Re: [petsc-dev] build of manual

The problem is in line 5216 \noindent\textbf{\trl{TSAdapt} basic.} If you change the word TSAdapt (e.g. add a random character), the error would disappear. Probably it is conflicting with something else. Hong > On Sep 12, 2016, at 10:01 AM, Barry Smith wrote: > > >

Re: [petsc-dev] question about time integrators, TS

ht? > > On Wed, Aug 3, 2016 at 3:01 PM, Hong Zhang <hongzh...@anl.gov> wrote: >> If you use a fully implicit method such as backward Euler, the G Jacobian >> will be used by PETSc. If you switch to an explicit method, the G Jacobian >> function will not be used. For

Re: [petsc-dev] BDF implementation

If there are state changes in the post event callback, then multistep methods would not be a good choice for the application. I would use multistage methods such as RK type instead. However, restarting the time stepper may still be necessary for other types of discontinuities, e.g. changes in

[petsc-dev] mpich-3.2 broken on OS X 10.11

I am not sure if I am the only one getting segmentation faults when building PETSc with mpich-3.2 (by default) on OS X 10.11. 'make testing' in mpich directory also fails. After I switch back to mpich-3.1, everything goes back to normal. Hong

Re: [petsc-dev] src/ts/examples/tutorials/ex19adj.c missing?

Author: Hong Zhang hongzh...@anl.gov Date: Sun Nov 23 08:19:16 2014 -0600 change names for the quadrature term in the cost function include/petsc-private/tsimpl.h | 2 +- include/petscts.h | 4 ++-- src/ts/examples/tutorials/makefile | 16 +--- src

Re: [petsc-dev] TSSolve web page JED and EMIL READ THIS!

This is a good heads-up for me. Actually I wanted that our adjoint models could handle forward integrations like this: TSSolve(ts,u); TSStep(ts); TSSolve(ts,u); Then the reverse run would look like: TSAdjointSolve(ts); TSAdjointStep(ts); TSAdjointSolve(ts); This flexibility should be very

[petsc-dev] summer students

Dear PETSc developers, Please send me your summer student's name, email, and project direction (optional). I like to hold bi-weekly informal gatherings for them. Thanks, Hong

Re: [petsc-dev] getting rid of annoying old branches

Barry, The branch origin/barry/saws-options is the one we are currently working on. Do NOT remove it. Hong On Fri, Apr 11, 2014 at 5:44 PM, Smith, Barry F. bsm...@mcs.anl.gov wrote: How do I get rid of these meaningless old branches? ~/Src/petsc next $ git branch -D

Re: [petsc-dev] Chebyshev hybrid option has no functional interface or man pages

Barry, I sent this email out, but apparently it failed to reach you. On Tue, Mar 11, 2014 at 10:46 PM, Hong Zhang hzh...@mcs.anl.gov wrote: Barry, The hybrid Chebyshev was implemented for experimentation, but had not been found useful, so the default is set as FALSE. I can add a functional

Re: [petsc-dev] Chebyshev hybrid option has no functional interface or man pages

PM, Hong Zhang hzh...@mcs.anl.gov wrote: Barry, I sent this email out, but apparently it failed to reach you. On Tue, Mar 11, 2014 at 10:46 PM, Hong Zhang hzh...@mcs.anl.gov wrote: Barry, The hybrid Chebyshev was implemented for experimentation, but had not been found useful, so the default

Re: [petsc-dev] Chebyshev hybrid option has no functional interface or man pages

Barry, The hybrid Chebyshev was implemented for experimentation, but had not been found useful, so the default is set as FALSE. I can add a functional interface though. Hong On Tue, Mar 11, 2014 at 9:15 PM, Smith, Barry F. bsm...@mcs.anl.gov wrote: There should be a functional interface for

Re: [petsc-dev] Chebyshev hybrid option has no functional interface or man pages

-pc_gamg_reuse_interpolation true 0 KSP Residual norm 2884.32 ... 11 KSP Residual norm 0.00529973 adding '-mg_levels_ksp_chebyshev_hybrid' may skew the convergence: 0 KSP Residual norm 3327.84 ... 12 KSP Residual norm 0.0197856 I'll remove it. Hong On Mar 14, 2014, at 2:20 PM, Hong Zhang hzh

[petsc-dev] Fwd: [MCS Staff] Jed Brown wins the SIAG/Supercomputing Junior Scientist Prize

Jed, Congratulates!!! Hong -- Forwarded message -- From: Snir, Marc s...@anl.gov Date: Sat, Jan 18, 2014 at 3:12 PM Subject: [MCS Staff] Jed Brown wins the SIAG/Supercomputing Junior Scientist Prize To: m...@mcs.anl.gov m...@mcs.anl.gov Please join me in congratulating Jed Brown

