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<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Folks:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">I'm developing an application using the SNES, and overall it's working great, as many of our other PETSc-based projects. But, I'm having a problem related to (presumably)
pre-allocation, block matrices and SNES.<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Without going into details about the actual problem we are solving, here are the symptoms/characteristics/behavior.<o:p></o:p></span></p>
</div>
<div>
<ul type="disc">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">For the SNES Jacobian, I'm using MatCreateBAIJ for a block size=3, and letting "PETSC_DECIDE" the partitioning. Actual call is:
<o:p></o:p></span></li></ul>
<ul type="disc">
<ul type="circle">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">ierr = MatCreateBAIJ(PETSC_COMM_WORLD, bs, PETSC_DECIDE, PETSC_DECIDE, (int)3 * numNodesSAM, (int)3 * numNodesSAM, PETSC_DEFAULT, NULL, PETSC_DEFAULT, NULL, &J);<o:p></o:p></span></li></ul>
</ul>
<ul type="disc">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">When registering the SNES jacobian function, I set the B and J matrices to be the same.
<o:p></o:p></span></li></ul>
<ul type="disc">
<ul type="circle">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ierr = SNESSetJacobian(snes, J, J, SAMformSNESJ, (void *)this); CHKERRQ(ierr);<o:p></o:p></span></li></ul>
</ul>
<ul type="disc">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">I can either let PETSc figure out the allocation structure:
<o:p></o:p></span></li></ul>
<ul type="disc">
<ul type="circle">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">ierr = MatMPIBAIJSetPreallocation(J, bs, PETSC_DEFAULT, NULL,PETSC_DEFAULT, NULL);<o:p></o:p></span></li></ul>
</ul>
<ul type="disc">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> or, do it myself, since I know the fill pattern,
<o:p></o:p></span></li></ul>
<ul type="disc">
<ul type="circle">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo1">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">ierr = MatMPIBAIJSetPreallocation(J, bs, d_nz_dum,&d_nnz[0],o_nz_dum,&o_nnz[0]);<o:p></o:p></span></li></ul>
</ul>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">The symptoms/problems are as follows:<o:p></o:p></span></p>
</div>
<div>
<ul type="disc">
<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo2">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Whether I do preallocation or not, the "setup" time is pretty long. It might take 2 minutes before SNES starts doing its thing. After this setup, convergence and speed is great. But this first
phase takes a long time. I'm assuming this has to be related to some poor preallocation setup so it's doing tons of mallocs where it’s not needed.<o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo2">
<span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">If I <b><u>don't</u></b> call my Jacobian formulation before calling SNESSolve, I get a segmentation violation in a PETSc routine. (If I DO call my Jacobian first, things work great, although
slow for the setup phase.) Here's a snippet of the traceback:<o:p></o:p></span></li></ul>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">0 0x00000000009649fc in MatMultAdd_SeqBAIJ_3 (A=<optimized out>,
<br>
xx=0x3a525b0, yy=0x3a531b0, zz=0x3a531b0)<br>
at /home/jstutts/Downloads/petsc-3.11.1/src/mat/impls/baij/seq/baij2.c:1424<br>
#1 0x00000000006444cb in MatMult_MPIBAIJ (A=0x15da340, xx=0x3a542a0, <br>
yy=0x3a531b0)<br>
at /home/jstutts/Downloads/petsc-3.11.1/src/mat/impls/baij/mpi/mpibaij.c:1380<br>
#2 0x00000000005b2c0f in MatMult (mat=0x15da340, x=x@entry=0x3a542a0, <br>
y=y@entry=0x3a531b0)<br>
at /home/jstutts/Downloads/petsc-3.11.1/src/mat/interface/matrix.c:2396<br>
#3 0x0000000000c61f2e in PCApplyBAorAB (pc=0x1ce78c0, side=PC_LEFT, <br>
x=0x3a542a0, y=y@entry=0x3a548a0, work=0x3a531b0)<br>
at /home/jstutts/Downloads/petsc-3.11.1/src/ksp/pc/interface/precon.c:690<br>
#4 0x0000000000ccb36b in KSP_PCApplyBAorAB (w=<optimized out>, y=0x3a548a0, <br>
x=<optimized out>, ksp=0x1d44d50)<br>
at /home/jstutts/Downloads/petsc-3.11.1/include/petsc/private/kspimpl.h:309<br>
#5 KSPGMRESCycle (itcount=itcount@entry=0x7fffffffc02c, <br>
ksp=ksp@entry=0x1d44d50)<br>
at /home/jstutts/Downloads/petsc-3.11.1/src/ksp/ksp/impls/gmres/gmres.c:152<br>
#6 0x0000000000ccbf6f in KSPSolve_GMRES (ksp=0x1d44d50)<br>
at /home/jstutts/Downloads/petsc-3.11.1/src/ksp/ksp/impls/gmres/gmres.c:237<br>
#7 0x00000000007dc193 in KSPSolve (ksp=0x1d44d50, b=b@entry=0x1d41c70, <br>
x=x@entry=0x1cebf40)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">I apologize if I’ve missed something in the documentation or examples, but I can’t seem to figure this one out. The “setup” seems
to take too long, and from my previous experiences with PETSc, this is due to a poor preallocation strategy.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Any and all help is appreciated!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy">-----------------------------------------------------------------------</span><span style="color:navy"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">William J. Coirier, Ph.D.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">Director, Aerosciences and Engineering Analysis Branch<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">Advanced Concepts Development and Test Division<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">Kratos Defense and Rocket Support Services<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">4904 Research Drive<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">Huntsville, AL 35805<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">256-327-8170<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy">256-327-8120 (fax)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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