MatCreateMPIAIJ Pre-allocation Query

[Tim Stitt]

Cheers...perfect.

On Sunday 17 June 2007 18:16, Matthew Knepley wrote:
> On 6/17/07, Tim Stitt <timothy.stitt at ichec.ie> wrote:
> > Matt,
> >
> > We are investigating 32-qubit fault-tolerant quantum computation which
> > results in 2^32 basis states and hence our large Hamiltonian matrix.
> >
> > I just ran into problems passing 2^32 in as the global row an column
> > argument so I assumed I need to rebuild PETSc to accept 64-bit integers.
>
> Yes, reconfigure with --with-64-bit-indices and rebuild. You can do
> this in another
> arch if you want to keep your old build using --PETSC_ARCH=<new arch name>
>
>    Matt
>
> > Tim.
> >
> > On Sunday 17 June 2007 17:54, Matthew Knepley wrote:
> > > On 6/17/07, Tim Stitt <timothy.stitt at ichec.ie> wrote:
> > > > Actually my sparse matrix has >2^32 rows and columns hence the global
> > > > row and column arguments need to be 64-bit.
> > >
> > > Cool. What problem is that big?
> > >
> > >   Matt
> > >
> > > > On Sunday 17 June 2007 17:36, Barry Smith wrote:
> > > > >   If your problem is so big that you need integers that represent
> > > > > numbers more than about 2 billion then yes you will need to rebuild
> > > > > PETSc.
> > > > >
> > > > >   Barry
> > > > >
> > > > > You'll be the first PETSc user who solves a problem with more than
> > > > > 2 billion unknowns.
> > > > >
> > > > > On Sun, 17 Jun 2007, Tim Stitt wrote:
> > > > > > Thanks for that Matt...will check it out.
> > > > > >
> > > > > > Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ.
> > > > > > Do I need to rebuild PETSc using a 64-bit integer option switch?
> > > > > >
> > > > > > Tim.
> > > > > >
> > > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote:
> > > > > > > On 6/17/07, Tim Stitt <timothy.stitt at ichec.ie> wrote:
> > > > > > > > Hi All,
> > > > > > > >
> > > > > > > > Currently I am using MatCreateMPIAIJ to create a distributed
> > > > > > > > sparse matrix for use in my parallel sparse eigensolver. If I
> > > > > > > > understand things correctly, it is important to specify the
> > > > > > > > correct pre-allocation values for (o_nz,d_nz) or (o_nnz,
> > > > > > > > d_nnz) respectively to obtain optimum memory usage per node.
> > > > > > > >
> > > > > > > > For information my matrix redistribution routine generates
> > > > > > > > each row in the sparse matrix (associated with a given node)
> > > > > > > > "on-the-fly" and then uses MatSetValues to apply the
> > > > > > > > elements.
> > > > > > > >
> > > > > > > > My question is: does anyone have a standard code template for
> > > > > > > > the calculating the d_nz or d_nnz values (along with o_nz or
> > > > > > > > o_nnz respectively) so that optimum pre-allocation is
> > > > > > > > obtained? Is there a simple way of determining if a given
> > > > > > > > non-zero value in a row is part of the diagonal or
> > > > > > > > off-diagonal regions for a given distributed topology?
> > > > > > > >
> > > > > > > > Any assistance gratefully received.
> > > > > > >
> > > > > > > Basically, you run through the construction algorithm once to
> > > > > > > calculate d_nnz and o_nnz, and then again to set values. You
> > > > > > > can see my code for doing it in preallocateOperator() in
> > > > > > > src/dm/mesh/mesh.c.
> > > > > > >
> > > > > > >    Matt
> > > > > > >
> > > > > > > > Thanks in advance,
> > > > > > > >
> > > > > > > > Tim.
> > > > > > > >
> > > > > > > > --
> > > > > > > > Dr. Timothy Stitt <timothy_dot_stitt_at_ichec.ie>
> > > > > > > > HPC Application Consultant - ICHEC (www.ichec.ie)
> > > > > > > >
> > > > > > > > Dublin Institute for Advanced Studies
> > > > > > > > 5 Merrion Square - Dublin 2 - Ireland
> > > > > > > >
> > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427
> > > > > > > > (mobile)
> > > >
> > > > --
> > > > Dr. Timothy Stitt <timothy_dot_stitt_at_ichec.ie>
> > > > HPC Application Consultant - ICHEC (www.ichec.ie)
> > > >
> > > > Dublin Institute for Advanced Studies
> > > > 5 Merrion Square - Dublin 2 - Ireland
> > > >
> > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile)
> >
> > --
> > Dr. Timothy Stitt <timothy_dot_stitt_at_ichec.ie>
> > HPC Application Consultant - ICHEC (www.ichec.ie)
> >
> > Dublin Institute for Advanced Studies
> > 5 Merrion Square - Dublin 2 - Ireland
> >
> > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile)

-- 
Dr. Timothy Stitt <timothy_dot_stitt_at_ichec.ie>
HPC Application Consultant - ICHEC (www.ichec.ie)

Dublin Institute for Advanced Studies
5 Merrion Square - Dublin 2 - Ireland

+353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile)