[petsc-users] Accessing Vector's ghost values

[Mohammad Mirzadeh]

glad to hear that :)

On Thu, Feb 23, 2012 at 3:38 PM, Bojan Niceno <bojan.niceno at psi.ch> wrote:

>  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> 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.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>
>>>
>>>   --
>>>
>>
>>
>>
>>   --
>>
>
>
>
> --
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/41bf10f5/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 6515 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/41bf10f5/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 6515 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/41bf10f5/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 6515 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/41bf10f5/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 6515 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120223/41bf10f5/attachment-0007.png>