Trilinos issueshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues2019-04-10T14:22:11Zhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/4251ROL test timing out on ATDM intel-18 mpich build2019-04-10T14:22:11ZJames WillenbringROL test timing out on ATDM intel-18 mpich build*Created by: fryeguy52*
CC: @trilinos/rol, @rppawlo (Trilinos Nonlinear Solvers Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
## Description
As shown in [this query](https://testing.sandia.gov/cdash-dev-v...*Created by: fryeguy52*
CC: @trilinos/rol, @rppawlo (Trilinos Nonlinear Solvers Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
## Description
As shown in [this query](https://testing.sandia.gov/cdash-dev-view/queryTests.php?project=Trilinos&date=2018-10-09&filtercount=4&showfilters=1&filtercombine=and&field1=buildname&compare1=61&value1=Trilinos-atdm-cee-rhel6_intel-18.0.2_mpich2-3.2_openmp_static_opt&field2=testname&compare2=61&value2=ROL_adapters_tpetra_test_sol_TpetraSimulatedConstraintInterfaceCVaR_MPI_4&field3=buildstarttime&compare3=84&value3=2019-01-23&field4=buildstarttime&compare4=83&value4=2019-01-01) the test:
* ROL_adapters_tpetra_test_sol_TpetraSimulatedConstraintInterfaceCVaR_MPI_4
is timing out in the build:
* Trilinos-atdm-cee-rhel6_intel-18.0.2_mpich2-3.2_openmp_static_opt
## Current Status on CDash
The current status of this test in this build for the current testing day can be found [here](https://testing.sandia.gov/cdash-dev-view/queryTests.php?project=Trilinos&date=2018-10-09&filtercount=4&showfilters=1&filtercombine=and&field1=buildname&compare1=61&value1=Trilinos-atdm-cee-rhel6_intel-18.0.2_mpich2-3.2_openmp_static_opt&field2=testname&compare2=61&value2=ROL_adapters_tpetra_test_sol_TpetraSimulatedConstraintInterfaceCVaR_MPI_4&field3=buildstarttime&compare3=84&value3=today&field4=buildstarttime&compare4=83&value4=yesterday)
## Steps to Reproduce
One should be able to reproduce this failure on a machine with a cee rhel6 environment as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for a machine with a cee rhel6 environment are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#cee-rhel6-environment
The exact commands to reproduce this issue should be:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh Trilinos-atdm-cee-rhel6_intel-18.0.2_mpich2-3.2_openmp_static_opt
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_Rol=ON \
$TRILINOS_DIR
$ make NP=16
$ ctest -j16
```
Initial cleanup of new ATDM builds of Trilinoshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/3844ATDM_CONFIG_MPI_EXEC Causes Problems on Chama2019-04-10T14:10:28ZJames WillenbringATDM_CONFIG_MPI_EXEC Causes Problems on Chama*Created by: jmgate*
Hey @bartlettroscoe, I'm having trouble getting a build of EMPIRE up and running on `chama`. It'll build, but I'm seeing all of EMPIRE-PIC's tests fail (see [EMPIRE_EM-Plasma-Trilinos-chama-test-all-of-EMPIRE-intel...*Created by: jmgate*
Hey @bartlettroscoe, I'm having trouble getting a build of EMPIRE up and running on `chama`. It'll build, but I'm seeing all of EMPIRE-PIC's tests fail (see [EMPIRE_EM-Plasma-Trilinos-chama-test-all-of-EMPIRE-intel-opt-openmp](https://jenkins-srn.sandia.gov/user/jmgate/my-views/view/EMPIRE/job/EMPIRE_EM-Plasma-Trilinos-chama-test-all-of-EMPIRE-intel-opt-openmp/9/consoleFull)). I think what's happening is on `chama` the `ATDM_CONFIG_MPI_EXEC` variable gets set to `srun` in [cmake/std/atdm/common/toss3/environment.sh](https://github.com/trilinos/Trilinos/blob/7e0342c8d2ab8855fe5112b483284a8837911d20/cmake/std/atdm/common/toss3/environment.sh#L74). When we test EMPIRE, we wind up submitting the `ctest` command via `srun`. Unfortunately each EMPIRE-PIC regression test winds up running
```
$Trilinos_MPI_EXEC -n $NUM_PROCS $EXE --i=$INPUT
```
where `$TRILINOS_MPI_EXEC` is `$ATDM_CONFIG_MPI_EXEC`, which is `srun`, so we're effectively invoking `srun` within something that's been submitted via `srun`. I don't know slurm inside and out, but that sounds like a problem.
