[petsc-users] PetscArraycpy only copies half of the entries of the matrix rows

Thu Dec 17 10:05:37 CST 2020

MatDense is stored by column. Is that causing the problem?
--Junchao Zhang

On Thu, Dec 17, 2020 at 6:00 AM Roland Richter <roland.richter at ntnu.no>
wrote:

> Dear all,
>
> I wanted to use PetscArraycpy for copying a part of one complex matrix A
> with a row length of a_len and an offset of a_off into another matrix B
> with a row length of b_len (smaller than a_len - a_off), using the
> following code snippet:
>
> *        PetscScalar *A_ptr, *B_ptr;*
> *        MatDenseGetArray(A, &A_ptr);*
> *        MatDenseGetArray(B, &B_ptr);*
> *        MatView(A, PETSC_VIEWER_STDOUT_WORLD);*
> *        for(size_t i = 0; i < num_local_rows; ++i) {*
> *            PetscArraycpy(B_ptr + i * b_len, (2 * a_off + A_ptr) + i *
> a_len, b_len);*
> *        }*
>
> *        MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY);*
> *        MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY);*
> *        MatView(B, PETSC_VIEWER_STDOUT_WORLD);*
>
> When printing the first row of matrix A (with a_len = 128, a_off = 76 and
> b_len = 26), I get
>
> *0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i -0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i -0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i -0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i -0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i -0.0000000000000000e+00 +
> 0.0000000000000000e+00i -7.5118186821231378e-02 + -1.2515848507502547e-01i
> 5.7593629917958706e+00 + 1.6535197175842331e+00i -6.3062119866941906e+01 +
> 3.2118985283369987e+01i 1.6228535942636518e+02 + -4.4588492144691378e+02i
> 8.7350162264986420e+02 + 2.0568440963147814e+03i -7.4258479521622921e+03 +
> -3.3031631388498363e+03i 2.2699374989663269e+04 + -7.8289291098031481e+03i
> -2.7846379282467926e+04 + 5.2456793075148809e+04i -3.2554674832896777e+04 +
> -1.2108819252524960e+05i 1.9430868047197413e+05 + 1.2114559011378702e+05i
> -3.5831799834334152e+05 + 7.0086227392363056e+04i 3.0028983479603863e+05 +
> -4.1447894788669585e+05i 7.8224949502036819e+04 + 6.2926756374162808e+05i
> -5.3474873053744854e+05 + -4.4718914789259754e+05i 6.8111038372267899e+05 +
> -3.6947593166740131e+04i -4.1287212326113920e+05 + 4.2925417635846150e+05i
> 7.1098224367113344e+03 + -4.6490743916366581e+05i 2.1807010096419850e+05 +
> 2.4106178223450572e+05i -2.0304162108015743e+05 + -1.7254769976182859e+04i
> 9.0164628688356752e+04 + -7.0830186001321214e+04i -8.9050769071193699e+03 +
> 5.7267241933255813e+04i -1.4789632694550470e+04 + -2.1786332309775924e+04i
> 1.0491004489879153e+04 + 2.3873712516742830e+03i -3.4183915782335853e+03 +
> 1.9886861075931499e+03i 3.7807432692260045e+02 + -1.2521184263406540e+03i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> -0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i -0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i*
>
> and for the first row of B I get
>
> *-0.0000000000000000e+00 + 0.0000000000000000e+00i -7.5118186821231378e-02
> + -1.2515848507502547e-01i 5.7593629917958706e+00 + 1.6535197175842331e+00i
> -6.3062119866941906e+01 + 3.2118985283369987e+01i 1.6228535942636518e+02 +
> -4.4588492144691378e+02i 8.7350162264986420e+02 + 2.0568440963147814e+03i
> -7.4258479521622921e+03 + -3.3031631388498363e+03i 2.2699374989663269e+04 +
> -7.8289291098031481e+03i -2.7846379282467926e+04 + 5.2456793075148809e+04i
> -3.2554674832896777e+04 + -1.2108819252524960e+05i 1.9430868047197413e+05 +
> 1.2114559011378702e+05i -3.5831799834334152e+05 + 7.0086227392363056e+04i
> 3.0028983479603863e+05 + -4.1447894788669585e+05i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 6.9004764357806349e-310 +
> 6.9004764357806349e-310i 6.9004764365446580e-310 + 6.9004764300000669e-310i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i 0.0000000000000000e+00 + 0.0000000000000000e+00i
> 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 +
> 0.0000000000000000e+00i*
>
> Apparently, only 13 complex values have been copied, and not 26. Moreover,
> if my source destination is chosen to be (a_off + A_ptr) instead, I will
> just copy 0-values. When increasing the number of values I would like to
> copy, nothing changes (except getting a segfault for sufficient large
> values).
>
> Why does that happen? And how can I copy all values into the second
> matrix, and not only half of them?
>
> Another question: Is there a parallel version of that function, to copy
> all local rows in parallel, or do I have to write it myself, for example by
> using OpenMP?
>
> Thanks!
>
> Roland
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20201217/a0715d4a/attachment.html>