Starting from version 3.5 the matrix parameters in SNESSetJacobian are
no longer pointers, hence my question:
What is the most appropriate place to call SNESSetJacobian if I need to
change the Jacobian during solution?
What about FormFunction?
Thanks,
Anton
On 09/23/2014 06:11 PM, Barry Smith wrote:
On Sep 23, 2014, at 9:50 AM, anton po...@uni-mainz.de wrote:
Starting from version 3.5 the matrix parameters in SNESSetJacobian are no
longer pointers, hence my question:
What is the most appropriate place to call SNESSetJacobian if I need
:
-bf_fieldsplit_0_ksp_type preonly
-bf_fieldsplit_0_pc_type lu
Doesn't work (ignored), because bf_ prefix isn't pass to inner solver
ksp (checked in the debugger).
Indeed, the following works:
-fieldsplit_0_ksp_type preonly
-fieldsplit_0_pc_type lu
Observed with 3.5 but not with 3.4
Thanks.
Anton
This is what I get for 3.5.0:
anton@anton ~/LIB/petsc-3.5.0-deb/src/snes/examples/tutorials $ ./ex19
-bf_pc_type fieldsplit -bf_snes_view
lid velocity = 0.0625, prandtl # = 1, grashof # = 1
Number of SNES iterations = 2
WARNING! There are options you set that were not used!
WARNING! could
Hi,
can I call DMLocalToLocalBegin\End on the same vector (g and l) in the
INSERT_VALUES mode?
The motivation is not to create the global buffer vector to be used with
DMGlobalToLocalBegin\End.
I just need to scatter ghost values to the neighbors.
Thanks,
Anton
On 11/14/2014 03:37 PM, Matthew Knepley wrote:
On Fri, Nov 14, 2014 at 8:18 AM, anton po...@uni-mainz.de
mailto:po...@uni-mainz.de wrote:
Hi,
can I call DMLocalToLocalBegin\End on the same vector (g and l) in
the INSERT_VALUES mode?
The motivation is not to create the global
On 3/5/15 4:18 PM, Matthew Knepley wrote:
On Thu, Mar 5, 2015 at 5:01 AM, anton po...@uni-mainz.de
mailto:po...@uni-mainz.de wrote:
Hi,
Does the near-null-space get attached to the internal ksp object
of redundant preconditioner, or a user has to scatter and attach
Hi,
Does the near-null-space get attached to the internal ksp object of
redundant preconditioner, or a user has to scatter and attach it manually?
If so, what would be a suggested way to do that?
Thanks,
Anton
On 04/23/2015 01:36 PM, Matthew Knepley wrote:
On Thu, Apr 23, 2015 at 6:28 AM, anton po...@uni-mainz.de
mailto:po...@uni-mainz.de wrote:
Hi,
I'm currently calling DMDAVecGet(Restore)Array on a subset of
processors. It seems to work correctly. So why does documentation
say
on a safe side, or I'm seriously violating something that's
not immediately obvious.
Thanks,
Anton
On 04/23/2015 07:38 PM, Barry Smith wrote:
On Apr 23, 2015, at 8:41 AM, anton po...@uni-mainz.de wrote:
On 04/23/2015 01:36 PM, Matthew Knepley wrote:
On Thu, Apr 23, 2015 at 6:28 AM, anton po...@uni-mainz.de wrote:
Hi,
I'm currently calling DMDAVecGet(Restore)Array on a subset
with MatSetValuesStencil in the usual
way if I don't use DM_BOUNDARY_PERIODIC boundary type?
Thanks,
Anton
On 07/22/2015 12:43 AM, Barry Smith wrote:
On Jul 21, 2015, at 5:13 PM, Jed Brown j...@jedbrown.org wrote:
anton po...@uni-mainz.de writes:
Hi,
Applying -snes_mf_operator to a Stokes problem is quite sensitive to
scaling of the velocity and pressure unknown (residual) blocks.
Apart from
someone suggest how it can be best implemented (or probably already
implemented) in PETSc.
