I am more than happy to share.
On 1/22/24 20:30, Matthew Knepley wrote:
On Mon, Jan 22, 2024 at 2:26 PM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
The problem is that I haven't figured out how to write a polyhedral
DMplex in parallel. So, curren
r?
Thanks and best regards,
Berend.
On 1/22/24 20:30, Matthew Knepley wrote:
On Mon, Jan 22, 2024 at 2:26 PM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
The problem is that I haven't figured out how to write a polyhedral
DMplex in parallel. So, curren
.
Best, Berend.
On 1/22/24 20:03, Matthew Knepley wrote:
On Mon, Jan 22, 2024 at 1:57 PM Berend van Wachem mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
Thanks for your quick response.
I have a DMPlex with a polyhedral mesh, and have defined a number of
vectors wit
very often.
But reading your response, this may not be a bad way of doing it?
Thanks,
Berend.
On 1/22/24 18:58, Matthew Knepley wrote:
On Mon, Jan 22, 2024 at 10:49 AM Berend van Wachem mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Petsc-Team,
Is there a good way to define a
Dear Petsc-Team,
Is there a good way to define a unique integer number in each element
(e.g. a cell) of a DMPlex mesh, which is in the same location,
regardless of the number of processors or the distribution of the mesh
over the processors?
So, for instance, if I have a DMPlex box mesh,
wrote:
> On Wed, May 17, 2023 at 11:20 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>
<mailto:berend.vanwac...@ovgu.de <mailto:berend.vanwac...@ovgu.de>>>
wrote:
>
> Dear Matt,
>
> Is there a way to 'redo' the D
Knepley wrote:
On Wed, May 17, 2023 at 11:20 AM Berend van Wachem mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
Is there a way to 'redo' the DMLocalizeCoordinates() ? Or to undo it?
Alternatively, can we make the calling of DMLocalizeCoordinates() in the
DMPlexCreate...() ro
() and DMGetCellCoordinatesLocal() before
scaling them.
Best regards, Berend.
On 5/17/23 16:35, Matthew Knepley wrote:
On Wed, May 17, 2023 at 10:21 AM Berend van Wachem mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
Thanks for getting back to me so quickly.
If I scal
, Berend.
On 5/17/23 16:10, Matthew Knepley wrote:
On Wed, May 17, 2023 at 10:02 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear PETSc Team,
We are using DMPlex, and we create a mesh using
DMPlexCreateBoxMesh ( );
and get a uniform mesh. Th
Dear PETSc Team,
We are using DMPlex, and we create a mesh using
DMPlexCreateBoxMesh ( );
and get a uniform mesh. The mesh is periodic.
We typically want to "scale" the coordinates (vertices) of the mesh, and
to achieve this, we call
DMGetCoordinatesLocal(dm, );
and scale the entries
Dear Petsc-Team,
Since Petsc-3.18 our code no longer runs successfully with periodic
geometries. Since this version, the call to DMGetPeriodicity has changed
arguments, but even after adapting our code, for some reason calling
DMLocalizeCoordinates, at least the way we do, no longer works. To
version?
3) This is strange, as it works fine for me.
Thanks, best, Berend.
On 12/15/22 18:56, Matthew Knepley wrote:
On Wed, Dec 14, 2022 at 3:58 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear PETSc team and users,
I have asked a few times about this
ERRQ(ierr);
/*** End of writing /
PetscFunctionReturn(0);
}
On 29/12/2022 21:54, Mark Adams wrote:
Have you tried using the DMForest as you would use a DMPLex?
That should work. Forst has extra stuff but it just makes a Plex and the
end of the day.
On Tue, Dec 27, 2022 at 5:21 AM Berend
Dear Petsc-team/users,
I am trying to save a DMForest which has been used for a calculation (so
refined/coarsened in places) to a file and later read it from the file
to continue a calculation with.
My question is: how do I do this? I've tried a few things, such as using
DMView and DMLoad,
Dear PETSc team and users,
I have asked a few times about this before, but we haven't really gotten
this to work yet.
In our code, we use the DMPlex framework and are also interested in
periodic geometries.
As our simulations typically require many time-steps, we would like to
be able to
Dear PETSc team and users,
I have asked a few times about this before, but we haven't really gotten
this to work yet.
In our code, we use the DMPlex framework and are also interested in
periodic geometries.
As our simulations typically require many time-steps, we would like to
be able to
? Or is the best way to call
DMPlexDistributeSetDefault(*NewDM, PETSC_FALSE), and call
DMPlexDistribute() with the required value of the overlap?
