[petsc-users] MatMumpsSetIcntl from Fortran

2011-12-01 Thread Hong Zhang
>> PetscMallocAlign, >>>>>> ?FP=7fff342ca080 >>>>>> PetscTrMallocDefault, >>>>>> ?FP=7fff342ca180 >>>>>> PetscStrallocpy, >>>>>> FP=7fff342ca230 >>>>>> PetscFListGetPathAndFunction, >>>>>> ?FP=7fff342cb2e0 >>>>>> PetscFListFind, >>>>>> ?FP=7fff342cb520 >>>>>> PetscObjectQueryFunction_Petsc, >>>>>> ?FP=7fff342cb590 >>>>>> PetscObjectQueryFunction, >>>>>> ?FP=7fff342cb620 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cb720 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cb820 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cb920 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cba20 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cbb20 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cbc20 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cbd20 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cbe20 >>>>>> MatMumpsSetIcntl, >>>>>> ?FP=7fff342cbf20 >>>>>> ... (Hundreds of MatMumpsSetIcntl) ... >>>>>> >>>>>> What can I do about that? >>>>>> >>>>>> Regards, >>>>>> Alexander >>>> >>>> > -- next part -- A non-text attachment was scrubbed... Name: ex57f.F Type: application/octet-stream Size: 13471 bytes Desc: not available URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/0dc52308/attachment.obj>

[petsc-users] zeros in sparse aij

2011-12-01 Thread Xiangdong Liang
Thanks. If this is the case, will the option MAT_IGNORE_ZERO_ENTRIES be helpful? Xiangdong On Thu, Dec 1, 2011 at 8:00 PM, Barry Smith wrote: > > On Dec 1, 2011, at 6:44 PM, Xiangdong Liang wrote: > >> Hello everyone, >> >> I have a question about whether zeros will change the sparse pattern. >>

[petsc-users] zeros in sparse aij

2011-12-01 Thread Barry Smith
The checks in the code are lines like if (value == 0.0 && ignorezeroentries && (is == ADD_VALUES)) continue; hence changing the source code to ignore small values is not difficult. But I think this is a terribly cheesy hack and would hope people would not do this. Barry On De

[petsc-users] zeros in sparse aij

2011-12-01 Thread Barry Smith
On Dec 1, 2011, at 8:46 PM, Xiangdong Liang wrote: > Thanks. If this is the case, will the option MAT_IGNORE_ZERO_ENTRIES be > helpful? What do you mean by "be helpful"? Sometimes you do want those "zero" locations represented and sometimes you don't, so sometimes you would use the option

[petsc-users] zeros in sparse aij

2011-12-01 Thread Xiangdong Liang
Hello everyone, I have a question about whether zeros will change the sparse pattern. Suppose I am generating two sparse matrices A and B. A is generated with exactly number of nonzeros, say 10 nnz per row. When I generate matrix B, I specify 12 nonzeros, but two of them are given zero values by M

[petsc-users] zeros in sparse aij

2011-12-01 Thread Barry Smith
On Dec 1, 2011, at 6:44 PM, Xiangdong Liang wrote: > Hello everyone, > > I have a question about whether zeros will change the sparse pattern. > Suppose I am generating two sparse matrices A and B. A is generated > with exactly number of nonzeros, say 10 nnz per row. When I generate > matrix B,

[petsc-users] zeros in sparse aij

2011-12-01 Thread Mohamad M. Nasr-Azadani
introduce an increase in the pattern. > > >BTW: if you then load the matrix via a binary file to MATLAB it may be > that MATLAB silently removes those locations so you don't see them. > Barry > > > Thanks. > > > > Best, > > Xiangdong > > ---

[petsc-users] VecGet/RestoreArray and related functions

2011-12-01 Thread Chetan Jhurani
write accessors so that I can do the following: Vector a (PETSC_COMM_WORLD, PETSC_DECIDE,10); // make a petsc vector of global length 10 using my own wrappers for (int i=0; ihttp://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/9db53cf2/attachment.htm>

[petsc-users] VecGet/RestoreArray and related functions

2011-12-01 Thread Barry Smith
On Dec 1, 2011, at 4:48 PM, Mohammad Mirzadeh wrote: > Hi guys, > > I am having a conceptual problem trying to design my vector wrappers for my > application. The problem is some of vector functionality in PETSc require > extra function calls which makes it hard to design a good wrapper. One

[petsc-users] VecGet/RestoreArray and related functions

2011-12-01 Thread Matthew Knepley
re they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/1110a18f/attachment.htm>

[petsc-users] VecGet/RestoreArray and related functions

2011-12-01 Thread Mohammad Mirzadeh
omehow nullify the pointer to prevent accidental use of pointer? > Since all pointers all private members of my class I assume this is safe > then unless these two functions are actually doing some extra work? > > > > 2) Is there any better way of writing these wrappers and get around the > problem of having to call "supplemental" functions safely? > > > > Sorry if my lack of knowledge is causing all these confusion. > > > > Thanks, > > Mohammad > > > > > > -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/349256ac/attachment.htm>

