Hi,
Thanks. That is not easy for me. I will move the right preconditioner to
the left which will lead to a similar preconditioned system with almost the
same eigenvalues. Is there any example to do the multiplicative composite
preconditioners on different preconditioner matrices from the origin
Hi,
I want to use both left and right preconditioners for a linear system. Both
the preconditioners are based on part of the matrix. How can I implement
it? I can construct the preconditioner matrices. Thanks.
Bests,
Hui
On May 13 2010, hxie at umn.edu wrote:
>
>>
>>On 12 May 2010 19:18, wrote:
>>> Hi,
>>>
>>> If I use MatCopy to get a new matrix, can i use MatSetValues to change
>>> some
>>> entries of that matrix and do the assemble after that? Or if I just
>>> need to
>>> change some diagonal entries, can I
>
>On 12 May 2010 19:18, wrote:
>> Hi,
>>
>> If I use MatCopy to get a new matrix, can i use MatSetValues to change
>> some
>> entries of that matrix and do the assemble after that? Or if I just
>> need to
>> change some diagonal entries, can I use MatDiagonalSet to change the
>> entries
>> w
Hi,
If I use MatCopy to get a new matrix, can i use MatSetValues to change some
entries of that matrix and do the assemble after that? Or if I just need to
change some diagonal entries, can I use MatDiagonalSet to change the
entries without assembling? Thanks.
Bests,
Hui
Hi,
Is the mumps the best option as a direct solver? Should the size of the
linear system be less than 1d5 for mumps? Should I run the following to set
mumps as the solver for the preconditioner?
mpirun -np 6 ~/bin/cats3d.1 -pc_type asm -ksp_type gmres -sub_ksp_type
preonly -sub_pc_type lu -su
Hi,
The Matshift will shift all the diagonals. Is there a function to shift
only the zero diagonals?
Bests,
Hui
>Date: Mon, 19 Apr 2010 16:08:34 -0500
>From: Barry Smith
>Subject: Re: [petsc-users] zero diagonals
>To: PETSc users list
>Message-ID: <8CCA772D-DD35-4396-9951-DF23AC833863 at
Hi,
I have a matrix with some zero diagonals. Now I create a new matrix for
preconditioner and use Matshift to avoid the zero diagonals in the
preconditioner matrix. It works fine. Is that possible to just use the
command line options? If I just want to shift the zero diagonals, how can I
do
When I use -ksp_monitor_true_residual, I get
-
1 223 KSP preconditioned resid norm 7.587441767451e-05 true resid norm
1.919239379677e-07 ||Ae||/||Ax|| 4.636852053066e-07
2 500 500 KSP preconditioned resid norm 2.984438235355e-06 true resid norm
1.067989408349e-08 ||Ae||/||Ax|| 9.2166808670
I use left preconditioner. So the preconditioned residual should be less
than 10e-6||b||_2+10e^-10. How to print the final preconditioned residual
using the command line options? Or I will use -ksp_mpnitor to show all the
residuals.
Hui
On Mar 8 2010, Jed Brown wrote:
>On 08 Mar 2010 11:50:
I printed the real residuals by computing ||b-Ax||_2 at the last column:
equation itergm_itsgmres
Linear solve converged due to CONVERGED_RTOL iterations 223
field 1 223 0.414E+00
Linear solv
On Mar 8 2010, Jed Brown wrote:
>On 06 Mar 2010 15:41:12 -0600, hxie at umn.edu wrote:
>> Hi,
>>
>> I am solving incompressible navier-stokes equations. The code implements
>> the Newton iteration and just uses the KSP solver for each iteration. It
>> takes 14 nonlinear iterations (~8min) to
Hi,
I am solving incompressible navier-stokes equations. The code implements
the Newton iteration and just uses the KSP solver for each iteration. It
takes 14 nonlinear iterations (~8min) to converge using the default solver
in PETSc. But it takes 6 nonlinear iterations (~30min) using boomeramg
Hi,
I got the option for pilut from help:
-pc_hypre_pilut_maxiter <-2> -pc_hypre_pilut_tol <-2>
-pc_hypre_pilut_factorrowsize <-2 >
What are the default values? "-pc_hypre_pilut_tol " is 0.001?
"-pc_hypre_pilut_factorrowsize" is 20? And I do not understand the option
Hi,
I'd like to put the command line options into a file and let the PETSc read
it. Any example for this? Thanks.
Hui
Hi,
It takes about 8min to solve my problem using the default solver in PETSc
and 14min using pilut from hypre. But it takes 132min to get the result if
using the option "-pc_type hypre -pc_hypre_type boomeramg -ksp_type gmres".
Should I change the default options for amg?
Any suggestions are w
Hi,
Is the ilut preconditioner included in Petsc? If so, could you show me how
to use it with command line options? Thanks.
Bests,
Hui
Hi,
If I want to use hypre, should the runtime option be
"-pc_type hypre -pc_type_hypre boomeramg -ksp_type gmres"? And I do not
know how to use the ml package. Any example for this? Thanks.
Bests,
Hui
I run with the following command:
mpirun -np 4 ~/bin/cats3d.1 -ksp_type preonly -pc_type lu
-pc_factor_mat_solver_package mumps
I use ftp to upload the file matrix.gz to incoming. But I cannot see it
using 'ls'.
Hui
-
Likely SuperLU_Dist is failing on the provided matrix. Could you
use -ksp_view_binary on the run and copy the resulting file
binaryoutput to the anonymous ftp site ftp.mcs.anl.gov in the
> 1) The solution norm you report is NaN, which indicates memory corruption
> in
your code
I guess the reason may be a division by zero. The diagonals of the matrix
have some zeros.