Great thanks,
Anton
P.S. assembled preconditioner matrix with a multigrid solver applied to
it we already have, because it's also essential for convergence of
-snes_mf_operator
SNESSetConvergenceTest
Best,
Anton
On 12/11/2015 04:29 PM, Xiangdong wrote:
Hello everyone,
Instead of using the standard atol, rtol, stol etc, can user define a
new stopping criterion for snes? For example, if I want to use a
specialized norm as my snes stopping criteria, which functions
On 03/11/2016 11:25 PM, Barry Smith wrote:
Boris,
We will add this support to the DMShell and its usage from PCMG within a
few days.
Barry
Tanks Barry. This is super-fast and very helpful.
Cheers,
Anton
On Mar 11, 2016, at 3:39 PM, Boris Kaus <k...@uni-mainz.de>
is it that DMShellSetCreateRestriction can be
implemented and included in 3.7 release?
Please, please.
Thanks,
Anton
On 10/24/16 8:21 PM, Hong wrote:
Anton :
If replacing superlu_dist with mumps, does your code work?
yes
Hong
On 10/24/2016 05:47 PM, Hong wrote:
Barry,
Your change indeed fixed the error of his testing code.
As Satish tested, on your branch, ex16 runs smooth.
I do
Jason,
I guess you can let PETSc partition the first DMDA, then access the
partitioning data using DMDAGetOwnershipRanges, and pass this to
subsequent calls to DMDACreat3D via lx, ly, lz parameters.
Thanks,
Anton
On 11/29/16 12:30 AM, Jason Lefley wrote:
I’m developing an application
which is a week old
and includes bug fixes.
Maybe we're facing a problem that is already solved.
Thanks,
Anton
On Oct 11, 2016, at 12:19 PM, Satish Balay <ba...@mcs.anl.gov> wrote:
This log looks truncated. Are there any valgrind mesages before this?
[like from your application code - o
=memcheck --leak-check=yes --num-callers=20
--track-origins=yes
[and if there were more valgrind messages from MPI - rebuild petsc
There are no messages originating from our code, just a few MPI related
ones (probably false positives) and from SuperLU_DIST (most of them).
Thanks,
Anton
be helpful,
Anton
On 1/20/12 4:45 PM, Matthew Knepley wrote:
On Fri, Jan 20, 2012 at 9:43 AM, Dominik Szczerba
dominik at itis.ethz.ch mailto:dominik at itis.ethz.ch wrote:
I am building on a Cray system with crayftn fortran compiler. I
specify --with-fc
Well, I simply gave up on Cray compilers, as well as on the other
compilers installed on this machine (Intel, Portland, Pathscale). After
many attempts only GNU compilers were functional with PETSc.
On 1/20/12 6:12 PM, Dominik Szczerba wrote:
Hi Anton,
Many thanks for your hints. I am
(say 4096 or
more). If it is supported, how can I use it?
Thank you,
Anton Popov
Try adding -lgfortran to LFLAGS variable
On 3/20/12 3:18 AM, Roc Wang wrote:
Hello,
I am trying to compile the example source code of
~\petsc-3.2-p7\src\ksp\ksp\examples\tutorials\ex2f.F. However the
error information shows:
ex2f.o: In function `MAIN__':
ex2f.F90:(.text+0x1b):
you'll be surprised.
Cheers,
Anton
On 4/3/12 3:57 AM, Barry Smith wrote:
On Apr 2, 2012, at 8:10 PM, Tabrez Ali wrote:
Hello
I am trying to debug a program using the switch '-on_error_attach_debugger'
but the vendor/sysadmin built PETSc 3.2.00 is unable to start the debugger
in xterm
, then this thing - HSL
MA87 - is even better than PARDISO. It's a commercial solver, but it's
free for academic use.
The only problem I see here is that both of them are difficult to use
together with PETSc, since they're OMP-based. But difficult probably
doesn't mean impossible.
Cheers,
Anton
the error, but doesn't
solve the problem, because I actually need to KEEP_NONZERO_PATTERN
Running the code sequentially, also vanishes the error.
Please check whether it's a bug in petsc-3.3, or I should set this
option in a different way.
