[petsc-dev] EM solver in XGC
Mark Adams
mfadams at lbl.gov
Tue Apr 14 17:19:07 CDT 2015
Matt, in looking at MatConvert_Nest_AIJ, the code looks like it is 2 years
old.
I need a MatConvert_Nest_MPIAIJ, should I write this or does it exist
someplace?
Mark
On Tue, Apr 14, 2015 at 2:54 PM, Mark Adams <mfadams at lbl.gov> wrote:
> Also, this is with MPI so I need MPIAIJ. Is that supposed to work?
>
> On Tue, Apr 14, 2015 at 2:53 PM, Mark Adams <mfadams at lbl.gov> wrote:
>
>> It looks like MatConvert is looking for "MatConvert_nest_aij_C"
>>
>> but I see:
>>
>> > git grep MatConvert_Nest
>> impls/nest/matnest.c:#define __FUNCT__ "MatConvert_Nest_AIJ"
>> impls/nest/matnest.c:PETSC_EXTERN PetscErrorCode MatConvert_Nest_AIJ(Mat
>> A,MatType newtype,MatReuse reuse,Mat *newmat)
>>
>> Is there a problems with "Nest" vs "nest" here?
>>
>> Mark
>>
>>
>> On Tue, Apr 14, 2015 at 2:46 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>
>>> I have tried
>>>
>>> call
>>> MatConvert(a_ts%FJacobian,MATMPIAIJ,MAT_INITIAL_MATRIX,a_ts%FJacobian2,ierr);CHKERRQ(ierr)
>>>
>>> and
>>>
>>> call
>>> MatConvert(a_ts%FJacobian,MATAIJ,MAT_INITIAL_MATRIX,a_ts%FJacobian2,ierr);CHKERRQ(ierr)
>>>
>>> in 'next' and it is not finding the specialized routine.
>>>
>>> I will look into it.
>>>
>>> Mark
>>>
>>>
>>> On Tue, Apr 14, 2015 at 1:41 PM, Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Tue, Apr 14, 2015 at 12:40 PM, Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Tue, Apr 14, 2015 at 12:33 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>
>>>>>> MatNest does not support convert because it does not have a getrow.
>>>>>>
>>>>>
>>>>> I think this got fixed in dev. Anyhow, this supports my contention
>>>>> that MatNest is a piece of shit.
>>>>>
>>>>
>>>> Use 'next', it has
>>>>
>>>> PETSC_EXTERN PetscErrorCode MatConvert_Nest_AIJ(Mat A,MatType
>>>> newtype,MatReuse reuse,Mat *newmat)
>>>>
>>>> so it should work.
>>>>
>>>> Matt
>>>>
>>>>
>>>>>
>>>>>
>>>>>> Should we use a 4 block fieldsplit?
>>>>>>
>>>>>
>>>>> We give up our ability to check using exact solves, but go ahead and
>>>>> try it if you think it will make
>>>>> the physicists happy for now.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> On Tue, Apr 14, 2015 at 1:26 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>
>>>>>>> OK,
>>>>>>>
>>>>>>> On Tue, Apr 14, 2015 at 1:25 PM, Matthew Knepley <knepley at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> On Tue, Apr 14, 2015 at 12:23 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I moved this to after the setup, which it has to do because it
>>>>>>>>> does not have the prefix or set options.
>>>>>>>>>
>>>>>>>>> It is not failing with not finding the IS. Will MatNest be able
>>>>>>>>> to merge two matrices together like this?
>>>>>>>>>
>>>>>>>>> I create a 4x4 MatNext but have just two fields in fieldSplit.
>>>>>>>>>
>>>>>>>>
>>>>>>>> Yep, I believe that will work. If not, just convert the MatNest to
>>>>>>>> an AIJ for now with MatConvert().
>>>>>>>>
>>>>>>>> Matt
>>>>>>>>
>>>>>>>>
>>>>>>>>> On Tue, Apr 14, 2015 at 1:18 PM, Matthew Knepley <
>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> On Tue, Apr 14, 2015 at 12:13 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> I get an error where it looks like the number fields in field
>>>>>>>>>>> split is < 2. Do I need to set the size?
