[petsc-users] 3-dimension to matrix

[Peter Lichtner]

I found a similar problem solving Laplace's equation: using MatCreate took forever, whereas using MatCreateAIJ instead the time for MatSetValues was essentially negligible. I set up MatCreate with a call to MatSetSizes.
...Peter

On May 17, 2013, at 2:50 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Fri, May 17, 2013 at 3:40 PM, Joon hee Choi <choi240 at purdue.edu> wrote:
> My petsc version is 3.3.5.
> And I made nnz using the number of each row. When I wrote the matrix using MatSetValues, I wrote from low row and column to high row and column. However, when I changed the order writing the matrix, it took much more time (up to 3hrs). So I am concerned that the slowness is because the big size of matrix (2.6*10^7, 1.248*10^15) is related to reading from or writing to the cache, ram, or hard.
> 
> No, it is bad preallocation. This should be simple to fix. First, turn on errors
> 
>   MatSetOption(MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE)
> 
> and second run with -info.
> 
>   Thanks,
> 
>      Matt
>  
> Anyway, the following code is the part that I read the data from a file and set up tuples and nnz:
> 
>         FILE *fp = fopen("data.txt", "r");
>         while (fscanf(fp, "%d %d %d %d", &x, &y, &z, &v) == 4)
>         {
>                 tups.push_back(std::tr1::make_tuple (x-1, z-1, y-1, v));
>                 nzrow[i-1] += 1;
>                 if (x > X) X = x;
>                 if (y > Y) Y = y;
>                 if (z > Z) Z = z;
>         }
>         fclose(fp);
>         PetscMalloc(X*sizeof(PetscInt), &nnz);
>         memset(nnz, 0, X);
>         for (itnz=nzrow.begin(); itnz!=nzrow.end(); ++itnz) {
>                 nnz[itnz->first] = itnz->second;
>         }
>         sort(tups.begin(), tups.end());
> 
> If my code is wrong, then please let me know.
> 
> Thank you,
> Joon
> 
> ----- Original Message -----
> From: "Jed Brown" <jedbrown at mcs.anl.gov>
> To: "Joon hee Choi" <choi240 at purdue.edu>
> Cc: petsc-users at mcs.anl.gov
> Sent: Friday, May 17, 2013 3:24:09 PM
> Subject: Re: [petsc-users] 3-dimension to matrix
> 
> Joon hee Choi <choi240 at purdue.edu> writes:
> 
> > Thank you for your fast reply. Your last comments looks like my first
> > code. The full size of the matrix is (X, Y*Z). Also, I used SEQAIJ as
> > matrix type and (X, Y) as block size. Also, I implemented
> > SeqAIJpreallocating with nnz. Nevertheless, it was very slow. The
> > Matrix-Set-Up part of the first code is as follows:
> >
> >         sort(tups.begin(), tups.end());
> >         MatCreate(PETSC_COMM_SELF, &A);
> >         MatSetType(A, MATSEQAIJ);
> >         MatSetSizes(A, PETSC_DECIDE, PETSC_DECIDE, X, Y*Z);
> >         MatSetBlockSizes(A, X, Y);
> >         MatSeqAIJSetPreallocation(A, PETSC_DEFAULT, nnz);
> >
> >         sz = tups.size();
> >         for (i=0; i<sz; i++) {
> >                 x = std::tr1::get<0>(tups[i]);
> >                 y = std::tr1::get<2>(tups[i]) + std::tr1::get<1>(tups[i])*Y;
> >                 val = std::tr1::get<3>(tups[i]);
> >                 MatSetValues(A, 1, &x, 1, &y, &val, INSERT_VALUES);
> >         }
> >         MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
> >         MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
> >
> >
> > I used tuple (x, z, y, value) and vector of c++. I didn't get any
> > errors from this code. However, it took about 9 minutes in this
> > part.
> 
> What version of PETSc?  Your preallocation was almost certainly not
> sufficient.
> 
> 
> 
> -- 
> 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

________________
Peter Lichtner
Santa Fe, NM 87507
(505) 692-4029 (c)
OFM Research/LANL Guest Scientist

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