On Fri, Apr 5, 2013 at 11:32 AM, Barry Smith wrote:
>
> On Apr 5, 2013, at 10:18 AM, Dmitry Karpeev wrote:
>
> > Should PetscInitialize() take a comm argument, then?
>
>No, this is such an uncommon case that it shouldn't be exposed to
> everyone.
It seems to m
Should PetscInitialize() take a comm argument, then?
On Fri, Apr 5, 2013 at 10:15 AM, Barry Smith wrote:
>
> On Apr 5, 2013, at 10:09 AM, Dmitry Karpeev wrote:
>
> >
> > On Thu, Apr 4, 2013 at 7:42 PM, Jed Brown wrote:
> >
> > It seems to me this is related t
On Thu, Apr 4, 2013 at 7:42 PM, Jed Brown wrote:
>
It seems to me this is related to Moose's new MultiApp capability: solving
different systems on subcommunicators (with the interaction between the
systems handled outside of PETSc)? It may be that the cleaner approach is
to have the subsystems (
On Thu, Mar 7, 2013 at 11:00 AM, Jed Brown wrote:
>
> On Thu, Mar 7, 2013 at 10:53 AM, Dmitry Karpeev wrote:
>
>> -pc_true is pretty ambiguous. how about
>>>
>>> -pc_true_op
>>>
>>> ? or if you prefer.
>>>
>> Name
On Thu, Mar 7, 2013 at 10:08 AM, Mark F. Adams wrote:
> >
> >
> > So you could add PCMGSetUseTrue(PC) and -pc_mg_true that would trigger
> setting the true (outer) operator inside the PCSetUp_MG() even if it was
> already set. You would still change/fix the current GAMG to always set the
> opera
On Mar 6, 2013 10:29 PM, "Barry Smith" wrote:
>
>
> On Mar 6, 2013, at 10:19 PM, Dmitry Karpeev wrote:
>
> > I suggested using 'exact' in place of 'true'. I guess it might have
gotten folded into "quoted text" or otherwise squeezed out
On Mar 6, 2013 10:05 PM, "Barry Smith" wrote:
>
>
> On Mar 6, 2013, at 9:36 PM, "Mark F. Adams"
wrote:
>
> >>
> >> Presumbly when you call PCReset() it zeros out all the pointers. If
you do not set the operators on the finest level again then it will use the
"outer" operator on the smoothest leve
ionally read this list, but for questions
> that are this advanced you would probably have better luck mailing the
> petsc developers list directly.
>
> And of course if you do find a good block preconditioning strategy for
> systems_of_equations_ex1, please feel free to report it here!
>
>
>
>> On Wed, Oct 17, 2012 at 3:01 PM, Dmitry Karpeev > mcs.anl.gov>wrote:
>>
>>>
>>>
>>> On Wed, Oct 17, 2012 at 2:56 PM, Peter Brune wrote:
>>>
>>>>
>>>>
>>>> On Wed, Oct 17, 2012 at 2:40 PM, Dmitry Karpeev >
On Wed, Oct 17, 2012 at 2:56 PM, Peter Brune wrote:
>
>
> On Wed, Oct 17, 2012 at 2:40 PM, Dmitry Karpeev wrote:
>
>>
>>
>> On Wed, Oct 17, 2012 at 2:11 PM, Jed Brown wrote:
>>
>>> On Wed, Oct 17, 2012 at 2:02 PM, Shiyuan Gu wrote:
>>&
On Wed, Oct 17, 2012 at 2:11 PM, Jed Brown wrote:
> On Wed, Oct 17, 2012 at 2:02 PM, Shiyuan Gu wrote:
>
>> Hi,
>> I am using petsc-3.3-p2. For my particular equation, for the first
>> few iterations, the residual norm is effectively reduced and the solution X
>> is very close to the exact
It would be good to have a meaningful test case to motivate the further
development.