The question, then, is what should we do about it? In the CMake file that's used for all of EMPIRE-PIC's regression tests, do we need to replace `$Trilinos_MPI_EXEC` with `$(which mpiexec)` or something to that effect? Or do we need to do something more clever with the `$ATDM_CONFIG_MPI_EXEC` variable in `cmake/std/atdm/common/toss3/environment.sh` such that it works for whatever you need it to do, but then it doesn't also mess up EMPIRE's testing on `toss3` systems?
@bathmatt, did you set up our CMake stuff to use `$Trilinos_MPI_EXEC`? Do you know the rationale behind it?https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4809Framework: Non-framework machines no longer able to report to Cdash2019-04-09T23:16:48ZJames WillenbringFramework: Non-framework machines no longer able to report to Cdash*Created by: csiefer2*
And for that matter, the entire Nightly track is gone. SAD!
(Originally noticed by @lucbv)
@trilinos/framework
@trilinos/tpetra This will impact deprecation work after the release if it is not resolved...*Created by: csiefer2*
And for that matter, the entire Nightly track is gone. SAD!
(Originally noticed by @lucbv)
@trilinos/framework
@trilinos/tpetra This will impact deprecation work after the release if it is not resolved by then.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4813Zoltan2: example passes extra arguments to Kokkos::View constructor2019-04-06T09:36:26ZJames WillenbringZoltan2: example passes extra arguments to Kokkos::View constructor*Created by: mhoemmen*
@trilinos/zoltan2 @kddevin
`Trilinos/packages/zoltan2/example/block/kokkosBlock.cpp`, line 147, creates a 1-D `Kokkos::View`, but passes it two run-time dimensions. The second dimension is zero, which is why ...*Created by: mhoemmen*
@trilinos/zoltan2 @kddevin
`Trilinos/packages/zoltan2/example/block/kokkosBlock.cpp`, line 147, creates a 1-D `Kokkos::View`, but passes it two run-time dimensions. The second dimension is zero, which is why it still builds, but it throws if you disable deprecated Kokkos code.
I am working on a fix.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4814Tpetra: Hide all currently deprecated code with TPETRA_ENABLE_DEPRECATED_CODE...2019-04-06T09:36:26ZJames WillenbringTpetra: Hide all currently deprecated code with TPETRA_ENABLE_DEPRECATED_CODE macro*Created by: mhoemmen*
@trilinos/tpetra
- [x] For anything in Tpetra marked with `TPETRA_DEPRECATED`, wrap it in `#ifdef TPETRA_ENABLE_DEPRECATED_CODE ... #endif`.
- [x] Make sure that all downstream code builds with `TPETRA_EN...*Created by: mhoemmen*
@trilinos/tpetra
- [x] For anything in Tpetra marked with `TPETRA_DEPRECATED`, wrap it in `#ifdef TPETRA_ENABLE_DEPRECATED_CODE ... #endif`.
- [x] Make sure that all downstream code builds with `TPETRA_ENABLE_DEPRECATED_CODE` not defined (it is currently defined by default; set the CMake option `Tpetra_ENABLE_DEPRECATED_CODE` (case significant) to `OFF`, in order to build with the macro not defined).
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4785Zoltan2: MJ giving unbalanced parts for large structured data2019-04-06T09:36:26ZJames WillenbringZoltan2: MJ giving unbalanced parts for large structured data*Created by: kddevin*
<!---
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pertains to a particular package in Trilinos, it's worthwhile to start the
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<!---
Note that an...*Created by: kddevin*
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@trilinos/zoltan2
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## Expectations
For uniformly weighted input, MJ should return balanced parts when not using rectilinear blocks.