Thanks,
Anton Popov
Thanks Matt, it's clear now
On 6/19/12 6:49 PM, Matthew Knepley wrote:
On Tue, Jun 19, 2012 at 10:06 AM, Anton Popov popov at uni-mainz.de
mailto:popov at uni-mainz.de wrote:
Hi petsc team!
I've recently upgraded to 3.3, and currently experience problems.
One of them follows
don't, petsc says Unhandled case,
must have at least two fields, not 1!?
Do I need to explicitly specify the blocksize, if I want to use the
filedsplit preconditioner for the velocity block?
A small example would be extremely helpful
Thanks a lot,
Anton
named mac11-005.geo.uni-mainz.de
by anton Thu Jun 28 17:06:53 2012
[0]PETSC ERROR: Libraries linked from
/Users/anton/LIB/petsc-3.3-p0/int32-debug/lib
[0]PETSC ERROR: Configure run at Tue Jun 12 15:32:21 2012
[0]PETSC ERROR: Configure options
PETSC_DIR=/Users/anton/LIB/petsc-3.3-p0 PETSC_ARCH
Thanks Barry,
We'll send the code to petsc-maint in a moment.
But we really don't want to bother you a lot.
Anton and Boris
On 6/28/12 8:55 PM, Barry Smith wrote:
Anton,
This came about because we are now being much more pedantic about the
blocksizes of PETSc objects and not allowing
,
Anton
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= VecLoad(V3, view_in);
Comment out one of vectors, your code works fine.
Hong
On Wed, Jul 18, 2012 at 7:54 AM, Anton Popov popov at uni-mainz.de
mailto:popov at uni-mainz.de wrote:
Dear petsc team,
could you please tell me what's wrong with the attached example file?
I run
, just makes it more obvious,
after scaling the matrix A will be:
A = [1, 1; 1, 1] - clearly the rows are linearly dependent.
Scaling may help you, but of course, this is not an always working solution
Anton
On 10/18/12 8:38 PM, Nachiket Gokhale wrote:
On Thu, Oct 18, 2012 at 2:28 PM, Matthew
for using PARALLEL SDM debugger with PETSc applications.
If you're interested, I can send detailed configuration / setup
instructions.
Anton
Barry
On Nov 15, 2012, at 4:52 PM, Fande Kong fd.kong at siat.ac.cn wrote:
Got it. Thanks.
On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley
,
Anton
On 11/18/12 4:43 PM, Fande Kong wrote:
yeap, It sounds very interesting. Could you please give some
instructions on how to use eclipse link both Petsc and MPI?
On Sat, Nov 17, 2012 at 3:08 AM, Anton Popov popov at uni-mainz.de
mailto:popov at uni-mainz.de wrote:
On 11/16/12 2
On 3/5/13 9:23 PM, Dharmendar Reddy wrote:
Hello,
Has any one installed petsc on the AMD 6200 series processor
systems? I have a small cluster with quad socket AMD 6274 (16Core)
processors. Should i use any special optimization flags or let petsc
configure script decide ?
I
On 3/5/13 11:38 PM, Dharmendar Reddy wrote:
Hello Anton,
For me the problem is with gfortran. I use certain object oriented
features available in Fortran 2003. When i last tested few months
agao, my code does not compile with gfortran. I guess it is
required/suggested to use the same
done work on packaging 3.3-version, so that
will probably be soon uploaded as well.
Best regards,
Anton
[1]
http://anonscm.debian.org/gitweb/?p=debian-science/packages/petsc.git;a=commit;h=6d043c23c3eea30e327543a5189a8602d24467ec
On 04/26/2013 06:12 PM, Alexei Matveev wrote:
Dear Debian Science
Hi guys,
I need GlobalToLocal simultaneously about five vectors composed with
different DMs.
What do you think will do better?
1) post all Begins first, followed by all Ends
2) post each Begin-End couple one after another
Many thanks,
Anton
Hi guys,
just a quick question. I'm upgrading to 3.4.2 and it complains about
PetscViewerBinaryMatlabOutputVecDA
What to use instead? I couldn't find it in Changes 3.4
Thanks,
Anton
: schurcomplement!