I initially wrote it to enable GAMG for KKT systems, but that is still on
the back burner,
although it might be coming back to the front, since elastic contact is
becoming more
important for MOOSE. With a good test
On Wed, Oct 10, 2012 at 8:33 AM, Jed Brown wrote:
> The best way, by far, is to assemble the matrix as AIJ if that is what you
> want to use. See MatGetLocalSubMatrix and SNES ex28. Using MATNEST should
> he a run-time choice.
>
The caveat here is that currently there is no good way (that I know
On Wed, Oct 10, 2012 at 11:38 AM, Barry Smith wrote:
>
> On Oct 10, 2012, at 8:50 AM, Jed Brown wrote:
>
> > How did you get the MatNest?
> >
> > What you describe is the right approach, but proper preallocation is
> messy in the general case. There is a partial implementation in petsc-dev,
> bu
On Thu, Sep 27, 2012 at 1:22 PM, Matthew Knepley wrote:
> On Thu, Sep 27, 2012 at 2:13 PM, Zou (Non-US), Ling inl.gov>wrote:
>
>> Thank you Matt.
>>
>> I've noticed that there is a different option '-snes_fd', and I guess
>> PETSc will use finite difference method for both Jacobian (action) and
I use Moose with petsc-3.3 essentially every day, and it works for
everything I do.
There shouldn't be a problem in building the whole herd stack with
petsc-3.3.
Dmitry.
On Wed, Sep 19, 2012 at 3:43 PM, Zou (Non-US), Ling wrote:
> good to know, I will try it.
>
> Ling
>
>
> On Wed, Sep 19, 2012
On Sat, Aug 11, 2012 at 6:36 PM, Subramanya Gautam Sadasiva <
ssadasiv at purdue.edu> wrote:
> Hi,
> I was trying the snes solver on the obstacle problem by modifying
> miscellaneous ex 7 and I get only linear convergence times.Is this what is
> expected from the virs solver?
>
Yes, in the sense t
On Thu, Aug 9, 2012 at 10:02 AM, Colin McAuliffe wrote:
> Sanjay, thanks for the reply but I am avoiding using blocked format since
> my problem has 10 dofs per node but only has either dofs 1-3 or 4-10 active
> on a particular node. If I use block the equations I run out of memory
> pretty quickl
Have you looked at MatSetValuesLocal()
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatSetValuesLocal.html?
That routine might be close enough to what you need.
Dmitry.
On Sun, May 27, 2012 at 4:01 AM, Hui Zhang wrote:
> Also, in the case that only a *subset* of v[] is used, t
It sounds like you need to write a new PC implementation, possibly reusing
pieces of PCASM.
Then you have control of what is being set up and when. Otherwise you are
essentially hacking
PCASM and using its internal subsolvers, which are only available after
PCSetUp(). PCCOMPOSITE
doesn't look like
t;
>> The above matrix is obtained from PCASMGetSubKSP(pc,subksp) and
>> KSPGetOperators(subksp[0], ...).
>>
>
> This is odd. Can you explain a bit more what leads up to this, so we can
> try and reproduce the problem?
> Thanks.
> Dmitry.
>
>>
>> Thank
alues for the column 1, is this normal?
>>
>> The above matrix is obtained from PCASMGetSubKSP(pc,subksp) and
>> KSPGetOperators(subksp[0], ...).
>>
>
> This is odd. Can you explain a bit more what leads up to this, so we can
> try and reproduce the problem?
> Thank
is normal?
>
> The above matrix is obtained from PCASMGetSubKSP(pc,subksp) and
> KSPGetOperators(subksp[0], ...).
>
This is odd. Can you explain a bit more what leads up to this, so we can
try and reproduce the problem?
Thanks.
Dmitry.
>
> Thanks!
