Hello Hong, There is no problem. You can add the following description:
"The matrices come from Jifeng Zhao, Northwestern University, [email protected]. The stiffness and mass matrices arise from a extended finite element model to predict phononic band gap of a three-dimensional two-phase composite with periodic SCC crystal structure. In addition, periodic boundary conditions are applied on the primary unit cell by employing Bloch wave analysis." ---------------------------- In addition, do want to let you know that I tried the runtime command you gave me using PETSC/3.4.4 (3.5 is not ready yet for me), it failed to converge. PETSC ERROR: ! PETSC ERROR: KSP did not converge (reason=DIVERGED_ITS)*!* *I also tried to different preconditioners:* minres/bjacobi/ icc minres/bjacobi/ asm minres/bjacobi/ gamg All of them failed by the same error. I can try to increase the maximum iteration number to remove this error message, but it will converge very slow for sure. Since I am already using -aij command, I am not sure if these slow convergence performance will disappear if I upgrade to PETSC/3.5. Is there anything else I can try on? Thank you so much, Jifeng Zhao On Mon, Aug 4, 2014 at 11:18 PM, [email protected] <[email protected]> wrote: > jifeng : > > > > I just want to check with you if there is any updates on why the code > > crashes under -sbaij? > > It is a bug in petsc. I've fixed it in the brach hzhang/mataxpy-bugfix: > https://bitbucket.org/petsc/petsc/branch/hzhang/mataxpy-bugfix > > which will be merged to 'next' branch for tests, then patch to petsc-3.5. > You can use this branch if you like. > > Again, I like to add your matrices into petsc matrix collection. > Can you give me a short sentence describing your matrices, e.g., > "The following matrices come from Rick Dean, Arco E&P Technology, > [email protected]. They arise from multiphase flow modeling of oil > reservoirs,..." > > Thanks, > Hong > > > > > > At the meanwhile, unfortunately PETSC-3.5 hasn't been installed on my > server > > due to some technical problems. I hope technicians can get it done as > soon > > as possible. I will update you when I have any new results. Thanks so > much. > > > > Best regards, > > Jifeng > > > > > > On Wed, Jul 30, 2014 at 2:53 PM, jifeng zhao > > <[email protected]> wrote: > >> > >> Hello Hong, > >> > >> Thanks a lot. The result makes sense, but I think I will need higher > >> accuracy (smaller tolerance). I will take a try myself at the meanwhile. > >> > >> Best regards, > >> Jifeng Zhao > >> > >> > >> On Wed, Jul 30, 2014 at 1:16 PM, [email protected] < > [email protected]> > >> wrote: > >>> > >>> Jifeng, > >>> Using petsc-3.5 and slepc-3.5 (maint branch), I tested your matrices > >>> > >>> mpiexec -n 32 ./ex7 -f1 $data/zhao/petsc_stiff20.dat -f2 > >>> $data/zhao/petsc_mass20.dat -mat_view ascii::ascii_info -mat_type aij > >>> -eps_gen_hermitian -eps_type krylovschur -eps_target -0.1 -st_ksp_type > >>> minres -st_pc_type bjacobi -st_sub_pc_type icc -st_ksp_rtol 1.e-2 > >>> -eps_tol 1.e-2 -eps_nev 40 -st_type sinvert -log_summary |& tee > >>> log.mat20.ex7.np32.tol-2 > >>> > >>> The output is attached. > >>> > >>> When using '-mat_type sbaij', I got same error as reported, which > >>> might be a bug in our libraries. I'll investigate it. > >>> Switching to '-mat_type aij' works (I'm not sure if the computed > >>> eigenvalues are meaningful though), but the linear solver > >>> minres/bjacobi/icc converges very slow, takes around 500 - 1000 linear > >>> iterations for each eps iteration. You may experiment with stronger > >>> pc_type, e.g., '-pc_type asm' etc. > >>> > >>> I'll let you know why sbaij crashes. > >>> > >>> Hong > >>> > >>> On Mon, Jul 28, 2014 at 4:52 PM, Jose E. Roman <[email protected]> > >>> wrote: > >>> > > >>> > El 28/07/2014, a las 23:48, jifeng zhao escribió: > >>> > > >>> >> Hi Barry, > >>> >> > >>> >> Thanks for the reply. I see. I am still testing it and looking for > the > >>> >> bug. > >>> >> > >>> >> It is pretty weird that the error appears, since the code I am > running > >>> >> is ex7 and I didn't change anything. > >>> >> > >>> >> My matrices are assembled in binary files separately. As I explained > >>> >> earlier, I have a series of matrices to solve, each of them have > the same > >>> >> patterns but with different values. The way I assembly the matrix > has proven > >>> >> to be correct for all the other cases. Only for this one, when the > matrix > >>> >> has an zero eigenvalue, ex7 failed to solve it. > >>> >> > >>> >> In fact, I don't understand why this "Out of range" error could > >>> >> possibly appear? 1. my matrices have the correct parrellel lay up. > 2. In > >>> >> ex7, I am not explicitly accessing to any elements at all! All I > did is > >>> >> EPSSolve(); > >>> >> > >>> >> Any ideas? > >>> >> > >>> >> Best regards, > >>> >> Jifeng Zhao > >>> >> > >>> > > >>> > Tomorrow we will release slepc-3.5. I would suggest trying with the > new > >>> > version. If the problem persist we can help to track down the > problem. > >>> > > >>> > Jose > >>> > > >> > >> > >> > >> > >> -- > >> Jifeng Zhao > >> PhD candidate at Northwestern University, US > >> Theoretical and Applied Mechanics Program > > > > > > > > > > -- > > Jifeng Zhao > > PhD candidate at Northwestern University, US > > Theoretical and Applied Mechanics Program > -- Jifeng Zhao PhD candidate at Northwestern University, US Theoretical and Applied Mechanics Program
