On 25 October 2016 at 19:59, Matthew Knepley <[email protected]> wrote:
> On Tue, Oct 25, 2016 at 6:22 PM, Barry Smith <[email protected]> wrote: > >> >> > On Oct 25, 2016, at 5:39 PM, Olivier Mesnard < >> [email protected]> wrote: >> > >> > On 25 October 2016 at 17:51, Barry Smith <[email protected]> wrote: >> > >> > Olivier, >> > >> > In theory you do not need to change anything else. Are you using a >> different matrix object for the velocity_ksp object than the poisson_ksp >> object? >> > >> > The matrix is different for the velocity_ksp and the poisson_ksp. >> > >> > The code change in PETSc is very little but we have a report from >> another CFD user who also had problems with the change so there may be some >> subtle bug that we can't figure out causing things to not behave properly. >> > >> > First run the 3.7.4 code with -poisson_ksp_view and verify that when >> it prints the matrix information it prints something like has attached null >> space if it does not print that it means that somehow the matrix is not >> properly getting the matrix attached. >> > >> > When running with 3.7.4 and -poisson_ksp_view, the output shows that >> the nullspace is not attached to the KSP (as it was with 3.5.4); however >> the print statement is now under the Mat info (which is expected when >> moving from KSPSetNullSpace to MatSetNullSpace?). >> >> Good, this is how it should be. >> > >> > Though older versions had MatSetNullSpace() they didn't necessarily >> associate it with the KSP so it was not expected to work as a replacement >> for KSPSetNullSpace() with older versions. >> > >> > Because our other user had great difficulty trying to debug the >> issue feel free to send us at [email protected] your code with >> instructions on building and running and we can try to track down the >> problem. Better than hours and hours spent with fruitless email. We will, >> of course, not distribute the code and will delete in when we are finished >> with it. >> > >> > The code is open-source and hosted on GitHub ( >> https://github.com/barbagroup/PetIBM). >> > I just pushed the branches `feature-compatible-petsc-3.7` and >> `revert-compatible-petsc-3.5` that I used to observe this problem. >> > >> Thanks, I'll get back to you if I discover anything > > > Obviously GAMG is behaving quite differently (1 vs 2 levels and a much > sparser coarse problem in 3.7). > > Could you try one thing for me before we start running it? Run with > > -poisson_mg_coarse_sub_pc_type svd > > and see what happens on 2 procs for 3.7? > > Hi Matt, With -poisson_mg_coarse_sub_pc_type svd , it ran normally on 1 proc but not on 2 procs the end of the output says: "** On entry to DGESVD parameter number 6 had an illegal value " I attached the log file. > Thanks, > > Matt > > >> >> > PETSc (both 3.5.4 and 3.7.4) was configured as follow: >> > export PETSC_ARCH="linux-gnu-dbg" >> > ./configure --PETSC_ARCH=$PETSC_ARCH \ >> > --with-cc=gcc \ >> > --with-cxx=g++ \ >> > --with-fc=gfortran \ >> > --COPTFLAGS="-O0" \ >> > --CXXOPTFLAGS="-O0" \ >> > --FOPTFLAGS="-O0" \ >> > --with-debugging=1 \ >> > --download-fblaslapack \ >> > --download-mpich \ >> > --download-hypre \ >> > --download-yaml \ >> > --with-x=1 >> > >> > Our code was built using the following commands: >> > mkdir petibm-build >> > cd petibm-build >> > export PETSC_DIR=<directory of PETSc> >> > export PETSC_ARCH="linux-gnu-dbg" >> > export PETIBM_DIR=<directory of PetIBM git repo> >> > $PETIBM_DIR/configure --prefix=$PWD \ >> > CXX=$PETSC_DIR/$PETSC_ARCH/bin/mpicxx \ >> > CXXFLAGS="-g -O0 -std=c++11" >> > make all >> > make install >> > >> > Then >> > cd examples >> > make examples >> > >> > The example of the lid-driven cavity I was talking about can be found >> in the folder `examples/2d/convergence/lidDrivenCavity20/20/` >> > >> > To run it: >> > mpiexec -n N <path-to-petibm-build>/bin/petibm2d -directory >> <path-to-example> >> > >> > Let me know if you need more info. Thank you. >> > >> > Barry >> > >> > >> > >> > >> > >> > >> > >> > >> > > On Oct 25, 2016, at 4:38 PM, Olivier Mesnard < >> [email protected]> wrote: >> > > >> > > Hi all, >> > > >> > > We develop a CFD code using the PETSc library that solves the >> Navier-Stokes equations using the fractional-step method from Perot (1993). >> > > At each time-step, we solve two systems: one for the velocity field, >> the other, a Poisson system, for the pressure field. >> > > One of our test-cases is a 2D lid-driven cavity flow (Re=100) on a >> 20x20 grid using 1 or 2 procs. >> > > For the Poisson system, we usually use CG preconditioned with GAMG. >> > > >> > > So far, we have been using PETSc-3.5.4, and we would like to update >> the code with the latest release: 3.7.4. >> > > >> > > As suggested in the changelog of 3.6, we replaced the routine >> `KSPSetNullSpace()` with `MatSetNullSpace()`. >> > > >> > > Here is the list of options we use to configure the two solvers: >> > > * Velocity solver: prefix `-velocity_` >> > > -velocity_ksp_type bcgs >> > > -velocity_ksp_rtol 1.0E-08 >> > > -velocity_ksp_atol 0.0 >> > > -velocity_ksp_max_it 10000 >> > > -velocity_pc_type jacobi >> > > -velocity_ksp_view >> > > -velocity_ksp_monitor_true_residual >> > > -velocity_ksp_converged_reason >> > > * Poisson solver: prefix `-poisson_` >> > > -poisson_ksp_type cg >> > > -poisson_ksp_rtol 1.0E-08 >> > > -poisson_ksp_atol 0.0 >> > > -poisson_ksp_max_it 20000 >> > > -poisson_pc_type gamg >> > > -poisson_pc_gamg_type agg >> > > -poisson_pc_gamg_agg_nsmooths 1 >> > > -poissonksp_view >> > > -poisson_ksp_monitor_true_residual >> > > -poisson_ksp_converged_reason >> > > >> > > With 3.5.4, the case runs normally on 1 or 2 procs. >> > > With 3.7.4, the case runs normally on 1 proc but not on 2. >> > > Why? The Poisson solver diverges because of an indefinite >> preconditioner (only with 2 procs). >> > > >> > > We also saw that the routine `MatSetNullSpace()` was already >> available in 3.5.4. >> > > With 3.5.4, replacing `KSPSetNullSpace()` with `MatSetNullSpace()` >> led to the Poisson solver diverging because of an indefinite matrix (on 1 >> and 2 procs). >> > > >> > > Thus, we were wondering if we needed to update something else for the >> KSP, and not just modifying the name of the routine? >> > > >> > > I have attached the output files from the different cases: >> > > * `run-petsc-3.5.4-n1.log` (3.5.4, `KSPSetNullSpace()`, n=1) >> > > * `run-petsc-3.5.4-n2.log` >> > > * `run-petsc-3.5.4-nsp-n1.log` (3.5.4, `MatSetNullSpace()`, n=1) >> > > * `run-petsc-3.5.4-nsp-n2.log` >> > > * `run-petsc-3.7.4-n1.log` (3.7.4, `MatSetNullSpace()`, n=1) >> > > * `run-petsc-3.7.4-n2.log` >> > > >> > > Thank you for your help, >> > > Olivier >> > > <run-petsc-3.5.4-n1.log><run-petsc-3.5.4-n2.log><run-petsc-3 >> .5.4-nsp-n1.log><run-petsc-3.5.4-nsp-n2.log><run-petsc-3.7.4 >> -n1.log><run-petsc-3.7.4-n2.log> >> > >> > >> >> > > > -- > 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 >
run-petsc-3.7.4-n2.log
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