hat are the
> recommended data formats to use to save Vecs for visualization?
>
> Thanks
>
> Barry
>
--
----
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
On Wed, 2011-07-06 at 12:24 -0300, Lisandro Dalcin wrote:
> On 6 July 2011 11:41, Ethan Coon wrote:
> > Both Paraview and Visit generally make ugly axes/colorbars/keys/etc. In my
> > opinion they both look fine for presentations and my own viewing, but are
> > not
ase.
>
> I have played with matplotlib some to view Petsc output (vtk), with mixed
> results. I wonder if Ethan would be willing to share an example or two?
>
> Best,
>
> Andrew
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
e
> message needs to be passed between communicating processes on update, but
> this still results in passing 5X the data that I have to. Any comment on
> this would be much appreciated.
>
> Thank you,
> Kevin
--
--------
Ethan Coon
Post-Doctoral Rese
ed this on Vecs, but not Mats or ISs, and I haven't thoroughly
tested degenerate cases. Will do some testing, but I wanted Lisandro to
take a look at it as well...
Thanks,
Ethan
On Wed, 2011-07-06 at 12:24 -0300, Lisandro Dalcin wrote:
> On 6 July 2011 11:41, Ethan Coon wrote:
>
>
>Excellent.
>
>I have the matlab programs in a subdirectory called matlab. Will there be
> several of these? So should we have a bin/python subdirectory for them?
>
> Barry
>
>
> On Jul 14, 2011, at 2:22 PM, Ethan Coon wrote:
>
> >
I have to finish up some other crap first, but will get these fixes done
soon.
Note that this should work for people using the release version with no
modifications, if Andrew is still reading this.
Thanks,
Etha
>
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
a string to identify what it is ('Vec', 'Mat',
or 'IS') and a numpy representation of the data.
You then can reshape the array to any shape you want:
In [5]: da_vec = petsc_objs[0][1].reshape((NZ, NY, NX, NDOFS))
Note the order!
Ethan
> Best,
> Ata
t;
> Which is peculiar since when I try to read the header myself using:
>
> header=numpy.fromfile('V-018.bin',dtype='>i4',count=1)
> print header[0]
>
> I get:
>
> 1211214
>
> which is a Vec identifier.
>
> Any thoughts on what goes w
ile is empty.
However, I screwed up the line in my last email -- it should read:
except (MemoryError, IndexError):
That should fix your problem, and will be fixed in dev.
Ethan
> Is it normal for PetscBinaryRead to try to read header twice?
>
>
> Best,
> Ata
> On Jul 18, 2011
path for mpi with ./config/configure.py
> --with-mpi-dir=/home/likunt/petsc-3.1-p8/externalpackages/mpich2-1.0.8,
> but it shows 'unable to configure with given options'.
>
> Any suggestions on this?
>
> Thanks,
> Likun
>
>
>
>
>
>
--
sc-as/snapshots/petsc-current/docs/manualpages/DA/DAGetGhostCorners.html#DAGetGhostCorners
So yes, you should only do the local portion of the calculation to set
set the values.
Ethan
> Thanks in advance,
> Likun
>
>
>
>
--
----
Ethan Coon
Post-
al and the post-processing is not too
expensive, you may find it easier to use the matlab or numpy/python
scripts in $PETSC_DIR/bin/matlab and $PETSC_DIR/bin/pythonscripts
respectively.
Ethan
>
> Thanks in advance,
> Best
> Mohamad
>
>
>
>
>
>
>
>
--
-
4 processors, he'd find
that his Y-direction would get split in 4 instead of splitting both X
and Y in 2.
Ethan
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
On Tue, 2011-10-11 at 11:22 -0500, Barry Smith wrote:
> On Oct 11, 2011, at 11:19 AM, Ethan Coon wrote:
>
> >
> >
> > On Sat, 2011-10-08 at 08:32 -0500, Jed Brown wrote:
> >
> >>
> >> I'm a little surprised it doesn't find the "
recision, then you can still solve big problems this way
> > (2^53 is a big number), but I still find it aesthetically displeasing.
>
> So let's increase the complexity of PETSc exponentially JUST so one
> little thing won't be "aesthetically displeasing"?
>
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
SetSizes(v2, PETSC_DECIDE, 5000);
> VecSetFromOptions(v1);
> VecSetFromOptions(v2);
>
> VecSet(v1,1.0);
> VecSet(v2,2.0);
>
> VecAssemblyBegin(v1);
> VecAssemblyEnd(v1);
> VecAssemblyBegin(v2);
> VecAssemblyEnd(v2);
>
> VecDot(v1, v2, &r);
> return r;
> }
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
> >> cdef extern from "c_files/dot.h":
> >>void init()
> >>double dot()
> >>
> >> def mydot():
> >>#init();
> >>return dot();
> >>
> >> --- C Code ---
> >>
> >&
cLoad() to load the entries of K.
> >
> >Barry
> >
> >>
> >> second one is that do you have any similar examples?