>
>
>
> On May 11, 201
On Sat, May 19, 2012 at 4:10 AM, Hui Zhang wrote:
> If PCASMSetSortIndices is used to set false, i.e. DO NOT sort indices,
> is that true rows of submatrices are in the same order as the IS we passed
> to
> PCASMSetLocalSubdomains?
>
Yes.
Dmitry.
>
> Thanks!
-- next part -
In principle, you can implement any type of line search in PETSc by
subclassing SNESLineSearch (although it requires going under the hood some,
as we generally think of LineSearch as a private object). If you can
elaborate on what you need, we can work with you guys to see how to
accomplish it wit
On Tue, May 15, 2012 at 11:25 AM, Hui Zhang wrote:
>
> On May 15, 2012, at 6:20 PM, Jed Brown wrote:
>
> On Tue, May 15, 2012 at 10:11 AM, Hui Zhang hotmail.com>wrote:
>
>> Yes, see Mandel & Dorhamann' paper
>> http://ccm.ucdenver.edu/reports/rep194.pdf ,
>>
>
> BDDC needs to solve pinned Neumann
On Tue, May 15, 2012 at 11:05 AM, Hui Zhang wrote:
>
> On May 15, 2012, at 5:42 PM, Dmitry Karpeev wrote:
>
>
>
> On Tue, May 15, 2012 at 10:30 AM, Hui Zhang hotmail.com>wrote:
>
>> thanks for reply!
>> On May 15, 2012, at 5:19 PM, Dmitry Karpeev wrote:
>
that last scatter would be for you, since the details of the structure
of the direct sum vector are internal to GASM.
Dmitry.
>
> Thanks!
>
> On May 15, 2012, at 3:29 PM, Dmitry Karpeev wrote:
>
> There are some additional minor fixes that mostly have to do with
> outputting t
Fri, May 11, 2012 at 12:31 PM, Hui Zhang hotmail.com>wrote:
>
>> Hi Dmitry,
>>
>> thanks for useful hints. Good day!
>>
>> Hui
>>
>> On May 11, 2012, at 7:17 PM, Dmitry Karpeev wrote:
>>
>> You can call PCSetUp(pc) on either ASM or GASM,
i Dmitry,
>
> thanks for useful hints. Good day!
>
> Hui
>
> On May 11, 2012, at 7:17 PM, Dmitry Karpeev wrote:
>
> You can call PCSetUp(pc) on either ASM or GASM, and that will destroy and
> recreate the matrices (including calling
> your modification subroutine), b
SM I can re-use it because the partition of subdomains remain
> the same.
>
> Thanks!
>
>
> On May 10, 2012, at 6:37 PM, Dmitry Karpeev wrote:
>
> Hui,
> There've been several changes to PCGASM ahead of the new release.
> Let me go back and see if it affected the co
; On Feb 20, 2012, at 6:38 PM, Dmitry Karpeev wrote:
>
> Okay, thanks.
> I'll take a look.
>
> Dmitry.
>
> On Mon, Feb 20, 2012 at 11:30 AM, Hui Zhang hotmail.com>wrote:
>
>> For reference, my results are attached.
>>
>> asm1.txt for asm with 1 proc
MatCreate probably gets called inside SNES via MatDuplicate. Set a
breakpoint in MatCreate to catch it.
Dmitry.
On Thu, Mar 1, 2012 at 10:16 AM, Derek Gaston wrote:
> In trying to track down where all of our memory usage is coming from I
> noticed that PETSc is saying that more matrices than I e
ferent
> from others)
> gasm2.txt for gasm with 2 processes
>
>
>
>
>
>
> thank you,
> Hui
>
> On Feb 20, 2012, at 3:06 PM, Dmitry Karpeev wrote:
>
>
>
> On Mon, Feb 20, 2012 at 12:59 AM, Hui Zhang hotmail.com>wrote:
>
>>
>> On Feb
On Mon, Feb 20, 2012 at 12:59 AM, Hui Zhang wrote:
>
> On Feb 20, 2012, at 12:41 AM, Dmitry Karpeev wrote:
>
>
>
> On Sun, Feb 19, 2012 at 3:08 PM, Hui Zhang hotmail.com>wrote:
>
>> I have a new problem: the results from ASM and GASM are different and it
>> se
you solving?