Re: [petsc-dev] Invalid read in PetscSubcommSetTypeGeneral

Stefano: Hong, currently in master there's an error in PetscSubcommSetTypeGeneral, namely in the loop starting at line 188 for (i=0; i2*size; i++) {subsize[recvbuf[i]] = recvbuf[i+1];} recvbuf is allocated at line 178 as 2*size*sizeof(PetscMPIInt), and the loop tries to read at

Re: [petsc-dev] Mat_CheckInode_FactorLU has malloc in inner inner loops

I'll investigate it. Hong On Wed, Aug 14, 2013 at 12:39 PM, Barry Smith bsm...@mcs.anl.gov wrote: Mat_CheckInode_FactorLU() has mallocs inside very tight loops and spends a lot of time in them. Surely a single large enough malloc could be done initially? Barry

Re: [petsc-dev] future of PetscSubcomm

Yes, I'm working on it. Hong On Wed, Jul 31, 2013 at 4:45 PM, Barry Smith bsm...@mcs.anl.gov wrote: https://bitbucket.org/petsc/petsc/issue/46/replace-petscsubcomm-with-the-information On Jul 31, 2013, at 10:59 AM, Jed Brown jedbr...@mcs.anl.gov wrote: Barry Smith bsm...@mcs.anl.gov

Re: [petsc-dev] fun plots

Why Satish and several petsc developers are missing from the list of contributors? Hong On Tue, Jul 30, 2013 at 12:11 AM, Aron Ahmadia a...@ahmadia.net wrote: In which Barry discovers the joys of GitHub :) Have you gotten started with hub yet? https://github.com/github/hub On Tue, Jul

[petsc-dev] All petsc-dev users will need to do a reclone of petsc-dev on Tuesday or later

No matter what new/better model is being introduced, please also try to make the model as SIMPLE as possible. Below is what I learned from Jed this morning (correct me if I'm wrong): 1. a stable branch of petsc-dev for users 2. a dynamic branch, e.g., named 'next', for group of internal petsc

[petsc-dev] MtPtAPSymbolic_SeqAIJ_SeqAIJ_SparseAxpy does not set MatInfo

Jed, The missing MatInfo is added: https://bitbucket.org/petsc/petsc-dev/commits/36c73b56b0b354c030fe1d6381374f66 Hong On Thu, Feb 7, 2013 at 1:06 AM, Jed Brown jedbrown at mcs.anl.gov wrote: Hong, this commit made -matptap_scalable the default, but the function does not set MatInfo,

[petsc-dev] example broken for a while src/mat/examples/tests/ex104.c

On my MacAir without elemental installed, I get clean 'make runex104' and anticipated message from 'make runex104_elemental' 0a1,28 [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing external

[petsc-dev] Interface for HIPS

A summer student project? Hong On Mon, Dec 10, 2012 at 9:27 PM, John Fettig john.fettig at gmail.com wrote: http://hips.gforge.inria.fr/ Has anybody thought about making an interface for this? I am guessing the interface would be very similar to some of the existing interfaces, so it

[petsc-dev] Please stop checking in debugging code

Sorry, I accidentally pushed my local temp work to petsc-dev. Removed https://bitbucket.org/petsc/petsc-dev/commits/8a26212be9cc66c7e51ce8f4615a9c32 Hong On Sat, Dec 8, 2012 at 1:43 PM, Jed Brown jedbrown at mcs.anl.gov wrote: On Sat, Dec 8, 2012 at 11:16 AM, Barry Smith bsmith at mcs.anl.gov

[petsc-dev] MatMatSolve_MUMPS

Eric : I just want to know if there is a known difficulty or unfeasible task if someone would like to implement MatMatSolve_MUMPS? MatMatSolve_MUMPS is supported in petsc-dev. It calls MatMatSolve_Basic() with then calls MatSolve_MUMPS in a loop. MUMPS own matmatsolve requires entire rhs

[petsc-dev] testing problems please checking them

First two, ifbcgs and tfibcgs and Broken MatPtAP are fixed and pushed. Hong On Wed, Nov 14, 2012 at 8:57 PM, Barry Smith bsmith at mcs.anl.gov wrote: There are a bunch of nightly tests with errors. Please check through them and see which ones you are guilty of and fix. Thanks

[petsc-dev] Fwd: [mumps-dev] support for distributed right-hand vectors?

: Wed, Nov 7, 2012 at 11:06 AM Subject: Re: [mumps-dev] support for distributed right-hand vectors? To: mumps-dev at listes.ens-lyon.fr, Hong Zhang hzhang at mcs.anl.gov Dear Hong, We are well aware that supporting distributed right-hand side vectors is a functionality requested by some of MUMPS

[petsc-dev] Fwd: [mumps-dev] support for distributed right-hand vectors?

