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</o:shapelayout></xml><![endif]--></head><body lang=DA link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> petsc-users-bounces@mcs.anl.gov [mailto:petsc-users-bounces@mcs.anl.gov] <b>On Behalf Of </b>Matthew Knepley<br><b>Sent:</b> Friday, December 02, 2011 4:32 PM<br><b>To:</b> PETSc users list<br><b>Subject:</b> Re: [petsc-users] newbie question on the parallel allocation of matrices<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>On Fri, Dec 2, 2011 at 9:25 AM, Treue, Frederik <<a href="mailto:frtr@risoe.dtu.dk">frtr@risoe.dtu.dk</a>> wrote:<o:p></o:p></p><div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <a href="mailto:petsc-users-bounces@mcs.anl.gov" target="_blank">petsc-users-bounces@mcs.anl.gov</a> [mailto:<a href="mailto:petsc-users-bounces@mcs.anl.gov" target="_blank">petsc-users-bounces@mcs.anl.gov</a>] <b>On Behalf Of </b>Matthew Knepley<br><b>Sent:</b> Friday, December 02, 2011 4:01 PM<br><b>To:</b> PETSc users list<br><b>Subject:</b> Re: [petsc-users] newbie question on the parallel allocation of matrices</span><o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Fri, Dec 2, 2011 at 8:58 AM, Treue, Frederik <<a href="mailto:frtr@risoe.dtu.dk" target="_blank">frtr@risoe.dtu.dk</a>> wrote:<o:p></o:p></p><div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <a href="mailto:petsc-users-bounces@mcs.anl.gov" target="_blank">petsc-users-bounces@mcs.anl.gov</a> [mailto:<a href="mailto:petsc-users-bounces@mcs.anl.gov" target="_blank">petsc-users-bounces@mcs.anl.gov</a>] <b>On Behalf Of </b>Jed Brown<br><b>Sent:</b> Friday, December 02, 2011 1:32 PM<br><b>To:</b> PETSc users list<br><b>Subject:</b> Re: [petsc-users] newbie question on the parallel allocation of matrices</span><o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Fri, Dec 2, 2011 at 03:32, Treue, Frederik <<a href="mailto:frtr@risoe.dtu.dk" target="_blank">frtr@risoe.dtu.dk</a>> wrote:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>OK, but that example seems to assume that you wish to connect only one matrix (the Jacobian) to a DA – I wish to specify many and I think I found this done in ksp ex39, is that example doing anything deprecated or will that work for me, e.g. with the various basic mat routines (matmult, matAXPY etc.) in a multiprocessor setup?<o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>What do you mean by wanting many matrices? How do you want to use them? <span lang=EN-US>There is DMCreateMatrix() (misnamed DMGetMatrix() in petsc-3.2), which you can use as many times as you want.<span style='color:#1F497D'>`</span></span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>And this was the one I needed. However I have another question: What does DMDA_BOUNDARY_GHOSTED do, compared to DMDA_BOUNDARY_PERIODIC? From experience I now know that the PERIODIC option automagically does the right thing when I’m defining matrices so I can simply specify the same stencil at all points. Does DMDA_BOUNDARY_GHOSTED do something similar? And if so, how is it controlled, ie. How do I specify if I’ve got Neumann or Dirichlet conditions, and what order extrapolation you want, and so forth? And if not, does it then ONLY make a difference if I’m working with more than on processor, ie. If everything is sequential, is DMDA_BOUNDARY_GHOSTED and DMDA_BOUNDARY_NONE equivalent?</span><o:p></o:p></p></div></div></div></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><br>GHOSTED adds extra space at the boundary so you can always use the same stencil, but you decide what goes in there. <o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Does this apply to both matrices and vectors, ie. Will the ghost points be considered part of my computational domain or not?</span><o:p></o:p></p></div></div></div></blockquote></div><p class=MsoNormal><br clear=all><o:p></o:p></p><div><p class=MsoNormal>The ghost nodes only exist in local vectors, not the global vectors for the solver.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><span lang=EN-US style='color:#1F497D'>OK? So how does one implement boundary conditions? Normally I would include (say) one extra point over the edge of the domain (the ghost point) and then implement the equation (if I start out with Ax=b, A and b known, x desired, and dirichlet boundary conditions)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>x_G+x_1=2*b_B, where x_G is the unknown at the ghost point, x_1 is the unknown at the first “real” point, and b_B is my dirichlet boundary condition.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thus, I need to a special stencil in the first and last row (ie. The -1 and nx row, with nx internal points) of my matrix, but this leads to memory errors. Is this possible while using GHOSTED? As I understand it, GHOSTED also deals with the MPI communication, so I’d like to retain it, instead of working with NONE.<o:p></o:p></span></p></div></body></html>