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<p class="MsoNormal">Hello team,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m debugging my code using gdb. The program runs just fine if I don’t debug it, but when I use gdb, it seg faults at a place where it never experienced any seg fault when I debugged it 1-2 years ago. I wonder if this might be caused by
the PETSc version change? Or something wrong with gdb itself? I’ve included the code block that is problematic for you to take a look at what might be wrong – seg fault happens when this function is called. For context, Spmat is a class of sparse matrices
in the code:</p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="p1"><span class="s1">// calculate the exact nonzero structure which results from the kronecker outer product of left and</span><span class="s2">
</span><span class="s3">right </span><span class="apple-converted-space"> </span></p>
<p class="p1"><span class="s1">// d_nnz = diagonal nonzero structure, o_nnz = off-diagonal nonzero structure</span><span class="apple-converted-space"> </span><span class="s2">
</span><span class="apple-converted-space"><span style="color:#EAEAEA"> </span></span></p>
<p class="p3"><span class="s4">void</span><span class="s2"> </span><span class="s1">kronConvert_symbolic</span><span class="s2">(</span><span class="s5">const</span><span class="s2">
</span><span class="s4">Spmat</span><span class="s2"> &</span><span class="s1">left</span><span class="s2">,
</span><span class="s5">const</span><span class="s2"> </span><span class="s4">Spmat</span><span class="s2"> &</span><span class="s1">right</span><span class="s2">,
</span><span class="s4">Mat</span><span class="s2"> &</span><span class="s1">mat</span><span class="s2">,
</span><span class="s4">PetscInt</span><span class="s2">* </span><span class="s1">d_nnz</span><span class="s2">,
</span><span class="s4">PetscInt</span><span class="s1">* </span><span class="s6">o_nnz</span><span class="s1">)</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="s1">{</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">size_t</span><span class="s1">
</span><span class="s6">rightRowSize</span><span class="s1"> = right.size(1); </span>
<span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">size_t</span><span class="s1">
</span><span class="s6">rightColSize</span><span class="s1"> = right.size(2); </span>
<span class="apple-converted-space"> </span></p>
<p class="p4"><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">PetscInt</span><span class="s1">
</span><span class="s6">Istart</span><span class="s1">,</span><span class="s6">Iend</span><span class="s1">;
</span><span class="s3">// rows owned by current processor </span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">PetscInt</span><span class="s1">
</span><span class="s6">Jstart</span><span class="s1">,</span><span class="s6">Jend</span><span class="s1">;
</span><span class="s3">// cols owned by current processor </span><span class="apple-converted-space"> </span></p>
<p class="p4"><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s3">// allocate space for mat</span><span class="apple-converted-space"><span style="color:#828282"> </span></span><span class="s1">
</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s1">MatGetOwnershipRange(mat,&Istart,&Iend);
</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s1">MatGetOwnershipRangeColumn(mat,&Jstart,&Jend);
</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">PetscInt</span><span class="s1">
</span><span class="s6">m</span><span class="s1"> = Iend - Istart;</span><span class="apple-converted-space"> </span></p>
<p class="p4"><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s5">for</span><span class="s1"> (</span><span class="s4">int</span><span class="s1">
</span><span class="s6">ii</span><span class="s1">=0; ii<m; ii++) { d_nnz[ii] = 0; }</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s5">for</span><span class="s1"> (</span><span class="s4">int</span><span class="s1">
</span><span class="s6">ii</span><span class="s1">=0; ii<m; ii++) { o_nnz[ii] = 0; }</span><span class="apple-converted-space"> </span></p>
<p class="p4"><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s3">// iterate over only nnz entries
</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s7">Spmat</span><span class="s1">::</span><span class="s4">const_row_iter</span><span class="s1">
</span><span class="s6">IiL</span><span class="s1">,</span><span class="s6">IiR</span><span class="s1">;
</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s7">Spmat</span><span class="s1">::</span><span class="s4">const_col_iter</span><span class="s1">
</span><span class="s6">JjL</span><span class="s1">,</span><span class="s6">JjR</span><span class="s1">;
</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">double</span><span class="s1">
</span><span class="s6">valL</span><span class="s1">=0, </span><span class="s6">valR</span><span class="s1">=0,
</span><span class="s6">val</span><span class="s1">=0;</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">PetscInt</span><span class="s1">
</span><span class="s6">row</span><span class="s1">,</span><span class="s6">col</span><span class="s1">;</span><span class="apple-converted-space"> </span></p>
<p class="p2"><span class="apple-converted-space"> </span><span class="s4">size_t</span><span class="s1">
</span><span class="s6">rowL</span><span class="s1">,</span><span class="s6">colL</span><span class="s1">,</span><span class="s6">rowR</span><span class="s1">,</span><span class="s6">colR</span><span class="s1">;</span><span class="apple-converted-space">
</span></p>
<p class="p4"><span class="apple-converted-space"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#828282">// loop over all values in left </span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">for</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> (IiL=left._mat.begin(); IiL!=left._mat.end(); IiL++) { <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">for</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> (JjL=(IiL->second).begin(); JjL!=(IiL->second).end(); JjL++) { <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> rowL = IiL->first; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> colL = JjL->first; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> valL = JjL->second; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">if</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> (valL==0) {
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">continue</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">; } <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#828282">// loop over all values in right
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">for</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> (IiR=right._mat.begin(); IiR!=right._mat.end(); IiR++) { <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">for</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> (JjR=(IiR->second).begin(); JjR!=(IiR->second).end(); JjR++) { <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> rowR = IiR->first; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> colR = JjR->first; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> valR = JjR->second; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#828282">// the new values and coordinates for the product matrix
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> </span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#828282"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> val = valL*valR; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> row = rowL*rightRowSize + rowR; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> col = colL*rightColSize + colR; <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#75A24D">PetscInt</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#CED074">ii</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> = row - Istart;
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#828282">// array index for d_nnz and o_nnz
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">if</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> (val!=0 && row >= Istart && row < Iend && col >= Jstart && col < Jend) { d_nnz[ii]++; \<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">} <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">
</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#77CDFF">if</span><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> ( (val!=0 && row >= Istart && row < Iend) && (col < Jstart || col >= Jend) ) { o_nnz[i\<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">i]++; } <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> } <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> } <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> } <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA"> } <o:p></o:p></span></p>
<p class="MsoNormal" style="background:#1D1D1D"><span style="font-size:11.5pt;font-family:"Andale Mono";color:#EAEAEA">} <o:p></o:p></span></p>
<p class="p4"><span class="apple-converted-space"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal">Thank you,</p>
<p class="MsoNormal">Yuyun</p>
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