[petsc-users] 3-dimension to matrix

[Joon hee Choi]

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.
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.