[petsc-users] Read/Write large dense matrix

[Matthew Knepley]

On Mon, Aug 5, 2024 at 1:10 PM Sreeram R Venkat <srvenkat at utexas.edu> wrote:

> I have a large dense matrix (size ranging from 5e4 to 1e5) that arises as
> a result of doing MatComputeOperator() on a MatShell. When the total number
> of nonzeros exceeds the 32 bit integer value, I get an error (MPI buffer
> size too big) when
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> I have a large dense matrix (size ranging from 5e4 to 1e5) that arises as
> a result of doing MatComputeOperator() on a MatShell. When the total number
> of nonzeros exceeds the 32 bit integer value, I get an error (MPI buffer
> size too big) when trying to do MatView() on this to save to binary. Is
> there a way I can save this matrix to load again for later use?
>

I think you need to reconfigure with --with-64-bit-indices.

  Thanks,

     Matt


> The other thing I tried was to save each column as a separate dataset in
> an hdf5 file. Then, I tried to load this in python, combine them to an np
> array, and then create/save a dense matrix with petsc4py. I was able to
> create the dense Mat, but the MatView() once again resulted in an error
> (out of memory).
>
> Thanks,
> Sreeram
>


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