Re: [petsc-users] ghost values

[Barry Smith]

> On Apr 14, 2015, at 7:43 PM, Gideon Simpson  wrote:
> 
> So in your example of the form function, is something happening where, when I 
> leave the scope of FormFunction, the invocation of DMGetLocalVector on the DM 
> keeps a note that it had been called previously and has that memory already 
> allocated?

   Yes, it just keeps a lists of available vectors and gives you the next one 
on the list. When you call RestoreLocalVector() it returns the vector to the 
list. If it has handed out all the vectors on the list to you (and you have not 
restored them) it creates a new one and gives it to you.

>  Does the design distinguish between different calls to DMGetLocalVector, 
> like if I called it in one subroutine and then in another subroutine, or 
> twice in a single subroutine?
> 

   Not sure what you mean by this but if you call it twice it gives you two 
different vectors (unless of course you restored the first before requesting 
the second) It does't matter from what function your request the vector or 
restore it (but passing around a vector you obtained with GetVector through a 
complicated set of function calls is generally bad because you will forget to 
restore it). Hence it is better to Get; Use; Restore

  Here is the entire routine.

PetscErrorCode  DMGetLocalVector(DM dm,Vec *g)
{
  PetscErrorCode ierr,i;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm,DM_CLASSID,1);
  PetscValidPointer(g,2);
  for (i=0; ilocalin[i]) {
  *g = dm->localin[i];
  dm->localin[i] = NULL;
  goto alldone;
}
  }
  ierr = DMCreateLocalVector(dm,g);CHKERRQ(ierr);

alldone:
  for (i=0; ilocalout[i]) {
  dm->localout[i] = *g;
  break;
}
  }
  PetscFunctionReturn(0);
}

> -gideon
> 
>> On Apr 14, 2015, at 8:23 PM, Barry Smith  wrote:
>> 
>> 
>>> On Apr 14, 2015, at 6:25 PM, Gideon Simpson  
>>> wrote:
>>> 
>>> So other than the minor point of it zeroing out the data, is there any 
>>> conceivable reason to use Create/Destroy over Get/Restore?
>> 
>> The design intends that Create/Destroy are for long lived objects. For 
>> example in main you might call Create to make a vector you will store the 
>> solution for the entire simulation run in then just before you exit the 
>> program you destroy it.
>> 
>>  The Get/Restore are for work vectors that are used within one routine. The 
>> most classic example is in FormFunction where you often have something like  
>> DMGetLocalVector() ;  DMGlobalToLocalBegin/End(global, local, ...) 
>> DMDAVecGetArray(local) /  DMRestoreLocalVector(). The idea is that 
>> rather creating work vectors in main and passing them around to use when 
>> needed, DM manages a "pool" of work vectors that you can grab whenever you 
>> need them and are low overhead to access.
>> 
>> There is nothing that enforces you follow this style, but if you don't you 
>> need to be careful to know which vectors to call VecDestroy() on and which 
>> ones to call DMRestoreLocalVector() on plus it will be easier for other 
>> people to follow your code.
>> 
>> Barry
>> 
>>> 
>>> -gideon
>>> 
 On Apr 14, 2015, at 7:16 PM, Matthew Knepley  wrote:
 
 On Tue, Apr 14, 2015 at 6:15 PM, Gideon Simpson  
 wrote:
 Other than zeroing things out, is there any substantive difference between 
 DMCreateLocalVector and DMGetLocalVector?
 
