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

Re: [petsc-dev] PGI errors with Fortran strings
by Satish Balay 07 Jul '20

07 Jul '20

> PETSC_EXTERN void dmswarmgetfield_(DM *dm, char *name, PetscInt *blocksize, PetscDataType *type, F90Array1d *ptr, int *ierr, PETSC_FORTRAN_CHARLEN_T lenN PETSC_F90_2PTR_PROTO(ptrd)) I don't see an example [in current code] for using both char and F90Array with the same function. So its not clear to me if the above is correct or if it should be: PETSC_EXTERN void dmswarmgetfield_(DM *dm, char *name, PetscInt *blocksize, PetscDataType *type, F90Array1d *ptr, int *ierr lenN PETSC_F90_2PTR_PROTO(ptrd), PETSC_FORTRAN_CHARLEN_T) And to disable: src/ksp/ksp/tutorials/ex54f.F90:! requires: !pgf90_compiler src/snes/tests/ex18f90.F90:! requires: !pgf90_compiler Satish On Tue, 7 Jul 2020, Mark Adams wrote: > DMSwarm has custom fortran wrappers in ftn-custom and f90-custom. I am > finding that the f90 one has junk in the string length with PGI compilers > (see attached). The ones in ftn-custom seem to work. > > Any ideas? > > Also, how can I disable a test for PGI? > > Thanks, > Mark >

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PGI errors with Fortran strings
by Mark Adams 07 Jul '20

07 Jul '20

DMSwarm has custom fortran wrappers in ftn-custom and f90-custom. I am finding that the f90 one has junk in the string length with PGI compilers (see attached). The ones in ftn-custom seem to work. Any ideas? Also, how can I disable a test for PGI? Thanks, Mark

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Re: [petsc-dev] Sphinx error
by Patrick Sanan 07 Jul '20

07 Jul '20

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 would make sense. > Am 07.07.2020 um 14:18 schrieb Barry Smith <bsmith(a)petsc.dev>: > > "Any Python package that you install with brew will install the Homebrew Python build." > > Sure in general with python on Apple, but you ignored my statement: > > $ which sphinx-build > /usr/local/opt/sphinx-doc/bin/sphinx-build > ~/Src/petsc/src/ksp/ksp/interface (master=) arch-master > $ more /usr/local/opt/sphinx-doc/bin/sphinx-build > #!/usr/local/Cellar/sphinx-doc/3.0.4/libexec/bin/python3.8 > # -*- coding: utf-8 -*- > import re > import sys > from sphinx.cmd.build import main > > sphinx seems to be carrying around its own python internally, thus quite rightly getting Jed upset about packaging on Apple of open source software. Or perhaps I misunderstand that line. > > Barry > > >> On Jul 7, 2020, at 2:40 AM, Lisandro Dalcin <dalcinl(a)gmail.com <mailto:[email protected]>> wrote: >> >> >> >> On Tue, 7 Jul 2020 at 05:37, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >> >> My fault, for some reason sphinx from brew installed its own private python so I had to do the pip at that. >> >> >> Any Python package that you install with brew will install the Homebrew Python build. Start using that one, and forget about the system Python install. >> From brew you get `/usr/local/bin/python3`, and then you can freely `python3 -m pip install <package>` >> I further symlink `/usr/local/bin/{python|pip}3` to `~/bin/{python|pip}`, so I don't have to deal ever again with the EOLed system Apple Python 2. >> >> -- >> Lisandro Dalcin >> ============ >> Research Scientist >> Extreme Computing Research Center (ECRC) >> King Abdullah University of Science and Technology (KAUST) >> http://ecrc.kaust.edu.sa/ <http://ecrc.kaust.edu.sa/> >

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Re: [petsc-dev] Sphinx error
by Barry Smith 07 Jul '20

07 Jul '20

"Any Python package that you install with brew will install the Homebrew Python build." Sure in general with python on Apple, but you ignored my statement: $ which sphinx-build /usr/local/opt/sphinx-doc/bin/sphinx-build ~/Src/petsc/src/ksp/ksp/interface (master=) arch-master $ more /usr/local/opt/sphinx-doc/bin/sphinx-build #!/usr/local/Cellar/sphinx-doc/3.0.4/libexec/bin/python3.8 # -*- coding: utf-8 -*- import re import sys from sphinx.cmd.build import main sphinx seems to be carrying around its own python internally, thus quite rightly getting Jed upset about packaging on Apple of open source software. Or perhaps I misunderstand that line. Barry > On Jul 7, 2020, at 2:40 AM, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: > > > > On Tue, 7 Jul 2020 at 05:37, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: > > My fault, for some reason sphinx from brew installed its own private python so I had to do the pip at that. > > > Any Python package that you install with brew will install the Homebrew Python build. Start using that one, and forget about the system Python install. > From brew you get `/usr/local/bin/python3`, and then you can freely `python3 -m pip install <package>` > I further symlink `/usr/local/bin/{python|pip}3` to `~/bin/{python|pip}`, so I don't have to deal ever again with the EOLed system Apple Python 2. > > -- > Lisandro Dalcin > ============ > Research Scientist > Extreme Computing Research Center (ECRC) > King Abdullah University of Science and Technology (KAUST) > http://ecrc.kaust.edu.sa/ <http://ecrc.kaust.edu.sa/>