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> No, each call to SetIS() just appends to the field list.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> I use this code but I do this before I have setup the TS.
>>>>>>>>>>> Should I do this after I setup the TS?
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> This is why I hate using the API since it is difficult to get all
>>>>>>>>>> the setup done at the right time. First,
>>>>>>>>>> when you call PCFieldSplitSetIS(), is the PC type set?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Matt
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> ! setup field split
>>>>>>>>>>> call TSGetSNES(a_ts,snes,ierr);CHKERRQ(ierr)
>>>>>>>>>>> call SNESGetKSP(snes,ksp,ierr);CHKERRQ(ierr)
>>>>>>>>>>> call KSPGetPC(ksp,pc,ierr);CHKERRQ(ierr)
>>>>>>>>>>>
>>>>>>>>>>> call
>>>>>>>>>>> MatGetSize(a_ts%mass,PETSC_NULL_INTEGER,npetsc,ierr);CHKERRQ(ierr)
>>>>>>>>>>> npetsc = 2*npetsc ! two blocks in each partition
>>>>>>>>>>> j = 0
>>>>>>>>>>> call ISCreateStride(w_comm,npetsc,j,ione,is,ierr);CHKERRQ(ierr)
>>>>>>>>>>> call PCFieldSplitSetIS(pc,'dt',is,ierr);CHKERRQ(ierr)
>>>>>>>>>>> call ISDestroy(is,ierr);CHKERRQ(ierr)
>>>>>>>>>>> j = npetsc
>>>>>>>>>>> call ISCreateStride(w_comm,npetsc,j,ione,is,ierr);CHKERRQ(ierr)
>>>>>>>>>>> call PCFieldSplitSetIS(pc,'aux',is,ierr);CHKERRQ(ierr)
>>>>>>>>>>> call ISDestroy(is,ierr);CHKERRQ(ierr)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Apr 14, 2015 at 12:24 PM, Matthew Knepley <
>>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Apr 14, 2015 at 11:16 AM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Should I just use
>>>>>>>>>>>>>
>>>>>>>>>>>>> PetscErrorCode VecGetSubVector(Vec X,IS is,Vec *Y)
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Yep, that is exactly what I use it for.
>>>>>>>>>>>>
>>>>>>>>>>>> Matt
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> ?
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Apr 14, 2015 at 12:15 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> I am thinking that I should create an IS that is my local
>>>>>>>>>>>>>> part of each field and then get a "sub vector" with that somehow. Looking
>>>>>>>>>>>>>> into this now.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Apr 14, 2015 at 12:00 PM, Mark Adams <mfadams at lbl.gov
>>>>>>>>>>>>>> > wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Whoop, old code still there.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I now have to get access to vectors somehow.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I now get vectors for a field and do stuff with them like:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> subroutine
>>>>>>>>>>>>>>> FormIFunction(ts,t_dummy,a_XX,a_Xdot,a_FF,a_ts,ierr)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> call TSGetDM(ts,dm,ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> call
>>>>>>>>>>>>>>> DMCompositeGetAccessArray(dm,a_FF,ifour,PETSC_NULL_INTEGER,Fsub,ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>> call
>>>>>>>>>>>>>>> DMCompositeGetAccessArray(dm,a_Xdot,ifour,PETSC_NULL_INTEGER,Xdotsub,ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>> one = 1d0
>>>>>>>>>>>>>>> call VecAXPY(Fsub(1),one,Xdotsub(1),ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>> call VecAXPY(Fsub(2),one,Xdotsub(2),ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>> call
>>>>>>>>>>>>>>> DMCompositeRestoreAccessArray(dm,a_Xdot,ifour,PETSC_NULL_INTEGER,Xdotsub,ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>> call
>>>>>>>>>>>>>>> DMCompositeRestoreAccessArray(dm,a_FF,ifour,PETSC_NULL_INTEGER,Fsub,ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> call
>>>>>>>>>>>>>>> MatMultAdd(a_ts%FJacobian,a_XX,a_FF,a_FF,ierr);CHKERRQ(ierr)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I need to get rid of DMCompositeGetAccessArray. What do I
>>>>>>>>>>>>>>> do?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, Apr 14, 2015 at 11:36 AM, Matthew Knepley <
>>>>>>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Tue, Apr 14, 2015 at 10:35 AM, Mark Adams <
>>>>>>>>>>>>>>>> mfadams at lbl.gov> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> And is this the solver (appended).