 The Get version caches vectors, so you are not continually 
 creating/destroying
 
  Matt
 
 -gideon
 
> On Apr 14, 2015, at 7:02 PM, Barry Smith  wrote:
> 
> 
> When PETSc vectors are created initially they always have 0 everywhere. 
> So if you use DMCreateLocalVector() it will have zero in all those ghost 
> places (as well as everywhere else).
> 
> But if you use DMGetLocalVector() it returns vectors that maybe dirty so 
> you need to fill in any locations you want to have a known value with 
> that known value. Or call VecSet() to clear the entire vector.
> 
> Barry
> 
>> On Apr 14, 2015, at 5:52 PM, Gideon Simpson  
>> wrote:
>> 
>> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array, 
>> are the ghosted values automatically set to zero, or should they be 
>> manually set to zero if that’s the desired ghost value?
>> 
>> -gideon
>> 
> 
 
 
 
 
 -- 
 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
>>> 
>> 
> 

Re: [petsc-users] ghost values

[Gideon Simpson]

So in your example of the form function, is something happening where, when I 
leave the scope of FormFunction, the invocation of DMGetLocalVector on the DM 
keeps a note that it had been called previously and has that memory already 
allocated?  Does the design distinguish between different calls to 
DMGetLocalVector, like if I called it in one subroutine and then in another 
subroutine, or twice in a single subroutine?

-gideon

> On Apr 14, 2015, at 8:23 PM, Barry Smith  wrote:
> 
> 
>> On Apr 14, 2015, at 6:25 PM, Gideon Simpson  wrote:
>> 
>> So other than the minor point of it zeroing out the data, is there any 
>> conceivable reason to use Create/Destroy over Get/Restore?
> 
>  The design intends that Create/Destroy are for long lived objects. For 
> example in main you might call Create to make a vector you will store the 
> solution for the entire simulation run in then just before you exit the 
> program you destroy it.
> 
>   The Get/Restore are for work vectors that are used within one routine. The 
> most classic example is in FormFunction where you often have something like  
> DMGetLocalVector() ;  DMGlobalToLocalBegin/End(global, local, ...) 
> DMDAVecGetArray(local) /  DMRestoreLocalVector(). The idea is that rather 
> creating work vectors in main and passing them around to use when needed, DM 
> manages a "pool" of work vectors that you can grab whenever you need them and 
> are low overhead to access.
> 
>  There is nothing that enforces you follow this style, but if you don't you 
> need to be careful to know which vectors to call VecDestroy() on and which 
> ones to call DMRestoreLocalVector() on plus it will be easier for other 
> people to follow your code.
> 
>  Barry
> 
>> 
>> -gideon
>> 
>>> On Apr 14, 2015, at 7:16 PM, Matthew Knepley  wrote:
>>> 
>>> On Tue, Apr 14, 2015 at 6:15 PM, Gideon Simpson  
>>> wrote:
>>> Other than zeroing things out, is there any substantive difference between 
>>> DMCreateLocalVector and DMGetLocalVector?
>>> 
>>> The Get version caches vectors, so you are not continually 
>>> creating/destroying
>>> 
>>>   Matt
>>> 
>>> -gideon
>>> 
 On Apr 14, 2015, at 7:02 PM, Barry Smith  wrote:
 
 
 When PETSc vectors are created initially they always have 0 everywhere. So 
 if you use DMCreateLocalVector() it will have zero in all those ghost 
 places (as well as everywhere else).
 
  But if you use DMGetLocalVector() it returns vectors that maybe dirty so 
 you need to fill in any locations you want to have a known value with that 
 known value. Or call VecSet() to clear the entire vector.
 
 Barry
 
> On Apr 14, 2015, at 5:52 PM, Gideon Simpson  
> wrote:
> 
> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array, 
> are the ghosted values automatically set to zero, or should they be 
> manually set to zero if that’s the desired ghost value?
> 
> -gideon
> 
 
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> 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
>> 
> 

Re: [petsc-users] ghost values

[Barry Smith]

> On Apr 14, 2015, at 6:25 PM, Gideon Simpson  wrote:
> 
> So other than the minor point of it zeroing out the data, is there any 
> conceivable reason to use Create/Destroy over Get/Restore?

  The design intends that Create/Destroy are for long lived objects. For 
example in main you might call Create to make a vector you will store the 
solution for the entire simulation run in then just before you exit the program 
you destroy it.

