April 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] empty space on left side of website pages
by Patrick Sanan 23 Apr '21

23 Apr '21

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.ht… Other projects using this theme have the mostly-empty left sidebar: https://numpy.org/doc/stable/ <https://numpy.org/doc/stable/> https://jupyter.readthedocs.io/en/latest/ <https://jupyter.readthedocs.io/en/latest/> (They also have fancier landing pages, though, which we have been discussing). It goes away on mobile devices or small windows, at least. > Am 23.04.2021 um 19:21 schrieb Barry Smith <bsmith(a)petsc.dev>: > > > There is a lot of empty space on the left side of the website pages; under the Search slot. Does this empty left side need to be so large, seems to waste a lot of the screen? > > Barry >

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Re: [petsc-dev] commenting on/asking questions on documentation pages
by Scott Kruger 23 Apr '21

23 Apr '21

I do not know much about these: https://sphinx-comments.readthedocs.io/en/latest/ I'm still not sure a link to a gitlab "New Issue" wouldn't be superior however. Scott On 2021-04-23 12:16, Barry Smith did write: > > Maybe the "edit" code could be copied and modified to go to a new issue window (and stick the URL into the issue) and then let people type. Could it even be clever enough to stick the issue number into the displayed webpage as clickable. Not perfect, but at least we would get notifications for each comment. > > Then the page might have a sidebar like > > Edit this page > Comment, ask question on page > > Comment !2345 > Comment !4555 > > Shouldn't Sphinx have such a beast? > > > Barry > > > > > On Apr 23, 2021, at 8:50 AM, Patrick Sanan <patrick.sanan(a)gmail.com> wrote: > > > > > > > >> Am 23.04.2021 um 04:45 schrieb Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>>: > >> > >> > >> 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" button that anyone can click on to make a comment or ask a question about the page. It would be super fantastic if they could refer to particular people in their comments but perhaps that is too difficult. > > > > > >> For example I am looking at https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview… <https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview…> and I immediately want to ask > >> > >> Where is the TS solver table in the list of solver tables? > >> > >> Barry > >> > >> Note the pre-historic PETSc html manual pages which everyone despises have a button in the upper right hand corner to report problems/ask questions so what I am asking for is not unprecedented. Our old code uses email which is not ideal but not ideal is better than not. Surely modern systems like Sphinx have this support built in? > >> > > > > I think the intended way to do this with our Sphinx template would be to add custom HTML templates, which can then be added to the sidebar. > > https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/sections.ht… <https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/sections.ht…> > > > > I'm worried that this involves too much scripting and customization, though. For example here's the way the "edit this page" link is done: > > https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the… <https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the…> > > > > Doesn't seem too bad but it relies on a pretty big chunk of Python as well: > > https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the… <https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the…> > > > > > > > > I'll open an issue on this, though, since it's entirely possible that someone else (or me, later) will think of a simple way to make this work, as it would indeed be a great feature. > -- Scott Kruger Tech-X Corporation kruger(a)txcorp.com 5621 Arapahoe Ave, Suite A Phone: (720) 466-3196 Boulder, CO 80303 Fax: (303) 448-7756

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empty space on left side of website pages
by Barry Smith 23 Apr '21

23 Apr '21

There is a lot of empty space on the left side of the website pages; under the Search slot. Does this empty left side need to be so large, seems to waste a lot of the screen? Barry

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Re: [petsc-dev] commenting on/asking questions on documentation pages
by Barry Smith 23 Apr '21

