Trilinos issueshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues2018-12-03T20:44:16Zhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/3981Belos: Add a users guide2018-12-03T20:44:16ZJames WillenbringBelos: Add a users guide*Created by: mhoemmen*
@hkthorn @trilinos/belos
Requested by @vbrunini. Current source of Belos documentation is Doxygen: https://trilinos.org/docs/dev/packages/belos/doc/html/index.html . This is a good start, but it's missing th...*Created by: mhoemmen*
@hkthorn @trilinos/belos
Requested by @vbrunini. Current source of Belos documentation is Doxygen: https://trilinos.org/docs/dev/packages/belos/doc/html/index.html . This is a good start, but it's missing the following features:
1. "How do I create a solver factory?" (Our recent DII work obfuscated the class hierarchy a bit.)
2. "How do I make the solver that I want?", i.e., "What is the mapping from solver string names to solvers?"
3. "What is a set of parameters that all Belos solvers accept?"
4. "Given a Belos solver, what parameters does it accept?" (This information exists only in the Doxygen documentation; its location may not be obvious to users.)
We could start with the existing Doxygen documentation, as it's the easiest to find and already exists.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3774Tpetra: improve BlockCrsMatrix documentation2018-10-30T16:34:11ZJames WillenbringTpetra: improve BlockCrsMatrix documentation*Created by: jhux2*
As mentioned in #3751, the documentation for Tpetra's BlockCrsMatrix could mislead a user or developer into thinking that fillComplete() is supported or required. The documentation should be improved.*Created by: jhux2*
As mentioned in #3751, the documentation for Tpetra's BlockCrsMatrix could mislead a user or developer into thinking that fillComplete() is supported or required. The documentation should be improved.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3664KokkosKernels: missing doxygen documentation2018-10-18T21:24:43ZJames WillenbringKokkosKernels: missing doxygen documentation*Created by: jhux2*
KokkosKernels doesn't have any links to its Doxygen documentation on trilinos.org, at least not that I could find. I think it would be useful to have doxygen available, similarly to what other Trilinos packages prov...*Created by: jhux2*
KokkosKernels doesn't have any links to its Doxygen documentation on trilinos.org, at least not that I could find. I think it would be useful to have doxygen available, similarly to what other Trilinos packages provide, e.g., [Tpetra](https://trilinos.org/docs/dev/packages/tpetra/doc/html/index.html).https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3494Epetra lessons don't show code2018-09-27T18:05:14ZJames WillenbringEpetra lessons don't show code*Created by: davydden*
PackageName: Epetra
HTML pages for Epetra Lessons (i.e. https://trilinos.org/docs/dev/packages/epetra/doc/html/Epetra_Lesson02.html) do not render the code. This works as expected for TPetra (i.e. https://trili...*Created by: davydden*
PackageName: Epetra
HTML pages for Epetra Lessons (i.e. https://trilinos.org/docs/dev/packages/epetra/doc/html/Epetra_Lesson02.html) do not render the code. This works as expected for TPetra (i.e. https://trilinos.org/docs/dev/packages/tpetra/doc/html/Tpetra_Lesson01.html)
@trilinos/epetra
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2801Amesos: reference guide is out-of-date2018-05-22T17:49:56ZJames WillenbringAmesos: reference guide is out-of-date*Created by: jhux2*
@trilinos/amesos
The Amesos 2.0 Reference Guide in `amesos/doc/AmesosReferenceGuide` has out-of-date configure and build instructions. This may confuse users - see #2770. Other parts may be out of date as well. ...*Created by: jhux2*
@trilinos/amesos
The Amesos 2.0 Reference Guide in `amesos/doc/AmesosReferenceGuide` has out-of-date configure and build instructions. This may confuse users - see #2770. Other parts may be out of date as well.
