Re: [petsc-dev] PETSc 3.8.2 and Sundials 3.0.0

In general PETSc will not work out of the box against newer versions of external packages. If you do not need the new features of Sundials then just use the default download of Sundials that PETSc uses automatically. If you need the latest Sundials then someone needs to go through the

Re: [petsc-dev] Copy scatter and change block size

Pierre, There is not. The block size is baked directly into the scatter data structure so not trivial to change in a copy. Barry > On Nov 25, 2017, at 7:41 AM, Pierre Jolivet > wrote: > > Hello, > Given a VecScatter inctx that operates on vectors x and

[petsc-dev] some change in DM plex output breaks next?

ftp://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2017/11/24/examples_full_next.log not ok diff-dm_impls_plex_tests-ex1_gmsh_6 # 8d7 # < Vertex Sets: 4 strata with value/size (1 (1), 2 (1), 3 (1), 4 (1)) # 10a10 # > Vertex Sets: 4 strata with value/size (1 (1), 2

Re: [petsc-dev] test harness with tests that depend on multiple source files

ic > On Nov 20, 2017, at 10:12 AM, Scott Kruger <kru...@txcorp.com> wrote: > > > > depends keyword: > > From: > dm/examples/tutorials/ex13f90.F90 > > !/*TEST > ! > ! build: > ! requires: !complex > ! depends: ex13f90aux.F90 > !

Re: [petsc-dev] composite vs. shell

Pierre, https://bitbucket.org/petsc/petsc/pull-requests/809/only-propagate-operators-into-inner-pcs-in/diff Sorry for the long delay in responding. Barry > On Nov 10, 2017, at 1:36 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.an

[petsc-dev] Add links to implementations from manual pages

Patrick, Automatically adding links to the manual pages to implementations is actually pretty straight forward. In lib/petsc/conf/rules look at, for example, manconcepts. You can just make a copy of that and have it use something like git grep -n "^PetscErrorCode MatMult_" to

Re: [petsc-dev] pnetcdf is a big problem

Do you really need to use pnetcdf? No one uses it and what usefulness does it really provide, best to be avoided. Barry > On Dec 19, 2017, at 1:12 PM, Satish Balay wrote: > > parallel-netcdf-1.9.0.pre1/INSTALL has: > > > 4. Reporting Installation or Usage

Re: [petsc-dev] pnetcdf is a big problem

in parallel. It would be better to use HDF5, >> but evidently >> it is broken in ExodusII. Thats what we get for using something from >> Sandia. They >> finally have their revenge. >> >> Matt >> >> On Tue, Dec 19, 2017 at 5:53 PM, Smith, Barry F. &

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

> On Nov 11, 2017, at 3:49 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >> You are arguing against a change in the abstract because you love >> next! You are making up stray men and attacking

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

> On Nov 11, 2017, at 11:17 AM, Matthew Knepley wrote: > > On Fri, Nov 10, 2017 at 4:50 PM, Satish Balay wrote: > > On Fri, 10 Nov 2017, Richard Tran Mills wrote: > > > Hi Satish, > > > > Thanks for taking the initiative to switch to testing next-tmp to

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

> On Nov 11, 2017, at 11:46 AM, Matthew Knepley wrote: > > On Sat, Nov 11, 2017 at 12:37 PM, Satish Balay wrote: > On Sat, 11 Nov 2017, Matthew Knepley wrote: > > > > In the long term - Barry wants to get rid of next.. > > > > > > 1) I think next really

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

> On Nov 11, 2017, at 11:33 AM, Jed Brown wrote: > > Matthew Knepley writes: > >>> Alternative is to delete/recreate next - if needed. [but it requires >>> all next users to do this delete/recreation] >>> >>> In the long term - Barry wants to get rid of

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

There is no reason to waste time protesting the attempt to change to the new model. The attempt will happen as soon as we have the new test harness fully working. So help out or get out of the way. Barry > On Nov 11, 2017, at 12:06 PM, Satish Balay wrote: > > On

