Re: [petsc-dev] [petsc-users] Mat created by DMStag cannot access ghost points

Sorry about the long delay on this. https://gitlab.com/petsc/petsc/-/merge_requests/5329 Am Do., 2. Juni 2022 um 15:01 Uhr schrieb Matthew Knepley : > On Thu, Jun 2, 2022 at 8:59 AM Patrick Sanan > wrote: > >> Thanks, Barry and Changqing! That seems reasonable to me, so I'l

[petsc-dev] Manual page improvements! (Docs MRs to main until PETSc 3.18 is released)

We just merged a large change to the documentation into the main branch. This integrates the manual pages into the documentation build with Sphinx, so you can do things like - Find manual page content with the website search box - Add images, inline code, equations, citations, links to the users

Re: [petsc-dev] Tutorials Question

We could include the ones that are somewhat complete at petsc.org/release/tutorials, but in addition to general cleanup to ensure they're clear enough to help more than hinder, I think it's essential to replace the hard-coded code examples with excerpts from the tutorial programs themselves, and

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

This makes that change to improve the behavior of the release branch: https://gitlab.com/petsc/petsc/-/merge_requests/4818 For reference in the future, also see this related issue: https://gitlab.com/petsc/petsc/-/issues/852 Am Fr., 4. Feb. 2022 um 12:03 Uhr schrieb Patrick Sanan < patrick

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Thanks for the feedback. > > > >> Gesendet: Donnerstag, den 03.02.2022 um 03:09 Uhr > >> Von: "Jed Brown" > >> An: "Marius Buerkle" , "Patrick Sanan" < > patrick.sa...@gmail.com> > >> Cc: "PETSc users list"

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Uhr schrieb Jed Brown : > Stefano Zampini writes: > > > Il giorno mar 1 feb 2022 alle ore 18:34 Jed Brown ha > > scritto: > > > >> Patrick Sanan writes: > >> > >> > Am Di., 1. Feb. 2022 um 16:20 Uhr schrieb Jed Brown >: > >&

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

That works, as in the attached example - Marius, would that work for your case? Am Di., 1. Feb. 2022 um 16:33 Uhr schrieb Jed Brown : > Patrick Sanan writes: > > > Am Di., 1. Feb. 2022 um 16:20 Uhr schrieb Jed Brown : > > > >> Patrick Sanan writes: > >> >

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Am Di., 1. Feb. 2022 um 16:20 Uhr schrieb Jed Brown : > Patrick Sanan writes: > > > Sorry about the delay on this. I can reproduce. > > > > This regression appears to be a result of this optimization: > > https://gitlab.com/petsc/petsc/-/merge_requests/4273 >

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Sorry about the delay on this. I can reproduce. This regression appears to be a result of this optimization: https://gitlab.com/petsc/petsc/-/merge_requests/4273 The changes there including having MatPreallocator destroy its internal hash structure within MatPreallocatorPreallocate(), which

Re: [petsc-dev] Gitlab workflow discussion with GitLab developers

Very much agreed that the biggest sort of friction is dealing with MRs from forks. I suspect that the reason many of the things we want don't work is because they would be too dangerous to allow a random, possibly malicious, user to do. E.g. setting labels seems innocuous enough, but all kinds of

Re: [petsc-dev] Speeding up building docs

https://gitlab.com/petsc/petsc/-/issues/1084 Am Sa., 15. Jan. 2022 um 07:07 Uhr schrieb Patrick Sanan < patrick.sa...@gmail.com>: > Yes, that's a good point - there's no reason to do the copy if we're > already assuming the source is up to date, so we can easily just check if >

Re: [petsc-dev] Speeding up building docs

Yes, that's a good point - there's no reason to do the copy if we're already assuming the source is up to date, so we can easily just check if the destination already has data! Also, while the build time certainly annoys me as well, it stopped being as much of a priority to improve because it now

[petsc-dev] Help tracking down unexpected Fortran behavior

I ran into an unexpected seg fault, which took me too long to realize was because of the old-school "you forgot the ierr" mistake! I was expecting the compiler to complain, since we've had better checking for a while. E.g. as in the attached code to reproduce, my compiler indeed errors on this