Dmitry.
>
>
> On Feb 15, 2012, at 6:46 PM, Dmitry Karpeev wrote:
>
> You should be able to.
> This behavior is the same as in PCASM,
> except in GASM the matrices live on subcommunicators.
> I am in transit right now, but I can take a closer look in Friday.
>
>
ng?
>
> As I tested, the row and col are always the same.
>
> I have a new question. Am I allowed to SetLocalToGlobalMapping() for the
> submat's
> in the above func()?
>
> thanks,
> Hui
>
>>
>> thanks,
>> Hui
>>
>>
>> On
Yes, that's right.
There is no good way to help the user assemble the subdomains at the moment
beyond the 2D stuff.
It is expected that they are generated from mesh subdomains.
Each IS does carry the subdomains subcomm.
There is ISColoringToList() that is supposed to convert a "coloring" of
indice
Good to hear you got it sorted out!
I understand that PetscLayoutSetup() and VecScatterCreate() problems were
unrelated, is that right?
The PetscLayoutSetup() was hanging because some nodes took too long to
enter the call -- they were waiting
for mutex locks somewhere else; VecScatterCreate() was
Since the processor count is down, can you run it with debugging and see
what the arguments to PetscLayout are?
Dmitry
On Tue, Feb 7, 2012 at 9:00 PM, Derek Gaston wrote:
>
>
> On Tue, Feb 7, 2012 at 7:56 PM, Matthew Knepley wrote:
>
>>
>> Same question: are you sure every process is there. I w
I think looking at the output of -snes_vi_monitor, as Barry suggested,
would be useful to see what really is going on.
What initial guess are you using? If you initialize V = 1 then whether a
degree of freedom belongs to the active set
or not will depend only on the sign of the residual there. I
It seems to me that the problem is that ultimately ALL of the degrees of
freedom are in the active set,
but they get added to it a few at a time -- and there may even be some
"chatter" there -- necessitating many SNESVI steps.
Could it be that the regularization makes things worse? When \epsilon \l
What is the solution that you end up converging to, and what are the
boundary conditions?
Thanks.
Dmitry.
On Mon, Jan 16, 2012 at 6:20 PM, Ataollah Mesgarnejad <
amesga1 at tigers.lsu.edu> wrote:
> Dear all,
>
> I'm trying to use SNESVI to solve a quadratic problem with box
> constraints. My pro
On Wed, Jan 4, 2012 at 2:28 PM, Barry Smith wrote:
>
> On Jan 4, 2012, at 1:18 PM, TAY wee-beng wrote:
>
> > Hi Barry and Jed,
> >
> > So the 1st step should be checking the load balancing. If it's more or
> less balanced, will slicing it in 3 directions further improve the speed?
> >
> > Another
s to others that might be interested.
Regards,
Dmitry
-----
Dmitry Karpeev, Ph.D.
Assistant Computational Mathematician
Mathematics and Computer Science
Argonne National Laboratory
Argonne, Illinois, USA
and
Fellow
Computation Institute
Universit
itry
-----
Dmitry Karpeev, Ph.D.
Assistant Computational Mathematician
Mathematics and Computer Science
Argonne National Laboratory
Argonne, Illinois, USA
and
Fellow
Computation Institute
University of Chicago
5735 S. Ellis Avenue
Chicago, IL 60637
---
Phone: 630
petsc-dev has PCGASM, which is a "generalization" of PCASM that allows for
subdomains that live on a subcommunicator of the PC's communicator. The API
is nearly identical to ASM's, and GASM will eventually replace ASM, once we
are reasonably sure
it works correctly (e.g., I'm chasing down a smal
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