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

> On Nov 11, 2017, at 11:49 AM, Jed Brown wrote: > > Matthew Knepley writes: > >> On Sat, Nov 11, 2017 at 12:37 PM, Satish Balay wrote: >> >>> On Sat, 11 Nov 2017, Matthew Knepley wrote: >>> > In the long term - Barry wants to

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

Jed wrote (with my ()) I'm sure I'm not the only one in a similar situation. We need an effective set of tests that runs in less than five minutes (on all systems with all compilers) so that we can fix problems and move on rather than having lots of open threads hanging around. Sure, this

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

> On Nov 11, 2017, at 3:26 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >> There is no reason to waste time protesting the attempt to change >> to the new model. The attempt will happen as s

Re: [petsc-dev] broken nightlybuilds (next vs next-tmp)

Let's please all stop wasting time arguing about next! We can argue when there is something to argue about. Not now. > On Nov 11, 2017, at 3:27 PM, Balay, Satish wrote: > > On Sat, 11 Nov 2017, Jed Brown wrote: > >> Removing next without a reliable substitute that

Re: [petsc-dev] proposed minor PetscPartitioner changes

> On Nov 10, 2017, at 8:51 AM, Vaclav Hapla <vaclav.ha...@erdw.ethz.ch> wrote: > > > >> 10. 11. 2017 v 14:56, Jed Brown <j...@jedbrown.org>: >> >> Vaclav Hapla <vaclav.ha...@erdw.ethz.ch> writes: >> >>

Re: [petsc-dev] composite vs. shell

> On Nov 9, 2017, at 11:13 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >> Jed, >> >>Please articulate in a bit more detail. From what I can interpolate you >> are saying >&

Re: [petsc-dev] nightlybuilds (next vs next-tmp)

A time out would/should/does have clear indication that it is a timeout, so it shouldn't be that. Satish, If the testing/fixing would be faster if we bought more machines then decide what machines we need and we order them now. Buying machines is far better than wasting even more

Re: [petsc-dev] PETSc blame digest (next) 2017-11-14

I've fixed this. Used "template" in a C++ program as a variable ;-) > On Nov 14, 2017, at 9:00 AM, PETSc checkBuilds > wrote: > > > > Dear PETSc developer, > > This email contains listings of contributions attributed to you by > `git blame` that caused

[petsc-dev] test harness chokes

on /*TEST test: test: suffix: 2 nsize: 2 TEST*/ with $ ./config/gmakegentest.py KeyError: 0

Re: [petsc-dev] test harness with tests that depend on multiple source files

> On Nov 20, 2017, at 9:37 PM, Jed Brown wrote: > > Scott Kruger writes: > >> depends keyword: >> >> From: >> dm/examples/tutorials/ex13f90.F90 >> >> !/*TEST >> ! >> ! build: >> ! requires: !complex >> ! depends: ex13f90aux.F90 >> ! >>

[petsc-dev] test harness with tests that depend on multiple source files

Scott, I asked you this before and you responded but I forgot and lost your response. For tests that rely on multiple source files can the test harness handle it? How? For example src/vec/vec/examples/tutorials/ex21f90.F90 Is there a list of all keywords that are searched for when

Re: [petsc-dev] nightlybuilds (next vs next-tmp)

> On Nov 15, 2017, at 8:30 PM, Matthew Knepley <knep...@gmail.com> wrote: > > On Wed, Nov 15, 2017 at 8:56 PM, Richard Tran Mills <rtmi...@anl.gov> wrote: > On Sun, Nov 12, 2017 at 9:54 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > > > > On Nov 12

Re: [petsc-dev] nightlybuilds (next vs next-tmp)

> On Nov 12, 2017, at 11:21 AM, Matthew Knepley wrote: > > On Sun, Nov 12, 2017 at 12:17 PM, Satish Balay wrote: > On Sun, 12 Nov 2017, Matthew Knepley wrote: > > > > > Have we tried histogramming test times? It would be nice to know how much > >

Re: [petsc-dev] CMake: make, install, find_package ?

