonlinear solve converged due to CONVERGED_ITS iterations 1 >>>>> 1 TS dt 0.01 time 0.01 >>>>> 0 SNES Function norm 1.433342292319e+02 >>>>> Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE iterations 0 >>>>> [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>> [0]PETSC ERROR: >>>>> [0]PETSC ERROR: TSStep has failed due to DIVERGED_NONLINEAR_SOLVE, increase -ts_max_snes_failures or make negative to attempt recovery >>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. >>>>> [0]PETSC ERROR: Petsc Development GIT revision: pre-tsfc-330-gda8116b GIT Date: 2016-02-23 15:17:17 -0600 >>>>> [0]PETSC ERROR: ./sd on a cplx named ivyamd.txcorp.com by dmeiser Fri Feb 26 11:46:29 2016 >>>>> [0]PETSC ERROR: Configure options --with-scalar-type=complex --with-x=0 --with-debugging=1 --with-ssl=0 --with-fortran-kernels=0 --with-pthread=0 --download-fftw=1 --with-mpi=1 --download-mpich=1 --with-mpiuni-fortran-binding=0 --with-fortran-interfaces >>>>> [0]PETSC ERROR: #1 TSStep() line 3346 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>>> [0]PETSC ERROR: #2 TSSolve() line 3544 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>>> [0]PETSC ERROR: #3 main() line 63 in /scr_ivyamd/dmeiser/SD/src/sd.c >>>>> [0]PETSC ERROR: PETSc Option Table entries: >>>>> [0]PETSC ERROR: -ksp_monitor_true_residual >>>>> [0]PETSC ERROR: -snes_converged_reason >>>>> [0]PETSC ERROR: -snes_monitor >>>>> [0]PETSC ERROR: -ts_max_steps 2 >>>>> [0]PETSC ERROR: -ts_monitor >>>>> [0]PETSC ERROR: -ts_type beuler >>>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- >>>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>>> [unset]: aborting job: >>>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>>> >>>>> >>>>> It seems that the linear system is being solved just fine. But >>>>> apparently it's the wrong linear problem because the SNES >>>>> function norm doesn't decrease. >>>>> >>>>> I think the problem might be related to the following behaviour >>>>> of `scr/ts/examples/tutorials/ex3.c`: >>>>> >>>>> >>>>> [dmeiser@ivyamd tutorials]$ ./ex3 -nox -ts_type beuler -ts_max_steps 2 -ksp_converged_reason -snes_monitor >>>>> Solving a linear TS problem on 1 processor >>>>> Timestep 0: step size = 0.000143637, time = 0., 2-norm error = 1.01507e-15, max norm error = 3.10862e-15 >>>>> 0 SNES Function norm 2.018485956680e+03 >>>>> Linear solve converged due to CONVERGED_RTOL iterations 1 >>>>> 1 SNES Function norm 1.207665524289e+05 >>>>> Timestep 1: step size = 0.000143637, time = 0.000143637, 2-norm error = 0.000599907, max norm error = 0.000863771 >>>>> 0 SNES Function norm 1.195422385486e+05 >>>>> Linear solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0 >>>>> PCSETUP_FAILED due to FACTOR_NUMERIC_ZEROPIVOT >>>>> [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>> [0]PETSC ERROR: >>>>> [0]PETSC ERROR: TSStep has failed due to DIVERGED_NONLINEAR_SOLVE, increase -ts_max_snes_failures or make negative to attempt recovery >>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. >>>>> [0]PETSC ERROR: Petsc Development GIT revision: pre-tsfc-330-gda8116b GIT Date: 2016-02-23 15:17:17 -0600 >>>>> [0]PETSC ERROR: ./ex3 on a cplx named ivyamd.txcorp.com by dmeiser Fri Feb 26 11:36:28 2016 >>>>> [0]PETSC ERROR: Configure options --with-scalar-type=complex --with-x=0 --with-debugging=1 --with-ssl=0 --with-fortran-kernels=0 --with-pthread=0 --download-fftw=1 --with-mpi=1 --download-mpich=1 --with-mpiuni-fortran-binding=0 --with-fortran-interfaces >>>>> [0]PETSC ERROR: #1 TSStep() line 3346 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>>> [0]PETSC ERROR: #2 TSSolve() line 3544 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>>> [0]PETSC ERROR: #3 main() line 216 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/examples/tutorials/ex3.c >>>>> [0]PETSC ERROR: PETSc Option Table entries: >>>>> [0]PETSC ERROR: -ksp_converged_reason >>>>> [0]PETSC ERROR: -nox >>>>> [0]PETSC ERROR: -snes_monitor >>>>> [0]PETSC ERROR: -ts_max_steps 2 >>>>> [0]PETSC ERROR: -ts_type beuler >>>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- >>>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>>> [unset]: aborting job: >>>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>>> >>>>> >>>>> I'm aware of Jed's commit e1244c6 which I thought was supposed to >>>>> enable constant linear rhs without IFunction and IJacobian. Note >>>>> that e1244c6 also added tests that apparently produced very >>>>> different output (see e.g. >>>>> src/ts/examples/tutorials/output/ex3_4.out). >>>>> >>>>> Is constant rhs without IFunction and IJacobian no longer >>>>> supported or did it just breat at some point? Do I need to call >>>>> TSRHSJacobianSetReuse in addition to the lines of code above? Is >>>>> it better to treat such systems using TSComputeIFunctionLinear >>>>> and TSComputeIJacobianConstant? >>>>> >>>>> Thanks, >>>>> Dominic >>>>> >>>>> -- >>>>> Dominic Meiser >>>>> Tech-X Corporation - 5621 Arapahoe Avenue - Boulder, CO 80303 >>>> >>>

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Re: [petsc-dev] Problem with assembly of Jacobian in ex12 & ex77
by Sander Arens 28 Jun '16

28 Jun '16

Please reply to all, so that other people can also read this discussion on the mailing list. I do currently have problems understanding the inner workings of PetscFE. > For example how the element matrix is assembled. As far as I could deduce > from your example, g3_uu_3d is the fourth-order elasticity tensor which > means that we should form the double-dot product of it with the strain for > it to be the integrand of the gradient of the basis functions ( int_omega > [g3:epsilon]•grad(v) d omega). So for a linear elastic problem, according > to my understanding, g3 *should* be the elasticity tensor and g0,g1,g2 = > NULL if there is no volumetric force. And the residual should be f0 = 0 ; > f1= the cauchy stress tensor. > > Yes, that seems correct. I also have troubles understanding how to apply boundary conditions. There > seems to be the concept of DMAddBoundary() and the PetscDSSetBdJacobian() > and PetscDSSetBdResidual(). I struggle to understand what sets them apart > from each other. My impression is that DMAddBoundary() is for Dirichlet and > Neumann conditions and that PetscDSSetBdJacobian() and > PetscDSSetBdResidual() are for BC types that do not fall in those > categories? Note that you can also use PetscDSAddBoundary now (if you use the master branch). DMAddBoundary is basically used to tell which boundary region to apply which bc. If it's a Dirichlet bc you have to provide a function to prescribe the values on the boundary, if it's a Neumann bc you just give it NULL. PetscDSSetBdJacobian() and PetscDSSetBdResidual() are for Neumann bcs. The reason why there's this difference for Dirichlet and Neumann bcs is because for finite elements you need to assemble stuff for non-zero Neumann bcs while for Dirichlet you set some dofs to some prescribed value. ex77 works with the options you provided me with. However the solver does > not seem to converge. > What do you mean that it works but it doesn't converge? Did you use all the options I provided you? In case not, you should send the output of -snes_view. The problem I have with the documentation online so far is that I fail to > fully understand how to apply petscFE. I did for example not know that you > had to set the order of the finite element space and I have the feeling > that there is much more I am missing. > I don't really understand what you mean with "applying PetscFE". I think the simplest way to learn how to use it is to start from one of the examples and if you don't understand what a function does you look it up in the documentation. If