Jed, However, the broken routine is still used for Cholesky. Why not delete MatMatSolve_MUMPS entirely? Pushed fix for Cholesky. I'll implement sequential MatMatSolve_MUMPS there. For parallel, we may implement multiple VecScatter? Hong -- next part -- An HTML

[petsc-dev] PCRedundant problem

, PETSC_SUBCOMM_CONTIGUOUS cannot be used for PCRedundant. Hong On Mon, Oct 15, 2012 at 4:37 PM, Hong Zhang hzhang at mcs.anl.gov wrote: Stefano : Hong, INTERLACED is the default since http://petsc.cs.iit.edu/petsc/petsc-dev/rev/67df4fdba5bd See also http://petsc.cs.iit.edu/petsc/petsc-dev/rev/c04222d17a3d

[petsc-dev] PCRedundant problem

Stefano : is it possible to use PCRedundant with PETSC_SUBCOMM_CONTIGUOUS as subcomm type? I think PETSC_SUBCOMM_CONTIGUOUS is the default for PCRedundant. Hong -- next part -- An HTML attachment was scrubbed... URL:

[petsc-dev] PCRedundant problem

a stand-alone code that reproduces the malloc errors? Hong 2012/10/15 Hong Zhang hzhang at mcs.anl.gov Stefano : is it possible to use PCRedundant with PETSC_SUBCOMM_CONTIGUOUS as subcomm type? I think PETSC_SUBCOMM_CONTIGUOUS is the default for PCRedundant. Hong -- Stefano

[petsc-dev] MatTransposeMatMult and MatTranspose

Jed: Impressive! Do you ever sleep? Hong I added proper preallocation for MatTranspose_MPIAIJ(), which speeds it up greatly. https://bitbucket.org/petsc/petsc-dev/changeset/486d50ec62fbd732c0049cb5f09b2b5709b8

[petsc-dev] Enabling single precision for MUMPS and SUPERLU

attached the patches made with the latest dev (changeset 2 92061a43c7a4) Stefano 2012/9/21 Hong Zhang hzhang at mcs.anl.gov Stefano: Are you sure these patches are made out of the latest petsc-dev? I get petsc:/sandbox/hzhang/petsc-devpatch -Np1 superlu_patch_single.diff

[petsc-dev] Enabling single precision for MUMPS and SUPERLU

Stefano: Thanks for sending us the patch. Is this for petsc-3.3 or petsc-dev? I'll test the patch first, then push to the repository. Yesterday it was the first time I try to build a single-precision version of PETSc with some external packages. I noticed that SuperLU and MUMPS, which are

[petsc-dev] Enabling single precision for MUMPS and SUPERLU

Stefano: When Hong has finished testing, I will split the patches and commit them. Please let me know what macro name you'll choose (or the ugly choice of course) How about split the patches now? Then I'll test one package at a time. Hong There is also pastix which can be enabled, but

[petsc-dev] Runtime errors for spooles on BlueGene/Q

Yes, we should remove PETSc support for Spools and DSCPack. Should we remove all relevant source codes? Hong On Sun, Sep 9, 2012 at 10:16 AM, Barry Smith bsmith at mcs.anl.gov wrote: On Sep 9, 2012, at 9:00 AM, Aron Ahmadia aron.ahmadia at kaust.edu.sa wrote: We can apply this patch, but

[petsc-dev] Runtime errors for spooles on BlueGene/Q

I On Sun, Sep 9, 2012 at 11:06 AM, Barry Smith bsmith at mcs.anl.gov wrote: On Sep 9, 2012, at 11:00 AM, Hong Zhang hzhang at mcs.anl.gov wrote: Yes, we should remove PETSc support for Spools and DSCPack. Should we remove all relevant source codes? Any source that would be dead code

[petsc-dev] Patch review

Sorry, my sloppiness. I should examining it before pushing. I'll clean it, and will ask Jie to provide regression tests. Hong On Fri, Aug 24, 2012 at 6:44 PM, Jed Brown jedbrown at mcs.anl.gov wrote: On Fri, Aug 24, 2012 at 6:38 PM, Jie Chen jiechen at mcs.anl.gov wrote: I am in fact

[petsc-dev] Patch review

Cleaned all except 5. Pushed to petsc-dev. Hong On Fri, Aug 24, 2012 at 5:42 PM, Jed Brown jedbrown at mcs.anl.gov wrote: http://petsc.cs.iit.edu/petsc/petsc-dev/rev/067c5dbc352e Just a couple requests regarding this patch: 1. Please split independent functionality into separate patches.