> On Nov 5, 2017, at 8:01 AM, Jed Brown wrote: > >> >> Sure - if you hunt arround the PETSc source tree - you will find bunch >> of stuff.. [but that would be ignoring the primary doc]. >> >> Also There was some reason Jed didn't want to strip out the cmake >> stuff.

Re: [petsc-dev] Recover from TS failure

> On Nov 1, 2017, at 1:13 PM, Mark Adams wrote: > > Yea, I don't understand the linear solve error: > > -ts_monitor -ts_type beuler -pc_type lu -pc_factor_mat_solver_package mumps > -ksp_type preonly -snes_monitor -snes_rtol 1.e-10 -snes_stol 1.e-10 > -snes_converged_reason

Re: [petsc-dev] proposed minor PetscPartitioner changes

> On Nov 7, 2017, at 1:33 AM, Lisandro Dalcin <dalc...@gmail.com> wrote: > > On 6 November 2017 at 16:37, Matthew Knepley <knep...@gmail.com> wrote: >> On Mon, Nov 6, 2017 at 8:34 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: >>> >>>

Re: [petsc-dev] composite vs. shell

Jed, Please articulate in a bit more detail. From what I can interpolate you are saying 1) that if we only propagate the outer matrices to inner matrices that the user has not set we will get a better more intuitive interface for users but 2) the whole idea of propagating in is

Re: [petsc-dev] proposed minor PetscPartitioner changes

> On Nov 8, 2017, at 3:52 AM, Vaclav Hapla <vaclav.ha...@erdw.ethz.ch> wrote: > > >> 8. 11. 2017 v 9:06, Lisandro Dalcin <dalc...@gmail.com>: >> >> On 8 November 2017 at 05:51, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: >>> >>>&

Re: [petsc-dev] PETSc communicators with MPI in Fortran

> On Oct 31, 2017, at 6:00 PM, Neelam Patel wrote: > > Hello PETSc users, > > Working in Fortran, I created 2 disjoint communicators with MPI_Group > operations using PETSC_COMM_WORLD as the "base" comm. I created parallel > vectors on each communicator, and set

Re: [petsc-dev] is this wrong?

Hmm, I think this perhaps an issue of documentation. It seems the various PetscOptionsGetXXX() DO NOT set the value unless the options database indicates it should be set (and when the options database does indicate it has been set the set flag is set). But this is only documented

Re: [petsc-dev] proposed minor PetscPartitioner changes

Vaclav, Please don't do this as proposed. Please learn about all the partitioner interfaces in PETSc before attempting a refactorization. Barry > On Nov 6, 2017, at 7:25 AM, Matthew Knepley wrote: > > On Mon, Nov 6, 2017 at 8:09 AM, Vaclav Hapla

Re: [petsc-dev] proposed minor PetscPartitioner changes

> On Nov 6, 2017, at 7:27 AM, Matthew Knepley <knep...@gmail.com> wrote: > > On Mon, Nov 6, 2017 at 8:24 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > >Vaclav, > > Actually you should not just do this! PETSc already has a full class >

Re: [petsc-dev] proposed minor PetscPartitioner changes

> On Nov 6, 2017, at 7:30 AM, Vaclav Hapla <vaclav.ha...@erdw.ethz.ch> wrote: > > >> 6. 11. 2017 v 14:27, Matthew Knepley <knep...@gmail.com>: >> >> On Mon, Nov 6, 2017 at 8:24 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: >> >>

Re: [petsc-dev] proposed minor PetscPartitioner changes

Vaclav, Actually you should not just do this! PETSc already has a full class for managing partitioning (that Matt ignored for no good reason) see MatPartitioningCreate(). Please look at all the functionality before doing anything. Any refactorization you do needs to combine,

Re: [petsc-dev] more next-tmp

Satish, Thanks for handling all the extra work of making subsets of next for test, without you PETSc would be drowning in its own excesses. Hopefully soon we won't need all this extra manual work needed to be done by you. Barry > On Dec 7, 2017, at 10:10 PM, Satish Balay

