[petsc-users] Out-of-memory, reading ASCII files using single processor

[jifeng zhao]

Hi Jed,

Actually the out-of-memory happened when converting ASCII files to petsc
format using a serial PETSc program.

It seems a single processor doesn't have enough memory to preallocate
enough space to store the matrices. Is there any way around it...?

Best regards,
Jifeng Zhao


On Sun, Aug 17, 2014 at 11:40 PM, Jed Brown <jed at jedbrown.org> wrote:

> jifeng zhao <jifengzhao2015 at u.northwestern.edu> writes:
>
> > Hello all,
> >
> > I am trying to read large matrices from ASCII files and save it into
> petsc
> > binary format using uni-processor.
> >
> > But I am encountered a out-of-memory error, when reading too-large ASCII
> > file.
>
> Don't use ASCII.  It is a monumentally bad format for parallel
> computing.  Convert your ASCII files to PETSc binary files (or HDF5, but
> PETSc binary is sufficient and simpler), then read in parallel.  You can
> do this easily in MATLAB or Python, or with a serial PETSc program.
>



-- 
Jifeng Zhao
PhD candidate at Northwestern University, US
Theoretical and Applied Mechanics Program
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