[petsc-dev] FieldSplit fixes in 3.3

Dmitry : I pushed a bugfix of mumps interface to 3.3. When merging it to petsc-dev, I get merging src/ksp/pc/impls/fieldsplit/fieldsplit.c failed! Hong On Mon, Aug 20, 2012 at 8:36 AM, Jed Brown jedbrown at mcs.anl.gov wrote: On Mon, Aug 20, 2012 at 4:02 AM, Dmitry Karpeev karpeev at

[petsc-dev] FieldSplit fixes in 3.3

for someone else does it :-( Hong On Tue, Aug 21, 2012 at 11:08 AM, Hong Zhang hzhang at mcs.anl.gov wrote: Dmitry : I pushed a bugfix of mumps interface to 3.3. When merging it to petsc-dev, I get merging src/ksp/pc/impls/fieldsplit/fieldsplit.c failed! Hong On Mon, Aug 20, 2012

[petsc-dev] Fwd: Changes in PETSc

Why yelling at me now? Most of you agreed for this name changing. Check the email thread on May 10, 2012:[petsc-dev] Spelling Chebyshev The change is posted at http://www.mcs.anl.gov/petsc/documentation/changes/33.html Hong On Tue, Aug 21, 2012 at 11:31 AM, Barry Smith bsmith at mcs.anl.gov

[petsc-dev] [petsc-users] GAMG setup scalability

John: Thanks for reporting your experience with petsc mat-mat operations, which are consistent with current status of these operations. Petsc mat-mat operations were written many years ago for users who wanted these operations for convenience on small size problems, not intended for huge size and

[petsc-dev] why does MatCreate_MPIDense still exist?

Barry, Elemental interface is not well tested yet. I would wait for few months to remove PLAPACK stuff. Hong On Mon, Aug 13, 2012 at 11:50 AM, Jed Brown jedbrown at mcs.anl.gov wrote: On Mon, Aug 13, 2012 at 10:40 AM, Barry Smith bsmith at mcs.anl.gov wrote: Should I remove all the MPIDense

[petsc-dev] why does MatCreate_MPIDense still exist?

, Matthew Knepley knepley at gmail.com wrote: On Mon, Aug 13, 2012 at 12:07 PM, Barry Smith bsmith at mcs.anl.gov wrote: On Aug 13, 2012, at 12:05 PM, Hong Zhang hzhang at mcs.anl.gov wrote: Barry, Elemental interface is not well tested yet. I would wait for few months to remove

[petsc-dev] Complex Cholesky

Jose : Thanks. I think the same error should go to MatGetFactor_seqaij_petsc otherwise my second sample run gives wrong results: Done for seqaij and seqbaij. Hong -- next part -- An HTML attachment was scrubbed... URL:

[petsc-dev] Jack has produced a scalable sparse direct solver

right-hand sides with the high-level interface: https://github.com/poulson/Clique/blob/master/tests/MultiVectorSolve.cpp Jack On Mon, Jul 23, 2012 at 11:53 AM, Hong Zhang hzhang at mcs.anl.gov wrote: Jack: I'm getting started on creating documentation right now; it should end up looking

[petsc-dev] Complex Cholesky

Jose : sbaij is for symmetric matrix, not Hermitian, as you noticed. Petsc does not have support for Hermitian operations for Cholesky solve yet. We need MatSolve_SeqSBAIJ_1_Hermitian(). Then why not give a PETSC_ERR_SUP error? I'll add it. Jose -- next part

[petsc-dev] Complex Cholesky

Jose : Then why not give a PETSC_ERR_SUP error? Patched 3.3 and petsc-dev. http://petsc.cs.iit.edu/petsc/petsc-dev/rev/ff096aff2a39 When I find time, I'll implement MatSolve() for seqsbaij_hermitian :-) Hong -- next part -- An HTML attachment was scrubbed... URL:

[petsc-dev] Jack has produced a scalable sparse direct solver

Xuan will take a look at this. Hong On Mon, Jul 23, 2012 at 9:47 AM, Matthew Knepley knepley at gmail.com wrote: I think we just need a small converter from AIJ: https://bitbucket.org/poulson/clique/src/dc417c7e9403/tests/DistSparseMatrix.cpp Matt -- What most experimenters take for

[petsc-dev] Jack has produced a scalable sparse direct solver

a look at it and give us your comments/suggests. Hong On Mon, Jul 23, 2012 at 10:12 AM, Hong Zhang hzhang at mcs.anl.gov wrote: Xuan will take a look at this. Hong On Mon, Jul 23, 2012 at 9:47 AM, Matthew Knepley knepley at gmail.comwrote: I think we just need a small converter from AIJ