Re: [petsc-dev] remove temporary output with new test-harness

Satish, I fixed the errors related to the DATAFILESPATH in ex37 Barry > On Dec 3, 2017, at 10:51 AM, Satish Balay wrote: > > Hm - how do we reproduce this? > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2017/12/03/examples_full_next.log > > There are a

[petsc-dev] test harness with alternative output files

Scott, It looks like you started to put in support for the test harness to compare output against multiple files. $ git grep altfile config/gmakegentest.py:if len(altlist)>1: subst['altfiles']=altlist config/gmakegentest.py: if 'altfiles' not in subst: config/gmakegentest.py:

[petsc-dev] type(*) not supported by multiple test fortran compilers we use

Jed, Unfortunately multiple fortran compilers we use do not support type(*) so we either configure check this stuff (annoying) or stop supporting lots of Fortran compilers. Satish, I guess you need to check all the failed Fortran compilers and see if they have versions that

Re: [petsc-dev] please don't mess up master by moving broken shit into

Thanks > On Oct 25, 2017, at 11:22 AM, Hong wrote: > > This should be cleaned by > https://bitbucket.org/petsc/petsc/commits/a0d1c92d1d6734b184005d635c14bf9895961849 > > Will merge it to master once it passes nightly tests. > > Hong > > On Tue, Oct 24, 2017 at 10:41

Re: [petsc-dev] PetscSF in Fortran

Adrian, I fixed some bugs but apparently broke something at the same time. At a meeting now, maybe you could use -start_in_debugger and get the traceback where it crashes for you? Barry > On Oct 30, 2017, at 5:21 PM, Adrian Croucher > wrote: > > hi, >

Re: [petsc-dev] PetscSF in Fortran

Please send the full traceback. Cut and paste > On Oct 31, 2017, at 3:37 PM, Adrian Croucher <a.crouc...@auckland.ac.nz> > wrote: > > > On 01/11/17 03:02, Smith, Barry F. wrote: >> Adrian, >> >> I fixed some bugs but apparently broke somet

Re: [petsc-dev] type(*) not supported by multiple test fortran compilers we use

through to see the failures and compiler specifics. There are six red lines. Barry > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >> Jed, >> >>Unfortunately multiple fortran compilers we use do not support type(*) so >> we eith

Re: [petsc-dev] type(*) not supported by multiple test fortran compilers we use

017, at 2:17 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >>> On Oct 26, 2017, at 7:55 AM, Jed Brown <j...@jedbrown.org> wrote: >>> >>> Which compilers don't work? >> >> Y

Re: [petsc-dev] calling petsc from a mex file

Push the branch that does this or send me the code and I'll debug it. I now have some vague memory about this behavior. Barry > On May 8, 2018, at 1:53 PM, Munson, Todd <tmun...@mcs.anl.gov> wrote: > > > >> On May 8, 2018, at 1:02 PM, Smith, Barry F. &l

Re: [petsc-dev] Nested XML logging and stages

I am fine with the suggested changes. > On May 13, 2018, at 1:06 PM, Lisandro Dalcin wrote: > > It took me a while to figure out why my xml -log_view was empty. Nested XML > logging and push/pop user-defined stages simply does not work, the > implementation cannot cope

Re: [petsc-dev] calling petsc from a mex file

t; To test, you should be able to start matlab and say "taopounders(); exit". > > Todd. > >> On May 8, 2018, at 2:21 PM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: >> >> >> Push the branch that does this or send me the code and I'll debug it. I now >&

Re: [petsc-dev] Proposed changes to TS API

> On May 12, 2018, at 1:17 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >>> On May 11, 2018, at 6:05 PM, Jed Brown <j...@jedbrown.org> wrote: >>> >>> "Smith, Barry F."

