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On 11/11/14 15:18, Jed Brown wrote:
...
Matt and I have a long-running disagreement about nullspace
handling in PETSc. He added the code that hangs it on an IS
despite it not logically belonging on IS, simply because the
implementation in
Hello,
I have a 3d DMDA and a vector created by DMCreateGlobalVector. I want to
visualize and therefore export a subset of the values, i.e. I want to
remove some points at the boundary. For example, if the DMDA
represents the domain [0,1]^3, I want to extract [0.25,0.75]^3.
I already tried to
On Wed, Nov 12, 2014 at 9:56 AM, Christopher Thiele
christopher.thi...@itwm.fraunhofer.de wrote:
Hello,
I have a 3d DMDA and a vector created by DMCreateGlobalVector. I want to
visualize and therefore export a subset of the values, i.e. I want to
remove some points at the boundary. For
I am trying to read in a sparse matrix file in binary format (.dat file) to set
it up as MPIBAIJ for MPIMatMult. I don't think I'm doing the file reading or
the matrix and vector setup correctly. Should the file loading, matrix setup,
and loading be done only on rank 0 together with the vector
1) remove all the preload stuff
2) MatLoad doesn't require or use the Mat preallocation stuff so remove all
of that
3) MatLoad determines the global matrix size from the binary file so do not
set that before calling MatLoad
4) All processes in the comm (in your case MPI_COMM_WORLD)
Hi,
I am solving an over-determined linear system Ax=b and b=0.
A size: 296856 x 14430
x (non-zero guess): 14430
b (zero): 296856
All of them are using seq mode to create, so one node will solve this.
However I got this error:
[0]PETSC ERROR: Nonconforming object sizes!
[0]PETSC ERROR: Mat
The calling sequence for KSPSolve is KSPSolve(KSP ksp,Vec b,Vec x), perhaps
you have the b and the x backwards in your call?
Barry
On Nov 12, 2014, at 2:23 PM, Brian Yang brianyang1...@gmail.com wrote:
Hi,
I am solving an over-determined linear system Ax=b and b=0.
A size:
Thank you for the prompt response. I checked and my usage of KSPSolve is
correct.
Besides, the assertion line is:
if (*mat-rmap-N* != *y-map-N*)
SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,Mat mat,Vec y: global dim %D
%D,mat-rmap-N,y-map-N);
On Wed, Nov 12, 2014 at 2:29 PM, Barry Smith
Oh, right CG only works for square matrices.
I think you should be using lsqr. See
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPLSQR.html
Note if you want to use preconditioning you need to pass for the second matrix
the product of the transpose of the matrix times
Wow, it works... LSQR is fine with the problem. Thanks!
On Wed, Nov 12, 2014 at 3:06 PM, Barry Smith bsm...@mcs.anl.gov wrote:
Oh, right CG only works for square matrices.
I think you should be using lsqr. See
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPLSQR.html
Thanks for your reply. I thought about changing the constructor
parameters, too, but I found it rather complicated and it exceeds my
current PETSc knowledge. So maybe you are right and I should use the
visualization tool if there is no other way to do it with PETSc.
Regards,
Christopher
On
Hello,
I have a DMDA vector and I need to set values in locations which are in
different processors. I am going over the mesh points in z,y and x directions
so I know the k,j,i indices of every point. However the 3D array obtained using
DMDAVecGetArray will not let me access the points
On Nov 12, 2014, at 3:48 PM, Ghosh, Swarnava sghosh2...@gatech.edu wrote:
Hello,
I have a DMDA vector and I need to set values in locations which are in
different processors. I am going over the mesh points in z,y and x directions
so I know the k,j,i indices of every point.
Thanks,
the option -help was quite useful and I got things to work fine with
icntl_14 50.
Best,
Luc
On 11/11/2014 11:07 AM, Hong wrote:
Luc:
Run your code with option '-help |grep mumps', then you'll see what
prefix should be used in your case with the mumps option
'-mat_mumps_icntl_14
Thank you, Barry. That took care of most of the issues. Two more things:
1) The code runs (MatMult executes) for block size =1. For block sizes 1. For
instance, block size = 3, throws:
PETSC ERROR: Arguments are incompatible!
[0]PETSC ERROR: Cannot change block size 3 to 1!
Matrix setup:
Lawrence Mitchell lawrence.mitch...@imperial.ac.uk writes:
So is the problem that the nullspace belongs to the appropriate
operator, but at the point you tell the solver, you don't necessarily
have all the operators to hand? Moreover, depending on the PC choice,
the nullspaces of the operator
I agree with what Jed says.
One could argue that if the matrix was represented as a MatNest, the null
space of the Schur complement is a property of the MatNest object and hence
could/should be something that is attached to the matrix. Now if the Mat
happens not to be a MatNest, the null
Barry Smith bsm...@mcs.anl.gov writes:
Perhaps we need a generic way of attaching null spaces to parts of
matrices and to parts of matrices in different basis (which is what
a Schur complement is). So (and this is likely overly simplistic)
one could supply a null space, an index
On Nov 12, 2014, at 7:49 PM, Jed Brown j...@jedbrown.org wrote:
Barry Smith bsm...@mcs.anl.gov writes:
Perhaps we need a generic way of attaching null spaces to parts of
matrices and to parts of matrices in different basis (which is what
a Schur complement is). So (and this is likely
Barry Smith bsm...@mcs.anl.gov writes:
Indeed it could. Perhaps we could start by unifying the concept of a
sub matrix and a Schur complement of the same part of the matrix?
I'm not sure how to do that.
We can certainly define an interface that works this way, but I'm not
sure it's
On Wed Nov 12 2014 at 7:49:28 PM Jed Brown j...@jedbrown.org wrote:
Barry Smith bsm...@mcs.anl.gov writes:
Perhaps we need a generic way of attaching null spaces to parts of
matrices and to parts of matrices in different basis (which is what
a Schur complement is). So (and this is
Ok, for now run with the additional command line option -matload_block_size
3 and I'll fix the code to take the size in the matrix.
Barry
On Nov 12, 2014, at 6:48 PM, Steena M stm8...@yahoo.com wrote:
Thank you, Barry. That took care of most of the issues. Two more things:
1) The
Dmitry Karpeyev karp...@mcs.anl.gov writes:
I think the problem-specific solver configuration can be carried out by an
additional user-specified callback (attached, e.g., using PCSetUserSetUp())
called from PCSetUp().
The problem of propagating it down the hierarchy can be solved by using DMs
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