August 2020 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Users manual update
by huabel 21 Aug '20

21 Aug '20

Thanks, I copied the ‘developer’ fold out and comment (#extensions.append('sphinxcontrib.bibtex’) this line, with few copy it works well, (no cite link), for me it enough. > On Aug 21, 2020, at 7:32 PM, Patrick Sanan <patrick.sanan(a)gmail.com> wrote: > > Note that we have only tested things with Sphinx 2.4.4, because we rely on a custom extension to add the links to man pages. > > We recently added a helper target in the top-level makefile, which sets up a virtual environment for you with the same packages used for the ReadTheDocs build. Perhaps you can try that, or it can give a hint as to how to set up your own Python environment? > > cd $PETSC_DIR > make sphinx-docs-clean > make sphinx-docs-html > open src/docs/sphinx_docs/_build/html/index.html > > > >> Am 21.08.2020 um 10:39 schrieb huabel <hu.ds.abel(a)icloud.com <mailto:[email protected]>>: >> >> Hi >> I run make dirhtml get some error >> >> ➜ sphinx_docs git:(maint) make dirhtml >> Running Sphinx v3.1.2 >> >> Found DOT install: /usr/local/bin/dot >> >> >> Extension error: >> Could not import extension sphinxcontrib.bibtex (exception: No module named 'sphinxcontrib.bibtex') >> gmake: *** [Makefile:29: dirhtml] Error 2 >> ➜ sphinx_docs git:(maint) pip3 show sphinxcontrib-bibtex >> Name: sphinxcontrib-bibtex >> Version: 1.0.0 >> Summary: A Sphinx extension for BibTeX style citations. >> Home-page: https://github.com/mcmtroffaes/sphinxcontrib-bibtex <https://github.com/mcmtroffaes/sphinxcontrib-bibtex> >> Author: Matthias C. M. Troffaes >> Author-email: matthias.troffaes(a)gmail.com <mailto:[email protected]> >> License: BSD >> Location: /usr/local/lib/python3.8/site-packages >> Requires: oset, Sphinx, pybtex-docutils, pybtex >> Required-by: >> ➜ sphinx_docs git:(maint) brew info graphviz >> graphviz: stable 2.44.1 (bottled), HEAD >> Graph visualization software from AT&T and Bell Labs >> https://www.graphviz.org/ <https://www.graphviz.org/> >> /usr/local/Cellar/graphviz/2.44.1 (506 files, 18MB) * >> Poured from bottle on 2020-07-12 at 16:47:06 >> From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/graphviz.rb <https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/graphviz.rb> >> License: EPL-1.0 >> ==> Dependencies >> Build: autoconf ✔, automake ✘, 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 days) >> build-error: 0 (30 days) >> >> >> >>> On Aug 21, 2020, at 3:14 PM, Patrick Sanan <patrick.sanan(a)gmail.com <mailto:[email protected]>> wrote: >>> >>> 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 manual via docs.petsc.org <http://docs.petsc.org/>, but Sphinx also allows you to build a PDF (via LaTeX) of the docs, which we'll maintain so as to have something citable. >>> >>> Most sections of the manual have a big ugly warning asking for volunteers, e.g. here: https://docs.petsc.org/en/latest/manual/mat/ <https://docs.petsc.org/en/latest/manual/mat/> . An expert reading through any of the chapters will certainly find things they can fix or remove as they go through. That said, the main objective for now is simply to provide the existing content in a web-friendly way. The minimal task mostly involves fixing references and tables (use list-table whenever possible). >>> >>> Probably the best example so far of good formatting is the SNES chapter which Jed has been working on: >>> https://docs.petsc.org/en/latest/manual/snes/ <https://docs.petsc.org/en/latest/manual/snes/> >>> >>> Regarding Sphinx, tips and useful conventions are being noted here: >>> https://docs.petsc.org/en/latest/developers/documentation/#sphinx-documenta… <https://docs.petsc.org/en/latest/developers/documentation/#sphinx-documenta…> >>> >>> (Note that for small docs changes like this, you can go to the ReadTheDocs drop-down in the bottom right and click a link to directly edit on GitLab) >>> >> >

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Re: [petsc-dev] Possible DMPLEX incorrect use of const
by Matthew Knepley 21 Aug '20