you want to see what kind of options there are for some object, for example petscspace, you add "-help|grep petscspace" to the command line. Thanks, Sander On 28 June 2016 at 17:47, <rickcha(a)googlemail.com> wrote: > Yes, that was vague, I should have formulated that better. > What I’m trying to accomplish is writing a FEM code to calculate > deformation and stress of structure. As a first step analysing a linear > elastic and static problem in 2D, which I plan to extend to a > elastic-plastic transient analysis for a 3D case. > > I do currently have problems understanding the inner workings of PetscFE. > For example how the element matrix is assembled. As far as I could deduce > from your example, g3_uu_3d is the fourth-order elasticity tensor which > means that we should form the double-dot product of it with the strain for > it to be the integrand of the gradient of the basis functions ( int_omega > [g3:epsilon]•grad(v) d omega). So for a linear elastic problem, according > to my understanding, g3 *should* be the elasticity tensor and g0,g1,g2 = > NULL if there is no volumetric force. And the residual should be f0 = 0 ; > f1= the cauchy stress tensor. > > I also have troubles understanding how to apply boundary conditions. There > seems to be the concept of DMAddBoundary() and the PetscDSSetBdJacobian() > and PetscDSSetBdResidual(). I struggle to understand what sets them apart > from each other. My impression is that DMAddBoundary() is for Dirichlet and > Neumann conditions and that PetscDSSetBdJacobian() and > PetscDSSetBdResidual() are for BC types that do not fall in those > categories? > > ex77 works with the options you provided me with. However the solver does > not seem to converge. > > The problem I have with the documentation online so far is that I fail to > fully understand how to apply petscFE. I did for example not know that you > had to set the order of the finite element space and I have the feeling > that there is much more I am missing. > > Thank you for your precious time, > > M. Hartig > > > On 28 Jun 2016, at 14:30, Sander Arens <Sander.Arens(a)ugent.be> wrote: > > What are you trying to do with it? I don't think there's more > documentation on how to use PetscFE than what's already in the online > documentation and in the examples. > What do you mean with "grasp the concept"? > > Thanks, > Sander > > On 27 June 2016 at 17:41, <rickcha(a)googlemail.com> wrote: > >> That did do the trick with the examples, thank you. I am still struggling >> with my own simple example however. Is there any documentation available on >> how to use petscFE? I could not find anything besides the three examples. >> And I yet have to grasp the concept. >> >> >> Thanks in advance, >> M. Hartig >> >> On 27 Jun 2016, at 15:49, Sander Arens <Sander.Arens(a)ugent.be> wrote: >> >> I think you forgot to set the order of the finite element spaces, which >> default to 0. Does it work if you try for example ex77 with the following >> options found here? >> <https://bitbucket.org/petsc/petsc/src/8bc5349a152c81f25b59a9592e1e5936c0186…> >> >> Thanks, >> Sander >> >> On 27 June 2016 at 15:28, <rickcha(a)googlemail.com> wrote: >> >>> Dear Petsc developer team, >>> >>> while learning the ways of the petscFE I came across a curiosity I’d >>> like to point out to you. The Jacobians that are created from the petscFE >>> object seem to have only 0-entries (apart from the obviously empty regions) >>> in examples 12 and 77. That might be due to a limited understanding from my >>> side on how exactly petscFE and the mentioned examples work, but it struck >>> me as unusual. >>> >>> Thanks in advance, >>> >>> M. Hartig >> >> >> >> > >

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Re: [petsc-dev] TSComputeRHSJacobianConstant issue
by Jed Brown 28 Jun '16

28 Jun '16