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Do not call SNESSetDM(). We are not using DM at all in this
>>>>>>>>>>>>>>>> code.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I am getting an error at this last line:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> .seealso: SNESGetDM(), KSPSetDM(), KSPGetDM()
>>>>>>>>>>>>>>>>> @*/
>>>>>>>>>>>>>>>>> PetscErrorCode SNESSetDM(SNES snes,DM dm)
>>>>>>>>>>>>>>>>> {
>>>>>>>>>>>>>>>>> PetscErrorCode ierr;
>>>>>>>>>>>>>>>>> KSP ksp;
>>>>>>>>>>>>>>>>> DMSNES sdm;
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> PetscFunctionBegin;
>>>>>>>>>>>>>>>>> PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
>>>>>>>>>>>>>>>>> if (dm) {ierr =
>>>>>>>>>>>>>>>>> PetscObjectReference((PetscObject)dm);CHKERRQ(ierr);}
>>>>>>>>>>>>>>>>> if (snes->dm) { /* Move the DMSNES context
>>>>>>>>>>>>>>>>> over to the new DM unless the new DM already has one */
>>>>>>>>>>>>>>>>> if (snes->dm->dmsnes && snes->dmAuto && !dm->dmsnes) {
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> The problem is that the argument 'dm' to this method is
>>>>>>>>>>>>>>>>> NULL so I get a segv at the last term of this conditional.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> -adv_ts_type beuler
>>>>>>>>>>>>>>>>> -adv_ts_monitor
>>>>>>>>>>>>>>>>> -adv_ts_view
>>>>>>>>>>>>>>>>> -adv_ts_max_step 1
>>>>>>>>>>>>>>>>> -adv_snes_max_it 1 # make >> 1 for
>>>>>>>>>>>>>>>>> nonlinear solve
>>>>>>>>>>>>>>>>> -adv_snes_lag_preconditioner -1 # make > 0 to update
>>>>>>>>>>>>>>>>> PC
>>>>>>>>>>>>>>>>> -adv_snes_lag_jacobian -1 # make > 0 for
>>>>>>>>>>>>>>>>> nonlinear Jacobian
>>>>>>>>>>>>>>>>> -adv_snes_monitor
>>>>>>>>>>>>>>>>> -adv_snes_converged_reason
>>>>>>>>>>>>>>>>> -adv_ksp_monitor
>>>>>>>>>>>>>>>>> -adv_ksp_converged_reason
>>>>>>>>>>>>>>>>> -adv_ksp_type richardson
>>>>>>>>>>>>>>>>> -adv_pc_type fieldsplit
>>>>>>>>>>>>>>>>> #-adv_pc_fieldsplit_type multiplicative
>>>>>>>>>>>>>>>>> -adv_pc_fieldsplit_type schur
>>>>>>>>>>>>>>>>> -adv_pc_fieldsplit_schur_fact_type full
>>>>>>>>>>>>>>>>> -adv_pc_fieldsplit_schur_precondition full
>>>>>>>>>>>>>>>>> #-adv_pc_fieldsplit_0_fields 0,1
>>>>>>>>>>>>>>>>> #-adv_pc_fieldsplit_1_fields 2,3
>>>>>>>>>>>>>>>>> -adv_fieldsplit_dt_pc_type lu
>>>>>>>>>>>>>>>>> -adv_fieldsplit_aux_pc_type lu
>>>>>>>>>>>>>>>>> -adv_fieldsplit_dt_pc_factor_mat_solver_package superlu
>>>>>>>>>>>>>>>>> -adv_fieldsplit_aux_pc_factor_mat_solver_package superlu
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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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