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 6:05 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >> Here is MY summary of the discussion so far. >> >> 1) the IFunction/IJacobian interface has its supporters. There

Re: [petsc-dev] Proposed changes to TS API

> On May 10, 2018, at 4:12 PM, Jed Brown wrote: > > "Zhang, Hong" writes: > >> Dear PETSc folks, >> >> Current TS APIs (IFunction/IJacobian+RHSFunction/RHSJacobian) were designed >> for the fully implicit formulation F(t,U,Udot) = G(t,U). >> Shampine's

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 7:05 AM, Matthew Knepley <knep...@gmail.com> wrote: > > On Fri, May 11, 2018 at 12:25 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > > > > On May 10, 2018, at 4:12 PM, Jed Brown <j...@jedbrown.org> wrote: > >

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 7:20 AM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >>> On May 10, 2018, at 4:12 PM, Jed Brown <j...@jedbrown.org> wrote: >>> >>> "Zhang, Hong"

Re: [petsc-dev] Proposed changes to TS API

o). Barry > > > >> On May 11, 2018, at 3:20 PM, Jed Brown <j...@jedbrown.org> wrote: >> >> "Smith, Barry F." <bsm...@mcs.anl.gov> writes: >> >>>> On May 10, 2018, at 4:12 PM, Jed Brown <j...@jedbrown.org> wro

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 10:17 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > > > >> On May 11, 2018, at 7:05 AM, Matthew Knepley <knep...@gmail.com> wrote: >> >> On Fri, May 11, 2018 at 12:25 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: &g

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 5:26 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >>> On May 11, 2018, at 5:09 PM, Jed Brown <j...@jedbrown.org> wrote: >>> >>> "Smith,

Re: [petsc-dev] Proposed changes to TS API

} ierr = MatAXPY(A,-1,Arhs,axpy);CHKERRQ(ierr); if (A != B) { ierr = MatAXPY(B,-1,Brhs,axpy);CHKERRQ(ierr); } } } Please comment and continue discussion. > On May 11, 2018, at 5:09 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith,

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 6:05 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >> Here is MY summary of the discussion so far. >> >> 1) the IFunction/IJacobian interface has its supporters. There

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 12:58 PM, Stefano Zampini <stefano.zamp...@gmail.com> > wrote: > > >> On May 11, 2018, at 6:20 PM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: >> >> >> >>> On May 11, 2018, at 8:03 AM, Stefano Zampini <s

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 1:01 PM, Lisandro Dalcin <dalc...@gmail.com> wrote: > > On Fri, 11 May 2018 at 19:34, Jed Brown <j...@jedbrown.org> wrote: > >> "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >>>>> >>>>&

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 5:09 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Smith, Barry F." <bsm...@mcs.anl.gov> writes: > >>>> The current IJacobian is essentially SNESJacobian. And the single-matrix >>>> SNESJacobian interface is alw

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 3:36 PM, Jed Brown wrote: > > "Zhang, Hong" writes: > >> We are not forcing users to do two matrix assemblies per time >> step. For most cases, there is even no need to update dF/dUdot at >> all. For extreme cases that the

Re: [petsc-dev] Proposed changes to TS API

> On May 11, 2018, at 3:38 PM, Matthew Knepley wrote: > > On Fri, May 11, 2018 at 4:36 PM, Jed Brown wrote: > "Zhang, Hong" writes: > > > We are not forcing users to do two matrix assemblies per time > > step. For most cases, there is

Re: [petsc-dev] GCC8 Fortran length changes from int to size_t

> On May 7, 2018, at 3:56 AM, Lisandro Dalcin wrote: > > On Mon, 7 May 2018 at 03:11, Jed Brown wrote: > >> Lisandro Dalcin writes: > > How do you exactly want to implement that? Totally replace these > special functions with

Re: [petsc-dev] calling petsc from a mex file

> On May 8, 2018, at 12:30 PM, Munson, Todd wrote: > > > Hi, > > I wonder if anyone has experience calling petsc from matlab using mex. I > have the > simplest possible mexFunction that just calls PetscInitialize() and > PetscFinalize(). That part seems to work