Thanks, Barry. My blunder with the tests. Should we still try to do the optimization? Barry Smith <bsmith(a)mcs.anl.gov> writes: > Fixed in barry/fix-tscomputerhsjacobianconstant/maint merged to next for nightly testing > > Had I any brains at all I would have had Dominic use git bisect to determine the cause (which was Barry who added an optimization that broke Jed's cool trick for constant Jacobians) and this would have been resolved long ago. Curse on Jed for not adding his test cases, that he did write at least, to the automatic testing list in the makefile. > > Barry > > >> On Mar 23, 2016, at 5:54 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: >> >> >> This problem still exists. What do we do? Broken code that a beginner could easily start with is not a good thing. >> >> Barry >> >>> On Feb 27, 2016, at 5:21 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: >>> >>> >>> Jed and Emil, >>> >>> Yes, this is a terrible mess. The TSComputeRHSJacobianConstant() will only work for methods that do not change entries in the Jacobian matrix. And for some reason the runex3_4 and _5 which do not work are turned off in the makefile ! It looks like Rosw does work because it does not change the matrix? And yet it is still turned off? >>> >>> I don't know what a good fix is. If we want to keep this capability then the TSComputeRHSJacobianConstant() interface has to keep a copy of the original user provided matrix and copy it into the matrices used by the method each time. This may lead to ugly special case code. >>> >>> Something has to be done about (simplest thing is just tossing the entire concept) because now there is a very broken API in TS that beginning users are likely to try and get upset with. >>> >>> Barry >>> >>> >>>> On Feb 26, 2016, at 11:04 AM, Dominic Meiser <dmeiser(a)txcorp.com> wrote: >>>> >>>> Hi all, >>>> >>>> I'm running into problems with TS with a time independent, linear >>>> rhs. Following the user's manual, I use >>>> >>>> ierr=TSSetProblemType(ts, TS_LINEAR);CHKERRQ(ierr); >>>> ierr=TSSetRHSFunction(ts, 0, TSComputeRHSFunctionLinear, 0);CHKERRQ(ierr); >>>> ierr=TSSetRHSJacobian(ts, mat, mat, TSComputeRHSJacobianConstant, 0);CHKERRQ(ierr); >>>> >>>> But running the code I get: >>>> >>>> [dmeiser@ivyamd src]$ ./sd -ts_monitor -snes_monitor -ksp_monitor_true_residual -snes_converged_reason -ts_type beuler -ts_max_steps 20 TS dt 0.01 time 0. >>>> 0 SNES Function norm 1.433485640883e+00 >>>> 0 KSP preconditioned resid norm 1.433485640883e-02 true resid norm 1.433485640883e+00 ||r(i)||/||b|| 1.000000000000e+00 >>>> 1 KSP preconditioned resid norm 6.528150237447e-18 true resid norm 6.122666587510e-16 ||r(i)||/||b|| 4.271173992185e-16 >>>> 1 SNES Function norm 1.419007435910e+02 >>>> Nonlinear solve converged due to CONVERGED_ITS iterations 1 >>>> 1 TS dt 0.01 time 0.01 >>>> 0 SNES Function norm 1.433342292319e+02 >>>> Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE iterations 0 >>>> [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>> [0]PETSC ERROR: >>>> [0]PETSC ERROR: TSStep has failed due to DIVERGED_NONLINEAR_SOLVE, increase -ts_max_snes_failures or make negative to attempt recovery >>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. >>>> [0]PETSC ERROR: Petsc Development GIT revision: pre-tsfc-330-gda8116b GIT Date: 2016-02-23 15:17:17 -0600 >>>> [0]PETSC ERROR: ./sd on a cplx named ivyamd.txcorp.com by dmeiser Fri Feb 26 11:46:29 2016 >>>> [0]PETSC ERROR: Configure options --with-scalar-type=complex --with-x=0 --with-debugging=1 --with-ssl=0 --with-fortran-kernels=0 --with-pthread=0 --download-fftw=1 --with-mpi=1 --download-mpich=1 --with-mpiuni-fortran-binding=0 --with-fortran-interfaces >>>> [0]PETSC ERROR: #1 TSStep() line 3346 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>> [0]PETSC ERROR: #2 TSSolve() line 3544 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>> [0]PETSC