[petsc-users] Petsc Binary Write - Memory
venkatesh g
venkateshgk.j at gmail.com
Wed Jun 10 09:04:14 CDT 2015
Hi,
Yes I will try Elemental but there is lots of complex routines and
functions with long codes in Matlab which goes in the creation of the A and
B matrices, so re-writing in C will take a long time.
Even if Matlab takes 128 GB out of 256 GB, and the matrix A to be written
is around 25 GB, then PetscBinaryWrite.m is using more than 100 GB just to
run.. This is the problem.
so is there any other way ?
cheers,
Venkatesh
On Wed, Jun 10, 2015 at 7:07 PM, Matthew Knepley <knepley at gmail.com> 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
>>> >
>>>
>>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
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