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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks, Jed.<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:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">So would you prefer to using MatCreateAIJ(…) or MatXAIJSetPreallocation(…)? I am having trouble to fill out the parameters. My
local dense matrix is A(LDA, LDB). The global size of square matrix is N. What would be the parameters to use them?<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" style="text-autospace:none"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I used
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:.5in;text-autospace:none"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MatCreateAIJ(PETSC_COMM_WORLD, LDA,LDB, N,N, d_nz, d_nnz,o_nz,o_nnz, &A);<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:.5in;text-autospace:none">MatXAIJSetPreallocation<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">(PETSC_COMM_WORLD, 1, d_nz, d_nnz,o_nz,o_nnz, &A);<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" style="text-autospace:none"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">However, I have trouble to figure out the values for
<b>d_nz, d_nnz,o_nz, o_nnz</b> since the local A is a block consisting of several sub-blocks from ScaLAPACK. I think MatCreateAIJ and MatXAIJSetPreallocation both take several rows together.
<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" style="text-autospace:none"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Do you think it is still doable to preallocate A using either function?<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" style="text-autospace:none"><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 12:22 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 1:00 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">This makes sense to me. I thought the preallocation only applies to MatCreateMPIAIJwithArrays(…)
and other more complicate functions.</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>
<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">The matrix coming out from ScaLAPACK will be repopulated into a sparse matrix in a much large scale. </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">I don't understand this exactly. You are taking the entries of the dense matrix and putting them into a much larger sparse matrix? In that case, you probably never need Elemental, but you definitely need to preallocate.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<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">Do I need to install elemental package in PETSc in order to use MATELEMENTAL? </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">Yes, just configure petsc-dev with --download-elemental.<o:p></o:p></p>
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