23 Apr '21

Maybe the "edit" code could be copied and modified to go to a new issue window (and stick the URL into the issue) and then let people type. Could it even be clever enough to stick the issue number into the displayed webpage as clickable. Not perfect, but at least we would get notifications for each comment. Then the page might have a sidebar like Edit this page Comment, ask question on page Comment !2345 Comment !4555 Shouldn't Sphinx have such a beast? Barry > On Apr 23, 2021, at 8:50 AM, Patrick Sanan <patrick.sanan(a)gmail.com> wrote: > > > >> Am 23.04.2021 um 04:45 schrieb Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>>: >> >> >> 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" button that anyone can click on to make a comment or ask a question about the page. It would be super fantastic if they could refer to particular people in their comments but perhaps that is too difficult. > > >> For example I am looking at https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview… <https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview…> and I immediately want to ask >> >> Where is the TS solver table in the list of solver tables? >> >> Barry >> >> Note the pre-historic PETSc html manual pages which everyone despises have a button in the upper right hand corner to report problems/ask questions so what I am asking for is not unprecedented. Our old code uses email which is not ideal but not ideal is better than not. Surely modern systems like Sphinx have this support built in? >> > > I think the intended way to do this with our Sphinx template would be to add custom HTML templates, which can then be added to the sidebar. > https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/sections.ht… <https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/sections.ht…> > > I'm worried that this involves too much scripting and customization, though. For example here's the way the "edit this page" link is done: > https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the… <https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the…> > > Doesn't seem too bad but it relies on a pretty big chunk of Python as well: > https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the… <https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the…> > > > > I'll open an issue on this, though, since it's entirely possible that someone else (or me, later) will think of a simple way to make this work, as it would indeed be a great feature.

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Re: [petsc-dev] commenting on/asking questions on documentation pages
by Patrick Sanan 23 Apr '21

23 Apr '21

> Am 23.04.2021 um 04:45 schrieb Barry Smith <bsmith(a)petsc.dev>: > > > 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" button that anyone can click on to make a comment or ask a question about the page. It would be super fantastic if they could refer to particular people in their comments but perhaps that is too difficult. > For example I am looking at https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview… <https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview…> and I immediately want to ask > > Where is the TS solver table in the list of solver tables? > > Barry > > Note the pre-historic PETSc html manual pages which everyone despises have a button in the upper right hand corner to report problems/ask questions so what I am asking for is not unprecedented. Our old code uses email which is not ideal but not ideal is better than not. Surely modern systems like Sphinx have this support built in? > I think the intended way to do this with our Sphinx template would be to add custom HTML templates, which can then be added to the sidebar. https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/sections.ht… I'm worried that this involves too much scripting and customization, though. For example here's the way the "edit this page" link is done: https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the… Doesn't seem too bad but it relies on a pretty big chunk of Python as well: https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the… <https://github.com/pydata/pydata-sphinx-theme/blob/master/pydata_sphinx_the…> I'll open an issue on this, though, since it's entirely possible that someone else (or me, later) will think of a simple way to make this work, as it would indeed be a great feature.

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Re: [petsc-dev] -info from just one process?
by Stefano Zampini 23 Apr '21