Re: [petsc-dev] Problem with l2g IS created by VecCreateGhostBlock

Garth, Sorry for the delay in responding. This is our bug, I have put the fix into the branch barry/fix-veccreateghostblockwitharray/maint which after testing tonight will go into the maint branch and then the next patch release. Please let us know if the fix in the branch

Re: [petsc-dev] Mat updating from 3.7 to 3.9.2 Fortran

Use -mat_view on the new and old code to verify that the same matrix is actually being generated. Barry > On May 23, 2018, at 6:18 PM, Hector E Barrios Molano > wrote: > > Thanks Jed for the Answer. > > I am still having problems with this code. In summary what I

Re: [petsc-dev] Tiny pull requests via Bitbucket web interface

> On Jun 6, 2018, at 10:06 AM, Karl Rupp wrote: > > Hi all, > > yes, I support Patrick's idea of actively encouraging such simple pull > requests. Particularly when it comes to documentation, it would be very handy > to also add a link to the manual pages on the top right. For example, >

Re: [petsc-dev] [petsc-users] Poor weak scaling when solving successive linearsystems

> VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD > ); > > > 1464: /* update rhs: bb1 = bb - B*x */ > 1465: VecScale > (mat->lvec,-1.0); > > 1466: (*mat->B->ops->multadd)(mat-> > B,mat->lvec,bb,bb1); >

Re: [petsc-dev] [petsc-users] Poor weak scaling when solving successive linearsystems

;>>> Hmm, it is certainly not intended at vectors be created and destroyed >>>> within each KSPSolve() could you please point us to the code that makes >>>> you think they are being created and destroyed? We create all the work >>>> vectors at KSPS

Re: [petsc-dev] [petsc-users] Poor weak scaling when solving successive linearsystems

;>>> Hmm, it is certainly not intended at vectors be created and destroyed >>>> within each KSPSolve() could you please point us to the code that makes >>>> you think they are being created and destroyed? We create all the work >>>> vectors at KSPS

Re: [petsc-dev] [petsc-users] Poor weak scaling when solving successive linearsystems

ut number of nonzeros in the matrix. Barry > > --Junchao Zhang > > On Thu, Jun 7, 2018 at 10:46 AM, Smith, Barry F. wrote: > So the only surprise in the results is the SOR. It is embarrassingly > parallel and normally one would not see a jump. > > The load balance f

Re: [petsc-dev] superlu_dist: update to version v5.4.0

arball release? >> >> Sherry >> >> >> On Tue, Jun 12, 2018 at 11:00 AM, Satish Balay wrote: >> >>> For now - removed from next [until I figureout how to handle it] >>> >>> One motivation for this change is xsdk@devel build [wrt

Re: [petsc-dev] changes for petsc tests for XL Fortran compiler

ple/user code uses: > > +call PetscFlush(6) > > [i.e with the 'call' statement explicitly listed in example/user code] This is fine (except for possibly one user who would just need to change their code). Barry > > Satish > > On Fri, 1 Jun 2018, Smith, B

Re: [petsc-dev] [petsc-users] Poor weak scaling when solving successive linearsystems

at show activity of each ranks along the time > axis in one KSPSove. White color means MPI wait. You can see white takes a > large space. > > I don't have a good explanation why at large scale (1728 cores), processors > wait longer time, as the communication pattern is sti

Re: [petsc-dev] superlu_dist: update to version v5.4.0

Complain to Sherry and have her fix it before moving the new release into PETSc Barry > On Jun 12, 2018, at 10:59 AM, Satish Balay wrote: > > > $ diff superlu/SRC/superlu_enum_consts.h > superlu_dist/SRC/superlu_enum_consts.h > 16a17 >> * January 28, 2018 > 28c29 > < typedef enum