Re: [petsc-dev] [DocTip!] #2: Aiming for self-updating docs

Am Fr., 5. Nov. 2021 um 19:18 Uhr schrieb Lawrence Mitchell : > > > On 5 Nov 2021, at 15:25, Patrick Sanan wrote: > > > > Good question. We don't have any that start at specific line numbers, > currently, as it is indeed too brittle - I suspect I removed some that w

[petsc-dev] [DocTip!] #3 CI docs build and preview

All MRs now build all the documentation. This is done with the "docs-review" job (defined in .gitlab-ci.yml ) . There is special logic associated with the "docs-only" label: if you add this to your MR, the usual heavy library tests will be skipped, and the docs will be built without you having to

Re: [petsc-dev] [DocTip!] #2: Aiming for self-updating docs

> below makes me realize that this is fragile. There is still some fragility > with function names, but that ostensibly can be caught by the > mechanism itself. > > Thanks, > > Matt > > On Fri, Nov 5, 2021 at 4:01 AM Patrick Sanan > wrote: > >> A big problem

[petsc-dev] [DocTip!] #2: Aiming for self-updating docs

A big problem with documentation is that it goes out of date. This quickly takes something that was useful to something which is actually harmful. Showing the user things that don't work exactly as described is worse than showing them nothing. So, it's good to aspire to writing docs in as

[petsc-dev] [DocTip!] #1 : What does the docs build build? What can I delete?

This is an experiment to try to disseminate information about the docs. Things here will be less formal and more practical than what might be at petsc.org/release/developers/documentation, and importantly, because this is a mailing list, I can describe things that will go out of date as we improve

Re: [petsc-dev] goggle still not good at finding petsc.org docs

For some reason for that term, Google returns a "petsc-3.5" URL instead of a "petsc-current" URL (which redirects). Maybe this was a problem even before we migrated to Sphinx? I don't have a great idea on how to fix, other than to slap a "THIS IS NOT CURRENT" label and a link on the top of all

[petsc-dev] Postdoctoral position at ETH Zurich: Geodynamics / HPC / Julia

The Geophysical Fluid Dynamics group at ETH Zurich (Switzerland) is seeking a postdoctoral appointee to work for about 2.5 years on an ambitious project involving developing a Julia-based library for GPU-accelerated multiphysics solvers based on pseudotransient relaxation. Of particular interest

Re: [petsc-dev] links from manual pages to users manual

> Am 26.05.2021 um 18:39 schrieb Jed Brown : > > Patrick Sanan mailto:patrick.sa...@gmail.com>> > writes: > >>> Am 25.05.2021 um 22:58 schrieb Barry Smith : >>> >>> >>> Now that the users manual is html and we can properly link into

Re: [petsc-dev] links from manual pages to users manual

currently have our custom plugin which adds the links in code snippets (for HTML only, not in the PDF), using the "htmlmap" generated by the "classic" docs build. My hope is that we could modify the plugin to create the correct internal links, once man pages are better integ

Re: [petsc-dev] links from manual pages to users manual

> Am 25.05.2021 um 22:58 schrieb Barry Smith : > > > Now that the users manual is html and we can properly link into it, it > would be great to have links from the manual pages to appropriate locations > in the users manual. For example SNESSetFunction.html would have a link to > the

Re: [petsc-dev] git worktree

Cool - I didn't know about this approach - If you still have your experiments sitting around, can you put numbers on what kind of space savings are we talking about vs the dumb approach (I have an independent clone for every branch I'm interested in working on simultaneously)? @Barry - thanks

Re: [petsc-dev] empty space on left side of website pages

ps://sphinx-themes.org/ >> >> I think alabaster, aiohttp, cloud_sptheme, ... meet Barry's complaint. >> >> There is a lot to like on the kotti_docs_theme for example although the >> bar is on the right instead of the left. >> >> Scott >> &g

Re: [petsc-dev] empty space on left side of website pages

It is possible to put things there, as in this link which is both documentation and example: https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/sections.html#the-left-sidebar Other projects using this theme have the mostly-empty left sidebar: https://numpy.org/doc/stable/

Re: [petsc-dev] commenting on/asking questions on documentation pages

> Am 23.04.2021 um 04:45 schrieb Barry Smith : > > >I can edit documentation pages directly from the page now, this is totally > awesome but I see no button to comment or ask questions on a page. > >I think every page should, by the edit button, have a "Comment, ask > questions"

Re: [petsc-dev] Regression in manualpages generation?

t of thing will become easier to work with, soon, as we'll have an automated doc build which can be examined for each MR.) P.S. nice email address! > Am 03.04.2021 um 11:19 schrieb Patrick Sanan : > > That isn't expected - thanks for pointing this out! I can reproduce locally > so will

Re: [petsc-dev] Regression in manualpages generation?