ERROR: #3 main() line 63 in /scr_ivyamd/dmeiser/SD/src/sd.c >>>> [0]PETSC ERROR: PETSc Option Table entries: >>>> [0]PETSC ERROR: -ksp_monitor_true_residual >>>> [0]PETSC ERROR: -snes_converged_reason >>>> [0]PETSC ERROR: -snes_monitor >>>> [0]PETSC ERROR: -ts_max_steps 2 >>>> [0]PETSC ERROR: -ts_monitor >>>> [0]PETSC ERROR: -ts_type beuler >>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- >>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>> [unset]: aborting job: >>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>> >>>> >>>> It seems that the linear system is being solved just fine. But >>>> apparently it's the wrong linear problem because the SNES >>>> function norm doesn't decrease. >>>> >>>> I think the problem might be related to the following behaviour >>>> of `scr/ts/examples/tutorials/ex3.c`: >>>> >>>> >>>> [dmeiser@ivyamd tutorials]$ ./ex3 -nox -ts_type beuler -ts_max_steps 2 -ksp_converged_reason -snes_monitor >>>> Solving a linear TS problem on 1 processor >>>> Timestep 0: step size = 0.000143637, time = 0., 2-norm error = 1.01507e-15, max norm error = 3.10862e-15 >>>> 0 SNES Function norm 2.018485956680e+03 >>>> Linear solve converged due to CONVERGED_RTOL iterations 1 >>>> 1 SNES Function norm 1.207665524289e+05 >>>> Timestep 1: step size = 0.000143637, time = 0.000143637, 2-norm error = 0.000599907, max norm error = 0.000863771 >>>> 0 SNES Function norm 1.195422385486e+05 >>>> Linear solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0 >>>> PCSETUP_FAILED due to FACTOR_NUMERIC_ZEROPIVOT >>>> [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>> [0]PETSC ERROR: >>>> [0]PETSC ERROR: TSStep has failed due to DIVERGED_NONLINEAR_SOLVE, increase -ts_max_snes_failures or make negative to attempt recovery >>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. >>>> [0]PETSC ERROR: Petsc Development GIT revision: pre-tsfc-330-gda8116b GIT Date: 2016-02-23 15:17:17 -0600 >>>> [0]PETSC ERROR: ./ex3 on a cplx named ivyamd.txcorp.com by dmeiser Fri Feb 26 11:36:28 2016 >>>> [0]PETSC ERROR: Configure options --with-scalar-type=complex --with-x=0 --with-debugging=1 --with-ssl=0 --with-fortran-kernels=0 --with-pthread=0 --download-fftw=1 --with-mpi=1 --download-mpich=1 --with-mpiuni-fortran-binding=0 --with-fortran-interfaces >>>> [0]PETSC ERROR: #1 TSStep() line 3346 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>> [0]PETSC ERROR: #2 TSSolve() line 3544 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/interface/ts.c >>>> [0]PETSC ERROR: #3 main() line 216 in /scr_ivyamd/dmeiser/SD/petsc/src/ts/examples/tutorials/ex3.c >>>> [0]PETSC ERROR: PETSc Option Table entries: >>>> [0]PETSC ERROR: -ksp_converged_reason >>>> [0]PETSC ERROR: -nox >>>> [0]PETSC ERROR: -snes_monitor >>>> [0]PETSC ERROR: -ts_max_steps 2 >>>> [0]PETSC ERROR: -ts_type beuler >>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- >>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>> [unset]: aborting job: >>>> application called MPI_Abort(MPI_COMM_WORLD, 91) - process 0 >>>> >>>> >>>> I'm aware of Jed's commit e1244c6 which I thought was supposed to >>>> enable constant linear rhs without IFunction and IJacobian. Note >>>> that e1244c6 also added tests that apparently produced very >>>> different output (see e.g. >>>> src/ts/examples/tutorials/output/ex3_4.out). >>>> >>>> Is constant rhs without IFunction and IJacobian no longer >>>> supported or did it just breat at some point? Do I need to call >>>> TSRHSJacobianSetReuse in addition to the lines of code above? Is >>>> it better to treat such systems using TSComputeIFunctionLinear >>>> and TSComputeIJacobianConstant? >>>> >>>> Thanks, >>>> Dominic >>>> >>>> -- >>>> Dominic Meiser >>>> Tech-X Corporation - 5621 Arapahoe Avenue - Boulder, CO 80303 >>> >>

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