[0]PETSC ERROR:
[0]PETSC ERROR: MatSetType() line 63 in
/Users/anton/LIB/petsc-3.4.2/src/mat/interface/matreg.c
[0]PETSC ERROR: MatCreateSchurComplement() line 180 in
/Users/anton/LIB/petsc-3.4.2/src/ksp/ksp/utils
On 10/1/13 9:45 PM, Jed Brown wrote:
Anton Popov po...@uni-mainz.de writes:
Dear all,
I guess MatCreateSchurComplement is somehow broken in PETSc 3.4.2
You can fix it by calling KSPMatRegisterAll() before
MatCreateSchurComplement,
Thanks, Jed. It solves the problem.
and the issue is now
Hi all,
do I need to call MatAssemblyBegin/End on a MATNEST matrix again after
the submatrices get updated by MatSetValues + MatAssemblyBegin/End?
Thanks,
Anton
On 10/14/13 11:47 AM, Dave May wrote:
Yes
Thanks Dave
On Monday, 14 October 2013, Anton Popov wrote:
Hi all,
do I need to call MatAssemblyBegin/End on a MATNEST matrix again
after the submatrices get updated by MatSetValues +
MatAssemblyBegin/End?
Thanks,
Anton
=1
--download-mumps=1
or:
--download-superlu_dist=1
Or just run sequentially
Anton
I run it with option |-snes_monitor -ksp_monitor_true_residual
-snes_converged_reason -ksp_converged_reason|. and received :
0 SNES Function norm 1.414213647226e-01
0 KSP preconditioned resid norm
-current/docs/manualpages/Vec/VecScatterBegin.html
Anton
Also, how can I solve the momentum eqn involving u,v,w using KSP?
What examples can I follow for the above requirements?
Thank you.
On 5/1/14 10:39 PM, Anush Krishnan wrote:
Hi Anton,
On 29 April 2014 05:14, Anton Popov po...@uni-mainz.de
mailto:po...@uni-mainz.de wrote:
You can do the whole thing much easier (to my opinion).
Since you created two DMDA anyway, just do:
- find first index on every processor
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecGetArray.html
On 9/28/14 1:15 PM, Parvathi M.K wrote:
Hey,
I am fairly new to PetSc. I was just curious as to how you can
directly access the data stored in a Petsc object, say a vector
without using VecGetValues().
I've
the data.
I think it's impossible for a good reason (or at least highly discouraged).
Why don't you want to use a prescribed interface? It's really light-weight.
But don't forget to call VecRestoreArray after directly manipulating the
data.
Anton
On Sun, Sep 28, 2014 at 4:45 PM, Parvathi M.K
://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecScatterCreateToZero.html#VecScatterCreateToZero
Anton
to stick to maint branch, and what are the chances for
these fixes to be included in 3.7.5?
Thanks,
Anton
On 10/07/2016 05:23 PM, Satish Balay wrote:
On Fri, 7 Oct 2016, Kong, Fande wrote:
On Fri, Oct 7, 2016 at 9:04 AM, Satish Balay <ba...@mcs.anl.gov> wrote:
On Fri, 7 Oct 2016, Anton Popov wrote:
Hi guys,
are there any news about fixing buggy behavior of SuperLU_DIST, exactly
add it, I (and other users probably too) would really
appreciate that.
Thanks a lot,
Anton
I'll check our interface to see if we can add flag-checking for Pr and
Pc, then set default accordingly.
Hong
On Wed, Oct 26, 2016 at 3:23 PM, Xiaoye S. Li <x...@lbl.gov
<mailto:x...@l
On 10/24/2016 10:32 PM, Barry Smith wrote:
Valgrind doesn't report any problems?
Valgrind hangs and never returns (waited hours for a 5 sec run) after
entering factorization for the second time.
On Oct 24, 2016, at 12:09 PM, Anton Popov <po...@uni-mainz.de> wrote:
On 10/2
On 10/25/2016 01:58 PM, Anton Popov wrote:
On 10/24/2016 10:32 PM, Barry Smith wrote:
Valgrind doesn't report any problems?
Valgrind hangs and never returns (waited hours for a 5 sec run) after
entering factorization for the second time.
Before it happens it prints this (attached
permutations for large diagonal even if
matrix values change significantly?