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Re: [petsc-dev] Sphinx error
by Lisandro Dalcin 07 Jul '20

07 Jul '20

On Tue, 7 Jul 2020 at 05:37, Barry Smith <bsmith(a)petsc.dev> wrote: > > My fault, for some reason sphinx from brew installed its own private > python so I had to do the pip at that. > > Any Python package that you install with brew will install the Homebrew Python build. Start using that one, and forget about the system Python install. >From brew you get `/usr/local/bin/python3`, and then you can freely `python3 -m pip install <package>` I further symlink `/usr/local/bin/{python|pip}3` to `~/bin/{python|pip}`, so I don't have to deal ever again with the EOLed system Apple Python 2. -- Lisandro Dalcin ============ Research Scientist Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/

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Re: [petsc-dev] Sphinx error
by Barry Smith 07 Jul '20

07 Jul '20

I never said there was anything wrong with Linux packaging, not at all. NextStep had Frameworks that were adopted by Apple when it migrated to Unix and they looked pretty much the same as today, a wrapping up of a package, library and includes or applications, with versioning and dependencies on other Frameworks and certainly not carrying around inside them other pieces of packages. My point is Apple has a packaging system that goes way back, it is just that the open source community doesn't use it much hence you and others think it doesn't have a packaging system. It isn't really hard at all to make a Framework, just doesn't happen. > On Jul 6, 2020, at 11:01 PM, Jed Brown <jed(a)jedbrown.org> wrote: > > Barry Smith <bsmith(a)petsc.dev> writes: > >> Apple introduced the concept of Framework for packaging long before >> Linux had half-way decent package managers. > > Debian debuted in 1996 with hundreds of packages and sufficient package management to enable continuous upgrades through to the modern era (no reinstall; e.g., https://lwn.net/Articles/226110/) > > You can blame Linux distros for lots of things, but reliable package management ain't one of them. > >> And it is not bad, manages versions, packaging, all the stuff you >> need. But because it is slightly different than the traditional Unix >> approaches and the Apple world used to be much smaller in open >> source users the open source community never adopted it as the way >> to deliver packages on Apple, they instead built Linux like package >> manager clones and totally by-passed the Framework approach. I don't >> think you can blame Apple; they do have a reasonable packaging >> system, the open source community just doesn't use it. I use to >> build PETSc frameworks for Apple but doubt that a single person used >> them so I stopped. >> >> >> >>> On Jul 6, 2020, at 10:08 PM, Jed Brown <jed(a)jedbrown.org> wrote: >>> >>> I don't envy the Brew developers who take the blame when Apple breaks things underneath them. I still boggle at the fact that the clear majority of people use operating systems that lack integrated package management. This problem has been solved for 25 years. >>> >>> Barry Smith <bsmith(a)petsc.dev> writes: >>> >>>> My fault, for some reason sphinx from brew installed its own private python so I had to do the pip at that. >>>> >>>> >>>> >>>>> On Jul 6, 2020, at 9:03 PM, Jed Brown <jed(a)jedbrown.org> wrote: >>>>> >>>>> Barry Smith <bsmith(a)petsc.dev> writes: >>>>> >>>>>> Apple's python 2 doesn't use pip >>>>>> >>>>>> $ sudo easy_install src/docs/sphinx_docs/requirements.txt >>>>>> Processing requirements.txt >>>>>> error: Not a recognized archive type: src/docs/sphinx_docs/requirements.txt >>>>>> >>>>>> Is this thing supported only for python3? >>>>> >>>>> Perhaps. Python2 is EOL. Try this >>>>> >>>>> python3 -m pip install --user -r src/docs/sphinx_docs/requirements.txt

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Re: [petsc-dev] Sphinx error
by Jed Brown 06 Jul '20