Thanks, best, Berend.
On 4/12/22 12:49, Matthew Knepley wrote:
On Tue, Apr 12, 2022 at 2:50 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de
within the code (our code determines the overlap required)?
Many thanks, best regards,
Berend.
On 4/11/22 16:23, Matthew Knepley wrote:
On Wed, Apr 6, 2022 at 9:41 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
I have made a small working example of
something wrong in the function CloneDMWithNewSection?
Many thanks for looking into this, best regards,
Berend.
On 4/4/22 23:05, Matthew Knepley wrote:
On Mon, Apr 4, 2022 at 3:36 PM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Petsc team,
Since about 2 years w
Dear Petsc team,
Since about 2 years we have been using Petsc with DMPlex, but since
upgrading our code to Petsc-3.17.0 something has broken.
First we generate a DM from a DMPlex with DMPlexCreateFromFile or
creating one with DMPlexCreateBoxMesh. Then the DM is distributed with
and see if
it works.
Thanks,
Koki
------------
*From:* Berend van Wachem
*Sent:* Thursday, February 17, 2022 9:06 AM
*To:* Sagiyama, Koki ; Hapla Vaclav
; PETSc users list ;
Lawrence Mitchell
*Subject:* Re: [petsc-users] DMView and DMLoad
Dear Koki,
Many thanks for your help and sorry for the slow reply.
I
Dear PETSc Team,
We are currently having a problem with the function DMSetGlobalSection -
this worked with v3.16.2 and 3.16.1, but doesn't seem to work anymore in
PETSc versions after 3.16.2.
I've attached an example which replicates the issue. It creates a box
with a random field is
l just by
modifying the dm(i.e., using the periodic mesh you are actually using)?
Thanks,
Koki
--------
*From:* Berend van Wachem
*Sent:* Monday, December 6, 2021 3:39 PM
*To:* Sagiyama, Koki ; Hapla Vaclav
; PETSc users list
ionally load coordinates directly on the distributed dm as (using
your notation):
/* Distribute dm */
...
PetscSFCompose(sfO, sfDist, );
DMPlexCoordinatesLoad(dm, viewer, sf);
To use this feature, we need to pass "-dm_plex_view_hdf5_storage_version
2.0.0" option when sav
;mailto:knep...@gmail.com>> wrote:
On Tue, Sep 14, 2021 at 5:15 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear PETSc-team,
We are trying to save and load distributed DMPlex and its associated
physical fields (created with DMCreateGlobalVector) (Uvelocity,
VVelocity,
.@gmx.li>> wrote:
Hi Berend,
On 14 Sep 2021, at 12:23, Matthew Knepley <mailto:knep...@gmail.com>> wrote:
On Tue, Sep 14, 2021 at 5:15 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear PETSc-team,
We are trying to save and load distributed DMPlex
Dear PETSc-team,
We are trying to save and load distributed DMPlex and its associated
physical fields (created with DMCreateGlobalVector) (Uvelocity,
VVelocity, ...) in HDF5_XDMF format. To achieve this, we do the following:
1) save in the same xdmf.h5 file:
DMView( DM ,
03 16:53, Jed Brown wrote:
Use the xml format (not the legacy format) by naming your file.vtu
instead of file.vtk
On Thu, Sep 3, 2020, at 8:17 AM, Berend van Wachem wrote:
Dear PETSc,
What is the best way to write data from a DMPLEX vector to file, so it
can be viewed with paraview?
I've foun
Dear PETSc,
What is the best way to write data from a DMPLEX vector to file, so it
can be viewed with paraview?
I've found that the standard VTK format works for a serial job, but if
there is more than 1 processor, the geometry data gets messed up.
I've attached a small working example for a
i, Mar 13, 2020 at 9:45 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
Thanks for your response. My understanding of the DM and DMClone
is the
same - and I have tested this with a DMPLEX DM without problems.
However, for
020 at 6:07 PM Matthew Knepley <mailto:knep...@gmail.com>> wrote:
On Fri, Mar 13, 2020 at 9:45 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
Thanks for your response. My understanding of the DM and DMClone
is the
s
Mar 12, 2020 at 7:40 AM Berend van Wachem
> mailto:berend.vanwac...@ovgu.de>
<mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de>>> wrote:
>
> Dear All,
>
> I have started to use
and my best wishes in these difficult times,
Berend.