That isn't expected - thanks for pointing this out! I can reproduce locally so will take a look. > Am 03.04.2021 um 11:10 schrieb Pierre Jolivet : > > Hello, > https://www.mcs.anl.gov/petsc/petsc-3.14/docs/manualpages/Mat/MatTranspose.html > >

Re: [petsc-dev] [petsc-users] [EXTERNAL] Re: Question about periodic conditions

Here's a simplistic solution, but one which might provide the most users with what they're expecting, which I think is important for a component like DMStag. It simply changes the behavior of the functions to set uniform coordinates to set all local coordinates, including ghosts, using linear

Re: [petsc-dev] [petsc-users] [EXTERNAL] Re: Question about periodic conditions

> Am 31.03.2021 um 12:11 schrieb Matthew Knepley : > > On Wed, Mar 31, 2021 at 3:21 AM Patrick Sanan <mailto:patrick.sa...@gmail.com>> wrote: > (moving to petsc-dev) > > To follow up further on this, Matt is correct as to what's happening now, but > periodic c

Re: [petsc-dev] [petsc-users] [EXTERNAL] Re: Question about periodic conditions

t; > > > I understand that degrees of freedom should be the same on both sides of the > boundary, but should the coordinates not be preserved? > > > I don't think so. The circle has coordinates in [0, 2\pi), so the point at > 2\pi is identified with the point at 0 and you must ch

Re: [petsc-dev] petsc release plan for march 2021

I added that milestone to some of the current docs MRs but it’s probably too tight, so I suggest to remove - it probably doesn’t matter much what’s in the tar all for docs so safer to have the current docs. We could have a patch release which updates the docs for release, once we’re happy with the

Re: [petsc-dev] configureLibrary fails for c++11 projects

I had a related (I think) issue trying to build with Kokkos. Those headers throw an #error if they're expecting OpenMP and the compiler doesn't have the OpenMP flag. I have an open MR here (number 60^2!) which thus adds the OpenMP flag to the CXXPPFLAGS:

Re: [petsc-dev] MatTransposeMatMult() bug

Sorry about the current mess but that page is halfway migrated, so any updates should go here: https://docs.petsc.org/en/main/install/externalsoftware_documentation/ > Am 18.03.2021 um 15:22 schrieb Zhang, Hong via

Re: [petsc-dev] integrate petsc4py tarball generation with petsc tarball generation

y generating the petsc4py docs with it. That would tell you > if it works? > >Yes, we do want to be able to build all the PETSc docs together in a > portable way. > >> On Mar 15, 2021, at 10:56 AM, Patrick Sanan > <mailto:patrick.sa...@gmail.com>> wrote: >

Re: [petsc-dev] integrate petsc4py tarball generation with petsc tarball generation

> Am 15.03.2021 um 16:26 schrieb Satish Balay : > > On Mon, 15 Mar 2021, Lisandro Dalcin wrote: > >> On Mon, 15 Mar 2021 at 07:06, Satish Balay wrote: >> >>> Lisandro, >>> >>> For the upcoming release its best to update lib/petsc/bin/maint/builddist >>> to also build petsc4py tarball in

Re: [petsc-dev] Argonne GPU Virtual Hackathon - Accepted

Another thing perhaps of interest is the stencil-based GPU matrix assembly functionality that Mark introduced. > Am 13.03.2021 um 07:59 schrieb Stefano Zampini : > > The COO assembly is entirely based on thrust primitives, I don’t have much > experience to say we will get a serious speedup by

Re: [petsc-dev] petsc release plan for march 2021

> Am 09.03.2021 um 19:58 schrieb Satish Balay via petsc-dev > : > > All, > > Its time for another PETSc release - due end of March. > > For this release [3.15], will work with the following dates: > > - feature freeze: March 28 say 5PM EST > - release: March 30 say 5PM EST > > Merges

Re: [petsc-dev] plan to transition to new documentation and webpages?

