[petsc-users] When to perform PETSc.Vec assembly with petsc4py

Tue Jul 15 10:26:04 CDT 2025

On Tue, Jul 15, 2025 at 10:44 AM SCOTTO Alexandre <
alexandre.scotto at irt-saintexupery.com> wrote:

> The place where the problem is quite deep in a large code, I will try to
> isolate the problematic behaviour but this may take some time.
>
>
>
> @Matthew, is there a way in the Python API to check whether a vector is
> assembled?
>

No. I will put in the wrapper for that.

  Thanks,

     Matt

> Regards,
>
> Alexandre.
>
>
>
> *De :* Matthew Knepley <knepley at gmail.com>
> *Envoyé :* mardi 15 juillet 2025 16:06
> *À :* Jose E. Roman <jroman at dsic.upv.es>
> *Cc :* SCOTTO Alexandre <alexandre.scotto at irt-saintexupery.com>;
> petsc-users at mcs.anl.gov
> *Objet :* Re: [petsc-users] When to perform PETSc.Vec assembly with
> petsc4py
>
>
>
> We check that the x argument is assembled in MatMultTranspose(), but not
> y. It seems possible that y could have stashed values that get communicated
> when the operation is performed. Why do we not check that y is assembled?
>
>
>
>   Thanks,
>
>
>
>      Matt
>
>
>
> On Tue, Jul 15, 2025 at 9:36 AM Jose E. Roman <jroman at dsic.upv.es> wrote:
>
> It is better if you can provide a full python script that we can run to
> reproduce the problem.
>
> Jose
>
>
> > El 15 jul 2025, a las 14:49, SCOTTO Alexandre <
> alexandre.scotto at irt-saintexupery.com> escribió:
> >
> > Ok I get it, Vec.assemble() is mandatory whenever MPI communications are
> required to get the values to appropriate processes.
> >  To provide more information, I am in a situation where I perform a
> A.multTranspose(x, y), where y is a vector that has been filled in with
> values earlier in the process. At this stage, I no longer care of these
> values and I expect the multTranspose() to override the values. But what I
> get is:
> > ·         if I do y.assemble() before the transpose multiplication, then
> y is filled-in with the correct result.
> > ·         if I do not perform y.assemble() before the transpose
> multiplication, I actually get y = y + A^T(x), i.e. a result rather of the
> form multTransposeAdd().
> > ·         If I do A.multTranspose(x, y) twice, then I get the correct
> result y = A^T(x).
> >  This makes me think that I am misusing something at some points, but it
> is not clear what. If someone has a hint to explain this behaviour that
> would help me better understand how to properly use PETSc!
> >  Regards,
> > Alexandre.
> >  De : Matthew Knepley <knepley at gmail.com>
> > Envoyé : mardi 15 juillet 2025 14:18
> > À : SCOTTO Alexandre <alexandre.scotto at irt-saintexupery.com>
> > Cc : Jose E. Roman <jroman at dsic.upv.es>; petsc-users at mcs.anl.gov
> > Objet : Re: [petsc-users] When to perform PETSc.Vec assembly with
> petsc4py
> >  On Tue, Jul 15, 2025 at 8:13 AM SCOTTO Alexandre via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> > Hello Jose,
> >
> > Thanks for your answer. Then it seems that I have under the hood usages
> of setValues() in my code since I do not explicitly make use of it but
> still has problems when not assembling my vector. Do I need to assemble
> vectors after Mat.mult or Scatter.scatter?
> >  No. The purpose of VecAsseblyBegin/End() is to move values from
> processes that do not own them to the processes that do. PETSc does this
> automatically for MatMult() and VecScatter routines because we know exactly
> where values are headed. However, when users call VecSetValues(), they may
> set locations that are owned by other processes. We could communicate these
> immediately, but that might be expensive for a series of VecSetValues()