On 2020-03-13 14:50, Matthew Knepley wrote:
On Fri, Mar 13, 2020 at 9:45 AM Berend van Wachem
mailto:berend.vanwac...@ovgu.de>> wrote:
Dear Matt,
Thanks for your response. My understanding of the DM and DMClone is the
same -
to
create a new section from the cloned P4EST DM. Is it not possible to
create/set a section on a P4EST DM? Or maybe I am doing something else
wrong? Do you suggest a workaround?
Many thanks, Berend.
On 2020-03-13 00:19, Matthew Knepley wrote:
On Thu, Mar 12, 2020 at 7:40 AM Berend van Wachem
Dear All,
I have started to use DMPLEX with P4EST for a computational fluid
dynamics application. I am solving a coupled system of 4 discretised
equations (for 3 velocity components and one pressure) on a mesh.
However, next to these 4 variables, I also have a few single field
variables
Dear Matt,
I use Eclipse and have eclipse make the makefiles.
It is just a matter of indicating to eclipse where the PETSc
headers/libraries are to be found, so if you have a C project which
needs PETSc headers and libraries:
To do this, click on your managed C project with the right sided
generated by the compiler, there is a PetscInitialize symbol that isn't
found in the library. But I'm soo confused at this point :(. How
did you guys all learn how to compile this?
Matt
On Wed, Jul 27, 2011 at 4:46 PM, Berend van Wachem
b.van-wachem at imperial.ac.uk mailto:b.van-wachem
believe it is failing during the linking step. I'm not 100% sure though.
Thanks for your quick response and help. Please advise,
Matt
On Wed, Jul 27, 2011 at 5:39 PM, Berend van Wachem
b.van-wachem at imperial.ac.uk mailto:b.van-wachem at imperial.ac.uk
wrote:
Dear Matt,
Does it say
/Documents/Research/codes/petsc/petsc-3.1-p8
In my source file I have included petsc.h:
#include petsc.h
Thanks,
Matt
On Wed, Jul 27, 2011 at 5:54 PM, Berend van Wachem
b.van-wachem at imperial.ac.uk mailto:b.van-wachem at imperial.ac.uk
wrote:
Dear Matt,
The error is definitely
pthread
rt
gcc_s
mpichf90
gfortran
m
m
dl
mpich
rt
gcc_s
dl
I used the exact order as I found in petscmachineinfo.h file (see here:
http://pastebin.com/cqzNgjJe)
Thank you very much for your help Berend,
Matt
On Wed, Jul 27, 2011 at 6:11 PM, Berend van Wachem
b.van-wachem
Dear Ryan,
I had a similar issue as you have. I am using KDE as a desktop manager
and found that I have to comment out the line
ServerArgsLocal=-nolisten tcp
in kdm, in the kdmrc file (on my system located at /etc/kde/kdm/kdmrc).
After restarting kdm, I get all windows of gdb coming up.
On Sun, Jul 19, 2009 at 2:59 AM, Berend van Wachem
b.van-wachem at imperial.ac.uk mailto:b.van-wachem at imperial.ac.uk
wrote:
Dear Ryan,
I had a similar issue as you have. I am using KDE as a desktop
manager and found that I have to comment out the line
ServerArgsLocal
Hi Barry,
http://www.intel.com/performance/server/xeon/hpc_ansys.htm
http://www.intel.com/performance/server/xeon/hpc_md_nastr.htm
Aren't both benchmarks run on Quads? The difference just being the cache
per processor? Or am I mistaken?
Berend.
these are the two benchmarks that
Hi Barry,
Perhaps you could describe how your matrix entries are generated and
we can suggest a
preallocation scheme?
Are there examples of preallocation schemes for PETSc? For instance, if
I would like to solve Poisson equation on an irregular grid (9 point
stencil in 2d and 27 in
Hi,
On the command
ierr = DACreateLocalVector(da,g); CHKERRQ(ierr);
I get the error
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
Memory requested 6050600
[0]PETSC ERROR: PETSC: Attaching gdb to Debug/MultiFlow of pid 19087 on
display :0.0 on machine tfdpc102
What
van Wachem berend at chalmers.se wrote:
Hi,
On the command
ierr = DACreateLocalVector(da,g); CHKERRQ(ierr);
I get the error
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
Memory requested 6050600
[0]PETSC ERROR: PETSC: Attaching gdb to Debug/MultiFlow of pid 19087
malloc?
On Tue, 9 Oct 2007, Berend van Wachem wrote:
Hi,
I ran the same command again, running top, and got the result
Mem: 6220940k total, 5879056k used, 341884k free, 143992k buffers
Swap: 1951888k total, 2584k used, 1949304k free, 2363516k cached
PID USER PR NI
Hi,
I am using 32 bit linux (slackware) on a 64 bit opteron. Would using a
64 bit linux distro help?
