[petsc-users] 3-dimension to matrix

[Joon hee Choi]

Thank you for your reply. Okay. I will try to check preallocation errors of my matrix.

Thanks,
Joon

----- Original Message -----
From: "Matthew Knepley" <knepley at gmail.com>
To: "Joon hee Choi" <choi240 at purdue.edu>
Cc: "Jed Brown" <jedbrown at mcs.anl.gov>, petsc-users at mcs.anl.gov
Sent: Friday, May 17, 2013 4:50:41 PM
Subject: Re: [petsc-users] 3-dimension to matrix


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