Surprisingly everything works even with:
-mat_superlu_dist_colperm PARMETIS
-mat_superlu_dist_parsymbfact TRUE
Thanks,
Anton
On 10/24/2016 09:06 PM, Hong wrote:
Anton:
If replacing superlu_dist with mumps, does
Thank you Barry, Satish, Fande!
Is there a chance to get this fix in the maintenance release 3.7.5
together with the latest SuperLU_DIST? Or next release is a more
realistic option?
Anton
On 10/24/2016 01:58 AM, Satish Balay wrote:
The original testcode from Anton also works [i.e
error otherwise).
Summary: we don't have a simple test code to debug superlu issue anymore.
Anton
Hong
On Mon, Oct 24, 2016 at 9:34 AM, Satish Balay <ba...@mcs.anl.gov
<mailto:ba...@mcs.anl.gov>> wrote:
On Mon, 24 Oct 2016, Barry Smith wrote:
>
> > [Or
On Tue, Oct 11, 2016 at 2:18 PM, Anton <po...@uni-mainz.de
<mailto:po...@uni-mainz.de>> wrote:
On 10/11/16 7:19 PM, Satish Balay wrote:
This log looks truncated. Are there any valgrind mesages
before this?
[like from your application code - or from M
Hong,
I checked out & compiled your new branch:
hzhang/fix-superlu_dist-reuse-factornumeric. Unfortunately it did not
solve the problem.
Sorry.
On 11/21/2016 04:43 AM, Hong wrote:
Anton,
I pushed a fix
https://bitbucket.org/petsc/petsc/commits/28865de08051eb99557d70672c208e14da23
DMShellSetCreateRestriction.
Replacing DMCreateInterpolation with DMCreateRestriction in
CreateRestriction also fails with a segfault:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: [0] DMCreateRestriction line 1064
/home/anton
Thanks, Hong.
I will try as soon as possible and let you know.
Anton
On 11/21/2016 04:43 AM, Hong wrote:
Anton,
I pushed a fix
https://bitbucket.org/petsc/petsc/commits/28865de08051eb99557d70672c208e14da23c8b1
in branch hzhang/fix-superlu_dist-reuse-factornumeric.
Can you give it a try to see
is not stack'd, malloc'd or (recently) free'd
==25674==
[1]PETSC ERROR:
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
On 10/11/2016 03:26 PM, Anton Popov wrote
On 10/10/2016 07:11 PM, Satish Balay wrote:
Thats from petsc-3.5
Anton - please post the stack trace you get with
--download-superlu_dist-commit=origin/maint
I guess this is it:
[0]PETSC ERROR: [0] SuperLU_DIST:pdgssvx line 421
/home/anton/LIB/petsc/src/mat/impls/aij/mpi/superlu_dist
,
Anton
On 15.10.2018 23:22, Manuel Valera wrote:
Thanks Matthew, i have made some progress but i am still unsure on how
to proceed to make the DMDAs work as intended, i will try to lay out
what i am trying now:
I was able to port the interpolation into the DMDA model but it works
only
option is being ignored?
Best wishes,
Anton
tion. The Picard matrix still does a good job as a
preconditioner. But it is important to start the iteration with Picard
and only change to MFFD later.
Is my workaround with the shell matrix acceptable, or there is a better
solution?
Thanks,
Anton
On 13.06.21 20:52, Barry Smith wrote:
A
On 14.06.21 15:02, Matthew Knepley wrote:
On Mon, Jun 14, 2021 at 8:45 AM Anton Popov <mailto:po...@uni-mainz.de>> wrote:
Hi Barry & Matt,
thanks for your quick response. These options were exactly what I
needed and expected:
-pc_mg_galerkin pmat
-pc_use_amat
On 14.06.21 15:04, Dave May wrote:
Hi Anton,
Hi Dave,
On Mon, 14 Jun 2021 at 14:47, Anton Popov <mailto:po...@uni-mainz.de>> wrote:
Hi Barry & Matt,
thanks for your quick response. These options were exactly what I
needed and expected:
-pc_mg_
the situation in a better way, if it is possible.
Thanks.