23 Apr '21

> I'm not talking about timings, I am talking about seeing where a code dies. > When codes die within the MPI implementation is basically impossible to provide a backtrace from PETSc, but the MPI implementation may offer some verbose messaging. If this happens quite early in the code (and I presume here we are failing somewhere in the 1-to-all pattern when distributing the plex data structure) running with -log_trace may get you some insight on where this is happening (provided that the offending PETSc routine calls LogEventBegin/End) In my experience, the sad story is that when there are software vendor failures with a large number of processes, I haven't found anything more efficient than a few bisection steps with good old printfs.... > > >> As a side note, one would expect that this kind of behavior is consistent >> across the library. >> But in fact, it isn’t. If you do something like -sub_ksp_view_pmat file >> with, for example, DD preconditioners, you end up with a single file with >> all local matrices scrambled in. >> It would be nice to have the same logic, i.e., file.%p, and be able to >> filter ranks that actually print to file like you suggest. >> These kind of options are less critical than -info so I can just insert >> them in the option database after initialization, if rank == view_this_rank >> PetscOptionsInsertString(), but doing that using command line arguments >> would be easier and more elegant, IMO. >> >> Thanks, >> Pierre >> >> Barry >> >> On Apr 22, 2021, at 11:14 AM, Mark Adams <mfadams(a)lbl.gov> wrote: >> >> OK, so -info out.%p would do what I asked. Alas, what I really need it to >> reduce the output with 128K processes. >> Thanks, >> >> On Thu, Apr 22, 2021 at 11:54 AM Pierre Jolivet <pierre(a)joliv.et> wrote: >> >>> >>> >>> On 22 Apr 2021, at 5:33 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> >>> wrote: >>> >>> Not out of the box no. There is -info ::self which makes info only print >>> from calls made on PETSC_COMM_SELF, but I don’t think that’s what you want. >>> Best advice would be to print to a file and grep the file for any lines >>> starting with the rank number you want. >>> >>> >>> There is no need for grep, IMHO, just do -info file and then open file.%p >>> >>> Thanks, >>> Pierre >>> >>> Best regards, >>> >>> Jacob Faibussowitsch >>> (Jacob Fai - booss - oh - vitch) >>> >>> On Apr 22, 2021, at 10:16, Mark Adams <mfadams(a)lbl.gov> wrote: >>> >>> Can I make -info only print from one process? >>> Mark >>> >>> >>> >>> >> >> -- Stefano

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Re: [petsc-dev] -info from just one process?
by Mark Adams 23 Apr '21

23 Apr '21

On Fri, Apr 23, 2021 at 2:57 AM Pierre Jolivet <pierre(a)joliv.et> wrote: > > > On 22 Apr 2021, at 7:45 PM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > It would be straightforward to add an option to -info to output only > from a particular MPI_COMM_WORLD global rank. > > Maybe an extra :rank at the end of the info options? > > Open 128k files is nuts. > > > It is what it is, I’ve made peace with the fact that I can’t expect any > meaningful timings for large runs when this option is on. > I'm not talking about timings, I am talking about seeing where a code dies. > As a side note, one would expect that this kind of behavior is consistent > across the library. > But in fact, it isn’t. If you do something like -sub_ksp_view_pmat file > with, for example, DD preconditioners, you end up with a single file with > all local matrices scrambled in. > It would be nice to have the same logic, i.e., file.%p, and be able to > filter ranks that actually print to file like you suggest. > These kind of options are less critical than -info so I can just insert > them in the option database after initialization, if rank == view_this_rank > PetscOptionsInsertString(), but doing that using command line arguments > would be easier and more elegant, IMO. > > Thanks, > Pierre > > Barry > > On Apr 22, 2021, at 11:14 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > > OK, so -info out.%p would do what I asked. Alas, what I really need it to > reduce the output with 128K processes. > Thanks, > > On Thu, Apr 22, 2021 at 11:54 AM Pierre Jolivet <pierre(a)joliv.et> wrote: > >> >> >> On 22 Apr 2021, at 5:33 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> >> wrote: >> >> Not out of the box no. There is -info ::self which makes info only print >> from calls made on PETSC_COMM_SELF, but I don’t think that’s what you want. >> Best advice would be to print to a file and grep the file for any lines >> starting with the rank number you want. >> >> >> There is no need for grep, IMHO, just do -info file and then open file.%p >> >> Thanks, >> Pierre >> >> Best regards, >> >> Jacob Faibussowitsch >> (Jacob Fai - booss - oh - vitch) >> >> On Apr 22, 2021, at 10:16, Mark Adams <mfadams(a)lbl.gov> wrote: >> >> Can I make -info only print from one process? >> Mark >> >> >> >> > >

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Re: [petsc-dev] -info from just one process?
by Mark Adams 23 Apr '21

