Dear Jed, The following is the result with the options you told me. The iteration has converged, while converged at a wrong solution, compared to the result from LU.
tutorials]$ time ./ex78 -Ain A_phi -rhs rhs_phi -solu solu_phi -noshift -pc_type hypre -pc_hypre_type parasails -ksp_gmres_restart 600 -ksp_rtol 1e-7 -ksp_typ gmres -ksp_monitor_true_residual -ksp_converged_reason Read matrix in ascii format ... m: 288399, n: 288399, nz: 4023176 read A completed rowNumber[0] = 13 rowNumber[1] = 13 rowNumber[2] = 19 read A is complete ! Read rhs in ascii format ... Read exact solution in ascii format ... 0 KSP preconditioned resid norm 1.311815748108e+00 true resid norm 3.838432566849e-03 ||r(i)||/||b|| 1.000000000000e+00 1 KSP preconditioned resid norm 5.507600629359e-01 true resid norm 1.878066463331e-03 ||r(i)||/||b|| 4.892795250727e-01 2 KSP preconditioned resid norm 4.013507277599e-01 true resid norm 1.785692106749e-03 ||r(i)||/||b|| 4.652138797934e-01 3 KSP preconditioned resid norm 3.186589484171e-01 true resid norm 1.939928539000e-03 ||r(i)||/||b|| 5.053960191341e-01 4 KSP preconditioned resid norm 2.533816267053e-01 true resid norm 2.182716525094e-03 ||r(i)||/||b|| 5.686478756839e-01 5 KSP preconditioned resid norm 1.956749847727e-01 true resid norm 2.436511231157e-03 ||r(i)||/||b|| 6.347672360328e-01 6 KSP preconditioned resid norm 1.489551919079e-01 true resid norm 2.625495747280e-03 ||r(i)||/||b|| 6.840020507214e-01 7 KSP preconditioned resid norm 1.129706022530e-01 true resid norm 2.726727688051e-03 ||r(i)||/||b|| 7.103753004809e-01 8 KSP preconditioned resid norm 8.528153693722e-02 true resid norm 2.764872691683e-03 ||r(i)||/||b|| 7.203129515839e-01 9 KSP preconditioned resid norm 6.419522418091e-02 true resid norm 2.765551151077e-03 ||r(i)||/||b|| 7.204897058665e-01 10 KSP preconditioned resid norm 4.793073337207e-02 true resid norm 2.754803244091e-03 ||r(i)||/||b|| 7.176896288040e-01 11 KSP preconditioned resid norm 3.590594904610e-02 true resid norm 2.738481920714e-03 ||r(i)||/||b|| 7.134375485361e-01 12 KSP preconditioned resid norm 2.683482240096e-02 true resid norm 2.722031760807e-03 ||r(i)||/||b|| 7.091519033880e-01 13 KSP preconditioned resid norm 2.001207136261e-02 true resid norm 2.709429246945e-03 ||r(i)||/||b|| 7.058686585627e-01 14 KSP preconditioned resid norm 1.493908729876e-02 true resid norm 2.699791991674e-03 ||r(i)||/||b|| 7.033579318265e-01 15 KSP preconditioned resid norm 1.111558666088e-02 true resid norm 2.692890954089e-03 ||r(i)||/||b|| 7.015600527536e-01 16 KSP preconditioned resid norm 8.272119255509e-03 true resid norm 2.688069519102e-03 ||r(i)||/||b|| 7.003039580057e-01 17 KSP preconditioned resid norm 6.143976425601e-03 true resid norm 2.684895702336e-03 ||r(i)||/||b|| 6.994771057136e-01 18 KSP preconditioned resid norm 4.563685459707e-03 true resid norm 2.682859292253e-03 ||r(i)||/||b|| 6.989465740324e-01 19 KSP preconditioned resid norm 3.394656398417e-03 true resid norm 2.681459888330e-03 ||r(i)||/||b|| 6.985819971124e-01 20 KSP preconditioned resid norm 2.518916365228e-03 true resid norm 2.680609739005e-03 ||r(i)||/||b|| 6.983605136526e-01 21 KSP preconditioned resid norm 1.872307188353e-03 true resid norm 2.680081243394e-03 ||r(i)||/||b|| 6.982228283859e-01 22 KSP preconditioned resid norm 1.390334828536e-03 true resid norm 2.679742748684e-03 ||r(i)||/||b|| 6.981346427259e-01 23 KSP preconditioned resid norm 1.034606694934e-03 true resid norm 2.679535108562e-03 ||r(i)||/||b|| 6.980805476966e-01 24 KSP preconditioned resid norm 7.710134967260e-04 true resid norm 2.679397134577e-03 ||r(i)||/||b|| 6.980446022989e-01 25 KSP preconditioned resid norm 5.725407938260e-04 true resid norm 2.679329449922e-03 ||r(i)||/||b|| 6.980269688889e-01 26 KSP preconditioned resid norm 4.272990427118e-04 true resid norm 2.679284171589e-03 ||r(i)||/||b|| 6.980151728414e-01 27 KSP preconditioned resid norm 3.181341598383e-04 true resid