21 Aug '20

Yep. Fixing. Thanks, Matt On Thu, Aug 20, 2020 at 10:39 PM Barry Smith <bsmith(a)petsc.dev> wrote: > > https://gitlab.com/petsc/petsc/-/jobs/696681024 > > > CC arch-ci-opensolaris-cmplx-pkgs-dbg/tests/ts/tutorials/ex10.o > 3680"/export/home/glci/builds/zxfiRCGf/0/petsc/petsc/include/petsc/private/sectionimpl.h", > line 21: warning: operands have incompatible types: > 3681 struct {pointer to int perm, pointer to int invPerm} ":" const > struct {pointer to int perm, pointer to int invPerm} > 3682"/export/home/glci/builds/zxfiRCGf/0/petsc/petsc/include/petsc/private/sectionimpl.h", > line 21: warning: operands have incompatible types: > 3683 struct {pointer to int perm, pointer to int invPerm} ":" const > struct {pointer to int perm, pointer to int invPerm} > 3684 CC > arch-ci-opensolaris-cmplx-pkgs-dbg/tests/ts/tutorials/ex16.o > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Users manual update
by Patrick Sanan 21 Aug '20

21 Aug '20

Note that we have only tested things with Sphinx 2.4.4, because we rely on a custom extension to add the links to man pages. We recently added a helper target in the top-level makefile, which sets up a virtual environment for you with the same packages used for the ReadTheDocs build. Perhaps you can try that, or it can give a hint as to how to set up your own Python environment? cd $PETSC_DIR make sphinx-docs-clean make sphinx-docs-html open src/docs/sphinx_docs/_build/html/index.html > Am 21.08.2020 um 10:39 schrieb huabel <hu.ds.abel(a)icloud.com>: > > Hi > I run make dirhtml get some error > > ➜ sphinx_docs git:(maint) make dirhtml > Running Sphinx v3.1.2 > > Found DOT install: /usr/local/bin/dot > > > Extension error: > Could not import extension sphinxcontrib.bibtex (exception: No module named 'sphinxcontrib.bibtex') > gmake: *** [Makefile:29: dirhtml] Error 2 > ➜ sphinx_docs git:(maint) pip3 show sphinxcontrib-bibtex > Name: sphinxcontrib-bibtex > Version: 1.0.0 > Summary: A Sphinx extension for BibTeX style citations. > Home-page: https://github.com/mcmtroffaes/sphinxcontrib-bibtex <https://github.com/mcmtroffaes/sphinxcontrib-bibtex> > Author: Matthias C. M. Troffaes > Author-email: matthias.troffaes(a)gmail.com <mailto:[email protected]> > License: BSD > Location: /usr/local/lib/python3.8/site-packages > Requires: oset, Sphinx, pybtex-docutils, pybtex > Required-by: > ➜ sphinx_docs git:(maint) brew info graphviz > graphviz: stable 2.44.1 (bottled), HEAD > Graph visualization software from AT&T and Bell Labs > https://www.graphviz.org/ <https://www.graphviz.org/> > /usr/local/Cellar/graphviz/2.44.1 (506 files, 18MB) * > Poured from bottle on 2020-07-12 at 16:47:06 > From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/graphviz.rb <https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/graphviz.rb> > License: EPL-1.0 > ==> Dependencies > Build: autoconf ✔, automake ✘, 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 days) > build-error: 0 (30 days) > > > >> On Aug 21, 2020, at 3:14 PM, Patrick Sanan <patrick.sanan(a)gmail.com <mailto:[email protected]>> wrote: >> >> 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 manual via docs.petsc.org <http://docs.petsc.org/>, but Sphinx also allows you to build a PDF (via LaTeX) of the docs, which we'll maintain so as to have something citable. >> >> Most sections of the manual have a big ugly warning asking for volunteers, e.g. here: https://docs.petsc.org/en/latest/manual/mat/ <https://docs.petsc.org/en/latest/manual/mat/> . An expert reading through any of the chapters will certainly find things they can fix or remove as they go through. That said, the main objective for now is simply to provide the existing content in a web-friendly way. The minimal task mostly involves fixing references and tables (use list-table whenever possible). >> >> Probably the best example so far of good formatting is the SNES chapter which Jed has been working on: >> https://docs.petsc.org/en/latest/manual/snes/ <https://docs.petsc.org/en/latest/manual/snes/> >> >> Regarding Sphinx, tips and useful conventions are being noted here: >> https://docs.petsc.org/en/latest/developers/documentation/#sphinx-documenta… <https://docs.petsc.org/en/latest/developers/documentation/#sphinx-documenta…> >> >> (Note that for small docs changes like this, you can go to the ReadTheDocs drop-down in the bottom right and click a link to directly edit on GitLab) >> >

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Re: [petsc-dev] Users manual update
by huabel 21 Aug '20