## Current Behavior
For large structured data, MJ can return unbalanced parts.
For example, running with 9M points selected as integers within a 1000x1000x1000 cube and dividing into 64 parts, MJ returns imbalance of 3, with half of the parts empty.
```
myGlobalId_t = i 4; localCount = 9000000; globalCount = 9000000
Test: no weights, scalar = double
Imbalance Metrics: (64 existing parts) (32 of which are non-empty)
min max avg imbalance
object count 0 4.219e+05 1.406e+05 3
```
This result is consistent regardless of whether the coordinates are given to MJ as integers or doubles.
## Motivation and Context
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I'd like to partition the nonzeros of a tensor with MJ, but for large-enough tensors, the resulting partition is not balanced.
## Definition of Done
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Tell us what needs to happen. If necessary, give us a task list along the
lines of:
- [ ] First do this.
- [ ] Then do that.
- [ ] Also this other thing.
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MJ returns balanced parts for this use case.
## Possible Solution
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ideas on how to implement the addition or change.
-->
## Steps to Reproduce
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this issue. Include code to reproduce, if relevant.
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New test problem zoltan2/test/partition/mj_imbalanced.cpp demonstrates the problem.
Running on one processor:
Zoltan2_mj_imbalanced.exe
## Your Environment
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issue.
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- **Relevant repo SHA1s:**
- **Relevant configure flags or configure script:**
- **Operating system and version:**
- **Compiler and TPL versions:**
77f266c4c5f8c2135b922c299ea531d221a2df5c
All platforms
## Related Issues
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* Blocks
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## Additional Information
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https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4797Tpetra::MultiVector: Deprecate getDualView & remove its use from Trilinos2019-04-05T20:34:29ZJames WillenbringTpetra::MultiVector: Deprecate getDualView & remove its use from Trilinos*Created by: mhoemmen*
@trilinos/tpetra
- [x] Deprecate `Tpetra::MultiVector::getDualView`.
- [x] Remove its use from Trilinos.
- [x] Explain (in the method's Doxygen documentation) how to get the same functionality.
## Motivat...*Created by: mhoemmen*
@trilinos/tpetra
- [x] Deprecate `Tpetra::MultiVector::getDualView`.
- [x] Remove its use from Trilinos.
- [x] Explain (in the method's Doxygen documentation) how to get the same functionality.
## Motivation and Context
The `getDualView` method exposes an implementation detail of `Tpetra::MultiVector`. This hinders fixing #364 and #333.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3715Tempus: Add Stepper Initial Conditions2019-04-05T20:00:01ZJames WillenbringTempus: Add Stepper Initial Conditions*Created by: ccober6*
Adding a Stepper initial conditions has several benefits:
* Ensure that the initial SolutionState is consistent, i.e., x, xDot, and xDotDot satisfy the governing equation at the initial time.
* Currently explic...*Created by: ccober6*
Adding a Stepper initial conditions has several benefits:
* Ensure that the initial SolutionState is consistent, i.e., x, xDot, and xDotDot satisfy the governing equation at the initial time.
* Currently explicit Steppers are not consistent until the next time step fills in the currentState. This change will make the SolutionState consistent within the time step.
* For explicit Steppers with a consistent SolutionState, the residual can be determined and compared to residuals from implicit Steppers. This is SPARC's main driver for this change.
* For DAEs, making the initial condition consistent is critical to obtain the correct solution.
@trilinos/tempus
## Expectations
* Changes for this issue should not effect solutions.
## Definition of Done
- [x] First convert Forward Euler.
- [x] Convert all other explicit Steppers, ERK, Leapfrog, ...
- [x] Convert all implicit Steppers
- [x] Passes all tests.
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4698Tempus: Fix Divide by Zero2019-04-05T19:59:39ZJames WillenbringTempus: Fix Divide by Zero*Created by: ccober6*
In the relative norm calculation, the denominator is not check if zero during the consistency check.
@trilinos/tempus *Created by: ccober6*
In the relative norm calculation, the denominator is not check if zero during the consistency check.
