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Yes, this works. Thanks a lot for your help.</div>
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Regards,</div>
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Edwin</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Barry Smith <bsmith@petsc.dev><br>
<b>Sent:</b> Wednesday, November 6, 2024 7:03 PM<br>
<b>To:</b> Weide, Edwin van der (UT-ET) <e.t.a.vanderweide@utwente.nl><br>
<b>Cc:</b> petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b> Re: [petsc-users] Matrix free SNES with user provided matrix vector product and preconditioner operation</font>
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You need to provide a callback function. Why? Otherwise your MatShell and PCshell have no way of knowing at what location the Jacobian is suppose to be evaluated at (in a matrix free way). That is the x for which J(x) is used.
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<div> Normally one puts the x into the application context of <span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif">mJac and accesses it every time the matmult is called. Similarly it needs to be accessed in </span><font face="Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif"><span style="">application
of your preconditioner.</span></font></div>
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<div>On Nov 6, 2024, at 12:01 PM, Weide, Edwin van der (UT-ET) <e.t.a.vanderweide@utwente.nl> wrote:</div>
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Barry,</div>
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If I do that, I get the following error</div>
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[0]PETSC ERROR: ------------------------------------------------------------------------</div>
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[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</div>
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[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</div>
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[0]PETSC ERROR: or see<span class="x_Apple-converted-space"> </span><a href="https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!dfJ_L4Ay2QlfGz0JU6uAfD7Zy_6a7x9D0bisHMG1T53fTy_gWL3Q8fzzLvWZ_TBK37FFmDYerLywkFOLtMnU1rISfF_VA3gxsDTm$" originalsrc="https://petsc.org/release/faq/#valgrind" shash="wFvUi8hdbkxZDEAndTEkSYVn5dDq78nzylp5SZxrOmUqOGVZIahk6fDUEbUG4FTFtZBp2X6YWuXdnhbUPzww7HCGgSNe2k8r/ZOEFkxTvqDCRopIySCSQGZGBKQlK/yfTbXSJyXDtmGyEuDm1+cb3FygRjYwmpYoNOVGgNwR4nE=">https://petsc.org/release/faq/#valgrind</a><span class="x_Apple-converted-space"> </span>and<span class="x_Apple-converted-space"> </span><a href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!dfJ_L4Ay2QlfGz0JU6uAfD7Zy_6a7x9D0bisHMG1T53fTy_gWL3Q8fzzLvWZ_TBK37FFmDYerLywkFOLtMnU1rISfF_VAwRW4W44$" originalsrc="https://petsc.org/release/faq/" shash="zmsWz26UayrClw/XfEeZSWqpBR0gBDo/J68Bbhn3dVV6/4sgHGrePRAv8YlR1RmQrNX39vcR+0N1yOUdm2506miJgwHzjtmtagM3Kl5dzGddNipxsR+Hp+S1+lsUn9qVyGfwnj8V/+bopfAh5GsR+JLBaWDF2vp6zNV67XzP+3o=">https://petsc.org/release/faq/</a></div>
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[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------</div>
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[0]PETSC ERROR: The line numbers in the error traceback are not always exact.</div>
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[0]PETSC ERROR: #1 SNES callback Jacobian</div>
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[0]PETSC ERROR: #2 SNESComputeJacobian() at /home/vdweide/petsc/src/snes/interface/snes.c:2966</div>
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[0]PETSC ERROR: #3 SNESSolve_NEWTONLS() at /home/vdweide/petsc/src/snes/impls/ls/ls.c:218</div>
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[0]PETSC ERROR: #4 SNESSolve() at /home/vdweide/petsc/src/snes/interface/snes.c:4841</div>
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[0]PETSC ERROR: #5 SolveCurrentStage() at SolverClass.cpp:502</div>
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[0]PETSC ERROR: #6 main() at Condensation.cpp:20</div>
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So SNES tries to call the call back function for the Jacobian, but that is not provided. Hence the failure.</div>
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Regards,</div>
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Edwin</div>
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<font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span class="x_Apple-converted-space"> </span>Barry Smith <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</a>><br>
<b>Sent:</b><span class="x_Apple-converted-space"> </span>Wednesday, November 6, 2024 5:52 PM<br>
<b>To:</b><span class="x_Apple-converted-space"> </span>Weide, Edwin van der (UT-ET) <<a href="mailto:e.t.a.vanderweide@utwente.nl">e.t.a.vanderweide@utwente.nl</a>><br>
<b>Cc:</b><span class="x_Apple-converted-space"> </span><a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><span class="x_Apple-converted-space"> </span><<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b><span class="x_Apple-converted-space"> </span>Re: [petsc-users] Matrix free SNES with user provided matrix vector product and preconditioner operation</font>
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Just pass <span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif">mJac, mJac instead of </span><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif">mJac, nullptr
and it will be happy. In your case, the second </span><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif">mJac won't be used in your preconditioner it is just a place holder so other parts of SNES won't try
to create a matrix.</span>
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<div><font face="Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif"><span> Barry</span></font></div>
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<div>On Nov 6, 2024, at 11:36 AM, Weide, Edwin van der (UT-ET) via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> wrote:</div>
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Hi,</div>
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I am trying to solve a nonlinear problem with matrix-free SNES where I would like to provide both the matrix vector product and the preconditioner myself. For that purpose, I use the following construction.</div>
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// Set up the matrix free evaluation of the Jacobian times a vector</div>
