[petsc-users] Moving from KSPSetNullSpace to MatSetNullSpace

Tue Oct 25 17:39:08 CDT 2016

On 25 October 2016 at 17:51, Barry Smith <bsmith at mcs.anl.gov> 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?).

    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 petsc-maint at mcs.anl.gov 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.

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 <olivier.mesnard8 at gmail.com>
> 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>
>
>
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