[petsc-users] Accessing Vector's ghost values

[Mohammad Mirzadeh]

You also need calls to VecGhostUpdateBegin()/VecGhostUpdateEnd() functions
to update the ghost values if you change them in the global representation.
See Petsc Manual 3.2 pp 55-56

Mohammad

On Thu, Feb 23, 2012 at 3:18 PM, Bojan Niceno <bojan.niceno at psi.ch> wrote:

>  On 2/23/2012 11:49 PM, Mohammad Mirzadeh wrote:
>
> based on,
>
>  VecCreateGhost(PETSC_COMM_WORLD, n, PETSC_DECIDE, nghost, &ghosts[0],
> &x);
>
>
>  it seems to me that x is your actual ghosted vector. If this is true,
> then you need to get its "local" form via VecGhostGetLocalForm<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecGhostGetLocalForm.html#VecGhostGetLocalForm>().
> Once you have done, you should be able to access the ghosted nodes. Are you
> calling this function anywhere?
>
>
> I tried that before.  I did:
>
> Vec lx;
> VecGhostGetLocalForm(x, &lx)
>
> then I copied "lx" to my variable, like
>
> for(Int i=1; i<N; i++)    /* N includes buffer cells */
>   unk[i] = lx[i]
>
> but ghost values were also zero.   I am thinking that PETSc somehow clears
> the ghost values after a call to KSP.  Is it the case?
>
>
>     Kind regards,
>
>
>     Bojan
>
>
>
> On Thu, Feb 23, 2012 at 2:32 PM, Bojan Niceno <bojan.niceno at psi.ch> wrote:
>
>>  Dear Mohammad,
>>
>>
>> it doesn't help me, or I did not understand your explanation.
>>
>> If I do this:
>>
>>   /* copy internal values (THIS WORKS, BUT COPIES NO BUFFER VALUES) */
>>
>>   for(Int i=0; i<n; i++) {
>>     Int gi = mesh.nodes[i].global_number;
>>     VecGetValues(x, 1, &gi, &unk[i]);
>>   }
>>
>>    /* copy ghost values (CREATES MANY WARNINGS */
>>
>>   for(Int i=n; i<N; i++) {
>>      VecGetValues(x, 1, &i, &unk[i]);
>>   }
>>
>> I get arnings are like this.
>>
>>  [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]PETSC ERROR: Argument out of range!
>>  [0]PETSC ERROR: Can only get local values, trying 3518!
>> [3]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> [3]PETSC ERROR: Argument out of range!
>> [3]PETSC ERROR: Can only get local values, trying 3511!
>> [3]PETSC ERROR:
>> ------------------------------------------------------------------------
>>
>> What am I doing wrong here?
>>
>>
>>     Cheers,
>>
>>
>>     Bojan
>>
>>
>>
>> On 2/23/2012 11:23 PM, Mohammad Mirzadeh wrote:
>>
>> just index x with the local numberings. if you have 'n' local nodes and
>> 'g' ghost nodes in x, ghost nodes indecies run from 'n' to 'n+g-1'
>> On Feb 23, 2012 1:16 PM, "Bojan Niceno" <bojan.niceno at psi.ch> wrote:
>>
>>>  Dear Jed,
>>>
>>> thanks.
>>>
>>> Now I have the following:
>>>
>>> - Array unk, which should hold values inside the partition and in ghost
>>> cells.  It is big enough to hold both
>>> - Vec x, created by command VecCreateGhost, with proper padding for
>>> ghost cells
>>> - Successful call to linear solver in parallel.
>>>
>>> But I need to copy ghost values from x to my array unk.
>>>
>>> How can I do it?
>>>
>>>
>>>     Kind regards,
>>>
>>>
>>>     Bojan
>>>
>>> On 2/23/2012 10:10 PM, Jed Brown wrote:
>>>
>>> On Thu, Feb 23, 2012 at 15:05, Bojan Niceno <bojan.niceno at psi.ch> wrote:
>>>
>>>> No, I use global.
>>>>
>>>
>>>  The local form is just a local vector. It doesn't even know that a
>>> global problem exists. You can't index into it using global indices. (In
>>> general, there is no efficient way to look up information in the local
>>> vector (includes ghost points) using global indices.)
>>>
>>>
>>>>
>>>>   for(Int i=0; i<n; i++) {
>>>>     Int gi = mesh.nodes[i].global_number;
>>>>     VecGetValues(x, 1, &gi, &unk[i]);
>>>>   }
>>>>
>>>> "n" is defined as the number of cells inside, i.e. without buffers.
>>>> "unk" is my external array.  If I try to access buffer values, I use:
>>>>
>>>>   for(Int i=0; i<N; i++) {
>>>>     Int gi = mesh.nodes[i].global_number;
>>>>     VecGetValues(x, 1, &gi, &unk[i]);
>>>>   }
>>>>
>>>> But then I end up with tons of warnings, presumably because I am going
>>>> beyond "n".  Vector x was created with VecCreateGhost.
>>>>
>>>
>>>
>>>
>>> --
>>>
>>
>>
>>   --
>>
>
>
>
> --
>
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