Re: [petsc-users] petsc4py: Passing command line switches

2015-03-25 Thread Florian Lindner
Am Mittwoch, 25. März 2015, 10:17:45 schrieb Matthew Knepley: On Wed, Mar 25, 2015 at 10:13 AM, Florian Lindner mailingli...@xgm.de wrote: Hello, I'm using the petsc4py. It works fine after some hurdling with missing documentation. (were not able to find API doc anywhere, I generated

Re: [petsc-users] petsc4py: Passing command line switches

2015-03-25 Thread Matthew Knepley
On Wed, Mar 25, 2015 at 10:13 AM, Florian Lindner mailingli...@xgm.de wrote: Hello, I'm using the petsc4py. It works fine after some hurdling with missing documentation. (were not able to find API doc anywhere, I generated it myself now). I try to use the switches like -ksp_monitor like

Re: [petsc-users] Load Vec from 1D HDF5 dataset MATT READ THIS EMAIL!

2015-03-25 Thread Håkon Strandenes
Did you come to any conclusion on this issue? Regards, Håkon On 20. mars 2015 22:02, Håkon Strandenes wrote: On 20. mars 2015 20:48, Barry Smith wrote: Why is 1 dimension a special case that is not worthy of its own format? The same thing would hold for 2d and 3d. One could then argue that we

[petsc-users] petsc4py: Passing command line switches

2015-03-25 Thread Florian Lindner
Hello, I'm using the petsc4py. It works fine after some hurdling with missing documentation. (were not able to find API doc anywhere, I generated it myself now). I try to use the switches like -ksp_monitor like that: import petsc4py from petsc4py import PETSc petsc4py.init(sys.argv) but no

Re: [petsc-users] petsc4py: Passing command line switches

2015-03-25 Thread Matthew Knepley
On Wed, Mar 25, 2015 at 10:29 AM, Florian Lindner mailingli...@xgm.de wrote: Am Mittwoch, 25. März 2015, 10:17:45 schrieb Matthew Knepley: On Wed, Mar 25, 2015 at 10:13 AM, Florian Lindner mailingli...@xgm.de wrote: Hello, I'm using the petsc4py. It works fine after some hurdling

Re: [petsc-users] Column #j is wrong in parallel from message Inserting a new nonzero (i, j) into matrix

2015-03-25 Thread Matthew Knepley
On Wed, Mar 25, 2015 at 1:03 PM, Eric Chamberland eric.chamberl...@giref.ulaval.ca wrote: Hi, while looking for where in the world do I insert the (135,9) entry in my matrix, I have discovered that the column # shown is wrong in parallel! We have talked about this before. It is certainly

Re: [petsc-users] Column #j is wrong in parallel from message Inserting a new nonzero (i, j) into matrix

2015-03-25 Thread Eric Chamberland
On 03/25/2015 02:06 PM, Matthew Knepley wrote: On Wed, Mar 25, 2015 at 1:03 PM, Eric Chamberland eric.chamberl...@giref.ulaval.ca mailto:eric.chamberl...@giref.ulaval.ca wrote: Hi, while looking for where in the world do I insert the (135,9) entry in my matrix, I have discovered

Re: [petsc-users] Column #j is wrong in parallel from message Inserting a new nonzero (i, j) into matrix

2015-03-25 Thread Barry Smith
Eric, This is a good idea. I've fixed it for MatSetValues, MatSetValuesLocal, and MatSetValuesStencil, for AIJ,BAIJ, and SBAIJ matrices in the branch barry/fix-inserting-new-nonzero-column-location. Fixing for the MatSetValuesBlocked family of methods for BAIJ and SBAIJ is tricky

Re: [petsc-users] SLEPc - Generalized symmetric eigenproblem using ARPACK

2015-03-25 Thread Jose E. Roman
El 25/03/2015, a las 21:29, Harshad Sahasrabudhe escribió: Hi, I'm trying to use the ARPACK interface in SLEPc for calculating smallest eigenvalues with eigenvectors of a generalized eigenproblem. The matrices are symmetric. What are the suggested linear solvers/preconditioners for

Re: [petsc-users] SLEPc - Generalized symmetric eigenproblem using ARPACK

2015-03-25 Thread Harshad Sahasrabudhe
Absolutely. Also, with Krylov-Schur you can adjust the restart parameter (which is hidden in ARPACK); it may help improve convergence in some cases. Awesome. I'll just use Krylov-Schur then. Thanks. On Wed, Mar 25, 2015 at 5:18 PM, Jose E. Roman jro...@dsic.upv.es wrote: El 25/03/2015, a

Re: [petsc-users] SLEPc - Generalized symmetric eigenproblem using ARPACK

2015-03-25 Thread Harshad Sahasrabudhe
With MUMPS you should not get spurious eigenvalues. I get only a few spurious eigenvalues when using MUMPS with ARPACK, but the eigenvectors are definitely wrong. Did you try the krylovschur solver? Yes, Krylov-Schur gives me correct results. How do you know the eigenvalues are wrong? I'm

Re: [petsc-users] SLEPc - Generalized symmetric eigenproblem using ARPACK

2015-03-25 Thread Jose E. Roman
El 25/03/2015, a las 21:47, Harshad Sahasrabudhe escribió: With MUMPS you should not get spurious eigenvalues. I get only a few spurious eigenvalues when using MUMPS with ARPACK, but the eigenvectors are definitely wrong. Did you try the krylovschur solver? Yes, Krylov-Schur gives me

Re: [petsc-users] SLEPc - Generalized symmetric eigenproblem using ARPACK

2015-03-25 Thread Harshad Sahasrabudhe
Anyway, why do you insist in using ARPACK when SLEPc's Krylov-Schur work? ARPACK will not give you any further advantage. I thought ARPACK was faster when the system size is large and number of eigenvalues required is small. I will be working with sparse matrices of size ~60,000. Does SLEPC's

[petsc-users] SLEPc - Generalized symmetric eigenproblem using ARPACK

2015-03-25 Thread Harshad Sahasrabudhe
Hi, I'm trying to use the ARPACK interface in SLEPc for calculating smallest eigenvalues with eigenvectors of a generalized eigenproblem. The matrices are symmetric. What are the suggested linear solvers/preconditioners for this type of a system when using ARPACK? I am using shift and invert

Re: [petsc-users] SLEPc - Generalized symmetric eigenproblem using ARPACK

2015-03-25 Thread Jose E. Roman
El 25/03/2015, a las 22:06, Harshad Sahasrabudhe escribió: I thought ARPACK was faster when the system size is large and number of eigenvalues required is small. I will be working with sparse matrices of size ~60,000. Does SLEPC's Krylov-Schur have about the same performance as ARPACK

Re: [petsc-users] How do I set PETSc LU reuse factorization

2015-03-25 Thread Sun, Hui
Thank you Barry. Hui From: Barry Smith [bsm...@mcs.anl.gov] Sent: Wednesday, March 25, 2015 5:38 PM To: Sun, Hui Cc: petsc-users@mcs.anl.gov Subject: Re: [petsc-users] How do I set PETSc LU reuse factorization On Mar 25, 2015, at 6:50 PM, Sun, Hui