21 Aug '20

Hi I run make dirhtml get some error ➜ sphinx_docs git:(maint) make dirhtml Running Sphinx v3.1.2 Found DOT install: /usr/local/bin/dot Extension error: Could not import extension sphinxcontrib.bibtex (exception: No module named 'sphinxcontrib.bibtex') gmake: *** [Makefile:29: dirhtml] Error 2 ➜ sphinx_docs git:(maint) pip3 show sphinxcontrib-bibtex Name: sphinxcontrib-bibtex Version: 1.0.0 Summary: A Sphinx extension for BibTeX style citations. Home-page: https://github.com/mcmtroffaes/sphinxcontrib-bibtex Author: Matthias C. M. Troffaes Author-email: matthias.troffaes(a)gmail.com License: BSD Location: /usr/local/lib/python3.8/site-packages Requires: oset, Sphinx, pybtex-docutils, pybtex Required-by: ➜ sphinx_docs git:(maint) brew info graphviz graphviz: stable 2.44.1 (bottled), HEAD Graph visualization software from AT&T and Bell Labs https://www.graphviz.org/ /usr/local/Cellar/graphviz/2.44.1 (506 files, 18MB) * Poured from bottle on 2020-07-12 at 16:47:06 From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/graphviz.rb License: EPL-1.0 ==> Dependencies Build: autoconf ✔, automake ✘, 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 days) build-error: 0 (30 days) > On Aug 21, 2020, at 3:14 PM, Patrick Sanan <patrick.sanan(a)gmail.com> wrote: > > 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 manual via docs.petsc.org <http://docs.petsc.org/>, but Sphinx also allows you to build a PDF (via LaTeX) of the docs, which we'll maintain so as to have something citable. > > Most sections of the manual have a big ugly warning asking for volunteers, e.g. here: https://docs.petsc.org/en/latest/manual/mat/ <https://docs.petsc.org/en/latest/manual/mat/> . An expert reading through any of the chapters will certainly find things they can fix or remove as they go through. That said, the main objective for now is simply to provide the existing content in a web-friendly way. The minimal task mostly involves fixing references and tables (use list-table whenever possible). > > Probably the best example so far of good formatting is the SNES chapter which Jed has been working on: > https://docs.petsc.org/en/latest/manual/snes/ <https://docs.petsc.org/en/latest/manual/snes/> > > Regarding Sphinx, tips and useful conventions are being noted here: > https://docs.petsc.org/en/latest/developers/documentation/#sphinx-documenta… <https://docs.petsc.org/en/latest/developers/documentation/#sphinx-documenta…> > > (Note that for small docs changes like this, you can go to the ReadTheDocs drop-down in the bottom right and click a link to directly edit on GitLab) >

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Users manual update
by Patrick Sanan 21 Aug '20

21 Aug '20

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 manual via docs.petsc.org, but Sphinx also allows you to build a PDF (via LaTeX) of the docs, which we'll maintain so as to have something citable. Most sections of the manual have a big ugly warning asking for volunteers, e.g. here: https://docs.petsc.org/en/latest/manual/mat/ . An expert reading through any of the chapters will certainly find things they can fix or remove as they go through. That said, the main objective for now is simply to provide the existing content in a web-friendly way. The minimal task mostly involves fixing references and tables (use list-table whenever possible). Probably the best example so far of good formatting is the SNES chapter which Jed has been working on: https://docs.petsc.org/en/latest/manual/snes/ Regarding Sphinx, tips and useful conventions are being noted here: https://docs.petsc.org/en/latest/developers/documentation/#sphinx-documenta… (Note that for small docs changes like this, you can go to the ReadTheDocs drop-down in the bottom right and click a link to directly edit on GitLab)

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Possible DMPLEX incorrect use of const
by Barry Smith 20 Aug '20

20 Aug '20

https://gitlab.com/petsc/petsc/-/jobs/696681024 CC arch-ci-opensolaris-cmplx-pkgs-dbg/tests/ts/tutorials/ex10.o 3680"/export/home/glci/builds/zxfiRCGf/0/petsc/petsc/include/petsc/private/sectionimpl.h", line 21: warning: operands have incompatible types: 3681 struct {pointer to int perm, pointer to int invPerm} ":" const struct {pointer to int perm, pointer to int invPerm} 3682"/export/home/glci/builds/zxfiRCGf/0/petsc/petsc/include/petsc/private/sectionimpl.h", line 21: warning: operands have incompatible types: 3683 struct {pointer to int perm, pointer to int invPerm} ":" const struct {pointer to int perm, pointer to int invPerm} 3684 CC arch-ci-opensolaris-cmplx-pkgs-dbg/tests/ts/tutorials/ex16.o

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CI error with OMP code - sycl problem?
by Mark Adams 14 Aug '20