norm 2.679247206576e-03 ||r(i)||/||b|| 6.980055426050e-01 28 KSP preconditioned resid norm 2.368729933003e-04 true resid norm 2.679233163958e-03 ||r(i)||/||b|| 6.980018841799e-01 29 KSP preconditioned resid norm 1.766017339700e-04 true resid norm 2.679224053276e-03 ||r(i)||/||b|| 6.979995106376e-01 30 KSP preconditioned resid norm 1.313377419946e-04 true resid norm 2.679217016981e-03 ||r(i)||/||b|| 6.979976775210e-01 31 KSP preconditioned resid norm 9.789603459870e-05 true resid norm 2.679213290696e-03 ||r(i)||/||b|| 6.979967067380e-01 32 KSP preconditioned resid norm 7.275708495896e-05 true resid norm 2.679210423371e-03 ||r(i)||/||b|| 6.979959597340e-01 33 KSP preconditioned resid norm 5.412802491776e-05 true resid norm 2.679209810847e-03 ||r(i)||/||b|| 6.979958001573e-01 34 KSP preconditioned resid norm 4.026672785271e-05 true resid norm 2.679209362635e-03 ||r(i)||/||b|| 6.979956833876e-01 35 KSP preconditioned resid norm 2.990907253308e-05 true resid norm 2.679208426592e-03 ||r(i)||/||b|| 6.979954395269e-01 36 KSP preconditioned resid norm 2.226822676398e-05 true resid norm 2.679208136434e-03 ||r(i)||/||b|| 6.979953639342e-01 37 KSP preconditioned resid norm 1.654703590780e-05 true resid norm 2.679208182746e-03 ||r(i)||/||b|| 6.979953759996e-01 38 KSP preconditioned resid norm 1.229268254949e-05 true resid norm 2.679208209944e-03 ||r(i)||/||b|| 6.979953830852e-01 39 KSP preconditioned resid norm 9.149145951039e-06 true resid norm 2.679208050822e-03 ||r(i)||/||b|| 6.979953416303e-01 40 KSP preconditioned resid norm 6.813825018110e-06 true resid norm 2.679207932900e-03 ||r(i)||/||b|| 6.979953109089e-01 41 KSP preconditioned resid norm 5.075333494970e-06 true resid norm 2.679208029175e-03 ||r(i)||/||b|| 6.979953359907e-01 42 KSP preconditioned resid norm 3.770609781438e-06 true resid norm 2.679208069198e-03 ||r(i)||/||b|| 6.979953464175e-01 43 KSP preconditioned resid norm 2.808924777973e-06 true resid norm 2.679208000517e-03 ||r(i)||/||b|| 6.979953285246e-01 44 KSP preconditioned resid norm 2.094599249993e-06 true resid norm 2.679207985642e-03 ||r(i)||/||b|| 6.979953246492e-01 45 KSP preconditioned resid norm 1.559223301396e-06 true resid norm 2.679208018840e-03 ||r(i)||/||b|| 6.979953332981e-01 46 KSP preconditioned resid norm 1.160309778657e-06 true resid norm 2.679208029228e-03 ||r(i)||/||b|| 6.979953360044e-01 47 KSP preconditioned resid norm 8.638154916854e-07 true resid norm 2.679208013013e-03 ||r(i)||/||b|| 6.979953317800e-01 48 KSP preconditioned resid norm 6.436084879799e-07 true resid norm 2.679208008459e-03 ||r(i)||/||b|| 6.979953305937e-01 49 KSP preconditioned resid norm 4.797395939888e-07 true resid norm 2.679208018385e-03 ||r(i)||/||b|| 6.979953331796e-01 50 KSP preconditioned resid norm 3.573839482305e-07 true resid norm 2.679208020910e-03 ||r(i)||/||b|| 6.979953338374e-01 51 KSP preconditioned resid norm 2.662426448119e-07 true resid norm 2.679208017655e-03 ||r(i)||/||b|| 6.979953329896e-01 52 KSP preconditioned resid norm 1.984893339085e-07 true resid norm 2.679208016597e-03 ||r(i)||/||b|| 6.979953327137e-01 53 KSP preconditioned resid norm 1.484050273141e-07 true resid norm 2.679208018006e-03 ||r(i)||/||b|| 6.979953330809e-01 54 KSP preconditioned resid norm 1.106994152625e-07 true resid norm 2.679208019541e-03 ||r(i)||/||b|| 6.979953334807e-01 Linear solve converged due to CONVERGED_RTOL iterations 54 Accuracy of the soltuion on the solution from LU: | u -U_lu |_2 : 3321.15 Iteration number is : 54 Accuracy of the soltuion: | b - A*u |_2 : 0.004681 real 0m15.393s user 0m14.895s sys 0m0.251s > Message: 8 > > Date: Thu, 10 Nov 2011 14:10:14 +0000 > > From: Matthew Knepley <knepley at gmail.com> > > Subject: Re: [petsc-users] Any suggestion for this kinds of matrix? > > To: PETSc users list <petsc-users at mcs.anl.gov> > > Message-ID: > > < > CAMYG4GnxR2A+TcVzmsiOgD4wp4P+a_GRnPBg1YQKz7bJT5XiDw at mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > On Thu, Nov 10, 2011 at 1:48 PM, Bao Kai <paeanball at gmail.com> wrote: > > > > > Dear all, > > > > > > I have been trying with PETSC to solve the linear system from mixed > > finite > > > element method. > > > > > > The pattern of the matrix is as the following, but due to the irregular > > > boundary involved, the matrix A is not strictly symmetric. > > > > > > A dt* C > > > > > > C^T 0 > > > > > > As a result of the matrix pattern, the diagonal entries of the > > > bottom-right portion are all zero. > > > > > > I am just wondering if there are any suggestion of the type of the > solver > > > and preconditioner for this kinds of linear system? Thank you very > much. > > > > > > When I tried to solve the system with PETSC, I got the following > > > information. ( PCType PCASM, KSPType, KSPFGMRES ) > > > > > > > ILU is jsut not going to work for this type of matrix (a saddle point). I > > suggest reading about PCFIELDSPLIT. > > > > Matt > > > > > > > [0]PETSC ERROR: --------------------- Error Message > > > ------------------------------------ > > > [0]PETSC ERROR: Object is in wrong state! > > > [0]PETSC ERROR: Matrix is missing diagonal entry 288398! > > > [0]PETSC ERROR: > > > > ------------------------------------------------------------------------ > > > [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 4, Sun Oct 23 > 12:23:18 > > > CDT 2011 > > > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > > > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > [0]PETSC ERROR: See docs/index.html for manual pages. > > > [0]PETSC ERROR: > > > > ------------------------------------------------------------------------ > > > [0]PETSC ERROR: Libraries linked from > > > /home/baok/software/petsc-3.2-p4/arch-linux2-c-debug-withhypre/lib > > > [0]PETSC ERROR: Configure run at Thu Nov 10 11:49:03 2011 > > > [0]PETSC ERROR: Configure options --download-hypre=yes > > > [0]PETSC ERROR: > > > > ------------------------------------------------------------------------ > > > [0]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ_ilu0() line 1636 in > > > /home/baok/software/petsc-3.2-p4/src/mat/impls/aij/seq/aijfact.c > > > [0]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 1740 in > > > /home/baok/software/petsc-3.2-p4/src/mat/impls/aij/seq/aijfact.c > > > [0]PETSC ERROR: MatILUFactorSymbolic() line 6092 in > > > /home/baok/software/petsc-3.2-p4/src/mat/interface/matrix.c > > > [0]PETSC ERROR: PCSetUp_ILU() line 216 in > > > /home/baok/software/petsc-3.2-p4/src/ksp/pc/impls/factor/ilu/ilu.c > > > [0]PETSC ERROR: PCSetUp() line 819 in > > > /home/baok/software/petsc-3.2-p4/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: KSPSetUp() line 260 in > > > /home/baok/software/petsc-3.2-p4/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: PCSetUpOnBlocks_ASM() line 339 in > > > /home/baok/software/petsc-3.2-p4/src/ksp/pc/impls/asm/asm.c > > > [0]PETSC ERROR: PCSetUpOnBlocks() line 852 in > > > /home/baok/software/petsc-3.2-p4/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in > > > /home/baok/software/petsc-3.2-p4/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: KSPSolve() line 380 in > > > /home/baok/software/petsc-3.2-p4/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: main() line 261 in > src/ksp/ksp/examples/tutorials/ex78.c > > > > > > > > > Best Regards, > > > Kai > > > > > > > > > > > > -- > > What most experimenters take for granted before they begin their > > experiments is infinitely more interesting than any results to which > their > > experiments lead. > > -- Norbert Wiener > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > > > http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111110/2ea2b385/attachment.htm > > > > > > > ------------------------------ > > > > _______________________________________________ > > petsc-users mailing list > > petsc-users at mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/petsc-users > > > > > > End of petsc-users Digest, Vol 35, Issue 29 > > ******************************************* > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111110/da069f92/attachment-0001.htm > > > > ------------------------------ > > Message: 2 > Date: Thu, 10 Nov 2011 14:49:55 -0600 > From: Jed Brown <jedbrown at mcs.anl.gov> > Subject: Re: [petsc-users] Any suggestion for this kinds of matrix? > To: PETSc users list <petsc-users at mcs.anl.gov> > Message-ID: > <CAM9tzSkW7PZaBLH_sXpxToYv6x3seupTQcY+sPj=fHc_ax-AjA at mail.gmail.com > > > Content-Type: text/plain; charset="utf-8" > > On Thu, Nov 10, 2011 at 14:45, Bao Kai <paeanball at gmail.com> wrote: > > > PCFIELDSPLIT seems a little more complex, I will try that. > > > > I tried some different preconditioners, only lu can get right results. > > > > With some pc, some wrong results can be obtained, such as the following > > one. > > > > tutorials]$ time ./ex78 -Ain A_in -rhs rhs -solu solu -noshift -pc_type > > hypre -pc_hypre_type parasails -ksp_gmres_restart 600 -ksp_rtol 1e-5 > > -ksp_typ gmres > > > > Always run with -ksp_monitor_true_residual -ksp_converged_reason when > checking whether a preconditioner is working. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111110/3d5e1de6/attachment-0001.htm > > > > ------------------------------ > > Message: 3 > Date: Thu, 10 Nov 2011 22:11:01 -0700 > From: Xiang Hao <haoxiang at yahoo.cn> > Subject: [petsc-users] Problem with including petscdmda.h > To: PETSc users list <petsc-users at mcs.anl.gov> > Message-ID: > <CAL-Bv1oxfJhXrrxJxGz1+mEGbnP7fRREGHpqsyB+rk0jTfpFCw at mail.gmail.com > > > Content-Type: text/plain; charset="windows-1252" > > Hi, > > I have a question about petscdmda.h. > > I have a program using PETSc, which is running well. Now I just add a new > line #include <petscdmda.h> in my code and get the following error. I don't > understand what's going on here. Any help? > > > ------------------------------------------------------------------------------------------------------------- > In file included from /home/sci/hao/software/PETSc/include/petscdmda.h:4:0, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.h:18, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.cxx:9: > /home/sci/hao/software/PETSc/include/petscdm.h:27:8: error: ?PetscClassId? > does not name a type > /home/sci/hao/software/PETSc/include/petscdm.h:48:8: error: ?PetscBool? > does not name a type > /home/sci/hao/software/PETSc/include/petscdm.h:120:55: error: ?PetscBool? > has not been declared > /home/sci/hao/software/PETSc/include/petscdm.h:144:46: error: ?PetscBool? > has not been declared > /home/sci/hao/software/PETSc/include/petscdm.h:145:42: error: ?PetscBool? > has not been declared > /home/sci/hao/software/PETSc/include/petscdm.h:146:42: error: ?PetscBool? > has not been declared > In file included from /home/sci/hao/software/PETSc/include/petscdm.h:157:0, > from /home/sci/hao/software/PETSc/include/petscdmda.h:4, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.h:18, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.cxx:9: > /home/sci/hao/software/PETSc/include/petscbag.h:44:60: error: ?PetscBool? > has not been declared > In file included from /home/sci/hao/software/PETSc/include/petscdmda.h:5:0, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.h:18, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.cxx:9: > /home/sci/hao/software/PETSc/include/petscpf.h:41:8: error: ?PetscClassId? > does not name a type > In file included from /home/sci/hao/software/PETSc/include/petscdmda.h:5:0, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.h:18, > from > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.cxx:9: > /home/sci/hao/software/PETSc/include/petscpf.h:52:8: error: ?PetscBool? > does not name a type > > ------------------------------------------------------------------------------------------------------------------- > > > The