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</o:shapelayout></xml><![endif]--></head><body lang=DA link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> petsc-users-bounces@mcs.anl.gov [mailto:petsc-users-bounces@mcs.anl.gov] <b>On Behalf Of </b>Matthew Knepley<br><b>Sent:</b> Wednesday, November 30, 2011 5:05 PM<br><b>To:</b> PETSc users list<br><b>Subject:</b> Re: [petsc-users] newbie question on the parallel allocation of matrices<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>On Wed, Nov 30, 2011 at 9:59 AM, Treue, Frederik <<a href="mailto:frtr@risoe.dtu.dk">frtr@risoe.dtu.dk</a>> wrote:<o:p></o:p></p><div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi everyone,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>Caveat: I have just started using petsc, so the answer to my question may very well be fairly trivial.</span><o:p></o:p></p></div></div></blockquote><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>See <a href="http://www.mcs.anl.gov/petsc/petsc-dev/src/snes/examples/tutorials/ex5.c.html">SNES ex5</a> for the right way to interact with the DMDA. We will preallocate the matrix for you and allow<o:p></o:p></p></div><div><p class=MsoNormal>you to set values using a stencil.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> Matt<o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>OK, but that example seems to assume that you wish to connect only one matrix (the Jacobian) to a DA – I wish to specify many and I think I found this done in ksp ex39, is that example doing anything deprecated or will that work for me, e.g. with the various basic mat routines (matmult, matAXPY etc.) in a multiprocessor setup?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> <o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>I’m trying to run the following bits of code:</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_BOX,10,10,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>[snip]</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US>MatCreate(PETSC_COMM_WORLD,&((*FD).ddx));</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> MatSetSizes((*FD).ddx,PETSC_DECIDE,PETSC_DECIDE,100,100);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> </span>MatSetFromOptions((*FD).ddx);<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> for (i=0;i<10;i++) {<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <span lang=EN-US>col[0]=i*10;col[1]=i*10+1; row[0]=i*10;</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> val[0]=1;val[1]=1;</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> MatSetValues((*FD).ddx,1,row,2,col,val,INSERT_VALUES);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> for (j=1;j<10-1;j++) {<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> col[0]=i*10+j-1;col[1]=i*10+j+1; row[0]=i*10+j;<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <span lang=EN-US>val[0]=-1;val[1]=1;</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> MatSetValues((*FD).ddx,1,row,2,col,val,INSERT_VALUES);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> }</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> col[0]=i*10+10-2;col[1]=i*10+10-1; row[0]=i*10+10-1;</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> val[0]=-1;val[1]=-1;</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> MatSetValues((*FD).ddx,1,row,2,col,val,INSERT_VALUES);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> }</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> MatAssemblyBegin((*FD).ddx,MAT_FINAL_ASSEMBLY);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US>MatAssemblyEnd((*FD).ddx,MAT_FINAL_ASSEMBLY);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'>MatScale((*FD).ddx,1/(2*(1/9)));<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'>[snip]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'> DMCreateGlobalVector(da,&tmpvec2);<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'> <span lang=EN-US>VecSet(tmpvec2,1.0);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> VecAssemblyBegin(tmpvec2);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> VecAssemblyEnd(tmpvec2);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> </span>DMCreateGlobalVector(da,&tmpvec3);<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'> VecSet(tmpvec3,1.0);<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'> <span lang=EN-US>VecAssemblyBegin(tmpvec3);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> VecAssemblyEnd(tmpvec3);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> MatView((*FD).ddx,PETSC_VIEWER_STDOUT_WORLD);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> VecView(tmpvec2,PETSC_VIEWER_STDOUT_WORLD);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> MatMult((*FD).ddx,tmpvec2,tmpvec3);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> VecView(tmpvec3,PETSC_VIEWER_STDOUT_WORLD);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> int tid,first,last;</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> MPI_Comm_rank(PETSC_COMM_WORLD, &tid);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> sleep(1);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> MatGetOwnershipRange((*FD).ddx,&first,&last);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> printf("rank: %d,first: %d,last: %d\n",tid,first,last);</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US>When running it on a single processor, everything works as expected, see attached file seqRes</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US>However when running with 4 processors (mpirun –np 4 ./progname) I get the output in mpiRes. Notice that there really is a difference, its not just a surprising division of points between the processes – I checked this with PETSC_VIEWER_DRAW_WORLD. How come? I notice that although in the end each process postulates that it has 25 rows, the result of matview is</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US>Matrix Object: 1 MPI processes</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US>type: mpiaij</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US>Is this OK? And if not, what am I doing wrong, presumably in the matrix allocation code?</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:4.5pt'><span lang=EN-US> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>---<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>yours sincerily<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Frederik Treue<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></blockquote></div><p class=MsoNormal><br><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener<o:p></o:p></p></div></body></html>