Possible resolutions:
1. Delete the guide.
1. Put a warning at the beginning that parts of the guide are invalid.
1. Update the incorrect parts of the guide.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2795Epetra requires C++11 now; update documentation2018-05-22T20:13:48ZJames WillenbringEpetra requires C++11 now; update documentation*Created by: mhoemmen*
I merged the following pull request that fixes GLIBCXX debug checking for deal.II's tests:
https://github.com/trilinos/Trilinos/pull/2783
This pull request introduces a modest C++11 requirement into Epetra. ...*Created by: mhoemmen*
I merged the following pull request that fixes GLIBCXX debug checking for deal.II's tests:
https://github.com/trilinos/Trilinos/pull/2783
This pull request introduces a modest C++11 requirement into Epetra. Please see discussion there for rationale. In particular, no one could come up with a current use case demanding that Epetra be built with a C++98 compiler. Even the Epetra-only MueLu build for Windows requires Teuchos, which in turn requires C++11. More importantly, we have no idea if Epetra builds with a C++98 compiler, since we have not tested this use case for a long time.
@trilinos/epetra @trilinos/framework @trilinos/muelu @maherou @trilinos/tpetra
If y'all have a problem with that, now might be a good time to say something. Otherwise, I hereby declare that Epetra now requires C++11. Next step is to update Epetra's documentation to make this clear.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2502Consistent Documentation2018-04-03T21:49:21ZJames WillenbringConsistent Documentation*Created by: jmgate*
@trilinos/framework
## Expectations
It'd be great if there was a single, comprehensive set of instructions for interacting with Trilinos.
## Current Behavior
At the moment, we have [README.md](https://githu...*Created by: jmgate*
@trilinos/framework
## Expectations
It'd be great if there was a single, comprehensive set of instructions for interacting with Trilinos.
## Current Behavior
At the moment, we have [README.md](https://github.com/trilinos/Trilinos/blob/master/README.md), which people will see rendered when they first navigate to [Trilinos on GitHub](https://github.com/trilinos/Trilinos). This file then links to [CONTRIBUTING.md](https://github.com/trilinos/Trilinos/blob/master/CONTRIBUTING.md), which also shows up linked on the new issue or new pull request creation pages. For instance, on the right-hand-side, at the bottom, you should see:
<img width="237" alt="screen shot 2018-04-03 at 3 43 19 pm" src="https://user-images.githubusercontent.com/20327215/38277489-ceb53f16-3755-11e8-94ad-c2c876e1e153.png">
In addition to these sources, we also have information spread out across the [wiki](https://github.com/trilinos/Trilinos/wiki). For instance, [here](https://github.com/trilinos/Trilinos/wiki/Pull-Request-Workflow) and [here](https://github.com/trilinos/Trilinos/wiki/Committing-Changes-to-the-Trilinos-Repository).
## Motivation and Context
At the very least, we need to make sure all these sources of information stay in sync. From what I've seen of other open source software projects, everything a potential user should need to know should show up in the README.md or CONTRIBUTING.md file. If either of those gets too lengthy and it seems prudent to break the information up over the wiki, everything should still be linked back into those files.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2228Tempus: update TSC documention for TSCS ordering issue2018-02-08T18:08:01ZJames WillenbringTempus: update TSC documention for TSCS ordering issue*Created by: sconde*
<!---
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Using Time Step Cont...*Created by: sconde*
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Using Time Step Control Strategy (TSCS) allows for applications to define their very own time step control strategy and add it to a vector of strategies and the Time Step Control will iterate and call each strategy. Essentially, this could be an `and` case if each strategies does a `min` with the step size `dt = metaData->getDt()` and a new computed step size `dt_new` before updating the step size with `metaData->setDt( DT )`.
<!--
Yes, this is an `and`. My understanding is that each strategy will just update (or override) the step size `dt` with `metadata->setDt(dt)`. In the `and` case, we just take the minimum of the step size from `metaData->getDt()` and new computed step size by the strategy.
-->
If the application wanted an `or` case, they can just appropriately update the `metaData->setDt(dt)`. The TSC, after calling all the TSCS, gets the updated `dt` by calling `metaData->getDt()`.
Note the ordering in the `Time Step Control Strategy List` (is important). A final TSCS that is called last can get just negate all previous TSCS updates.
The documentation needs to be updated to make this clear.