06 Jul '20

Barry Smith <bsmith(a)petsc.dev> writes: > Apple introduced the concept of Framework for packaging long before > Linux had half-way decent package managers. Debian debuted in 1996 with hundreds of packages and sufficient package management to enable continuous upgrades through to the modern era (no reinstall; e.g., https://lwn.net/Articles/226110/) You can blame Linux distros for lots of things, but reliable package management ain't one of them. > And it is not bad, manages versions, packaging, all the stuff you > need. But because it is slightly different than the traditional Unix > approaches and the Apple world used to be much smaller in open > source users the open source community never adopted it as the way > to deliver packages on Apple, they instead built Linux like package > manager clones and totally by-passed the Framework approach. I don't > think you can blame Apple; they do have a reasonable packaging > system, the open source community just doesn't use it. I use to > build PETSc frameworks for Apple but doubt that a single person used > them so I stopped. > > > >> On Jul 6, 2020, at 10:08 PM, Jed Brown <jed(a)jedbrown.org> wrote: >> >> I don't envy the Brew developers who take the blame when Apple breaks things underneath them. I still boggle at the fact that the clear majority of people use operating systems that lack integrated package management. This problem has been solved for 25 years. >> >> Barry Smith <bsmith(a)petsc.dev> writes: >> >>> My fault, for some reason sphinx from brew installed its own private python so I had to do the pip at that. >>> >>> >>> >>>> On Jul 6, 2020, at 9:03 PM, Jed Brown <jed(a)jedbrown.org> wrote: >>>> >>>> Barry Smith <bsmith(a)petsc.dev> writes: >>>> >>>>> Apple's python 2 doesn't use pip >>>>> >>>>> $ sudo easy_install src/docs/sphinx_docs/requirements.txt >>>>> Processing requirements.txt >>>>> error: Not a recognized archive type: src/docs/sphinx_docs/requirements.txt >>>>> >>>>> Is this thing supported only for python3? >>>> >>>> Perhaps. Python2 is EOL. Try this >>>> >>>> python3 -m pip install --user -r src/docs/sphinx_docs/requirements.txt

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Re: [petsc-dev] Sphinx error
by Barry Smith 06 Jul '20

06 Jul '20

Apple introduced the concept of Framework for packaging long before Linux had half-way decent package managers. And it is not bad, manages versions, packaging, all the stuff you need. But because it is slightly different than the traditional Unix approaches and the Apple world used to be much smaller in open source users the open source community never adopted it as the way to deliver packages on Apple, they instead built Linux like package manager clones and totally by-passed the Framework approach. I don't think you can blame Apple; they do have a reasonable packaging system, the open source community just doesn't use it. I use to build PETSc frameworks for Apple but doubt that a single person used them so I stopped. > On Jul 6, 2020, at 10:08 PM, Jed Brown <jed(a)jedbrown.org> wrote: > > I don't envy the Brew developers who take the blame when Apple breaks things underneath them. I still boggle at the fact that the clear majority of people use operating systems that lack integrated package management. This problem has been solved for 25 years. > > Barry Smith <bsmith(a)petsc.dev> writes: > >> My fault, for some reason sphinx from brew installed its own private python so I had to do the pip at that. >> >> >> >>> On Jul 6, 2020, at 9:03 PM, Jed Brown <jed(a)jedbrown.org> wrote: >>> >>> Barry Smith <bsmith(a)petsc.dev> writes: >>> >>>> Apple's python 2 doesn't use pip >>>> >>>> $ sudo easy_install src/docs/sphinx_docs/requirements.txt >>>> Processing requirements.txt >>>> error: Not a recognized archive type: src/docs/sphinx_docs/requirements.txt >>>> >>>> Is this thing supported only for python3? >>> >>> Perhaps. Python2 is EOL. Try this >>> >>> python3 -m pip install --user -r src/docs/sphinx_docs/requirements.txt

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Re: [petsc-dev] Sphinx error
by Jed Brown 06 Jul '20

06 Jul '20

I don't envy the Brew developers who take the blame when Apple breaks things underneath them. I still boggle at the fact that the clear majority of people use operating systems that lack integrated package management. This problem has been solved for 25 years. Barry Smith <bsmith(a)petsc.dev> writes: > My fault, for some reason sphinx from brew installed its own private python so I had to do the pip at that. > > > >> On Jul 6, 2020, at 9:03 PM, Jed Brown <jed(a)jedbrown.org> wrote: >> >> Barry Smith <bsmith(a)petsc.dev> writes: >> >>> Apple's python 2 doesn't use pip >>> >>> $ sudo easy_install src/docs/sphinx_docs/requirements.txt >>> Processing requirements.txt >>> error: Not a recognized archive type: src/docs/sphinx_docs/requirements.txt >>> >>> Is this thing supported only for python3? >> >> Perhaps. Python2 is EOL. Try this >> >> python3 -m pip install --user -r src/docs/sphinx_docs/requirements.txt

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Re: [petsc-dev] Sphinx error
by Barry Smith 06 Jul '20

06 Jul '20

My fault, for some reason sphinx from brew installed its own private python so I had to do the pip at that. > On Jul 6, 2020, at 9:03 PM, Jed Brown <jed(a)jedbrown.org> wrote: > > Barry Smith <bsmith(a)petsc.dev> writes: > >> Apple's python 2 doesn't use pip >> >> $ sudo easy_install src/docs/sphinx_docs/requirements.txt >> Processing requirements.txt >> error: Not a recognized archive type: src/docs/sphinx_docs/requirements.txt >> >> Is this thing supported only for python3? > > Perhaps. Python2 is EOL. Try this > > python3 -m pip install --user -r src/docs/sphinx_docs/requirements.txt

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