[petsc-dev] Jack has produced a scalable sparse direct solver

Jack: FYI, Petsc examples for testing elemental interfaces are petsc-dev/src/mat/examples/tests/ex38.c, ex39.c and ex145.c petsc-dev/src/ksp/ksp/examples/tests/ex40.c Hong On Mon, Jul 23, 2012 at 11:53 AM, Hong Zhang hzhang at mcs.anl.gov wrote: Jack: I'm getting started on creating

[petsc-dev] [petsc-users] FFT Matrix Examples/Tests: Compiletime error

Thomas: Thx Hong. I tried the ex148, but I doesn't work as I have complex petsc scalars. Instead I tried ex154, where I did the following modification to be able to compile it ex148.c only works with real precision: #if defined(PETSC_USE_COMPLEX) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,

[petsc-dev] [petsc-users] FFT Matrix Examples/Tests: Compiletime error

Thomas: I removed src/mat/examples/tests/ex145.c and ex154.c from petsc-3.3 and petsc-dev because these tests are covered by other FFTW examples. This would reduce our maintenance and confusion to users. For complex precision, see ex143.c Hong On Wed, Jul 11, 2012 at 8:12 AM, Hong Zhang hzhang

[petsc-dev] [petsc-users] FFT Matrix Examples/Tests: Compiletime error

Sorry, ex148.c should be taken off. The examples of using petsc/FFTW interfaces are real precision: ex142.c, ex144, ex158 complex precision: ex112, ex143, ex145 (see petsc-dev/src/mat/examples/tests/makefile). I'll clean it. Hong On Tue, Jul 10, 2012 at 12:50 PM, Thomas Hisch t.hisch at

[petsc-dev] [petsc-users] FFT Matrix Examples/Tests: Compiletime error

I fixed this problem in petsc-3.3 and petsc-dev. http://petsc.cs.iit.edu/petsc/petsc-dev/rev/3287ab3cb0ed Hong On Tue, Jul 10, 2012 at 1:03 PM, Sean Farley sean at mcs.anl.gov wrote: On Tue, Jul 10, 2012 at 12:50 PM, Thomas Hisch t.hisch at gmail.com wrote: However, compilation of the ex148

[petsc-dev] cheby.c

Barry, Do you recall the paper or detailed Chebyshev algorithm that you implemented the Chebyshev in petsc? I added 'hybrid' to it, which is not correct. Jie is helping to fix it. Having an original algorithm would help. On Tue, May 22, 2012 at 1:21 PM, Jie Chen jiechen at mcs.anl.gov wrote:

[petsc-dev] ex43_3 stokes problem FAIL

Barry, I sent an email to Mark this morning about runex43_3 (Mark might be off-line ...). It seems to me these errors relates to block size changes. Hong On Fri, May 11, 2012 at 9:31 PM, Barry Smith bsmith at mcs.anl.gov wrote: Please run make alltests before pushing changes! Who ever

[petsc-dev] Spelling Chebyshev

Jed : This rename needs to be documented in dev.html. http://petsc.cs.iit.edu/petsc/petsc-dev/rev/9ffb4f0fe85d Pushed. Should we register both spellings (they are both used, though Chebyshev is more common). I do not see Chebychev is being used. Good search ' Chebychev' fails as well.

[petsc-dev] MetSetBlockSize issue

is trial. Mark On Apr 24, 2012, at 11:14 PM, Barry Smith wrote: On Apr 24, 2012, at 8:14 PM, Mark F. Adams wrote: On Apr 24, 2012, at 5:01 PM, Barry Smith wrote: On Apr 24, 2012, at 2:38 PM, Mark F. Adams wrote: On Apr 24, 2012, at 3:28 PM, Hong Zhang wrote: Mark : Shall

[petsc-dev] How does this compare...

Entire paper discusses SpAMM, and compares with SGEMM. Sorry, I do not see anything about SpMV. Hong On Wed, Mar 28, 2012 at 9:52 PM, Matthew Knepley knepley at gmail.com wrote: On Wed, Mar 28, 2012 at 9:39 PM, Hong Zhang hzhang at mcs.anl.gov wrote: Matt: to the new scalable MatMatMult

[petsc-dev] How does this compare...