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@trilinos/tempus
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https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2223MueLu: trouble when building the tutorial2018-02-07T22:48:32ZJames WillenbringMueLu: trouble when building the tutorial*Created by: mayrmt*
I get an error when building the MueLu tutorial. Can anybody in @trilinos/muelu build the tutorial?
## Expectations
Being able to build the MueLu tutorial.
## Current Behavior
Following the step in the ```mu...*Created by: mayrmt*
I get an error when building the MueLu tutorial. Can anybody in @trilinos/muelu build the tutorial?
## Expectations
Being able to build the MueLu tutorial.
## Current Behavior
Following the step in the ```muelu/doc/Tutorial/README``` doesn't work for me.
Executing ```muelu/doc/Tutorial/tex/prepareTexTutorial.py``` results in the error
```
./prepareTexTutorial.py
Prepare files...
Split source files in src folder for inclusion in pdf...
Run test examples to include results in pdf...
Traceback (most recent call last):
File "./prepareTexTutorial.py", line 158, in <module>
splitfileintofragments('s1_easy.txt_3.fragment','--------------------------------------------------------------------------------')
File "./prepareTexTutorial.py", line 80, in splitfileintofragments
file = open( inputfile )
IOError: [Errno 2] No such file or directory: 's1_easy.txt_3.fragment'
```
The directory does not contain a file ```s1_easy.txt_3.fragment```, though I don't know why. Isn't it supposed to be created when configure/build MueLu?
## Steps to Reproduce
<!---
Provide a link to a live example, or an unambiguous set of steps to reproduce
this issue. Include code to reproduce, if relevant.
1. Do this.
1. Do that.
1. Shake fist angrily at computer.
-->
I followed the steps described in ```muelu/doc/Tutorial/README```:
1. Build MueLu with tests and examples enabled.
2. Run ```muelu/doc/Tutorial/tex/prepareTexTutorial.py```https://gitlab.osti.gov/jmwille/Trilinos/-/issues/1888Document best practices for linking apps against Trilinos with CUDA2017-10-25T21:12:28ZJames WillenbringDocument best practices for linking apps against Trilinos with CUDA*Created by: mhoemmen*
@trilinos/framework @trilinos/tpetra
It looks like applications are not linking against Trilinos with CUDA in the way that Trilinos itself builds and links with CUDA. See discussion here: https://github.com/g...*Created by: mhoemmen*
@trilinos/framework @trilinos/tpetra
It looks like applications are not linking against Trilinos with CUDA in the way that Trilinos itself builds and links with CUDA. See discussion here: https://github.com/gahansen/Albany/issues/195
This suggests that Trilinos needs to document best practices for linking applications against Trilinos with CUDA. It could be that applications have multiple good options, in which case Trilinos should document the strengths and weaknesses of each.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/1730MueLu: expand section on performance tips when running multigrid2017-09-13T20:57:10ZJames WillenbringMueLu: expand section on performance tips when running multigrid*Created by: aprokop*
We need a lot more tips for running at scale. *Created by: aprokop*
We need a lot more tips for running at scale. https://gitlab.osti.gov/jmwille/Trilinos/-/issues/1674Add Wiki page about GitHub notifications2017-09-01T23:22:59ZJames WillenbringAdd Wiki page about GitHub notifications*Created by: maherou*
GitHub notifications are essential for communication, especially for large projects. However, setting up your notifications and dealing with troubleshooting can be challenging. The wiki page:
https://github.co...*Created by: maherou*
GitHub notifications are essential for communication, especially for large projects. However, setting up your notifications and dealing with troubleshooting can be challenging. The wiki page:
https://github.com/trilinos/Trilinos/wiki/GitHub-Notifications
attempts to address the challenges.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/1233Create and publish an official Trilinos Change Management Policy2017-06-29T15:50:24ZJames WillenbringCreate and publish an official Trilinos Change Management Policy*Created by: maherou*
While the Trilinos project has a rigorous backward compatibility policy, other forms of change management are not well define. This issue is for creating a more comprehensive statement of how we manage changes. ...*Created by: maherou*
While the Trilinos project has a rigorous backward compatibility policy, other forms of change management are not well define. This issue is for creating a more comprehensive statement of how we manage changes. The policy should cover these things (and probably more):
- [ ] How we inform users of commits to the repository that could change numerical results.