Anton
;where);
/* must return 1 or 3 or 4*/
^~~
{PETSCDIR PATH REMOVED}/lib/include/revolve_c.h:14:49: note: passing argument
to parameter here
int revolve_action(int*,int*,int*,int,int*,int*);
Is revolve incompatible with 64bit indices by design?
Bes
On 04.02.22 17:39, Matthew Knepley wrote:
On Fri, Feb 4, 2022 at 11:35 AM Anton Popov wrote:
Hi Satish,
I just discovered that PETSc 3.16.4 fails to link against the
latest AMD
BLIS and LibFLAME libraries on a Linux box
this immediately.
After installing libgfortran.so.5, both PETSc versions install just
fine, however I get the warning mentioned by Satish.
Maybe it is indeed worth upgrading everything to the compatible versions.
Best,
Anton
On 04.02.22 18:33, Barry Smith wrote:
On Feb 4, 2022, at 12:27 PM
Am 04.02.2022 um 18:54 schrieb Satish Balay:
On Fri, 4 Feb 2022, Anton Popov wrote:
Thanks Matt, Barry and Satish, for your suggestions.
The problem was indeed in mismatch between the gfortran library version
(system has libgfortran.so.4 libflame needs libgfortran.so.5)
3.9.4 did
On 04.02.22 22:18, Satish Balay wrote:
On Fri, 4 Feb 2022, Anton Popov wrote:
Am 04.02.2022 um 18:54 schrieb Satish Balay:
On Fri, 4 Feb 2022, Anton Popov wrote:
Thanks Matt, Barry and Satish, for your suggestions.
The problem was indeed in mismatch between the gfortran library version
Dear petsc users.
I am attempting to solve a large, dense equation system. I would like to try
using the BiCGSTAB algorithm, and specifically, the petsc library, as it is
open source and seems to be well supported. I take it petsc is primarily aimed
at people solving partial differential
Dear petsc users.
I am attempting to solve a large, dense equation system. I would like to try
using the BiCGSTAB algorithm, and specifically, the petsc library, as it is
open source and seems to be well supported. I take it petsc is primarily aimed
at people solving partial differential
On 12. aug. 2011, at 15.51, Jed Brown wrote:
If by brute force, you mean volumetric discretizations of the differential
equations, then this is indeed the largest user base. But there are many
optimal methods in this category, such that I think brute force would be a
misnomer.
That's what
On 12. aug. 2011, at 16.42, Jed Brown wrote:
On Fri, Aug 12, 2011 at 10:09, Paul Anton Letnes paul.anton.letnes at
gmail.com wrote:
The problem is a discretized integral equation. It does not quite fall into
the boundary element category, but it's not too far off, in a sense. I did
On 12. aug. 2011, at 21.54, Jed Brown wrote:
On Fri, Aug 12, 2011 at 12:26, Paul Anton Letnes paul.anton.letnes at
gmail.com wrote:
I'm not 100% sure what you mean by second kind integral operator, but it is
a Fredholm equation of the first kind, as far as I understand (my background
On 14. aug. 2011, at 16.42, Jed Brown wrote:
On Sun, Aug 14, 2011 at 06:18, Paul Anton Letnes paul.anton.letnes at
gmail.com wrote:
I believe of the first kind - there is. Our approach is to discretize the
integral equation. The equations we are really solving are the Maxwell
equations
Let's start with a scatter plot of the eigenvalues. Can you do a problem that
is representative of the physics in less than, say, 1000 degrees of freedom?
If so, I would just use Matlab (or Octave, etc). You want to be able to plot
the eigenvector associated with a chosen eigenvalue in
This looks tricky. It certainly doesn't have the nice structure of a
second-kind integral operator with compact kernel (or even first-kind, which
would be the limit of vanishing regularization). If we're going to solve this
efficiently, we probably need either:
1. A sparse system that
On 24. aug. 2011, at 00.00, Jed Brown wrote:
On Mon, Aug 22, 2011 at 05:51, Paul Anton Letnes paul.anton.letnes at
gmail.com wrote:
Not that I know of. The operator contains integrals over a stochastically
rough surface. Due to its random nature, any sparsity structure will depend
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