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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What I am trying to say is that
<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">allocated 1D array A in PETSc<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">passed 1D A into ScaLAPACK<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">obtained the indices of A^-1 computed from ScaLAPACK and stored them in a 1D array<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">indexed A^-1 as a 1D array in PETSc using the indices obtained from ScaLAPACK<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">constructed a sparse matrix, including A^-1 and others, using a new set of indices for A^-1.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I can have the last step done in using
<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>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.5pt;font-family:Consolas"> ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.5pt;font-family:Consolas"> ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.5pt;font-family:Consolas"> ierr = MatSetFromOptions(A);CHKERRQ(ierr);<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.5pt;font-family:Consolas"> ierr = MatSetUp(A);CHKERRQ(ierr);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:1.5in;text-indent:.5in;text-autospace:none">
<span style="font-size:12.5pt;font-family:Consolas"> <o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:1.5in;text-indent:.5in;text-autospace:none">
<span style="font-size:12.5pt;font-family:Consolas"> ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.5pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It just took too long. This is the performance issue I am having.
<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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">To improve the performance, it is necessary for preallocation. The dilemma is:
<b>MatCreateAIJ</b> and <b>MatXCreateAIJ</b> complained the setting of </span><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">d_nz, d_nnz,o_nz, o_nnz</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
since there are no diagonal and off-diagonal parts defined in A^-1.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><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">Jinquan<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>
<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"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span 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>Jed Brown<br>
<b>Sent:</b> Wednesday, August 08, 2012 3:04 PM<br>
<b>To:</b> PETSc users list<br>
<b>Subject:</b> Re: [petsc-users] Customizeing MatSetValuesBlocked(...)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Wed, Aug 8, 2012 at 3:45 PM, Jinquan Zhong <<a href="mailto:jzhong@scsolutions.com" target="_blank">jzhong@scsolutions.com</a>> wrote:<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">It is a 1D matrix in PETSc. I just passed it as a 2D matrix in ScaLAPACK. It is still a 1D matrix
when get back into PETSc.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">What are you trying to say?<o:p></o:p></p>
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