[petsc-dev] Indexing only the most recent man pages

2011-06-07 Thread Jed Brown
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[petsc-dev] ILU factorization very slow

2011-06-07 Thread Barry Smith
Never mind. My fault. I was using -malloc_debug with the inode LU factorization On Jun 7, 2011, at 10:16 AM, Barry Smith wrote: > >The flop rate for ILU numeric for AIJ matrices seems to have dropped > through the floor in petsc-dev. Any thoughts on what was changed there > recently? >

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Jed Brown
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[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Jed Brown
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[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Jed Brown
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[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Jed Brown
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[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Jed Brown
ing in parallel, this step usually does a copy anyway (e.g. DMDA). -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20110607/d4dcb7ce/attachment.html>

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Jed Brown
ve that API and get the data to go directly into a PETSc format? -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20110607/aceeebc0/attachment.html>

[petsc-dev] SNESLineSearchSetPostCheck not being called in petsc 3.1-p8

2011-06-07 Thread Matthew Knepley
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[petsc-dev] SNESLineSearchSetPostCheck not being called in petsc 3.1-p8

2011-06-07 Thread David Andrs
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[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Boyce Griffith
On 6/7/11 2:32 PM, Jed Brown wrote: > On Tue, Jun 7, 2011 at 20:17, Boyce Griffith > wrote: > > At one point, I tried implementing the local part of the matrix-free > matrices use PETSc Mat's, but performance was modestly lower than a > pure Fortran i

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Philip, Bobby
From: petsc-dev-bounces at mcs.anl.gov [petsc-dev-bounces at mcs.anl.gov] On Behalf Of Jed Brown [j...@59a2.org] Sent: Tuesday, June 07, 2011 2:40 PM To: For users of the development version of PETSc Subject: Re: [petsc-dev] Integrating PFLOTRAN, PETSC & S

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Boyce Griffith
On 6/7/11 2:42 PM, Jed Brown wrote: > On Tue, Jun 7, 2011 at 20:41, Boyce Griffith > wrote: > > Nope; to keep SAMRAI stuff working like regular SAMRAI stuff, the > ghost values wind up in the middle of the vector. At least with the > standard data ty

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Boyce Griffith
On 6/7/11 2:32 PM, Jed Brown wrote: > An alternative, which I had in mind when I said that I was > interested in trying to use PETSc to provide the storage for the > SAMRAI data structures, is to use SAMRAI to provide basic grid > management, and to use PETSc to provide data stora

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Boyce Griffith
On 6/7/11 2:24 PM, Philip, Bobby wrote: > Jed: > > SAMRAI has a fairly typical structured AMR design.There is a list or array of > refinement levels that together form the AMR hierarchy and > each refinement level has a set of logically rectangular patches. Data is > only contiguous on a patch.

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Philip, Bobby
From: Boyce Griffith [griff...@cims.nyu.edu] Sent: Tuesday, June 07, 2011 2:35 PM To: For users of the development version of PETSc Cc: Philip, Bobby Subject: Re: [petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI On 6/7/11 2:24 PM, Philip, Bobby wrote: > Je

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Philip, Bobby
Jed: Realized I never addressed your question on matrices. I do use matrices on each refinement level storing them as stencils at each grid point. However, I never form a global matrix - this was something we did attempt a while ago for a particular problem and realized it is a nightmare. Most

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Philip, Bobby
Jed: SAMRAI has a fairly typical structured AMR design.There is a list or array of refinement levels that together form the AMR hierarchy and each refinement level has a set of logically rectangular patches. Data is only contiguous on a patch. Patches on different refinement levels can overlap o

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Boyce Griffith
On 6/7/11 1:43 PM, Jed Brown wrote: > On Tue, Jun 7, 2011 at 19:05, Boyce Griffith > wrote: > > Another might be easier access to CUDA. > > > What do SAMRAI matrices look like? In particular, how are they constructed? There is not a notion of matrices in SAM

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Philip, Bobby
Boyce: I recognize the benefits and we should talk about this more. In my case I do have my own data types too for interlaced data and it would be nice to have it all work well. As you know, it's non trivial maintaining all this. The reason this whole conversation started was difficulties in t

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Boyce Griffith
On 6/7/11 12:48 PM, Bobby Philip wrote: > > On Jun 6, 2011, at 4:26 PM, Boyce Griffith wrote: >> >> What I'd really like to do is to setup some SAMRAI stuff that actually >> uses Vec / Mat for data storage, so that most of this wrapper stuff is >> not necessary. (It would probably still be neces

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Boyce Griffith
On 6/7/11 12:47 PM, Bobby Philip wrote: >> >> All I can tell you is that, many years ago, at least some of these calls >> to PetscObjectStateIncrease() were needed in the Vec routines in order >> to get PETSc solvers to work with the SAMRAI PETSc Vec class. To try to >> avoid the issues that Bob

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Bobby Philip
Boyce: On Jun 6, 2011, at 4:26 PM, Boyce Griffith wrote: > > > On 6/6/11 4:09 PM, Barry Smith wrote: >> >> On Jun 6, 2011, at 2:57 PM, Boyce Griffith wrote: >> >>> Does anyone actually use the PETSc wrappers that are provided by SAMRAI? >>> (Even you, Bobby? :-) ) >>> >>> My impression is t

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Bobby Philip
> > All I can tell you is that, many years ago, at least some of these calls > to PetscObjectStateIncrease() were needed in the Vec routines in order > to get PETSc solvers to work with the SAMRAI PETSc Vec class. To try to > avoid the issues that Bobby is reporting, I went ahead and made any

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Bobby Philip
On Jun 6, 2011, at 3:57 PM, Boyce Griffith wrote: > Does anyone actually use the PETSc wrappers that are provided by SAMRAI? > (Even you, Bobby? :-) ) > I do - only I maintain my own version which is consistent with the release and dev versions of SAMRAI. However, each new update of PETSc o

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Bobby Philip
Barry: There might be bugs in the implementation. On the other hand when it is a user defined Vec as in SAMRAI it is unclear how you would/could make it more error-proof within changing some of the present structure. Bobby On Jun 6, 2011, at 3:55 PM, Barry Smith wrote: > > On Jun 6, 2011, a

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Bobby Philip
Barry: Them is SAMRAI. Not sure whether you should kick or use some gentler means :-) On Jun 6, 2011, at 3:47 PM, Barry Smith wrote: > > On Jun 6, 2011, at 2:40 PM, Bobby Philip wrote: > >> What usually breaks for me is VecNorm caching, arguments for functions, >> and introduction of new func

[petsc-dev] Compiling ML on windows

2011-06-07 Thread Matthew Knepley
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-dev/attachments/20110607/53037047/attachment.html>

[petsc-dev] ILU factorization very slow

2011-06-07 Thread Barry Smith
The flop rate for ILU numeric for AIJ matrices seems to have dropped through the floor in petsc-dev. Any thoughts on what was changed there recently? Barry

[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

2011-06-07 Thread Jed Brown
orState(y,y,axpy,(y,alpha,x)); -- next part -- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20110607/6518207f/attachment.html>