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Hi Dave,
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<div class="">Yes it is parallel so the preallocation calls are not lowered by the allocation.</div>
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<div class="">I am trying to use MatXAIJSetPreallocation, but not sure how, since the following link does not give an example:</div>
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<div class=""><a href="https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatXAIJSetPreallocation.html" class="">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatXAIJSetPreallocation.html</a></div>
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<div class="">If I have the following matrix:</div>
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<div class="">0 1 2 0 </div>
<div class="">1 0 0 0 </div>
<div class="">2 0 1 3</div>
<div class="">0 0 3 2 </div>
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<div class="">How should I put in the parameters of MatXAIJSetPreallocation?</div>
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<div class="">Thanks!</div>
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<div class="">Cheers,</div>
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<div class="">Yang Bo</div>
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<div class="">On 21 May 2020, at 5:42 PM, Dave May <<a href="mailto:dave.mayhem23@gmail.com" class="">dave.mayhem23@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">On Thu 21. May 2020 at 10:49, Yang Bo (Asst Prof) <<a href="mailto:yang.bo@ntu.edu.sg" class="">yang.bo@ntu.edu.sg</a>> wrote:<br class="">
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<div style="word-wrap: break-word; line-break: after-white-space;" class="">Hi Dave,
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<div class="">Thank you very much for your reply. That is indeed the problem. I have been working with matrices in Slepc but I don’t really understand it. I tried to preallocate but it still does not work.<span class="Apple-converted-space"> </span></div>
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<div dir="auto" class="">Meaning the number of reported mallocs is still non-zero?</div>
<div dir="auto" class="">Is the number reported with you preallocation calls lower than what you originally saw?</div>
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<div class="">If you look at my code below:</div>
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<div class="">ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);</div>
<div class="">ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,h_dim,h_dim);<span style="white-space: pre-wrap;" class="">
</span> // h_dim is the dimension of the square matrix A</div>
<div class="">ierr = MatSetFromOptions(A);CHKERRQ(ierr);</div>
<div class="">ierr = MatSetUp(A);CHKERRQ(ierr);</div>
<div class="">ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);</div>
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<div class="">MatSeqAIJSetPreallocation(A,0,nnz); <span class="Apple-converted-space"> </span><span style="white-space: pre-wrap;" class=""></span>// I try to preallocate here, where nnz is the array containing the number
of non-zero entries each row</div>
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<div class="">for (int i=0;i<row.size();i++) {</div>
<div class=""><span style="white-space: pre-wrap;" class=""></span>MatSetValue(A,row[i],column[i],h[i],INSERT_VALUES);</div>
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<div class="">I am not sure what other information I need to give for the pre-allocation…</div>
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<div dir="auto" class="">This looks fine. However MatSeqAIJSetPreallocation() has no effect if the Mat type is not SEQAIJ.</div>
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<div dir="auto" class="">Are you running in parallel? If yes then the Mat type will be MATMPIAIJ and you either have to call the MPI specific preallocator or use the generic one I pointed you too.</div>
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<div dir="auto" class="">Thanks</div>
<div dir="auto" class="">Dave</div>
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<div class="">Cheers,</div>
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<div class="">Yang Bo</div>
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<div class="">On 21 May 2020, at 4:08 PM, Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank" class="">dave.mayhem23@gmail.com</a>> wrote:</div>
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| grep malloc</b></div>
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