VecLoadIntoVector and double dispatch

Barry Smith bsmith at
Fri Dec 4 08:52:44 CST 2009

On Dec 4, 2009, at 2:58 AM, Jed Brown wrote:

> On Thu, 3 Dec 2009 16:40:10 -0600, Barry Smith <bsmith at>  
> wrote:
>>    The vector has a pointer to the DM so the VecView() for that
>> derived vector class has access to the DM information.  The same
>> viewer object can be used with a bunch of different sized Vecs since
>> it gets the DM information out of each vector. With your model when
>> the DM info is attached to the viewer you need to pass in a different
>> viewer for different vectors (of different sizes). This is just plan
>> nuts.
> The DM info is not attached to the viewer, I have plain Vecs with a DM
> composed so it can call DMView as in your snippet below.  The viewer
> holds no state with regard to the DM.  But VecView_MyViewer_DM needs  
> to
> get called somehow,


> it will in turn call DMView and use an internal
> Viewer API so that the file has a connection from the Vec to the DM.
>>    I say this is nonsense, it ain't more closely coupled to the  
>> viewer.
> VecGetArray is public, all vectors have to implement it in order to
> function in PETSc.

     This is not accurate. The SAMRAI vector class does not implement  
it. Yes, this means the SAMRAI vector class cannot use any PETSc built  
in matrix classes, but that is ok it provides its own. (note also that  
PETSc allows incomplete implementations of abstract classes where a  
new class implementaiton simply does not provide some methods and  
errors are generated if one tries to use them; I think this is a great  
design feature because it allows many-method base abstract classes,  
but I realize most of the computing world would be shocked and  
disgusted by this design feature).

> The internal Viewer API to write the bytes of a Vec
> with some connection to a DM is not public in the sense that users  
> never
> call it directly and no other viewers implement it.  You can  
> substitute
> any other Vec and this code will still write it correctly because your
> Vec would be broken if it didn't implement VecGetArray [1].
> DM currently monkey-patches Vec to set ops->view and
> ops->loadintovector, but it doesn't rely on the implementation of Vec
> (the definition of Vec_Seq/MPI is never used in src/dm) and in  
> principle
> DACreateGlobalVector could call VecSetFromOptions so that it's  
> actually
> operating with any Vec type (e.g. the Vec could implement it's
> operations on a GPU, only bringing the values to the CPU for
> VecGetArray).  Many viewers (formats) have no special representation  
> of
> vectors that come from a DM [2] which is the reason for having
> ops->viewnative and ops->loadintovectornative.
>>> But somehow, calling VecView needs to be able to call the viewer
>>> with enough context for the viewer to wire up the metadata.  Note
>>> that the coordinates of the nodes in the DM are part of the vector
>>> (it's an ALE formulation) so the metadata is nontrivial.
>>    Each vector has a pointer to its DM (DMComposite etc) so its
>> viewer can dump/read that info when needed. In fact, when writing a
>> vector it could do something like
>> myvecview(Vec v,Viewer viewer)
>> {
>>     DM dm = getreferencetoDMfrom(v);
>>     DMView(dm,viewer);
>>     ... now dump my vector with writes or whatever
> My code looks exactly like this, my point is that the elided part
> involves only the public Vec API, but a private Viewer API.  I can put
> this chunk of code anywhere, but it needs changes when I make private
> changes to the viewer, it doesn't need anything when I make private
> changes to the DM or Vec (it doesn't even need to know the types of
> those objects).  It is currently sitting with my DM, mostly because I
> wrote the DMView first.
>> You have to admit that it would be crazy to have the DM viewer method
>> stored inside a viewer object which seems to be what your model is.
> I wish I could get the dispatch with a symmetric relationship, but in
> lieu of that, I don't especially care where the function pointer is,
> what matters is that there is a way to get DMView_MyViewer_YourDM
> called [3].  As long as dispatch is happening via PetscTypeCompare  
> against
> all the known types, we are restricted in that we either have no way  
> to
> use a third-party Viewer, or no way to view a third-party DM.  The
> current choice is the former; I don't think it's inherently superior,
> it's just a choice of which component can be extended without  
> modifying
> every object it touches.
> If I was distributing a binary-only viewer plugin, I would have no
> choice but to put all these methods in with the viewer (but I would
> currently have no way to get them called).  Note that a viewer can be
> very functional without ever using a private API or looking underneath
> obj->data.  With all other PETSc objects (DM not so much because  
> nobody
> works with the generic DM interface), I can distribute a binary-only
> implementation which is first class after dynamic loading.
> My DMView is packaged up with my DM because it needs to know many
> internal details of the DM, but the higher level logic about how to
> write a time-dependent file with association between Vecs and DMs and
> possibly other objects is currently with my viewer.  Now I need to  
> write
> DMView_MyViewer_DMComposite, but I won't be able to get it called
> without modifying DMComposite (not okay since my viewer is not part of
> PETSc).
>>    You know my answer. The Viewers are abstractions of file IO, ;
>> except instead of having only methods like read()/write() bytes it  
>> has
>> somewhat "higher level" operations. Note: these methods can include
>> graphics operations for example that are still essentially like
>> writes(). YOU are making the viewers into these strange "all knowing"
>> beasts which I think is wrong.
> Current PETSc viewers put minimal metadata and associations into a  
> file,
> the application is mostly responsible for "knowing" what was in the  
> file
> and wiring everything up correctly.  I'm trying to get more of this in
> the file, partly to go with a VisIt plugin that is not tied to a
> specific model.  I don't want to maintain a bunch of manual calls to
> HDF5 to walk this file in the VisIt plugin especially when this
> functionality is useful in other contexts [4].  I also hate C++.  ;-)
> So I've been putting stuff like walking the header and attributes to
> find out what's there, selecting a time step, etc., into my viewer.   
> The
> viewer is able to offer up information like which fields are available
> on which meshes, the plugin is a wrapper that uses this, DMLoadIntoDM
> (but not this elegant), VecLoadIntoVector, etc., and stuffs it into
> avt/vtk data structures.  Note that this plugin makes no direct  
> calls to
> HDF5 and uses only the public API of the Viewer, DM, and Vec.