Interesting paper. I'll read it and get back to you on How does this compare to petsc MatMatMult(). Hong On Wed, Mar 21, 2012 at 2:43 PM, Matthew Knepley knepley at gmail.com wrote: to the new scalable MatMatMult() that is done in PETSc? Is it possible to even compare the flop rates

[petsc-dev] problem in MatMerge_Seq

fixed and pushed. Hong On Fri, Mar 2, 2012 at 4:54 PM, Barry Smith bsmith at mcs.anl.gov wrote: Hong, MatMerge_Seq() is not doing preallocation nor setting the flag that allows improper preallocation -*- mode: compilation; default-directory:

[petsc-dev] MatDestroy call in MatMerge

Vaclav: I feel that it is quite incorrect that MatMerge calls MatDestroy(inmat) since this corrupts garbage collection - inmat is destroyed but only nullified in MatMerge. It remains unchanged outside so subsequent MatDestroy call fails. I think that there is no reason for this destroy, if

[petsc-dev] MatMatMult gives different results

implement everything as it is written down on paper and then optimize once it works (I thought it's easier way). On 07.02.2012 20:44, Hong Zhang wrote: Alexander, I'm curious about why do you need parallel C=A^T*B? How large your matrices are? In petsc-dev, we have MatTransposeMatMult

[petsc-dev] MatMatMult gives different results

() line 8618 in /home/lib/petsc-dev/src/mat/interface/matrix.c On 08.02.2012 17:45, Hong Zhang wrote: Alexander : I can repeat the crash, and am working on it. I'll let you know after the bug is fixed. Thanks for your patience, Hong It seems now I know why I used MAT_REUSE_MATRIX

[petsc-dev] MatMatMult gives different results

depending on number of cores I use. My PETSc is: Using Petsc Development HG revision: 876c894d95f4fa6561d0a91310ca914592527960 HG Date: Tue Jan 10 19:27:14 2012 +0100 On 06.02.2012 17:13, Hong Zhang wrote: MatMatMult() in petsc is not well-tested for complex - could be buggy. Can you send us

[petsc-dev] MatMatMult gives different results

HG revision: 876c894d95f4fa6561d0a91310ca914592527960 HG Date: Tue Jan 10 19:27:14 2012 +0100 On 06.02.2012 17:13, Hong Zhang wrote: MatMatMult() in petsc is not well-tested for complex - could be buggy. Can you send us the matrices A and B in petsc binary format for investigation

[petsc-dev] MatMatMult gives different results

, 2012 at 1:18 PM, agrayver at gfz-potsdam.de agrayver at gfz-potsdam.de wrote: Hong, Thanks for explanation. I will try this tomorrow. Good to have this stuff in the help now. And sorry for misleading you initially. Regards, Alexander - Reply message - From: Hong Zhang hzhang

[petsc-dev] petsc-dev on bitbucket

The lab opens almost all the time - graduate students stay in the lab 7x24 ... Hong On Tue, Feb 7, 2012 at 9:09 PM, Sean Farley sean at mcs.anl.gov wrote: I'm sure Jed (or Matt in his prime) could have run over to IIT and restarted the machine in less time than this :-) Sure, and like

[petsc-dev] MatMatMult gives different results

MatMatMult() in petsc is not well-tested for complex - could be buggy. Can you send us the matrices A and B in petsc binary format for investigation? Hong On Mon, Feb 6, 2012 at 5:55 AM, Alexander Grayver agrayver at gfz-potsdam.dewrote: Dear PETSc team, I try to use: call

[petsc-dev] PETSc LU vs SuperLU

Dave : I've observed same performance. PETSc LU uses simple algorithm and implementation, and our recent releases pay particular attention to efficient data accessing in solve phase, thus it outperforms other packages sometime. SuperLU has built-in schemes, such at row/col permutation, equil etc,

[petsc-dev] wtf

? ?Why did I add that horrible #if defined() stuff? So I could run tests with MatMatMultSym() on your matrices without running the more memory using and time consuming part of the example. I am determined to beat Hong's best on the symbolic part :-). Have you achieved it? I saw

[petsc-dev] CHOLESKY with MUMPS doesn't work properly

Are you sure MUMPS is installed with petsc correctly? [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc CHOLESKY! Uses '-ksp_view' to check which solver is being used. Seems it calls petsc cholesky with

[petsc-dev] CHOLESKY with MUMPS doesn't work properly

On 09.12.2011 18:44, Hong Zhang wrote: Are you sure MUMPS is installed with petsc correctly? [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc CHOLESKY! Uses '-ksp_view' to check which solver is being

[petsc-dev] how come PETSc doesn't contain the SPIKE algorithm?

Hey, SPIKE_algorithm is a block version of the algorithm PPT and PPD we published almost 20 years ago http://www.cs.iit.edu/~scs/psfiles/efficient92.pdf I did this work at graduate school; the paper took 3+ years to appear ... Surprisingly, the SPIKE_algorithm uses the same notations as we did in

[petsc-dev] features of GAMG

Mark: I have made the suggested changes so you should now be able to specify the smoothers with gamg in the normal command line way (eg, -mg_levels_pc_type ilu) and your errors should be caught more elegantly. Unfortunately one of the regression tests is now failing, I'm working on that

[petsc-dev] Bug in MatMatMultTranspose for sequantial AIJ matrices from petsc-dev?