Re: [petsc-dev] superlu_dist: update to version v5.4.0

> On Jun 12, 2018, at 1:00 PM, Balay, Satish wrote: > > For now - removed from next [until I figureout how to handle it] > > One motivation for this change is xsdk@devel build [wrt ATPESC tutorials]. > > Satish > > On Tue, 12 Jun 2018, Smith, Barry F. wrote: &g

Re: [petsc-dev] Opening XML performance log files in browsers

Looks ok to me (I haven't tested it). You could make a pull request. I was able to use the manual process on my Mac, with Safari, Firefox, and Chrome in the past. Barry > On Jun 13, 2018, at 3:59 PM, Lisandro Dalcin wrote: > > Making it work with the official instructions is

Re: [petsc-dev] good partitioning packages?

Fande, This is a great question. I am forwarding it to Mike Heroux who has a high level position in the ECP; because I have similar concerns and also don't have a good answer. ParMetis does indeed have a poor license and essentially no support. Perhaps Mike has some ideas. Barry

Re: [petsc-dev] changes for petsc tests for XL Fortran compiler

Serban, Thanks for the patches. We'll get fixes into the maint branch and hence the next patch release. Satish, We have the macro PetscFlush() that should be used for the call flush(6) locations to make the Fortran example code portable. (But needs to be tested since

Re: [petsc-dev] faster and/or parallel build for petsc4py?

No way to separate into a bunch of independent small files? Barry > On Jun 6, 2018, at 4:24 PM, Stefano Zampini wrote: > > It is a simple huge file compiled. No way to do a parallel build > >> On Jun 6, 2018, at 4:19 PM, Smith, Barry F. wrote: >> >>

[petsc-dev] faster and/or parallel build for petsc4py?

Petsc4py takes a long time to build on my laptop (longer than PETSc itself?) It appears to not use a parallel build; any chance it can be changed to use a parallel build or to take less time to build? Thanks Barry

Re: [petsc-dev] VTK viewer design question

> On Jun 29, 2018, at 10:15 AM, Jed Brown wrote: > > Stefano Zampini writes: > >> Vec and DM classes should not be visible from Sys. This is why they are >> PetscObject. >> If they were visible, builds with --with-single-library=0 will be broken. >> >> 2018-06-29 17:06 GMT+03:00 Patrick

Re: [petsc-dev] GAMG and custom MatMults in smoothers

> On Jun 29, 2018, at 9:33 AM, Vaclav Hapla wrote: > > > >> 22. 6. 2018 v 17:47, Smith, Barry F. : >> >> >> >>> On Jun 22, 2018, at 5:43 AM, Pierre Jolivet >>> wrote: >>> >>> Hello, >>> I’m solvin

Re: [petsc-dev] building with MKL

Can you please do nm -o /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/*.* | grep mkl_blas_dtrsm > On Jul 1, 2018, at 3:14 PM, Mark Adams wrote: > > Sorry, I've sent several today. > > On Sun, Jul 1, 2018 at 2:59 PM Smith, Barry F. wrote: > >

Re: [petsc-dev] building with MKL

/madams/petsc_install/petsc/src/snes/interface/snes.c > > [0]PETSC ERROR: #6 SNESSetUp_NEWTONLS() line 296 in > > /global/u2/m/madams/petsc_install/petsc/src/snes/impls/ls/ls.c > > [0]PETSC ERROR: #7 SNESSetUp() line 2941 in > > /global/u2/m/madams/petsc_install/petsc/src/sn

Re: [petsc-dev] problem with hypre with '--with-openmp=1'

I hate OpenMP with a passion > On Jun 26, 2018, at 1:59 PM, Mark Adams wrote: > > > > On Tue, Jun 26, 2018 at 1:06 PM Satish Balay wrote: > I wonder if these jobs are scheduled in such a way so that they are not > oversubscribed. > > i.e number_mpi_jobs_per_node *

Re: [petsc-dev] running test harness under batch system

es. For example, Theta requires a minimum of 128 nodes. > > Hong (Mr.) > > >> On Jun 22, 2018, at 11:41 AM, Smith, Barry F. wrote: >> >> >> Has anyone run the entire test harness under a batch system? Is this >> possible, does it require specific commands that should be documented in the >> users manual? >> >> Thanks >> >> Barry >> >