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// by setting the appropriate function in snes.</div>
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PetscCall(MatCreateShell(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE,</div>
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nEqns, nEqns, this, &mJac));</div>
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PetscCall(MatShellSetOperation(mJac, MATOP_MULT,</div>
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(void (*)(void))JacobianTimesVector));</div>
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PetscCall(SNESSetJacobian(mSnes, mJac, nullptr, nullptr, nullptr));</div>
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// Set the function to be used as preconditioner for the krylov solver.</div>
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KSP ksp;</div>
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PC pc;</div>
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PetscCall(SNESGetKSP(mSnes, &ksp));</div>
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PetscCall(KSPGetPC(ksp, &pc));</div>
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PetscCall(PCSetType(pc, PCSHELL));</div>
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PetscCall(PCSetApplicationContext(pc, this));</div>
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PetscCall(PCShellSetApply(pc, Preconditioner));</div>
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For small problems this construction works, and it does exactly what I expect it to do. However, when I increase the problem size, I get a memory allocation failure in SNESSolve, because it looks like SNES attempts to allocate memory for a full dense matrix
for the preconditioner, which is not used. This is the call stack when the error occurs.</div>
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[0]PETSC ERROR: #1 PetscMallocAlign() at /home/vdweide/petsc/src/sys/memory/mal.c:53</div>
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[0]PETSC ERROR: #2 PetscTrMallocDefault() at /home/vdweide/petsc/src/sys/memory/mtr.c:175</div>
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[0]PETSC ERROR: #3 PetscMallocA() at /home/vdweide/petsc/src/sys/memory/mal.c:421</div>
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[0]PETSC ERROR: #4 MatSeqDenseSetPreallocation_SeqDense() at /home/vdweide/petsc/src/mat/impls/dense/seq/dense.c:3357</div>
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[0]PETSC ERROR: #5 MatSeqDenseSetPreallocation() at /home/vdweide/petsc/src/mat/impls/dense/seq/dense.c:3338</div>
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[0]PETSC ERROR: #6 MatDuplicateNoCreate_SeqDense() at /home/vdweide/petsc/src/mat/impls/dense/seq/dense.c:372</div>
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[0]PETSC ERROR: #7 MatDuplicate_SeqDense() at /home/vdweide/petsc/src/mat/impls/dense/seq/dense.c:399</div>
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[0]PETSC ERROR: #8 MatDuplicate() at /home/vdweide/petsc/src/mat/interface/matrix.c:4964</div>
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[0]PETSC ERROR: #9 DMCreateMatrix_Shell() at /home/vdweide/petsc/src/dm/impls/shell/dmshell.c:195</div>
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[0]PETSC ERROR: #10 DMCreateMatrix() at /home/vdweide/petsc/src/dm/interface/dm.c:1501</div>
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[0]PETSC ERROR: #11 SNESSetUpMatrices() at /home/vdweide/petsc/src/snes/interface/snes.c:794</div>
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[0]PETSC ERROR: #12 SNESSetUp_NEWTONLS() at /home/vdweide/petsc/src/snes/impls/ls/ls.c:290</div>
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[0]PETSC ERROR: #13 SNESSetUp() at /home/vdweide/petsc/src/snes/interface/snes.c:3395</div>
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[0]PETSC ERROR: #14 SNESSolve() at /home/vdweide/petsc/src/snes/interface/snes.c:4831</div>
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[0]PETSC ERROR: #15 SolveCurrentStage() at SolverClass.cpp:502</div>
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In the function SNESSetUpMatrices the source looks as follows</div>
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784 } else if (!snes->jacobian_pre) {</div>
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785 PetscDS prob;</div>
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786 Mat J, B;</div>
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787 PetscBool hasPrec = PETSC_FALSE;</div>
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788 </div>
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789 J = snes->jacobian;</div>
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790 PetscCall(DMGetDS(dm, &prob));</div>
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791 if (prob) PetscCall(PetscDSHasJacobianPreconditioner(prob, &hasPrec));</div>
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792 if (J) PetscCall(PetscObjectReference((PetscObject)J));</div>
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793 else if (hasPrec) PetscCall(DMCreateMatrix(snes->dm, &J));</div>
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794 PetscCall(DMCreateMatrix(snes->dm, &B));</div>
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795 PetscCall(SNESSetJacobian(snes, J ? J : B, B, NULL, NULL));</div>
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796 PetscCall(MatDestroy(&J));</div>
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797 PetscCall(MatDestroy(&B));</div>
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798 }</div>
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It looks like in line 794 it is attempted to create the preconditioner, because it was (intentionally) not provided. </div>
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Hence my question. Is it possible to use matrix-free SNES with a user provided matrix vector product (via MatShell) and a user provided preconditioner operation without SNES allocating the memory for a dense matrix? If so, what do I need to change in the construction
above to make it work?<br>
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If needed, I can provide the source code for which this problem occurs.</div>
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Thanks,</div>
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Edwin</div>
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</i>Edwin van der Weide
Department of Mechanical Engineering
University of Twente
Enschede, the Netherlands</div></pre>
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