[petsc-users] VecGet/RestoreArray and related functions

2011-12-01 Thread Mohammad Mirzadeh
;> problem of having to call "supplemental" functions safely? >> >> Sorry if my lack of knowledge is causing all these confusion. >> >> Thanks, >> Mohammad >> >> >> > > > -- > 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 > -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/34c4f649/attachment-0001.htm>

[petsc-users] VecGet/RestoreArray and related functions

2011-12-01 Thread Mohammad Mirzadeh
th is the following: I am trying to write accessors so that I can do the following: Vector a (PETSC_COMM_WORLD, PETSC_DECIDE,10); // make a petsc vector of global length 10 using my own wrappers for (int i=0; ihttp://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/e91b2754/attachment.htm>

[petsc-users] MATBDIAG in > 3.1

2011-12-01 Thread Parker, Andrew (UK Filton)
I have tried to use the following, this was before I had both you're emails (Barry, Matthew) ;-) 1) First I set this up PetscInt size = 7; MatCreate(MPI_COMM_SELF,&LHS); MatSetSizes(LHS,size,size,size,size); MatSetType(LHS,MATSEQDENSE); //**NOTE THIS LINE

[petsc-users] MATBDIAG in > 3.1

2011-12-01 Thread Barry Smith
My approach will be a million times faster. Barry On Dec 1, 2011, at 8:50 AM, Matthew Knepley wrote: > On Thu, Dec 1, 2011 at 8:44 AM, Parker, Andrew (UK Filton) baesystems.com> wrote: > I have tried to use the following, this was before I had both you're > emails (Barry, Matthew) ;-) >

[petsc-users] Questions about setting values for GPU based matrices

2011-12-01 Thread Fredrik Heffer Valdmanis
>>> >> Yes. The same matrices yields a speedup of 4-6x when solving the system >> on the GPU. >> > > Please confirm that the correct routine by running wth -info and sending > the output. > > Please send the output of -log_summary so I can confirm the results. > > You can run KSP ex4 and reproduce my results where I see a 5.5x speedup on > the GTX285 > > I am not sure what to look for in those outputs. I have uploaded the output of running my assembly program with -info and -log_summary, and the output of running ex4 with -log_summary. See http://folk.uio.no/fredva/assembly_info.txt http://folk.uio.no/fredva/assembly_log_summary.txt http://folk.uio.no/fredva/ex4_log_summary.txt Trying this on a different machine now, I actually see some speedup. 3rd order Poisson on 300x300 assembles in 0.211 sec on GPU and 0.4232 sec on CPU. For 1st order and 1000x1000 mesh, I go from 0.31 sec to 0.205 sec. I have tried to increase the mesh size to see if the speedup increases, but I hit the bad_alloc error pretty quick. For a problem of that size, should I expect even more speedup? Please let me know if you need any more output from test runs on my machine. -- Fredrik -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/460366cb/attachment.htm>

[petsc-users] A postdoctoral position at Argonne involving PETSc

2011-12-01 Thread Dmitry Karpeev
y of Chicago 5735 S. Ellis Avenue Chicago, IL 60637 --- Phone: 630-252-1229 Fax: 630-252-5986 -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/a1803c73/attachment.htm>

[petsc-users] A postdoctoral position at Argonne involving PETSc

2011-12-01 Thread Dmitry Karpeev
-252-1229 Fax: 630-252-5986 -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/0caf9b48/attachment.htm>

[petsc-users] MATBDIAG in > 3.1

2011-12-01 Thread Parker, Andrew (UK Filton)
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[petsc-users] MatMumpsSetIcntl from Fortran

2011-12-01 Thread Alexander Grayver
Hong, This should be enough to reproduce the problem: call KSPCreate(PETSC_COMM_WORLD,ksp,ierr);CHKERRQ(ierr) call KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN,ierr);CHKERRQ(ierr) call KSPSetType(ksp,KSPPREONLY,ierr);CHKERRQ(ierr) call KSPGetPC(ksp,pc,ierr);CHKERRQ(ierr) call

[petsc-users] MATBDIAG in > 3.1

2011-12-01 Thread Matthew Knepley
**** > > > > > > > > > > -- > > 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 > > > -- 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 -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/4275a819/attachment.htm>

[petsc-users] MATBDIAG in > 3.1

2011-12-01 Thread Barry Smith
On Dec 1, 2011, at 7:05 AM, Matthew Knepley wrote: > You can get this effect using PCBJACOBI, setting the number of local blocks, > and using -sub_pc_type lu -sub_ksp_type preonly. Do not do this. It will give bad performance since it explicitly pulls out each block with MatGetSubMatrices()

[petsc-users] MATBDIAG in > 3.1

2011-12-01 Thread Matthew Knepley
which their experiments lead. -- Norbert Wiener -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20111201/01fa51b5/attachment.htm>

[petsc-users] Questions about setting values for GPU based matrices

2011-12-01 Thread Matthew Knepley
dispatching to the CUDA version. The regular >>>> version just calls MatSetValues() in a loop. Are you >>>> using a SEQAIJCUSP matrix? >>>> >>> Yes. The same matrices yields a speedup of 4-6x when solving the system >>> on the GPU. >&g