> Am 07.03.2021 um 01:01 schrieb Barry Smith : > > > >> On Mar 6, 2021, at 4:46 PM, Jed Brown > > wrote: >> >> The one value-add that comes from ReadTheDocs is its version switcher, which >> we'd need to do ourselves. > >> >> I've been using this strategy (for

Re: [petsc-dev] plan to transition to new documentation and webpages?

Here's my WIP on having the sphinx build include a consistent set of HTML pages from the "classic" docs build. https://gitlab.com/petsc/petsc/-/merge_requests/3684 <https://gitlab.com/petsc/petsc/-/merge_requests/3684> > Am 07.03.2021 um 08:37 schrieb Patrick Sanan

Re: [petsc-dev] plan to transition to new documentation and webpages?

I'm working on this right now - I think I have a workable way, where we just use the "classic" docs system to build the man pages and HTML sources for each version on RTD, and then specify those HTML files as "extra" to Sphinx, so it just copies them over in the build and we can refer to them

Re: [petsc-dev] Commit squashing in MR

I have also been enjoying using lazygit (thanks, Lisandro, for the tip!). It's a similar sort of thing but runs in the terminal. I find it very useful for those things where the command line git tool falls down (staging parts of files, browsing large sets of changes), and I like that I don't

Re: [petsc-dev] Commit squashing in MR

The whole section on git in the dev manual needs some attention. (It was moved there in the consolidation of docs we had scattered in various places, but hasn't been expertly updated yet). Ideal, I think, would be to find some good, external instructions and link to them, under the idea that we

Re: [petsc-dev] headsup: switch git default branch from 'master' to 'main'

The answers to these were probably stated already, but the reminder might be useful to others, as well. What will happen to "master" after today? Will it be deleted immediately or at some planned time? If not immediately deleted, will it be updated to match main? > Am 23.02.2021 um 18:19

Re: [petsc-dev] Understanding Vecscatter with Kokkos Vecs

erimental. We need to decide whether >> they are good or not. >> >> --Junchao Zhang >> >> >> On Fri, Feb 19, 2021 at 4:32 AM Patrick Sanan >> wrote: >> >>> Thanks! That helps a lot. >>> >>> I assume "no," but

Re: [petsc-dev] Understanding Vecscatter with Kokkos Vecs

sume your vecscatter is not a throw away > object but you will reuse it many times. Once the setup is done, the indices > used internally by the implementation should be on gpu , or not? > > Il Ven 19 Feb 2021, 13:33 Patrick Sanan <mailto:patrick.sa...@gmail.com>> ha scrit

Re: [petsc-dev] Understanding Vecscatter with Kokkos Vecs

do not have an ISCUDA class. > > > Fande, > > When the SF is used to communicate device data, indices are copied to the > device.. > > --Junchao Zhang > > > On Thu, Feb 18, 2021 at 11:50 AM Patrick Sanan <mailto:patrick.sa...@gmail.com>> wrote:

[petsc-dev] Understanding Vecscatter with Kokkos Vecs

I'm trying to understand how VecScatters work with GPU-native Kokkos Vecs. Specifically, I'm interested in what will happen in code like in src/vec/vec/tests/ex22.c, ierr = VecScatterCreate(x,is1,y,is2,);CHKERRQ(ierr); (from

Re: [petsc-dev] error with flags PETSc uses for determining AVX

> Am 14.02.2021 um 07:22 schrieb Barry Smith : > > > >> On Feb 13, 2021, at 11:58 PM, Jed Brown wrote: >> >> I usually configure --with-debugging=0 COPTFLAGS='-O2 -march=native' or >> similar. There's a tension here between optimizing aggressively for the >> current machine and making

Re: [petsc-dev] behavior of PetscDefined(PETSC_HAVE_CUDA)

The man page for this seems to need fixing: "Either way evaluates true if PETSC_USE_DEBUG is defined (merely defined or defined to 1) or undefined. This macro should not be used if its argument may be defined to a non-empty value other than 1." Is a 0 value allowed? If so, does it also