14 Aug '20

I get this error with omp but it looks fine to me. I see its from a (new) sycl test. Is this a bug? /home/glci/builds/dDpd88Yu/0/petsc/petsc/src/dm/impls/plex/landau/plexland.c(1455): error #3180: unrecognized OpenMP #pragma 1781 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1781> #pragma omp parallel for private(j) 1782 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1782> ^ 1783 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1783>compilation aborted for /home/glci/builds/dDpd88Yu/0/petsc/petsc/src/dm/impls/plex/landau/plexland.c (code 2) 1784 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1784>gmake[3]: *** [gmakefile:172: arch-ci-linux-sycl-double/obj/dm/impls/plex/landau/plexland.o] Error 2 1785 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1785>gmake[3]: *** Waiting for unfinished jobs.... 1786 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1786> ..... 1796 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1796> **************************ERROR************************************* 1797 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1797> Error during compile, check arch-ci-linux-sycl-double/lib/petsc/conf/make.log 1798 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1798> Send it and arch-ci-linux-sycl-double/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov 1799 <https://gitlab.com/petsc/petsc/-/jobs/686976946#L1799> ********************************************************************

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Re: [petsc-dev] test harness failure make -f gmakefile.test test query='requires' queryval='kokkos'
by Scott Kruger 12 Aug '20

12 Aug '20

Ahhhh.ï¿½ gmakefile is not passing PETSC_DIR and PETSC_ARCH to query_tests.py like it should. The immediate fix is to set your env variables, but I'll do a quick MR to fix this. Scott On 8/11/20 8:11 PM, Barry Smith wrote: > > ï¿½ Scott, > > ï¿½ ï¿½Sometimes when I run the below test the harness mis-behaves. I > cannot say what is different when this happens and doesn't because > sometimes it also works. > > ï¿½ Thanks > > ï¿½ ï¿½Barry > > > > > make -f gmakefile.testï¿½ test query='requires' queryval='kokkos' > Traceback (most recent call last): > File "config/query_tests.py", line 226, in <module> > ï¿½ main() > File "config/query_tests.py", line 187, in main > ï¿½ petsc_full_arch = os.path.join(petsc_dir, petsc_arch) > File "/usr/lib64/python3.7/posixpath.py", line 94, in join > ï¿½ genericpath._check_arg_types('join', a, *p) > File "/usr/lib64/python3.7/genericpath.py", line 153, in _check_arg_types > ï¿½ (funcname, s.__class__.__name__)) from None > TypeError: join() argument must be str or bytes, not 'NoneType' > Using MAKEFLAGS: -- queryval=kokkos query=requires > # No tests run > # No tests run > # No tests run > > -- Tech-X Corporation kruger(a)txcorp.com 5621 Arapahoe Ave, Suite A Phone: (720) 974-1841 Boulder, CO 80303 Fax: (303) 448-7756

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test harness failure make -f gmakefile.test test query='requires' queryval='kokkos'
by Barry Smith 11 Aug '20

11 Aug '20

Scott, Sometimes when I run the below test the harness mis-behaves. I cannot say what is different when this happens and doesn't because sometimes it also works. Thanks Barry make -f gmakefile.test test query='requires' queryval='kokkos' Traceback (most recent call last): File "config/query_tests.py", line 226, in <module> main() File "config/query_tests.py", line 187, in main petsc_full_arch = os.path.join(petsc_dir, petsc_arch) File "/usr/lib64/python3.7/posixpath.py", line 94, in join genericpath._check_arg_types('join', a, *p) File "/usr/lib64/python3.7/genericpath.py", line 153, in _check_arg_types (funcname, s.__class__.__name__)) from None TypeError: join() argument must be str or bytes, not 'NoneType' Using MAKEFLAGS: -- queryval=kokkos query=requires # No tests run # No tests run # No tests run

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Re: [petsc-dev] PetscContainerSetPointer
by Barry Smith 10 Aug '20

10 Aug '20

> On Aug 10, 2020, at 3:27 PM, Mark Adams <mfadams(a)lbl.gov> wrote: > > I had some problems giving a container an PETSc object so I wrapped it in a struct. > I forget what problem I had. Maybe ISColoringDestroy can't take a void*. > I'd like to check if I was just missing something. > Should something like this work? > > ISColoring c; > .... > ierr = PetscContainerSetPointer(container,(void*)c);CHKERRQ(ierr); > ierr = PetscContainerSetUserDestroy(container, ISColoringDestroy);CHKERRQ(ierr); Mark ISColoring is a plain old C struct: struct _n_ISColoring { PetscInt refct; ... so it seems like this should work. But ISColoringDestroy(), like most PETSc destroy functions, takes the address of the pointer as the argument (as opposed to the pointer itself, this is so XXXDestroy() can set the pointer to null to prevent it getting used again accidentally with a now meaningless value.) So there is a disconnect in how PETSc handles destroying objects (take the address of a pointer) and the pointer for containers (take a pointer). Looking back I just made the container concept as simple as possible and did not think about the API difference. We could fix it now but it might break a tiny bit of user code. This should work static PetscErrorCode MyISColoringDestroy(void *is) { ISColoring tmp = (ISColoring)is; return ISColoringDestroy(&tmp); } ierr = PetscContainerSetUserDestroy(container, MyISColoringDestroy);CHKERRQ(ierr); then you won't need the dummy struct. Barry

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