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<p class="MsoNormal"><span style="color:black">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">I am doing calculations with version 3.12.0 of PETSc.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Using the finite-element method, I solve the Maxwell equations on the interior of a 3D domain, coupled with boundary condition auxiliary equations on the boundary of the domain. The auxiliary equations employ auxiliary
variables g.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">For ease of implementation of element matrix assembly, the auxiliary variables g are defined on the entire domain. However, only the basis functions for g with nonzero value at the boundary give nonzero entries
in the system matrix.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">The element matrices hence have the structure<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">[ A B; C D]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">at the boundary.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">In the interior the element matrices have the structure<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">[A 0; 0 0].<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">The degrees of freedom in the system matrix can be ordered by element [u_e1 g_e1 u_e2 g_e2 …] or by parallel process [u_p1 g_p1 u_p2 g_p2 …].<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">To solve the system matrix, I need to filter out zero rows and columns:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">error = MatFindNonzeroRows(stiffnessMatrix, &nonzeroRows);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">CHKERRABORT(PETSC_COMM_WORLD, error);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">error = MatCreateSubMatrix(stiffnessMatrix, nonzeroRows, nonzeroRows, MAT_INITIAL_MATRIX, &stiffnessMatrixSubMatrix);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">CHKERRABORT(PETSC_COMM_WORLD, error);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">I solve the system matrix in parallel on multiple nodes connected with InfiniBand.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">The problem is that the MUMPS solver frequently (nondeterministically) hangs during KSPSolve() (after KSPSetUp() is completed).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Running with the options -ksp_view and -info the last printed statement is:<o:p></o:p></span></p>
<p class="p1"><span class="s1">[0] VecScatterCreate_SF(): Using StarForest for vector scatter</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:black">In the calculations where the program does not hang, the calculated solution is correct. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">The problem doesn’t occur for calculations on a single node, or for calculations with the SuperLU solver (but SuperLU will not allow calculations that are as large).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">The problem also doesn’t seem to occur for small problems.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">The problem doesn’t occur either when I put ones on the diagonal, but this is computationally expensive:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">error = MatFindZeroRows(stiffnessMatrix, &zeroRows);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">CHKERRABORT(PETSC_COMM_WORLD, error);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">error = MatZeroRowsColumnsIS(stiffnessMatrix, zeroRows, diagEntry, PETSC_IGNORE, PETSC_IGNORE);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">CHKERRABORT(PETSC_COMM_WORLD, error);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Would you have any ideas on what I could check?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Sjoerd<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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