Re: [petsc-dev] pull request tutorial October 15 at 2pm central

This page is the home for documentation on these processes (and no longer the GitLab wiki): https://docs.petsc.org/en/latest/developers/integration/ > Am 14.10.2020 um 23:52 schrieb Munson, Todd via petsc-dev > : > > > Hi all, > > I forgot to send a reminder earlier. Our next tutorial

Re: [petsc-dev] Makefile.user and CUDA

gt; Matthew Knepley mailto:knep...@gmail.com>> writes: > >> On Mon, Oct 12, 2020 at 3:03 PM Patrick Sanan >> wrote: >> >>> >>> >>> Am 12.10.2020 um 20:11 schrieb Matthew Knepley : >>> >>> On Mon, Oct 12, 2020 at 3:47 AM P

Re: [petsc-dev] [petsc-users] About MAT_NEW_NONZERO_LOCATION[]

So we can just take the advice out of the manual about setting this, since it's the default behavior? https://gitlab.com/petsc/petsc/-/merge_requests/3344 > Am 13.10.2020 um 16:41 schrieb Barry Smith : > > > You only need to provide one of the options. > >The docs are slightly

Re: [petsc-dev] Makefile.user and CUDA

> Am 12.10.2020 um 20:11 schrieb Matthew Knepley : > > On Mon, Oct 12, 2020 at 3:47 AM Patrick Sanan <mailto:patrick.sa...@gmail.com>> wrote: > I have a toy application code built on PETSc which needs to compile and link > a .cu file. > > I'd love to be able

[petsc-dev] Makefile.user and CUDA

I have a toy application code built on PETSc which needs to compile and link a .cu file. I'd love to be able to configure PETSc (with CUDA), and then use a modified version of share/petsc/Makefile.user to compile and link my code, using a consistent set of compilers, libraries, and flags.

Re: [petsc-dev] sphinx tutorial October 1 at 2pm central

Hi all - thanks for listening! Here are the slides (including pdf with lots of links): https://gitlab.com/psanan/petsc-sphinx-slides > Am 01.10.2020 um 14:48 schrieb Munson, Todd via petsc-dev > : > > Hi all, > > A reminder that Patrick Sanan will be giving a

Re: [petsc-dev] reminder on managing your merge requests MR

> Am 29.09.2020 um 08:16 schrieb Barry Smith : > > > >> On Sep 29, 2020, at 12:43 AM, Patrick Sanan > <mailto:patrick.sa...@gmail.com>> wrote: >> >> >> >>> Am 29.09.2020 um 02:12 schrieb Barry Smith >> <mailto:bsm...@petsc.de

Re: [petsc-dev] reminder on managing your merge requests MR

> Am 29.09.2020 um 02:12 schrieb Barry Smith : > > > This is a reminder for everyone submitting MR. > > You are responsible to track the progress of the MR. Make sure you use the > > label workflow:review when you think it is ready to be reviewed for > merge, add additional

Re: [petsc-dev] petsc release plan for Sept/2020

Hi Satish - To follow up on the earlier discussion of what needs to be added the release checklist, as far as versioning: The aim is to delete the old LaTeX users manual before the release, so things related to that obviously wouldn''t apply anymore. The TAO manual remains for now. The

Re: [petsc-dev] Users manual update

> Am 25.08.2020 um 17:24 schrieb Barry Smith : > > > >> On Aug 25, 2020, at 9:26 AM, Patrick Sanan > <mailto:patrick.sa...@gmail.com>> wrote: >> >> >> >>> Am 25.08.2020 um 15:59 schrieb Barry Smith >> <mailto:bsm...@

Re: [petsc-dev] Users manual update

This is still up for debate. The main push right now is to try and move as many of the docs as possible (in particular, the users manual) to a web-friendlier format, using Sphinx and ReadTheDocs. Unlike the current "classic" docs at https://www.mcs.anl.gov/petsc/documentation/index.html

Re: [petsc-dev] Users manual update

ake ✘, pkg-config ✔ > Required: gd ✔, gts ✔, libpng ✔, libtool ✔, pango ✘ > ==> Options > --HEAD > Install HEAD version > ==> Analytics > install: 59,114 (30 days), 157,762 (90 days), 518,413 (365 days) > install-on-request: 48,388 (30 days), 125,480 (90 days), 390,556 (365