> >>
> >> Nothing with the mixed-discretization of the Laplacian.
> >>
> >>Matt
> >>
> >>
n
> Has anybody used a DMDA to create a dual DMDA?
>
> Any advice would be appreciated,
>
> Tim
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
b
I'll look a little closer into whether it is PETSc or petsc4py...
Thanks,
Ethan
--
----
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
and make a copy if not true before
it grabs the underlying c-array?
Ethan
On Fri, 2013-01-18 at 10:55 -0700, Ethan Coon wrote:
> First, apologies for not looking into this more closely, but I wanted to
> make sure I wasn't missing something stupid before I rebuilt petsc-dev
> and
tions?
Thanks,
Ethan
--
-
Ethan Coon
Post-Doctoral Researcher
Mathematical Modeling and Analysis
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
-
t, this is what I was missing. This should do the trick. Thanks
Barry.
Ethan
> to local_indices and you have a list of global indices depending on what you
> want you do with this beast you may need to scale by bs or 1/bs
>
>Barry
>
>
> On Dec 15, 2010, at 1:09 PM, Eth
l VecRestoreArrayF90(x,xx_v,ierr)
> > > >
> > > > ...
> > > >
> > > > But, the error keeps coming out when call VecGetArrayF90(x,xx_v,ierr)
> > > > and call VecRestoreArrayF90(x,xx_v,ierr) are not commented off.
> > > >
> > > >
> > > > The error information shows:
> > > > Caught signal number 11 SEGV: Segmentation Violation, probably memory
> > > > access out of range
> > > >
> > > > [0]PETSC ERROR: - Stack Frames
> > > >
> > > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> > > > available,
> > > > [0]PETSC ERROR: INSTEAD the line number of the start of the function
> > > > [0]PETSC ERROR: is given.
> > > > [0]PETSC ERROR: [0] F90Array1dCreate line 52 src/sys/f90-src/f90_cwrap.c
> > > > [0]PETSC ERROR: - Error Message
> > > >
> > > >
> > > > I checked the code according the example, but cannot see any difference
> > > > to that. Just don't know why the pointer array xx_v doesn't work here?
> > > > Thanks.
> > > >
> > > >
> > >
> >
>
--
-
Ethan Coon
Post-Doctoral Researcher
Mathematical Modeling and Analysis
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
-
\src\snes\examples\tutorials\ as following,
> > > > >
> > > > > PetscScalar, pointer :: xx_v(:)
> > > > >
> > > > > ...
> > > > > call KSPSolve(ksp,b,x,ierr)
> > > > > call VecView(x,PETSC_VIEWER_STDOUT_WOR
---
On Wed, 2011-01-05 at 13:21 -0600, Barry Smith wrote:
> I don't think this is correct. You are suppose to use the local indexing for
> each process. With the strange index starting at 1 instead of 0.
>
>
>Barry
>
>
> On Jan 5, 2011, at 1:03 PM, Ethan Coon
On Sat, 2011-02-05 at 19:19 -0500, Gaetan Kenway wrote:
> Hello
>
> I'm wondering if it is possible to put an external procedure reference
> in a ctx() in fortran.
>
> I'm in the process of writing a Newton--Krylov solver for an
> aero-structural system. My two different codes are wrapped with
: Hangup
(signal 1)
--
--------
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
On Thu, 2011-02-17 at 10:35 -0600, Matthew Knepley wrote:
> On Thu, Feb 17, 2011 at 10:06 AM, Ethan Coon wrote:
> So I thought I understood how VecScatters worked, but
> apparently not.
> Is it possible to create a general VecScatter from an
>
red-libraries=1 --download-hdf5=1
> > [0]PETSC ERROR:
> >
>
>
> > [0]PETSC ERROR: VecScatterCreate() line 1432 in
> > src/vec/
ed in that case. In that case, you still have to
pass something in to KSPSetOperators, so Amat for both is the likely
choice.
Ethan
>
> Thank you,
>
> Gaurish
>
>
>
>
>
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
l row %d value %d",i,nnz[i]);
> > > >if (nnz[i] > B->cmap->n)
> > > > SETERRQ3(PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater
> > > > than row length: local row %d value %d rowlength %
> > > > d",i,nnz[i],B->cmap->n);
> > > > }
> > > >}
> > > >
> > > > But why is nnz nonzero? I passed PETSC_NULL. It seems
> > > > like macros CHKFORTRANNULLINTEGER in matcreateseqaij_
> > > > should set it to zero, but it doesn't.
> > > >
> > > >
> > > >
> > > > Thanks.
> > > >
> > > > On 06.03.2011 16:49, Jed Brown wrote:
> > > >
> > > >
> > > > >
> > > > > On Sun, Mar 6, 2011 at 07:39, Alexander Grayver
> > > > wrote:
> > > > >>
> > > > >> Hello,
> > > > >...
> > > >
> > > >
> >
> >
> >
> >
> >
> > --
> > 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
>
--
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
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