> calls, so we wait until you call VecAssembly().
> >  Note that direct assignment to the array can only set local values.
> This is equivalent to VecGetArray().
> >    Thanks,
> >       Matt
> >  By the way, I did not know that PETSc.Vec objects supported direct
> assignments like x[i] = ..., so I rather use assignments of the form
> x.array = ...
> >
> > From what I understand from the GitHub page (
> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/binding/petsc4py/src/petsc4py/PETSc/Vec.pyx__;!!G_uCfscf7eWS!f3M5SmfhSqew4tgfvFDjdLnd3q3kT_KzcCitJTJC0HRl1YvbSNBr5Uuzv6OWP1pVQBgbi_WJlekerylpGcBHQ9vsbzL1suFBQHkoPIwhdw$
> <https://urldefense.us/v3/__https:/gitlab.com/petsc/petsc/-/blob/main/src/binding/petsc4py/src/petsc4py/PETSc/Vec.pyx__;!!G_uCfscf7eWS!f3M5SmfhSqew4tgfvFDjdLnd3q3kT_KzcCitJTJC0HRl1YvbSNBr5Uuzv6OWP1pVQBgbi_WJlekerylpGcBHQ9vsbzL1suFBQHkoPIwhdw$>
> ) it seems, that doing so, we only access the local portion of the array
> which should not require any assemble() am I right?
> >
> > Best regards,
> > Alexandre.
> >
> >
> > -----Message d'origine-----
> > De : Jose E. Roman <jroman at dsic.upv.es>
> > Envoyé : mardi 15 juillet 2025 12:21
> > À : SCOTTO Alexandre <alexandre.scotto at irt-saintexupery.com>
> > Cc : petsc-users at mcs.anl.gov
> > Objet : Re: [petsc-users] When to perform PETSc.Vec assembly with
> petsc4py
> >
> > Assembly is needed after a call to x.setValues() or any of its variants.
> >
> https://urldefense.us/v3/__https://petsc.org/main/petsc4py/reference/petsc4py.PETSc.Vec.html*petsc4py.PETSc.Vec.setValue__;Iw!!G_uCfscf7eWS!f3M5SmfhSqew4tgfvFDjdLnd3q3kT_KzcCitJTJC0HRl1YvbSNBr5Uuzv6OWP1pVQBgbi_WJlekerylpGcBHQ9vsbzL1suFBQHlKEPOyQg$
> <https://urldefense.us/v3/__https:/petsc.org/main/petsc4py/reference/petsc4py.PETSc.Vec.html*petsc4py.PETSc.Vec.setValue__;Iw!!G_uCfscf7eWS!f3M5SmfhSqew4tgfvFDjdLnd3q3kT_KzcCitJTJC0HRl1YvbSNBr5Uuzv6OWP1pVQBgbi_WJlekerylpGcBHQ9vsbzL1suFBQHlKEPOyQg$>
> > Take into account that in python the notation x[i] = ...  with call
> x.setValues() under the hood.
> >
> > Jose
> >
> >
> > > El 15 jul 2025, a las 12:02, SCOTTO Alexandre via petsc-users <
> petsc-users at mcs.anl.gov> escribió:
> > >
> > > Dear PETSc community,
> > >  As a beginner in the MPI world and with the PETSc library, I come
> with a possibly very naive question.
> > > I know from the documentation that assembling vectors must be done,
> but it is not clear to me when to perform this operation.
> > > Is there a simple way to know when a vector need be assembled and when
> it is not?
> > >  Thanks in advance.
> > > Regards,
> > > Alexandre.
> >  -- What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >  https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fWSWIHY4a4L2adD4fYqOth8uBeVB9CUKljMnzGrrzwXCW7Th4Iv_EdU7624bjBlHVSoaV6Ybdss-lakusLGJ$ 
>
>
>
>
> --
>
> 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
>
>
>
> https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fWSWIHY4a4L2adD4fYqOth8uBeVB9CUKljMnzGrrzwXCW7Th4Iv_EdU7624bjBlHVSoaV6Ybdss-lakusLGJ$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fWSWIHY4a4L2adD4fYqOth8uBeVB9CUKljMnzGrrzwXCW7Th4Iv_EdU7624bjBlHVSoaV6Ybdss-lUFG1TxU$ >
>

-- 
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

https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fWSWIHY4a4L2adD4fYqOth8uBeVB9CUKljMnzGrrzwXCW7Th4Iv_EdU7624bjBlHVSoaV6Ybdss-lakusLGJ$  <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fWSWIHY4a4L2adD4fYqOth8uBeVB9CUKljMnzGrrzwXCW7Th4Iv_EdU7624bjBlHVSoaV6Ybdss-lUFG1TxU$ >
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