[petsc-users] Matrix reuse with changing structure

[Smith, Kevin R.]

Barry - I need to avoid dynamic allocation because it results in too much of a slowdown.
Matt - The MatSetType thing did not work for some reason. It seems like PETSc wants me to set the preallocation after calling this method (suggested by the error below). I'm trying to reuse the original block of preallocated memory for the sparse matrix and blow away the structure each time. This would let me avoid repeated deallocate/allocate calls throughout my simulation. 

PETSc Function: MatGetOwnershipRange
 PETSc File: /share/maul-data/smithkr1/src/petsc-3.6.0/src/mat/interface/matrix.c
 PETSc Line: 6289
 PETSc Error Code: 73
 PETSc Error reference: http://www.mcs.anl.gov/petsc/petsc-dev/include/petscerror.h.html
 PETSc Message: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()

Kind regards,
 Kevin

-----Original Message-----
From: Barry Smith [mailto:bsmith at mcs.anl.gov] 
Sent: Tuesday, March 15, 2016 2:02 PM
To: Smith, Kevin R.
Cc: Matthew Knepley; petsc-users at mcs.anl.gov
Subject: Re: [petsc-users] Matrix reuse with changing structure


> On Mar 15, 2016, at 12:56 PM, Smith, Kevin R. <Kevin.R.Smith at jhuapl.edu> wrote:
> 
> 
> Barry - Yeah, I suspected it was doing this. In my original implementation I would get allocation errors. 

   You need to call a MatSetOption() to tell the matrix that it is allowed to allocate new nonzeros.


> 
> Matt - Thanks, I will try this solution out. 
> 
> Thanks for your help,
> 
>  Kevin
> 
> -----Original Message-----
> From: Barry Smith [mailto:bsmith at mcs.anl.gov] 
> Sent: Tuesday, March 15, 2016 1:48 PM
> To: Matthew Knepley
> Cc: Smith, Kevin R.; petsc-users at mcs.anl.gov
> Subject: Re: [petsc-users] Matrix reuse with changing structure
> 
> 
>> On Mar 15, 2016, at 12:28 PM, Matthew Knepley <knepley at gmail.com> wrote:
>> 
>> On Tue, Mar 15, 2016 at 12:24 PM, Smith, Kevin R. <Kevin.R.Smith at jhuapl.edu> wrote:
>> Hello,
>> 
>> 
>> 
>> Is it possible to reuse a sparse matrix and not reuse its non-zero structure?   I have a matrix whose sparse structure changes each time. I’m hoping to avoid destroying and allocating new matrices each time the structure changes.
> 
>   Sure you can just add new nonzero locations at a later time. But it won't take out any current entries even if they are zero. So effectively the nonzero structure grows over time.
> 
>   Barry
> 
>> 
>> 
>> Hmm, I can't find a toplevel API that does this (it would be something like MatReset()). You can get this effect using
>> 
>>  MatSetType(A, MATSHELL)
>>  MatSetType(A, <type you had before>)
>> 
>> A little messy but it will work.
>> 
>>  Thanks,
>> 
>>     Matt
>> 
>> 
>> 
>> Thanks,
>> 
>>  Kevin
>> 
>> 
>> 
>> 
>> -- 
>> 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
>