[petsc-dev] running test harness under batch system

Has anyone run the entire test harness under a batch system? Is this possible, does it require specific commands that should be documented in the users manual? Thanks Barry

Re: [petsc-dev] problem with hypre with '--with-openmp=1'

> On Jun 22, 2018, at 3:33 PM, Mark Adams wrote: > > We are using KNL (Cori) and hypre is not working when configured with > '--with-openmp=1', even when not using threads (as far as I can tell, I never > use threads). It does seem to run correctly without the --with-openmp option?

Re: [petsc-dev] GAMG and custom MatMults in smoothers

> On Jun 22, 2018, at 5:43 AM, Pierre Jolivet > wrote: > > Hello, > I’m solving a system using a MATSHELL and PCGAMG. > The MPIAIJ Mat I’m giving to GAMG has a specific structure (inherited from > the MATSHELL) I’d like to exploit during the solution phase when the smoother > on the finest

Re: [petsc-dev] building on Titan

LCFs - so its not > clear to me when cmake switched to requring C++11. [this issue never > came up with so far] > > So - suggest avoiding --download-cmake - and use 'module load cmake' > or whatever is appropriate on titan. > > Satish > > On Thu, 21 Jun 2018, Smith, Bar

Re: [petsc-dev] GAMG key not found in table

ote: > > > > On Sun, Jun 24, 2018 at 2:09 PM Smith, Barry F. wrote: > > > > On Jun 24, 2018, at 11:15 AM, Mark Adams wrote: > > > > First, -pc_gamg_threshold 0.8 is crazy. 0.08 is very high. probably best > > to start with 0. > > > > This thresh

Re: [petsc-dev] GAMG key not found in table

> On Jun 24, 2018, at 11:15 AM, Mark Adams wrote: > > First, -pc_gamg_threshold 0.8 is crazy. 0.08 is very high. probably best to > start with 0. > > This threshold will delete all of your edges in the coarsening graph, > probably, and GAMG will switch to a one level solve (silently

Re: [petsc-dev] Expensive VecDuplicate_MPI_DA

like VecDuplicate_MPI() does the right thing. > > > > On Jun 19, 2018, at 10:35 PM, Jed Brown wrote: > > > > "Smith, Barry F." writes: > > > >> Jed, > >> > >> You added these two lines. Any idea why they are needed? &

Re: [petsc-dev] Expensive VecDuplicate_MPI_DA

types including the DM ones to 1) prevent collective calls 2) reference the layout instead of making new ones. Barry It looks like VecDuplicate_MPI() does the right thing. > On Jun 19, 2018, at 10:35 PM, Jed Brown wrote: > > "Smith, Barry F." writes: > >>

Re: [petsc-dev] Expensive VecDuplicate_MPI_DA

Jed, You added these two lines. Any idea why they are needed? Thanks Barry 3e08d2bebf99 src/dm/impls/da/dadist.c (Barry Smith 2012-09-18 14) PetscFunctionBegin; c688c0463f6c src/dm/impls/da/dadist.c (Matthew Knepley 2012-11-11 15) ierr = VecGetDM(g,

[petsc-dev] (no subject)

The problem with this code from package.py is it rejects a package for a large variety of reasons but cannot print which reason it is rejecting it! Thus we waste hours and tons of emails debugging something that doesn't need to be debugged. Barry # if user did not request option,

Re: [petsc-dev] F90 code with PGI (Titan)

> On Jun 29, 2018, at 1:10 PM, Satish Balay wrote: > > https://bitbucket.org/petsc/petsc/commits/16d0e248c69a6e6dc72c61578459093d2bcb#Lsrc/snes/examples/tutorials/ex73f90t.F90T744 > > -! requires: !single > +! requires: !single !libpgf90 > > This example is marked as

  1   2   3   4   5   6   7   8   >