   The Get/Restore are for work vectors that are used within one routine. The 
most classic example is in FormFunction where you often have something like  
DMGetLocalVector() ;  DMGlobalToLocalBegin/End(global, local, ...) 
DMDAVecGetArray(local) /  DMRestoreLocalVector(). The idea is that rather 
creating work vectors in main and passing them around to use when needed, DM 
manages a "pool" of work vectors that you can grab whenever you need them and 
are low overhead to access.

  There is nothing that enforces you follow this style, but if you don't you 
need to be careful to know which vectors to call VecDestroy() on and which ones 
to call DMRestoreLocalVector() on plus it will be easier for other people to 
follow your code.

  Barry

> 
> -gideon
> 
>> On Apr 14, 2015, at 7:16 PM, Matthew Knepley  wrote:
>> 
>> On Tue, Apr 14, 2015 at 6:15 PM, Gideon Simpson  
>> wrote:
>> Other than zeroing things out, is there any substantive difference between 
>> DMCreateLocalVector and DMGetLocalVector?
>> 
>> The Get version caches vectors, so you are not continually 
>> creating/destroying
>> 
>>Matt
>>  
>> -gideon
>> 
>> > On Apr 14, 2015, at 7:02 PM, Barry Smith  wrote:
>> >
>> >
>> >  When PETSc vectors are created initially they always have 0 everywhere. 
>> > So if you use DMCreateLocalVector() it will have zero in all those ghost 
>> > places (as well as everywhere else).
>> >
>> >   But if you use DMGetLocalVector() it returns vectors that maybe dirty so 
>> > you need to fill in any locations you want to have a known value with that 
>> > known value. Or call VecSet() to clear the entire vector.
>> >
>> >  Barry
>> >
>> >> On Apr 14, 2015, at 5:52 PM, Gideon Simpson  
>> >> wrote:
>> >>
>> >> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array, 
>> >> are the ghosted values automatically set to zero, or should they be 
>> >> manually set to zero if that’s the desired ghost value?
>> >>
>> >> -gideon
>> >>
>> >
>> 
>> 
>> 
>> 
>> -- 
>> 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
> 

Re: [petsc-users] ghost values

[Matthew Knepley]

On Tue, Apr 14, 2015 at 6:25 PM, Gideon Simpson 
wrote:

> So other than the minor point of it zeroing out the data, is there any
> conceivable reason to use Create/Destroy over Get/Restore?
>

Nope, and calling VecSet(v, 0.0) is really cheap.

  Matt


> -gideon
>
> On Apr 14, 2015, at 7:16 PM, Matthew Knepley  wrote:
>
> On Tue, Apr 14, 2015 at 6:15 PM, Gideon Simpson 
> wrote:
>
>> Other than zeroing things out, is there any substantive difference
>> between DMCreateLocalVector and DMGetLocalVector?
>>
>
> The Get version caches vectors, so you are not continually
> creating/destroying
>
>Matt
>
>
>> -gideon
>>
>> > On Apr 14, 2015, at 7:02 PM, Barry Smith  wrote:
>> >
>> >
>> >  When PETSc vectors are created initially they always have 0
>> everywhere. So if you use DMCreateLocalVector() it will have zero in all
>> those ghost places (as well as everywhere else).
>> >
>> >   But if you use DMGetLocalVector() it returns vectors that maybe dirty
>> so you need to fill in any locations you want to have a known value with
>> that known value. Or call VecSet() to clear the entire vector.
>> >
>> >  Barry
>> >
>> >> On Apr 14, 2015, at 5:52 PM, Gideon Simpson 
>> wrote:
>> >>
>> >> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array,
>> are the ghosted values automatically set to zero, or should they be
>> manually set to zero if that’s the desired ghost value?
>> >>
>> >> -gideon
>> >>
>> >
>>
>>
>
>
> --
> 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

Re: [petsc-users] ghost values

[Gideon Simpson]

So other than the minor point of it zeroing out the data, is there any 
conceivable reason to use Create/Destroy over Get/Restore?

-gideon

> On Apr 14, 2015, at 7:16 PM, Matthew Knepley  wrote:
> 
> On Tue, Apr 14, 2015 at 6:15 PM, Gideon Simpson  > wrote:
> Other than zeroing things out, is there any substantive difference between 
> DMCreateLocalVector and DMGetLocalVector?
> 
> The Get version caches vectors, so you are not continually creating/destroying
> 
>Matt
>  
> -gideon
> 
> > On Apr 14, 2015, at 7:02 PM, Barry Smith  > > wrote:
> >
> >
> >  When PETSc vectors are created initially they always have 0 everywhere. So 
> > if you use DMCreateLocalVector() it will have zero in all those ghost 
> > places (as well as everywhere else).
> >
> >   But if you use DMGetLocalVector() it returns vectors that maybe dirty so 
> > you need to fill in any locations you want to have a known value with that 
> > known value. Or call VecSet() to clear the entire vector.
> >
> >  Barry
> >
> >> On Apr 14, 2015, at 5:52 PM, Gideon Simpson  >> > wrote:
> >>
> >> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array, are 
> >> the ghosted values automatically set to zero, or should they be manually 
> >> set to zero if that’s the desired ghost value?
> >>
> >> -gideon
> >>
> >
> 
> 
> 
> 
> -- 
> 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

Re: [petsc-users] ghost values

[Matthew Knepley]

On Tue, Apr 14, 2015 at 6:15 PM, Gideon Simpson 
wrote:

> Other than zeroing things out, is there any substantive difference between
> DMCreateLocalVector and DMGetLocalVector?
>

The Get version caches vectors, so you are not continually
creating/destroying

   Matt


> -gideon
>
> > On Apr 14, 2015, at 7:02 PM, Barry Smith  wrote:
> >
> >
> >  When PETSc vectors are created initially they always have 0 everywhere.
> So if you use DMCreateLocalVector() it will have zero in all those ghost
> places (as well as everywhere else).
> >
> >   But if you use DMGetLocalVector() it returns vectors that maybe dirty
> so you need to fill in any locations you want to have a known value with
> that known value. Or call VecSet() to clear the entire vector.
> >
> >  Barry
> >
> >> On Apr 14, 2015, at 5:52 PM, Gideon Simpson 
> wrote:
> >>
> >> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array,
> are the ghosted values automatically set to zero, or should they be
> manually set to zero if that’s the desired ghost value?
> >>
> >> -gideon
> >>
> >
>
>


-- 
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

Re: [petsc-users] ghost values

[Gideon Simpson]

Other than zeroing things out, is there any substantive difference between 
DMCreateLocalVector and DMGetLocalVector?

-gideon

> On Apr 14, 2015, at 7:02 PM, Barry Smith  wrote:
> 
> 
>  When PETSc vectors are created initially they always have 0 everywhere. So 
> if you use DMCreateLocalVector() it will have zero in all those ghost places 
> (as well as everywhere else). 
> 
>   But if you use DMGetLocalVector() it returns vectors that maybe dirty so 
> you need to fill in any locations you want to have a known value with that 
> known value. Or call VecSet() to clear the entire vector.
> 
>  Barry
> 
>> On Apr 14, 2015, at 5:52 PM, Gideon Simpson  wrote:
>> 
>> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array, are 
>> the ghosted values automatically set to zero, or should they be manually set 
>> to zero if that’s the desired ghost value?
>> 
>> -gideon
>> 
> 

Re: [petsc-users] ghost values

[Barry Smith]

  When PETSc vectors are created initially they always have 0 everywhere. So if 
you use DMCreateLocalVector() it will have zero in all those ghost places (as 
well as everywhere else). 

   But if you use DMGetLocalVector() it returns vectors that maybe dirty so you 
need to fill in any locations you want to have a known value with that known 
value. Or call VecSet() to clear the entire vector.

  Barry

> On Apr 14, 2015, at 5:52 PM, Gideon Simpson  wrote:
> 
> If i use the DM_BOUNDARY_GHOSTED flag in the creation of a DMDA array, are 
> the ghosted values automatically set to zero, or should they be manually set 
> to zero if that’s the desired ghost value?
> 
> -gideon
>