- [ ] When these kinds of changes can be pushed into the repository and how.
- [ ] As we start to introduce non-deterministic algorithms, how do we indicate when a function may produce results that vary from run to run.
cc: @trilinos/framework Improve productivity, stability, and quality of Trilinoshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/1232Create and publish an official Trilinos User Support Policy2017-09-19T16:55:37ZJames WillenbringCreate and publish an official Trilinos User Support Policy*Created by: maherou*
The user support policy for Trilinos has been implicit from project inception. We need to make an explicit policy. Basic elements are:
- [x] Expectations for the general community.
- [x] Expectations for fund...*Created by: maherou*
The user support policy for Trilinos has been implicit from project inception. We need to make an explicit policy. Basic elements are:
- [x] Expectations for the general community.
- [x] Expectations for funded projects.
- [x] Roles and accountability.
**CC:** @trilinos/frameworkImprove productivity, stability, and quality of Trilinoshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/1153MueLu tutorial has undefined references2017-05-14T03:35:53ZJames WillenbringMueLu tutorial has undefined references*Created by: VictorEijkhout*
`CMakeFiles/MueLu_tutorial_laplace2d.dir/laplace2d.cpp.o: In function `Teuchos::RCP<MueLu::SmootherPrototype<double, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> > > M...*Created by: VictorEijkhout*
`CMakeFiles/MueLu_tutorial_laplace2d.dir/laplace2d.cpp.o: In function `Teuchos::RCP<MueLu::SmootherPrototype<double, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> > > MueLu::GetIfpackSmoother<double, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Teuchos::ParameterList const&, int const&)':
laplace2d.cpp:(.text._ZN5MueLu17GetIfpackSmootherIdiiN6Kokkos6Compat23KokkosDeviceWrapperNodeINS1_6SerialENS1_9HostSpaceEEEEEN7Teuchos3RCPINS_17SmootherPrototypeIT_T0_T1_T2_EEEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS7_13ParameterListERKSB_[_ZN5MueLu17GetIfpackSmootherIdiiN6Kokkos6Compat23KokkosDeviceWrapperNodeINS1_6SerialENS1_9HostSpaceEEEEEN7Teuchos3RCPINS_17SmootherPrototypeIT_T0_T1_T2_EEEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS7_13ParameterListERKSB_]+0x36): undefined reference to `MueLu::IfpackSmoother<Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> >::IfpackSmoother(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Teuchos::ParameterList const&, int const&)'
CMakeFiles/MueLu_tutorial_laplace2d.dir/laplace2d.cpp.o: In function `MueLu::MutuallyExclusiveTime<MueLu::Level>::start(bool)':
laplace2d.cpp:(.text._ZN5MueLu21MutuallyExclusiveTimeINS_5LevelEE5startEb[_ZN5MueLu21MutuallyExclusiveTimeINS_5LevelEE5startEb]+0x3b8): undefined reference to `MueLu::myParent_[abi:cxx11]'
laplace2d.cpp:(.text._ZN5MueLu21MutuallyExclusiveTimeINS_5LevelEE5startEb[_ZN5MueLu21MutuallyExclusiveTimeINS_5LevelEE5startEb]+0x41b): undefined reference to `MueLu::myParent_[abi:cxx11]'
`
And fiddle. I can't attach the log file because it's too large. Beats me why you guys keep using github.