[petsc-dev] Users manual update

Hi all - We're working on getting the users manual fully migrated to Sphinx, so we can delete the pure-LaTeX version. So far, we've done most of the groundwork to set things up using Sphinx and ReadTheDocs, and to do some semi-automated conversion of the manual. Most people will access the

Re: [petsc-dev] Sphinx error

Sorry about the delay in seeing this thread - Barry, I assume that this means that despite the pain you have at least some sort of working Sphinx. I hesitated to add anything related to Sphinx to the existing docs build (controlled by the makefiles) yet, but as more things are ported there that

Re: [petsc-dev] Prediscusion of appropriate communication tool for discussion of PETSc 4 aka the Grand Refactorization

The Gitlab wiki (on whichever repo) might also be a good complement to whichever thread-based option is used. schrieb am Fr. 19. Juni 2020 um 20:39: > I'd expect we'd have a handful of issues with a common label. Easy to > customize notifications. I don't see the point of a special repository >

Re: [petsc-dev] Valgrind MPI-Related Errors

It's not the most satisfying solution but you can also pretty quickly generate and use suppression files to at least de-clutter the output: https://valgrind.org/docs/manual/manual-core.html#manual-core.suppress Am Di., 2. Juni 2020 um 18:59 Uhr schrieb Satish Balay via petsc-dev <

Re: [petsc-dev] Filter -help

Grep is the goto. If you are only interested in the help string, you can do -help intro Am Fr., 10. Apr. 2020 um 04:03 Uhr schrieb Mark Adams : > I use grep. > > On Thu, Apr 9, 2020 at 9:11 PM Jacob Faibussowitsch > wrote: > >> Hello All, >> >> Is there any built-in way to filter -help

[petsc-dev] Developers Documentation and Metadocumentation

tl:dr developer docs are now at docs.petsc.org, will be looking for help in moving the Users Manual Hi PETSc dev - I wanted to draw your attention to some work we've been doing with the documentation. The new home for developer's documentation is

Re: [petsc-dev] [petsc-users] About the interpolation and restriction matrix for cell-centered multigrid.

This sort of feedback is great in terms of learning what can move out of "tutorials" and into "tests". https://gitlab.com/petsc/petsc/-/merge_requests/2629 Am Di., 24. März 2020 um 16:22 Uhr schrieb Jed Brown : > Mark Adams writes: > > > Good question. It does look like there is Q1: > > > >

Re: [petsc-dev] Suggestions for MatProductCreate()

You can put whatever message you like when you deprecate the function, so perhaps here you could leave the old functions and say something like PETSC_DEPRECATED_FUNCTION("Use X() and Y() (since version 3.13)") PetscErrorCode

Re: [petsc-dev] lazygit

This looks like it could be very helpful, thanks! I usually end up doing these sorts of things (especially partial staging) with GitX, which works well for me but only on OS X, and I'm not sure if anyone is actively developing it anymore. I installed from MacPorts and looks like it's available

Re: [petsc-dev] Truly minimal configure

> Am 15.03.2020 um 16:06 schrieb Jed Brown : > > Patrick Sanan writes: > >> I want to generate docs/manualpages/htmlmap as quickly as possible, from >> scratch (a clone on ReadTheDocs), so I want a fast configure which will let >> me run "make allcite&quo

[petsc-dev] Truly minimal configure

I want to generate docs/manualpages/htmlmap as quickly as possible, from scratch (a clone on ReadTheDocs), so I want a fast configure which will let me run "make allcite". The below will work, I think, but I'm curious whether there's an even faster known way. Also note that I had to

Re: [petsc-dev] Request for comments: allow C99 internally

Perhaps naively, I‘d assume that while there may well be someone out there relying on compilers for which this would be a problem, that same person is also less likely to be able to upgrade PETSc. The benefits seem well worth it. It‘ll make things just that much easier to work with. +1 for the

Re: [petsc-dev] ccache tips?

