Re: [petsc-users] Could be a bug on hypre with petsc

2015-04-20 Thread Barry Smith
It could be a bug or it could just be sloppyness where they send uninitialized data that they never use at the other end. Either way you should submit it to the hypre team so they can decide if they want to fix it. Barry On Apr 19, 2015, at 6:55 PM, Sun, Hui hus...@ucsd.edu wrote: I'm

Re: [petsc-users] Tao iterations

2015-04-20 Thread Justin Chang
Jason, I am using TaoGetSolutionStatus(tao,its, ...) and it gives me exactly what I want. However, I seem to be having an issue with blmvm I wrote my own backward euler code for a transient linear diffusion problem with lower bounds = 0 and upper bounds = 1. For the first several time steps I am

[petsc-users] design philosophy question

2015-04-20 Thread Gideon Simpson
In cutting up a petsc code into subroutines, is there any design philosophy as to when to call global routines, like assemble? The problem I have in mind is that I want to build up a matrix, allowing for it to be of MPIAIJ type. Currently, I’m populating it row by row with a loop using

[petsc-users] Create identity IS

2015-04-20 Thread Florian Lindner
Hello, I use an index set for a row mapping but don't want to use one for the column mapping. I try to create an idenitity index set to supply to ISLocalToGlobalMappingCreateIS and MatSetLocalToGlobalMapping: IS is; ISCreate(PETSC_COMM_WORLD, is); ISSetIdentity(is); but I get an

Re: [petsc-users] Matrix assebly

2015-04-20 Thread Barry Smith
You would simply call MatSetValues() to change those values (or MatSetValuesBlocked, etc). There are no special routines for changing columns. Barry On Apr 20, 2015, at 3:05 AM, siddhesh godbole siddhesh4godb...@gmail.com wrote: Hello, I have created a matrix with initial values

Re: [petsc-users] Create identity IS

2015-04-20 Thread Florian Lindner
Am Montag, 20. April 2015, 14:57:58 schrieb Lisandro Dalcin: On 20 April 2015 at 14:35, Florian Lindner mailingli...@xgm.de wrote: Hello, I use an index set for a row mapping but don't want to use one for the column mapping. I try to create an idenitity index set to supply to

Re: [petsc-users] petsc 3.4.3 to 3.5.3

2015-04-20 Thread Barry Smith
On Apr 20, 2015, at 4:06 AM, carol.brick...@awe.co.uk carol.brick...@awe.co.uk wrote: All, I am switching to petsc 3.5.3 and finding some differences with 3.4.3. KSPSetOperators no longer has the MatStructure argument. I see for SAME_PRECONDITIONER that you now use

Re: [petsc-users] Create identity IS

2015-04-20 Thread Lisandro Dalcin
On 20 April 2015 at 14:35, Florian Lindner mailingli...@xgm.de wrote: Hello, I use an index set for a row mapping but don't want to use one for the column mapping. I try to create an idenitity index set to supply to ISLocalToGlobalMappingCreateIS and MatSetLocalToGlobalMapping: IS is;

[petsc-users] Matrix assebly

2015-04-20 Thread siddhesh godbole
Hello, I have created a matrix with initial values and i want to change the elements of the same matrix and in the iterations column wise. how do i insert new columns into the matrix when calls for assembly begin and end have already been made? I have used MatGetColumnVector to select which

Re: [petsc-users] Uninterpolating a distributed mesh

2015-04-20 Thread Justin Chang
Matt, I have attempted to implement this, called UninterpolateSF(), and attached is the code for the function. However, I suspect that there are bugs because when I refine the mesh via -dm_refine my program crashes. In my program I have the following lines for uninterpolating a distributed mesh:

[petsc-users] PhD position on developing software to model hydrofracturing in geothermal systems

2015-04-20 Thread Boris Kaus
Dear PETSC-users, I have an open PhD position in my group to develop codes to simulate hydrofracturing in visco-elasto-plastic rocks using massively parallel computers. We will use PETSC for this, so in case you are interested or you know someone that might be interested please let them know.

[petsc-users] petsc 3.4.3 to 3.5.3

2015-04-20 Thread Carol.Brickley
All, I am switching to petsc 3.5.3 and finding some differences with 3.4.3. KSPSetOperators no longer has the MatStructure argument. I see for SAME_PRECONDITIONER that you now use KSPSetReusePreconditioner with flag set to tru before the call to set to true KSPSetOperators. Is there any need

[petsc-users] EPS performance

2015-04-20 Thread siddhesh godbole
hello i am trying to solve generalized eigenvalue problem using eps solver. i have a monte carlo loop in the program which has to run for about 1000 times. matrix sizes are 15 X 15 as a dummy problem and 23040 X23040 in the real problem. as i run the program i see that eps takes increasingly more

Re: [petsc-users] EPS performance

2015-04-20 Thread Jose E. Roman
El 20/04/2015, a las 17:09, siddhesh godbole escribió: hello i am trying to solve generalized eigenvalue problem using eps solver. i have a monte carlo loop in the program which has to run for about 1000 times. matrix sizes are 15 X 15 as a dummy problem and 23040 X23040 in the real

[petsc-users] How to solve a matrix with zero diagonal entries?

2015-04-20 Thread Song Gao
Dear Petsc-users, I modified the code based on KSP ex1f. I'm solving a 2D stream function vorticity finite element problem. The problem is relatively small, around 2500x2500. I choose to use single processor and LU preconditioner. But the algorithm set some zeros on the diagonals. By checking the