23 Apr '21

On Thu, Apr 22, 2021 at 1:45 PM Barry Smith <bsmith(a)petsc.dev> wrote: > > It would be straightforward to add an option to -info to output only > from a particular MPI_COMM_WORLD global rank. > > Maybe an extra :rank at the end of the info options? > > Open 128k files is nuts. > Yep, and Fugaku can't deal with 128K MPI ranks then it should love 128K files > > Barry > > On Apr 22, 2021, at 11:14 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > > OK, so -info out.%p would do what I asked. Alas, what I really need it to > reduce the output with 128K processes. > Thanks, > > On Thu, Apr 22, 2021 at 11:54 AM Pierre Jolivet <pierre(a)joliv.et> wrote: > >> >> >> On 22 Apr 2021, at 5:33 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> >> wrote: >> >> Not out of the box no. There is -info ::self which makes info only print >> from calls made on PETSC_COMM_SELF, but I don’t think that’s what you want. >> Best advice would be to print to a file and grep the file for any lines >> starting with the rank number you want. >> >> >> There is no need for grep, IMHO, just do -info file and then open file.%p >> >> Thanks, >> Pierre >> >> Best regards, >> >> Jacob Faibussowitsch >> (Jacob Fai - booss - oh - vitch) >> >> On Apr 22, 2021, at 10:16, Mark Adams <mfadams(a)lbl.gov> wrote: >> >> Can I make -info only print from one process? >> Mark >> >> >> >> >

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Re: [petsc-dev] -info from just one process?
by Pierre Jolivet 23 Apr '21

23 Apr '21

> On 22 Apr 2021, at 7:45 PM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > It would be straightforward to add an option to -info to output only from a particular MPI_COMM_WORLD global rank. > > Maybe an extra :rank at the end of the info options? > > Open 128k files is nuts. It is what it is, I’ve made peace with the fact that I can’t expect any meaningful timings for large runs when this option is on. As a side note, one would expect that this kind of behavior is consistent across the library. But in fact, it isn’t. If you do something like -sub_ksp_view_pmat file with, for example, DD preconditioners, you end up with a single file with all local matrices scrambled in. It would be nice to have the same logic, i.e., file.%p, and be able to filter ranks that actually print to file like you suggest. These kind of options are less critical than -info so I can just insert them in the option database after initialization, if rank == view_this_rank PetscOptionsInsertString(), but doing that using command line arguments would be easier and more elegant, IMO. Thanks, Pierre > Barry > >> On Apr 22, 2021, at 11:14 AM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >> >> OK, so -info out.%p would do what I asked. Alas, what I really need it to reduce the output with 128K processes. >> Thanks, >> >> On Thu, Apr 22, 2021 at 11:54 AM Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >> >> >>> On 22 Apr 2021, at 5:33 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>> >>> Not out of the box no. There is -info ::self which makes info only print from calls made on PETSC_COMM_SELF, but I don’t think that’s what you want. Best advice would be to print to a file and grep the file for any lines starting with the rank number you want. >> >> There is no need for grep, IMHO, just do -info file and then open file.%p >> >> Thanks, >> Pierre >> >>> Best regards, >>> >>> Jacob Faibussowitsch >>> (Jacob Fai - booss - oh - vitch) >>> >>>> On Apr 22, 2021, at 10:16, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>> >>>> Can I make -info only print from one process? >>>> Mark >>> >> >

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commenting on/asking questions on documentation pages
by Barry Smith 22 Apr '21

22 Apr '21

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" button that anyone can click on to make a comment or ask a question about the page. It would be super fantastic if they could refer to particular people in their comments but perhaps that is too difficult. For example I am looking at https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview… <https://petsc.gitlab.io/-/petsc/-/jobs/1204309863/artifacts/public/overview…> and I immediately want to ask Where is the TS solver table in the list of solver tables? Barry Note the pre-historic PETSc html manual pages which everyone despises have a button in the upper right hand corner to report problems/ask questions so what I am asking for is not unprecedented. Our old code uses email which is not ideal but not ideal is better than not. Surely modern systems like Sphinx have this support built in?

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