Thanks a lot for all the tips! I'm trying things out now with an approach like Jed's, but attempting to use system MPI instead of a specific build of MPICH. > Am 17.01.2020 um 22:13 schrieb Jed Brown : > > "Balay, Satish" writes: > >> I guess you can just create links [from mpicc to ccache]

[petsc-dev] ccache tips?

I'm shamefully not using ccache. How do I do it? Is it as simple as ./configure --with-cc="ccache gcc" --with-cxx="ccache g++"? Works on OS X and various Linuxes? Any known issue with external packages or otherwise?

Re: [petsc-dev] Valgrind problems

I was actually wondering about this, as in some cases valgrind errors appear and sometimes they don't, but I didn't dig into it too deeply. Here's my workaround, FWIW, which shows some output for that test on master. I don't see any output when I just run the tests like this: VALGRIND=1

[petsc-dev] Sowing: proposed change to allow single-entry lists on man pages

Lists on the man pages don't seem to be able to have a single entry, because sowing requires you to start lists with "+" and end them with "-", requiring at least two entries. This leads to ugly-looking indentation for man pages for functions with a single input or output parameter, e.g.

Re: [petsc-dev] [petsc4py] Broken tests for DMStag

I will attempt to just fix the underlying issue here, that is allow DMStagSetUniformCoordinates() to work for period boundary conditions with a single rank in the corresponding dimension. Am Mi., 12. Juni 2019 um 19:10 Uhr schrieb Patrick Sanan < patrick.sa...@gmail.com>: > Ah, okay,

Re: [petsc-dev] [petsc4py] Broken tests for DMStag

Do you know if these arose because of the recent example bug fix, or have they potentially been around for a while? Am Mi., 12. Juni 2019 um 04:58 Uhr schrieb Lisandro Dalcin via petsc-dev < petsc-dev@mcs.anl.gov>: > $ python test/runtests.py -v -i dmstag TestDMStag_2D_PXY > [0@kl-18232] Python

Re: [petsc-dev] User(s) manual sections field in manual pages?

am, David A via petsc-dev" writes: > > > >> Firedrake is a very happy Sphinx user. Of course our primary language > is Python. I’m not sure how wonderful sphinx is if your primary language is > C (though support is, I believe, claimed). > >> > >> Fr

Re: [petsc-dev] Man pages usage of "Collective on XXX"

(Forgot to reply-all before) I'd propose to update the guidelines in the dev manual to say that unless otherwise specified, collectivity is wrt the communicator associated with the PETSc object in the first argument slot. Am Do., 7. Feb. 2019 um 10:35 Uhr schrieb Patrick Sanan < patrick

Re: [petsc-dev] Code of Conduct [ACTION REQUIRED]

In the first paragraph, with the list of characteristics that should not trigger harassment, suggest to add "native language" or similar, to underscore the point that, while the working language is English, the important things are the ideas, not the particulars of usage. Am Di., 23. Okt. 2018 um

Re: [petsc-dev] large bug in KSPSolve_Chebyshev() affects all multigrid solvers; all core developers including Mark please read this

2018-09-20 12:00 GMT+02:00 Mark Adams : > > > On Wed, Sep 19, 2018 at 7:44 PM Smith, Barry F. > wrote: > >> >> Look at the code in KSPSolve_Chebyshev(). >> >> Problem 1) VERY MAJOR >> >> Once you start running the eigenestimates it always runs them, this >> is because the routine begins

Re: [petsc-dev] Undefined symbols for _kspfgmresmodifypcksp_ and _kspfgmresmodifypcnochange_ when rebuilding

o 2018, a las 12:52, Matthew Knepley > escribió: > > > > On Wed, Aug 22, 2018 at 6:35 AM Lawrence Mitchell > wrote: > > > > > On 22 Aug 2018, at 10:04, Patrick Sanan > wrote: > > > > > > This happens fairly frequently when I try to switch/update branches of

[petsc-dev] Undefined symbols for _kspfgmresmodifypcksp_ and _kspfgmresmodifypcnochange_ when rebuilding

This happens fairly frequently when I try to switch/update branches of PETSc (here invoked by building my own code, but the error message looks the same with "make check"): $ make /Users/patrick/petsc-stagbl/arch-darwin-stagbl-double-extra-debug/bin/mpicc -o runme.o -c -Wall -Wwrite-strings