>2) The number of allocated nonzeros is really suspicious. There are only 2
nonzeros per row?
At least 5.
Hu
The information for superlu_dist
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=1000, initial guess is zero
tolerances: relative=1e-06, absolute=1e-10, divergence=100
left preconditioning
PC Object:
type: lu
LU: out-of-place f
Hi,
My code works when I use mumps option like
-ksp_type preonly -pc_type lu -pc_factor_mat_solver_package mumps .
But it does not work with
-ksp_type preonly -pc_type lu -pc_factor_mat_solver_package superlu_dist
It runs but cannot get anything. Are the options correct? Or the
superlu_di
I have fixed the link problem. Thanks.
Bests,
Hui
'make test' runs ok. But I cannot compile my own code. The problems I guess
are the conflict of libmetis and libparmetis. The error messages while
compiling my own code:
Undefined symbols:
"_METIS_mCPartGraphRecursive2", referenced from:
_ParMETIS_V3_PartKway in libparmetis.a(kmetis.o)
Hi,
No problems with the configuration for hypre:
./config/configure.py --COPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-debugging=0
--with-mpi-dir=/usr/local/mpich2-1.2.1 --with-fortran --with-shared=0
--PETSC_ARCH=mac-gnu-f-all --with-hypre=1 --download-hypre=1
But I met some problems when installing t
Hi,
Where can I find the examples (command line options) to use the external
packages like hypre, mumps, ml? Thanks.
Bests,
Hui
Hi,
Thanks. But if I try to dump it into an ascii file using the following:
---
call
PetscViewerASCIIOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_WRITE,viewer,pterr)
call PetscViewerSetFormat(viewer,PETSC_VIEWER_ASCII_MATLAB,pterr)
call MatView(ptMat,viewer,pterr)
---
It
Hi,
I am trying to dump the nonzero entries of matrix into a file. I did the
following:
-
call
PetscViewerBinaryOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_WRITE,viewer,pterr)
call MatView(ptMat,viewer,pterr)
-
Is that correct? The file has a very large size.
Bests,
Hui
Hi,
I put the following in my code:
--
PetscViewer viewer
...
call
PetscViewerBinaryOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_WRITE,viewer,pterr);
call MatView(ptMat,viewer,pterr)
call PetscViewerDestroy(viewer,pterr)
--
Still no window
Hi,
Thanks. When I try to run with the option "-ksp_xmonitor", no window pops
up. Do I need to reinstall the petsc with the option --with-x=1? BTW, if I
want to use some external packages, do I have to reinstall the petsc?
Happy holiday,
Hui
-
well if you need -mat_view_draw - t
Hi,
I installed all the packages in a mac machine. When I run " mpirun -np 4
~/bin/cats3d.1 -mat_view_draw -draw_pause -1" under X11, I get some errors:
--
[0]PETSC ERROR: - Error Message
[0]PETSC ERROR: Argument out of range!
[0]PETSC
When I run "make all", I saw many warnings like
---
f90_fwrap.F:124.72:
subroutine F90Array2dCreateScalar(array,start1,len1,
1
Warning: Line truncated at (1)
f90_fwrap.F:130.72:
real(kind=selected_r
Hi,
My operation system is Mac OS X 10.6.2. I unzip the petsc under
/usr/local/petsc-3.0.0-p10.
I use the following to configure petsc.
---
sudo ./config/configure.py --CFLAGS=-O3 --FFLAGS=-O3
--with-mpi-dir=/usr/local/mpich2-1.2.1 --with-fortran --with-shared=0
--with-fc=gfortran
---
Following your instruction, I got the error message:
X connection to localhost:15.0 broken (explicit kill or server shutdown).
mpirun_ssh -timeout 200 -paramfile paramfile.6617 -np 4 -hostfile hosts
/home/bc2/xieh2/bin/cats3d.1 -mat_view_draw -draw_pause -1 -display
localhost:15.0 failed!
Hi,
I use X11 to connect the server and I want to draw the nonzero structure of
matrix. The option '-mat_view_draw' gives some error messages. How to fix
it? Thanks.
Bests,
Hui
Hi,
I want to change the ilu levels for block jacobi method. What is the
command line option for it? Or should I use "PCFactorSetLevels" in the
code? The "-sub_pc_factor_levels 1" does not work in fortran. Thanks.
Bests,
Hui
Hi,
I compile the petsc by
-
./config/configure.py COPTFLAGS=-O3 FOPTFLAGS=-O3 --download-f-blas-lapack=1
-
(.bashrc:
export PETSC_DIR=$HOME/lib/petsc-3.0.0-p8
export PETSC_ARCH=linux-gnu-c-opt
)
and the "make all" runs OK but the "make test" always fails (probably
because the queueing
sy
Hi,
I try to customize the subksp for block jacobi method. Does anybody have an
fortran example for this?
For c language, we can declare "ksp *subksp". Then how for fortran? Thanks.
Bests,
Hui
Hi,
I want to change the method for orthogonalization for the default ksp
solver in fortran. I added the following in my code:
--
call
KSPGMRESSetOrthogonalization(ksp,KSPGMRESClassicalGramSchmidtOrthogonalization,pterr)
call
KSPGMRESSetCGSRefinementType(ksp,KSP_GMRES_CGS_RE
Hi,
I want to output the true residual norm after calling KSPSolve in a fortran
program. I know there is a command option '-ksp_final_residual', but I
cannot do this using the PBS job submission. What is the related fortran
subroutine for this? Thanks for your help.
Bests,
Hui
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