head file of my program begin with the following. The read line is the > one I just added. > > #include <fstream> > #include <iostream> > #include <itkImage.h> > #include <itkImageFileReader.h> > #include <itkImageFileWriter.h> > #include <itkVectorImage.h> > #include <itkRecursiveGaussianImageFilter.h> > #include <petscksp.h> > #include <petscdmda.h> > #include <itkMedianImageFilter.h> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111110/a9209e2e/attachment-0001.htm > > > > ------------------------------ > > Message: 4 > Date: Thu, 10 Nov 2011 23:17:27 -0600 > From: Jed Brown <jedbrown at mcs.anl.gov> > Subject: Re: [petsc-users] Problem with including petscdmda.h > To: PETSc users list <petsc-users at mcs.anl.gov> > Message-ID: > <CAM9tzSkbrwNLoMCu4p_eL9syVxMXdm6jtmgvts6WwohniREMJw at mail.gmail.com > > > Content-Type: text/plain; charset="utf-8" > > On Thu, Nov 10, 2011 at 23:11, Xiang Hao <haoxiang at yahoo.cn> wrote: > > > I have a program using PETSc, which is running well. Now I just add a new > > line #include <petscdmda.h> in my code and get the following error. I > don't > > understand what's going on here. Any help? > > > > > > > ------------------------------------------------------------------------------------------------------------- > > In file included from > /home/sci/hao/software/PETSc/include/petscdmda.h:4:0, > > from > > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.h:18, > > from > > /home/sci/hao/programming/C++/ITK/SolveAlpha/SolveAlpha.cxx:9: > > /home/sci/hao/software/PETSc/include/petscdm.h:27:8: error: > ?PetscClassId? > > does not name a type > > /home/sci/hao/software/PETSc/include/petscdm.h:48:8: error: ?PetscBool? > > does not name a type > > > > The most likely explanation is that a path to an old version of PETSc > appears before this one in the header search paths, therefore it finds the > file with a new name (petscdm.h) in the new directory, but finds all the > supporting headers (which did not change names) in the old directory. Check > the command line and environment. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111110/7c64d647/attachment-0001.htm > > > > ------------------------------ > > Message: 5 > Date: Fri, 11 Nov 2011 12:39:02 +0200 > From: Konstantinos Kontzialis <ckontzialis at lycos.com> > Subject: [petsc-users] configuration problem > To: petsc-users at mcs.anl.gov > Message-ID: <4EBCFB46.8050509 at lycos.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear all, > > I'm trying to configure petsc v3.2 with the following options: > > ./configure --with-debugging=1 --with-mpi-dir=/usr/lib64/mpich2/bin > --with-shared-libraries > --with-large-file-io=1 > --with-precision=__float128 > --with-blacs=1 > --download-blacs=yes > --download-f-blas-lapack=yes > --with-plapack=1 > --download-plapack=yes > --with-scalapack=1 > --download-scalapack=yes > --with-superlu=1 > --download-superlu=yes > --with-superlu_dist=1 > --download-superlu_dist=yes > --with-ml=1 --download-ml=yes > --with-umfpack=1 > --download-umfpack=yes > --with-sundials=1 > --download-sundials=1 > --with-parmetis=1 > --download-parmetis=1 > --with-hypre=1 > --download-hypre=1 > > > and I get: > > > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > for details): > > ------------------------------------------------------------------------------- > Could not use downloaded f-blas-lapack? > > ******************************************************************************* > > What should I do? > > Kostas > > > ------------------------------ > > _______________________________________________ > petsc-users mailing list > petsc-users at mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/petsc-users > > > End of petsc-users Digest, Vol 35, Issue 32 > ******************************************* > -------------- next part -------------- An HTML attachment was scrubbed... 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