    Ok so you are deriving a new Viewer that implements much higher  
level operations that are particular to PETSc (since it knows about  
Vecs and DMs). This is perhaps reasonable. But the vecload/view  
methods still belong in the Vec object :-)

> Jed
> [1] In my view, a Vec is just an element of some finite dimensional  
> linear
> space.  If you want to use a special format, or stuff extra info in
> there to make function evaluation easier or some operation faster,
> that's fine, but it's still just an element of this linear space and  
> it
> better satisfy the appropriate axioms.  The linear space that this
> vector lives in is defined by the DM and we need this to do anything
> useful (like visualization) with the vector.

    To the algebraic solvers I agree a " Vec is just an element of  
some finite dimensional ....." (since that is all the solvers need to  
know about them).  But to a specific application a Vec can be thought  
of as the linear algebra beast PLUS all kinds of grid information etc  
(like the DM).  So I think of a (application) Vec in the application  
as basically derived off of two classes:  the linear algebra beast  
PLUS a DM (it is implemented as a isA(linear algebra beast) and  
hasA(DM beast)).  This is why I feel so strongly that the VecView  
class that also reads/writes stuff related specifically to the Vec  
belongs with the Vec, not with the Viewer.

   Regarding where code needs to be changed/where : The reason for the  
"native/super" support for the VecLoadIntoVector() (which I admit is  
terribly crude and ugly) is exactly so that one can implement a new  
loader/writer directly for a specific Vec/DM combination IN THE  
APPLICATION CODE or another library. One does not have to add it to  
Do you have suggestions on how one could improve the "native/super"  
thing to satisfy you?

As I said before a Viewer in PETSc is just an abstraction/ 
generalization of a file pointer with read/write methods on the file  
pointer. So it disturbs me that a method in a Viewer would even know  
what a Vec. It leads to these loops of knowledge that make code much  
more complicated. I would do anything to prevent these loops of  
knowledge I consider them so troublesome.


> [2] Or the Vec doesn't use information about the DM when viewing on  
> that
> format if you like, I think this relationship is symmetric and
> conceptually owned by neither.
> [3] I think the location of the source for DMView_MyViewer_YourDM is
> mostly a packaging and distribution matter rather than a design  
> matter.
> I don't see a problem with it being distributed independently of  
> either
> MyViewer or YourDM (except for the technical issue of how it announces
> it's existence).
> [4] It's all slightly complicated by the fact that for visualization,
> it's important to be able to read chunks of the domain independently,
> whereas the analysis code would prefer to only define proper  
> collective
> operations.

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