Berend.
Barry Smith wrote:
Pressure your vendors, be they IBM or Redhat, to provide a 2007 OS instead
of a 2001 OS :-(.
Barry
On Tue, 9 Oct 2007, Berend van Wachem wrote:
Hi
Hi,
I'm not sure if it is optimal, but I usually go through the changes when
upgrading,
http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/changes/index.html
Maybe there is a more easy way, I'm not sure.
Berend.
Trivedi, Jagruti CIV 47D, 474300D wrote:
Hello there,
I am
Hi,
I have also used the VOF/level set model in our PETSc based code, and it does
require a lot more iterations than a single phase model because of the
stencil. I guess you are solving
d/dx 1/rho d/dx p = 0
? Which can result in a terrible coefficient structure.
Are you sure the
of freedom.
Barry
On Wed, 31 Jan 2007, Berend van Wachem wrote:
Hi Ben,
The challenge in your problem is how you glue the C grid in
the back; there you will need to do some additional scattering.
I would set-up the IS for this, and then use that to scatter the
values
? Is it to install as an external software thru PETSc or
just use HYPRE on its own?
Btw, it will be great if you can send me parts of your code
regarding DA.
Thank you very much!
On 1/26/07, Berend van Wachem berend at tfd.chalmers.se wrote:
Hi,
I am not an expert - but have used PETSc
Hi Ben,
Sure you can - it just means you will need to save the X,Y,Z locations
of the grid points as well. All a DA requires is a regular I,J,K
numbering over your grid.
Berend.
Hi,
just to clarify. I'm using structured grid but not cartesian ie
strictly horizontal/vertical. So I can't
Hi,
I am not an expert - but have used PETSc for both structured and
unstructured grids.
When you use an unstructured code for a structured grid, there is
additional overhead (addressing, connectivity) which is redundant; this
information is not required for solving on a structured grid. I would
-laptop:/PETSc3/petsc/petsc-dev/src/vec/vec/examples/
tutorials$ $MPIRUN -np 4 ./ex1001 -vec_view
Process [0]
3
Process [1]
Process [2]
Process [3]
Matt
On 1/18/07, Berend van Wachem berend at chalmers.se wrote:
Hi,
In one of the input/output routines, I want to write one number
Hi,
valgrind shows something related to open-mpi, see below. I'll try mpich
to see if the problem goes away.
Thanks,
Berend.
==3683== Syscall param writev(vector[...]) points to uninitialised
byte(s)
==3683==at 0x543A607: writev (in /lib64/tls/libc-2.3.6.so)
==3683==by 0x5BE0AEA:
dealing with
this.
Barry
On Fri, 19 Jan 2007, Berend van Wachem wrote:
Hi,
valgrind shows something related to open-mpi, see below. I'll try
mpich to see if the problem goes away.
Thanks,
Berend.
==3683== Syscall param writev(vector[...]) points to uninitialised
byte(s
Hi,
In one of the input/output routines, I want to write one number to a viewer. I
created a vector with global size one, wrote the number to the vector, and
then viewed the vector. In the latest version of Petsc, this does not seem to
work anymore. What do you suggest as a work around? Hereby
Hi Julian,
I am not affiliated to the petsc-team, but have been using petsc a
number of years.
The idea of MPI is that your whole program get executed on each
processor. So getting output twice on each processor is quite normal. So
not only PETSC functions are called by each processor, every
Dear Mat,
One other thing,
in your function VecOverGlobalToBlockGlobalBegin and
VecOverGlobalToBlockGlobalEnd:
i assume that Vec *A is a the pointer to the blockglobal Vector?
further Vec **B is an array of pointers to MPI vectors where each element of
the array is a MPI vector
Hi Mat,
Isn't that exactly what the function I sent you does? It just places a
series of pointers into the new vector.
Berend.
i was wondering if there exists a function that lets me assemble a vector.
Basically i would like to do the following:
I have several PETSc vectors on the same
what m and n are. It says they denote the process
partition in each direction and that m*n must be equal the total number of
processes in the communicator.
Sorry, i am almost sure this is something simple.
thanks
mat
On Thursday 13 July 2006 23:13, Berend van Wachem wrote:
Hi,
i
Hi,
I am using Petsc with Open-Mpi and have started to use valgrind to find
a bug. One of the things that I see is that there is memory lost in
PetscInitialize by calling MPI_Init and in DACreate (which I do quite
often in my project). The amounts of memory lost aren't huge; should I
be
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