<div dir="ltr"><div dir="ltr">On Thu, Jul 15, 2021 at 8:46 AM Fande Kong <<a href="mailto:fdkong.jd@gmail.com">fdkong.jd@gmail.com</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">"if (a->keepnonzeropattern)" branch does not change ilen so that A->ops->assemblyend will be fine. It would help if you made sure that elements have been inserted for these rows before you call MatZeroRows.<br></div></blockquote><div><br></div><div>So this is the crux of the problem. In ex11 let's say that I had not insert a value at (0,5) but I know I'm going to later and I've preallocated the space for it. MatZeroValues will erase that preallocation with its call to MatAssemblyEnd with MAT_FINAL_ASSEMBLY regardless of the value of keepnonzeropattern.</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br>However, I am not sure it is necessary to call A->ops->assemblyend if we already require a->keepnonzeropattern. That being said, we might have something like this<br><div><br></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><b>diff --git a/src/mat/impls/aij/seq/aij.c b/src/mat/impls/aij/seq/aij.c</b></span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><b>index 42c93a82b1..3f20a599d6 100644</b></span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><b>--- a/src/mat/impls/aij/seq/aij.c</b></span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><b>+++ b/src/mat/impls/aij/seq/aij.c</b></span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(56,185,199)">@@ -2203,7 +2203,9 @@</span><span style="font-variant-ligatures:no-common-ligatures"> PetscErrorCode MatZeroRows_SeqAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscSc</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>#if defined(PETSC_HAVE_DEVICE)</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>if (A->offloadmask != PETSC_OFFLOAD_UNALLOCATED) A->offloadmask = PETSC_OFFLOAD_CPU;</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>#endif</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(202,51,35)"><span style="font-variant-ligatures:no-common-ligatures">-<span> </span>ierr = (*A->ops->assemblyend)(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(57,192,38)"><span style="font-variant-ligatures:no-common-ligatures">+<span> </span>if (!a->keepnonzeropattern) {</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(57,192,38)"><span style="font-variant-ligatures:no-common-ligatures">+<span> </span>ierr = (*A->ops->assemblyend)(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(57,192,38)"><span style="font-variant-ligatures:no-common-ligatures">+<span> </span>}</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>PetscFunctionReturn(0);</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>}</span></p>
<br></div><div><br></div><div>Fande</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 15, 2021 at 9:30 AM Stefano Zampini <<a href="mailto:stefano.zampini@gmail.com" target="_blank">stefano.zampini@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Alexander<div><br></div><div>Do you have a small code to reproduce the issue?<div><br></div><div>Below is the output using a PETSc example (src/mat/tests/ex11). The pattern is kept. </div><div><br></div><div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">kl-18448:tests szampini$ ./ex11 </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Mat Object: 1 MPI processes</span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> type: seqaij</span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 0: (0, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 1: (0, -1.) (1, 4.) (2, -1.) (6, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 2: (2, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 3: (2, -1.) (3, 4.) (4, -1.) (8, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 4: (4, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 5: (0, -1.) (5, 4.) (6, -1.) (10, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 6: (6, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 7: (2, -1.) (6, -1.) (7, 4.) (8, -1.) (12, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 8: (8, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 9: (4, -1.) (8, -1.) (9, 4.) (14, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 10: (10, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 11: (6, -1.) (10, -1.) (11, 4.) (12, -1.) (16, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 12: (12, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 13: (8, -1.) (12, -1.) (13, 4.) (14, -1.) (18, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 14: (14, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 15: (10, -1.) (15, 4.) (16, -1.) (20, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 16: (16, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 17: (12, -1.) (16, -1.) (17, 4.) (18, -1.) (22, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 18: (18, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 19: (14, -1.) (18, -1.) (19, 4.) (24, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 20: (20, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 21: (16, -1.) (20, -1.) (21, 4.) (22, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 22: (22, 5.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 23: (18, -1.) (22, -1.) (23, 4.) (24, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 24: (19, -1.) (23, -1.) (24, 4.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">kl-18448:tests szampini$ ./ex11 -keep_nonzero_pattern</span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Mat Object: 1 MPI processes</span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> type: seqaij</span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 0: (0, 5.) (1, 0.) (5, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 1: (0, -1.) (1, 4.) (2, -1.) (6, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 2: (1, 0.) (2, 5.) (3, 0.) (7, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 3: (2, -1.) (3, 4.) (4, -1.) (8, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 4: (3, 0.) (4, 5.) (9, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 5: (0, -1.) (5, 4.) (6, -1.) (10, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 6: (1, 0.) (5, 0.) (6, 5.) (7, 0.) (11, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 7: (2, -1.) (6, -1.) (7, 4.) (8, -1.) (12, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 8: (3, 0.) (7, 0.) (8, 5.) (9, 0.) (13, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 9: (4, -1.) (8, -1.) (9, 4.) (14, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 10: (5, 0.) (10, 5.) (11, 0.) (15, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 11: (6, -1.) (10, -1.) (11, 4.) (12, -1.) (16, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 12: (7, 0.) (11, 0.) (12, 5.) (13, 0.) (17, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 13: (8, -1.) (12, -1.) (13, 4.) (14, -1.) (18, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 14: (9, 0.) (13, 0.) (14, 5.) (19, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 15: (10, -1.) (15, 4.) (16, -1.) (20, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 16: (11, 0.) (15, 0.) (16, 5.) (17, 0.) (21, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 17: (12, -1.) (16, -1.) (17, 4.) (18, -1.) (22, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 18: (13, 0.) (17, 0.) (18, 5.) (19, 0.) (23, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 19: (14, -1.) (18, -1.) (19, 4.) (24, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 20: (15, 0.) (20, 5.) (21, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 21: (16, -1.) (20, -1.) (21, 4.) (22, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 22: (17, 0.) (21, 0.) (22, 5.) (23, 0.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 23: (18, -1.) (22, -1.) (23, 4.) (24, -1.) </span></div><div style="margin:0px;font-stretch:normal;font-size:21px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">row 24: (19, -1.) (23, -1.) (24, 4.)</span></div><div><br><blockquote type="cite"><div>On Jul 15, 2021, at 4:41 PM, Alexander Lindsay <<a href="mailto:alexlindsay239@gmail.com" target="_blank">alexlindsay239@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div>My interpretation of the documentation page of MatZeroRows is that if I've set MAT_KEEP_NONZERO_PATTERN to true, then my sparsity pattern shouldn't be changed by a call to it, e.g. a->imax should not change. However, at least for sequential matrices, MatAssemblyEnd is called with MAT_FINAL_ASSEMBLY at the end of MatZeroRows_SeqAIJ and that does indeed change my sparsity pattern. Is my interpretation of the documentation page wrong?</div><div><br></div><div>Alex<br></div></div>
</div></blockquote></div><br></div></div></div></blockquote></div>
</blockquote></div></div>