Re: [petsc-dev] PETSc goes Jenkins

This is super cool - thanks Alp and Karl! Once tuning is complete, how is one intended to interpret the nice green check marks? "The library compiles" or "All the tests passed"? I ask because in the demo PR there is the reassuring check mark and "3 of 3 builds passed", even though failed tests

Re: [petsc-dev] VTK viewer design question

2018-06-29 17:15 GMT+02:00 Jed Brown : > 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

[petsc-dev] VTK viewer design question

I'm looking at the VTK viewer implementation and I notice that PetscViewerVTKAddField() [1] accepts a parameter which, despite being called "dm", is of type PetscObject. I think that this is used, amongst other things, to ensure that vectors being queued up to be written all come from the same

Re: [petsc-dev] Matt's Tutorial Slides from PETSc Users' Meeting

Sorry, I'm an idiot - I did indeed write down the wrong number and what I wanted is there on slide 195. 2018-06-20 14:22 GMT+02:00 Matthew Knepley : > On Wed, Jun 20, 2018 at 2:22 AM Patrick Sanan > wrote: > >> Matt, are your tutorial slides from the London Users' Meeting avail

[petsc-dev] Matt's Tutorial Slides from PETSc Users' Meeting

Matt, are your tutorial slides from the London Users' Meeting available? I made a note check out something from there (the highly-automated saddle point PC, which I'd like to use in an example/test) but either I wrote something down wrong in my notes, or the slides you showed are different from

Re: [petsc-dev] Testing system

And for more info make -f gmakefile.test help-test 2018-06-06 23:55 GMT+01:00 Jed Brown : > Use search, as in > > make -f gmakefile test search=mat_% > > Often you'll want to be more specific. > > "Kong, Fande" writes: > > > How to run tests for Mat examples only? > > > > "make

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

After Karl's nice talk on contributing to PETSc, I was reminded of a similar talk that I saw at the Julia conference. The title was also something like "Contributing is easy!" but used an even more extreme example of making your first contribution. It was (as Barry encouraged) a small

Re: [petsc-dev] [petsc-users] Segmentation Violation in getting DMPlex coordinates

For functions like this (only for one impl), should this new check be considered new best practices (as opposed to the composition approach, defining things with names like DMDASetUniformCoordinates_DMDA())? It seems like less boilerplate, as well as avoiding a function on the stack (and the check

Re: [petsc-dev] Figures 20, 21 in Chapter 13.1 of PETSc manual are out of date

Sorry I didn't catch this when cleaning up the manual recently. If you don't have time to update it yourself, let me know and I will. 2018-04-19 5:23 GMT+02:00 Karl Rupp : > Hi Junchao, > > 1) The manual says the example is src/ksp/ksp/examples/ex10.c, but it >> actually

Re: [petsc-dev] [petsc-users] PetscPrintf

.@mcs.anl.gov>: > On Thu, Apr 12, 2018 at 9:48 AM, Smith, Barry F. <bsm...@mcs.anl.gov> > wrote: > >> >> >> > On Apr 12, 2018, at 3:59 AM, Patrick Sanan <patrick.sa...@gmail.com> >> wrote: >> > >> > I also happened to stumble acr

Re: [petsc-dev] [petsc-users] PetscPrintf

I also happened to stumble across this yesterday. Is the length restriction for the default printer (l assume from the array of 8*1024 chars in PetscVFPrintfDefault() ) intended behavior to be documented, or a bug to be fixed? 2018-04-12 2:16 GMT+02:00 Rongliang Chen :

Re: [petsc-dev] upcoming release and testing

Spellcheck fixes for dev.html : - relavant --> relevant - diffencing --> differencing - seperately --> separately Patch also attached. 2018-04-05 17:03 GMT+02:00 Satish Balay : > Thanks Karl! > > BTW: Its best to update dev.html in master [and then I can rebase >

Re: [petsc-dev] Manual builds fail on master

ete MPIAdj > on each process (needed by sequential preconditioners) > > Logically Collective on MPI_Comm > <<<<<< > > Will check if this works.. > > Satish > > > On Thu, 22 Mar 2018, Smith, Barry F. wrote: > > > > >I'll

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