[petsc-users] Petsc Binary Write - Memory

[Satish Balay]

Just to add - the sparse matrix would be of size:

4*84500+(4+8)*2.7338e+09 bytes = 33GB [app]. So matlab - with the
intermediate represantations used in PetscBinaryWrite.m are perhaps
consuming 256GB - so a sequential assmebly of this matrix in C code
[with proper preallocation] should be more memory efficient..

Satish

On Wed, 10 Jun 2015, Matthew Knepley wrote:

> On Wed, Jun 10, 2015 at 8:32 AM, venkatesh g <venkateshgk.j at gmail.com>
> wrote:
> 
> > The size of the matrix is 84500 x 84500
> >
> > the no. of non-zero elements is 2.7338e+09
> >
> 
> This matrix is not sparse, it has 40% fill. You should treat it as dense.
> For dense matrices of this size,
> you should consider using Elemental. We have an interface to Elemental in
> PETSc.
> 
> I recommend writing the code to create these entries on the fly since it
> will probably be faster than loading
> them from disk.
> 
>   Thanks,
> 
>     Matt
> 
> 
> > cheers,
> > Venkatesh
> >
> > On Wed, Jun 10, 2015 at 6:35 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> >
> >> Whats the size of the matrix? How many non-zeros?
> >>
> >> Satish
> >>
> >> On Wed, 10 Jun 2015, venkatesh g wrote:
> >>
> >> > Hi
> >> >
> >> > I am trying to write very large sparse matrices A and B for solving
> >> > generalized Eigenvalue problem
> >> >
> >> > so that I can use SLEPC ex7.c code.
> >> >
> >> > I want to read matrices from file according to that code. And I generate
> >> > these matrices from Matlab using PetscBinaryWrite.m
> >> >
> >> > However, it exceeds my 256 GB RAM in one of the machines. So I am
> >> unable to
> >> > generate these binary matrices.
> >> >
> >> > Kindly let me know how to write them efficiently.
> >> >
> >> > cheers,
> >> >
> >> > Venkatesh
> >> >
> >>
> >>
> >
> 
> 
>