[petsc-users] Accessing Vector's ghost values
Bojan Niceno
bojan.niceno at psi.ch
Thu Feb 23 17:38:46 CST 2012
Yeeee-ha!
VecGhostUpdateBegin() / VecGhostUpdateEnd() was indeed what I was missing.
Thank you Mohammad, thank you all who helped me today!
Cheers
Bojan
On 2/24/2012 12:27 AM, Mohammad Mirzadeh wrote:
> 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
> <mailto: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 <mailto: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
>>> <mailto: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 <mailto: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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