Stefano: MatMatMultTranspose() has been renamed. With latest petsc-dev: MatTransposeMatMult - Performs Matrix-Matrix Multiplication C=A^T*B. MatMatTransposeMult - Performs Matrix-Matrix Multiplication C=A*B^T. I'm currently working on C=A*B^T. Report to us if you encounter problems. Hong Hi,

[petsc-dev] Bug in MatMatMultTranspose for sequantial AIJ matrices from petsc-dev?

Hong, please update?src/docs/website/documentation/changes/dev.html when you make API changes. Done and pushed to petsc-dev. Hong

[petsc-dev] Bug in MatMatMultTranspose for sequantial AIJ matrices from petsc-dev?

, 2011, at 10:47 AM, Hong Zhang wrote: Hong, please update src/docs/website/documentation/changes/dev.html when you make API changes. Done and pushed to petsc-dev. Hong

[petsc-dev] Bug in MatMatMultTranspose for sequantial AIJ matrices from petsc-dev?

?2 ?0 ?0 ?0 ?4 ? 6 ?3 ?0 ?0 ?4 ? ?55 KSPSolve ? ? ? ? ? ? ? 1 1.0 2.9164e+00 1.0 1.57e+09 1.0 0.0e+00 0.0e+00 0.0e+00 10 21 ?0 ?0 ?0 100100 ?0 ?0 ?0 ? 538 Mark On Nov 9, 2011, at 10:47 AM, Hong Zhang wrote: Hong, please update src/docs/website/documentation/changes/dev.html when you make

[petsc-dev] Questions about MatMatTransposeMult/MatMatMultTranspose

Dmitry : And a minor question: wouldn't it be better to name these two functions MatTransposeMatMult and MatMatTransposeMult respectively,?so that the Transpose operation sits next to the matrix it operates on? Barry agrees this name change. I'll rename these two routines as you suggest

[petsc-dev] Failure converting MPIBAIJ - MPIAIJ

Lisandro : I cannot reproduce this error using a C code (ex160.c attached). [dalcinl at trantor petsc4py-dev]$ mpiexec -n 1 python test-mat-baij.py Traceback (most recent call last): ?File test-mat-baij.py, line 11, in module ? ?A.convert('aij') ?File Mat.pyx, line 481, in

[petsc-dev] KSP Viewer problem in petsc3.1

Can you switch to petsc-dev? Quite few bugs have been fixed in petsc-dev and superlu_dist since petsc-3.1. You may try '-mat_superlu_dist_equil no -mat_superlu_dist_colperm NATURAL' first. Hong On Thu, Aug 25, 2011 at 11:19 AM, Satish Balay balay at mcs.anl.gov wrote: Its a patch to petsc - its

[petsc-dev] KSP Viewer problem in petsc3.1

-bounces at mcs.anl.gov [petsc-dev-bounces at mcs.anl.gov] on behalf of Hong Zhang [hzhang at mcs.anl.gov] Sent: Thursday, August 25, 2011 10:33 AM To: For users of the development version of PETSc Cc: Victor Eijkhout Subject: Re: [petsc-dev] KSP Viewer problem in petsc3.1 Can you switch

[petsc-dev] change to MatIsTranspose() and failing test

Pushed MatIsTranspose_SeqBAIJ(). Hong On Wed, Apr 27, 2011 at 2:04 PM, Lisandro Dalcin dalcinl at gmail.com wrote: After wasting as considerable amount of time debugging issues related to uninitialized variables passed to MatIsTranspose, I've pushed this: changeset: ? 18869:3bdc748ba073

[petsc-dev] change to MatIsTranspose() and failing test

Lisandro : BTW, do you fully agree with my previous fix? Should MatIsTranspose() generate an error if the test is not implemented? Or should it just return PETSC_FALSE? I agree with you: generate an error if the test is not implemented - consistent with entire petsc style 'PETSC_FALSE' is

[petsc-dev] failing test

I'll check this. Hong On Thu, Apr 28, 2011 at 4:38 PM, Lisandro Dalcin dalcinl at gmail.com wrote: Can any one take a look here? It is unlikely that is is caused by my commit dbddbea75f68. It smells as an issue with Viewers created on subcommunicators. [dalcinl at trantor tutorials]$ cd

[petsc-dev] failing test

Lisandro : Has this been fixed? I cannot reproduce it on petsc machine or my Mac. Hong Can any one take a look here? It is unlikely that is is caused by my commit dbddbea75f68. It smells as an issue with Viewers created on subcommunicators. [dalcinl at trantor tutorials]$ cd

[petsc-dev] change to MatIsTranspose() and failing test

I'll check it. Hong On Wed, Apr 27, 2011 at 2:04 PM, Lisandro Dalcin dalcinl at gmail.com wrote: After wasting as considerable amount of time debugging issues related to uninitialized variables passed to MatIsTranspose, I've pushed this: changeset: ? 18869:3bdc748ba073 tag: ? ? ? ? tip

