|
Many thanks Barry,
MatMPIAIJSetPreallocationCSR could be a good solution for
me.
It seems that to satisfy the
MatMPIAIJSetPreallocationCSR requirements I should convert the
nz array from a relative to an absolute representation of the row offsets
but ...
I think this implies a not negligible drawback: my matrix is
too large and offsets must be promoted to a long long int (64 bit)
type.
Moreover the idxn array type also must be
promoted to be compliant with a 64 bit PetscInt type.
This requires the double amount of memory for nz and
idxn.
What do you think about the opportunity to provide another
version of MatMPIAIJSetPreallocationCSR based on relative
offsets to save memory?
Absolute offsets could be managed internally
...
Finally I've look into the body
of MatMPIAIJSetPreallocationCSR_MPIAIJ function ad I found this
snippet of code
for (i=0; i<m; i++) {
ii
= i + rstart;
nnz = I[i+1]-
I[i];
ierr =
MatSetValues_MPIAIJ(B,1,&ii,nnz,J+I[i],values+(v ? I[i] :
0),INSERT_VALUES);CHKERRQ(ierr);
}
There's no way to avoid the copy of the values? This doubles
one more time the memory for the values array and spend time into the
loop.
Morevover nnz corresponds exactly to my nz[i] ...
----- Original Message -----
Sent: Monday, February 06, 2006 4:15
PM
Subject: Re: mat creation
On Mon, 6 Feb 2006, Roberto Gori wrote:
> Hi,
guys,
>
> I'm trying to solve a linear system with M equations and
N unknowns (M >> N) using the LSQR method.
>
> I have a C
parallel sparse matrix MxN with NZ nonzero elements stored in this
way:
>
> double values[NZ]; // the nonzero values
> int
idxn[NZ]; // the column indices
> int nz[M]; // the number of nonzero
values for each row
This needs to be instead indices to start of each
row in idxn and values
instead of the length of each row.
>
>
what is the best way to create a PETSc
matrix?
MatMPIAIJSetPreallocationCSR()
> > Do exists a statement like VecCreateMPIWithArray for
already distributed vectors that could do all the work in one shot without
copy? Yes > Just another detail. Initially M is
unknown. All my structures are > allocated dynamically because the
number of rows M (and the number > of nonzero NZ also) is determined
just before to solve the system, > so I think it's no feasible for me to
call MatCreateMPIAIJ at the > begin of my code and to perform the
MatSetValues loop. There is nothing saying that you must "call
MatCreateMPIAIJ at the beginning of your code", you can call it anytime
that you have the needed information.
Barry > > Roberto > >
================================================================ > |
Roberto
Gori
CINECA > | High Performance System
Group Via Magnanelli 6/3
40033 > | e-mail: r.gori@cineca.it
Casalecchio di Reno > | Tel:
051/6171522
Bologna - ITALY > | Fax:
051/6132198
http://www.cineca.it>
================================================================ > >
|