https://www.dropbox.com/s/i3bnbxj97kscmdl/trilinos-12_intel17_impi_17_0.log?dl=0
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/1071Fix Broken Video Links in TUG Pages2019-04-03T07:27:30ZJames WillenbringFix Broken Video Links in TUG Pages*Created by: jmgate*
Many of the video links in the Trilinos User Group annual meeting pages on the Trilinos website are missing. I noticed the problem when looking at the [2011 schedule](https://trilinos.org/community/events/trilinos-...*Created by: jmgate*
Many of the video links in the Trilinos User Group annual meeting pages on the Trilinos website are missing. I noticed the problem when looking at the [2011 schedule](https://trilinos.org/community/events/trilinos-user-group-meeting-2011/), but it looks like other years are affected as well. The videos can be found at http://digitalops.sandia.gov/Mediasite/Catalog/catalogs/TUG-2011 (with links to the other years on the left).https://gitlab.osti.gov/jmwille/Trilinos/-/issues/1040doxygen 1.8.13 incompatibility2017-10-05T22:43:50ZJames Willenbringdoxygen 1.8.13 incompatibility*Created by: ilovezfs*
I'm having to set `-DPyTrilinos_DOCSTRINGS:BOOL=OFF` due to an incompatibility with doxygen 1.8.13, which ultimately leads to
```
[ 91%] Built target PanzerDiscFE_SacadoExample
[ 92%] Built target pytrilinos
[...*Created by: ilovezfs*
I'm having to set `-DPyTrilinos_DOCSTRINGS:BOOL=OFF` due to an incompatibility with doxygen 1.8.13, which ultimately leads to
```
[ 91%] Built target PanzerDiscFE_SacadoExample
[ 92%] Built target pytrilinos
[ 92%] Swig source /tmp/trilinos-20170129-37787-ninfii/Trilinos-trilinos-release-12-10-1/packages/PyTrilinos/src/LOCA.Epetra.Interface.i
/tmp/trilinos-20170129-37787-ninfii/Trilinos-trilinos-release-12-10-1/packages/PyTrilinos/src/LOCA.Epetra.Interface.i:147: Error: Unable to find 'LOCA_dox.i'
/tmp/trilinos-20170129-37787-ninfii/Trilinos-trilinos-release-12-10-1/packages/PyTrilinos/src/Epetra.i:260: Error: Unable to find 'Epetra_dox.i'
make[2]: *** [packages/PyTrilinos/src/LOCA.Epetra.InterfacePYTHON_wrap.cpp] Error 1
make[1]: *** [packages/PyTrilinos/src/CMakeFiles/PyTrilinos_LOCA_Epetra_Interface.dir/all] Error 2
make: *** [all] Error 2
```
Looking back in the log, there are errors in the initial cmake configuration: https://gist.github.com/ilovezfs/a5f72851bbeecded8d4b87a996b1b3ad
This does not occur if I use doxygen 1.8.12 or 1.8.11.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/971Ifpack2: update user guide with new block relaxation options2018-07-23T15:44:34ZJames WillenbringIfpack2: update user guide with new block relaxation options*Created by: jhux2*
@trilinos/ifpack2 The Ifpack2 user's guide should be updated to reflect changes in options to block relaxation.*Created by: jhux2*
@trilinos/ifpack2 The Ifpack2 user's guide should be updated to reflect changes in options to block relaxation.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/817Belos ParameterList documentation broken2016-11-14T18:20:01ZJames WillenbringBelos ParameterList documentation broken*Created by: wfspotz*
The `ParameterList` documentation for the Belos `BlockGmresSolMgr` is not working. It is supposed to be a collapsible list of parameter descriptions, but nothing renders on the page. `ParameterList` documentation i...*Created by: wfspotz*
The `ParameterList` documentation for the Belos `BlockGmresSolMgr` is not working. It is supposed to be a collapsible list of parameter descriptions, but nothing renders on the page. `ParameterList` documentation is working for Stratimikos and Domi. Locally, we can get the documentation to render correctly. On the trilinos.org site, the generated HTML and XML look OK. So we think there is some issue with dependent javascript or XML files, but Dena can't look at those.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/741Teuchos: Move YAML ParameterList document into header file2017-10-17T15:33:22ZJames WillenbringTeuchos: Move YAML ParameterList document into header file*Created by: mhoemmen*
@trilinos/teuchos @DrBooom
It lives in Trilinos/packages/teuchos/doc/paramlist_yaml.tex. It should go into the YAML header file as Doxygen.
*Created by: mhoemmen*
@trilinos/teuchos @DrBooom
It lives in Trilinos/packages/teuchos/doc/paramlist_yaml.tex. It should go into the YAML header file as Doxygen.