[petsc-dev] petsc-dev/src/ksp/ksp/examples/tutorials/ex40.c crash

, Hong Zhang hzhang at mcs.anl.gov wrote: Matt, The reference counting is ASA must be wrong. I have fixed this, but the output does not seem to match. Did this work before? I got same thing - runs, but gives different output. I saw the crash from this Friday's nightly test, which did

[petsc-dev] PETSc Sorting with duplicate entries

Gautam: I'm was sorting an array which that has duplicate entries: (x = [39 9 19 39 29]). I noticed that for duplicate entries after sorting, the index returned are not in ascending. The example below will explain this further. Here is the code snippet:

[petsc-dev] Preconditioner side

-ksp_preconditioner_side LEFT (choose one of) LEFT RIGHT SYMMETRIC (KSPSetPCSide) Hong On Fri, Feb 25, 2011 at 9:10 AM, Desire NUENTSA WAKAM desire.nuentsa_wakam at inria.fr wrote: Hi all, what's the current command-line option to set the preconditioner side in PETSc-dev? It seems not to be

[petsc-dev] Fwd: Request for new PETSc capability

2D planes. Several years ago, when we were planning this project, we spoke with Hong Zhang about this solver strategy and she told us that if there was a demand for it, the present limitation restricting the block Jacobi preconditioner to a single processor could be lifted. ? ?We are now

[petsc-dev] error report from petsc-dev/src/dm/examples/tutorials/ex3.c

OK, pushed. Hong On Sun, Jan 9, 2011 at 11:36 AM, Barry Smith bsmith at mcs.anl.gov wrote: ?This is controversial but I guess you better change to the .5 one ? Barry On Jan 9, 2011, at 11:30 AM, Hong Zhang wrote: Barry, Nightly test report error in src/dm/examples/tutorials/ex3

[petsc-dev] SuperLU link error on BGP FEN

I'll do it. Hong On Fri, Dec 3, 2010 at 9:10 PM, Barry Smith bsmith at mcs.anl.gov wrote: ?Sherry, ? ?Thanks, we'll upgrade to use those versions with petsc-dev. ?Hong and Satish, ? ? Could you please update petsc-dev with these newest versions of superlu[_dist] ? Thanks ? ?Barry

[petsc-dev] Shifting in ICC, changes?

Jed, We replaced old numerical factorization and MatSolve with faster data structure, then cleaned up MatPivotCheck() (still using previous algorithm). Changes, such as changeset: 15909:fbc1ba94d8d9 user:hong at hong-zhangs-macbook-air.local date:Wed May 12 22:17:30 2010 -0500

[petsc-dev] Shifting in ICC, changes?

, Hong Zhang hzhang at mcs.anl.gov wrote: We replaced old numerical factorization and MatSolve with faster data structure, then cleaned up MatPivotCheck() (still using previous algorithm). Changes, such as changeset: ? 15909:fbc1ba94d8d9 user: ? ? ? ?hong at hong-zhangs-macbook-air.local date

[petsc-dev] Shifting in ICC, changes?

Jed: With the version from Feb 1, I get (using AIJ since SBAIJ had no shift logic at that time and just proceeded with negative pivots): [0] MatCholeskyFactorNumeric_SeqAIJ(): number of shiftpd tries 1, shift_amount 1.02086e+06 [0] MatCholeskyFactorNumeric_SeqAIJ(): number of shiftpd tries

[petsc-dev] using consistant username for commits

I changed mine to: username=Hong Zhang hzhang at mcs.anl.gov Hong On Thu, Aug 19, 2010 at 2:10 PM, Barry Smith bsmith at mcs.anl.gov wrote: ?? Satish, ?? Just tell Hong, Satish and Shri to add their ~/.hg properly but I won't make a big deal about it since inconsistencies will sometimes pop

[petsc-dev] MatDestroy_MUMPS

Jed, Thanks for the suggestion. I'll look into this. Hong On Thu, May 20, 2010 at 5:23 PM, Jed Brown jed at 59a2.org wrote: I'm not a fan of invalid frees so I pushed this thing which seems to Work for Me. ?Could one of you involved in this check if it's correct? ?changeset: ?

[petsc-dev] GCC warnings

This relates to my recent change. I'll take care of it. Hong On Sat, May 15, 2010 at 5:12 PM, Jed Brown jed at 59a2.org wrote: On Sat, 15 May 2010 18:25:10 -0300, Lisandro Dalcin dalcinl at gmail.com wrote: ... libfast in: /usr/local/petsc/dev/src/mat/impls/aij/seq aijfact.c: In function

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