@trilinos/tempus https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4776Apply for Google's Season of Docs2019-04-05T13:44:55ZJames WillenbringApply for Google's Season of Docs*Created by: jmgate*
## What is It?
The [Software Sustainability Institute](https://www.software.ac.uk/) recently had [a blog post](https://www.software.ac.uk/blog/2019-03-26-season-docs-fostering-open-source-collaboration-tech-writers...*Created by: jmgate*
## What is It?
The [Software Sustainability Institute](https://www.software.ac.uk/) recently had [a blog post](https://www.software.ac.uk/blog/2019-03-26-season-docs-fostering-open-source-collaboration-tech-writers?mc_cid=19c554b05e&mc_eid=96b055f1e9) introducing Google's [Season of Docs](https://developers.google.com/season-of-docs/). The goal of the project is to pair technical writers with open source projects in need of documentation for a three month period starting in September of this year.
> In case you're familiar with it, this is similar to Google's [Summer of Code](https://developers.google.com/open-source/gsoc/2008/) project from years ago.
## What's the Timeline Look Like?
The complete timeline [is available here](https://developers.google.com/season-of-docs/docs/timeline), but the parts we need to be aware of are:
* April 2nd–23rd: Submit application to Google
* April 30th: Selection of organizations announced
* September 2nd: Doc writing officially starts
* November 29th: Tech writer submits final work products
## Who Pays for What?
Google will pay the technical writer ~$6,000 (adjusted for cost of living) over the three month period. They also supply some smaller amount of funding to the institution for the sake of mentoring the technical writer over the course of the season.
## How Does the Tech Writer Do the Work?
They work remotely from wherever they happen to be, using whatever remote collaboration means the mentoring organization uses. For us, that'd mean we'd communicate via GitHub issues and pull requests, and if we need to speak in person, we could give them a call. If Sandia wants to fly them out to meet/work in person, that's on us. There's no need on our end for actual hiring, onboarding, etc.
## What Do We Need to Do?
- [ ] First we need to identify two organization administrators (a primary and a backup) to manage our participation in Season of Docs. I can be one of these, though I don't need to be.
- [ ] Generate a list of project ideas. These would be specific tasks that will be accomplished in the three-month program. There's no need to adhere to these 100% once the program starts, but they are intended to give technical writers an accurate idea of what they might be doing with us. To decide what we'd like to focus on, we probably want to bring this up at the next Trilinos leaders' meeting (@maherou, @rppawlo, @mperego, @kddevin, @srajama1, @jwillenbring). If that's too far away, we should probably set up a Skype meeting sooner, because we don't have too much time to get an application together.
- [ ] Given the specific tasks above, we need to identify at least two mentors to help bring the tech writer on board and oversee their work throughout the season.
- [ ] Then we need to submit our application within the next three weeks.
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4789Unused Tpetra var warning in header breaking SPARC Trilinos Integration build...2019-04-05T13:42:55ZJames WillenbringUnused Tpetra var warning in header breaking SPARC Trilinos Integration builds with -Werror*Created by: bartlettroscoe*
CC: @trilinos/tpetra, @kddevin (Trilinos Data Services Product Lead), @bartlettroscoe, @fryeguy52, @mhoemmen
## Next Action Status
<status-and-or-first-action>
## Description
Recently Tpetra wa...*Created by: bartlettroscoe*
CC: @trilinos/tpetra, @kddevin (Trilinos Data Services Product Lead), @bartlettroscoe, @fryeguy52, @mhoemmen
## Next Action Status
<status-and-or-first-action>
## Description
Recently Tpetra was updated to add a new unused var warning:
```
.../Tpetra_Details_StaticView.hpp:168:9: error: unused type alias 'host_device_type' [-Werror,-Wunused-local-typedef]
```
This is bringing down the [SPARC Trilinos Integration builds](https://snl-wiki.sandia.gov/display/CoodinatedDevOpsATDM/SPARC+Trilinos+Integration+Process) for Clang and GCC due to the SPARC setting `-Werror` in those builds. Therefore, we get no build or test results in those builds due to this.
## Current Status on CDash
The current status can only be seen in the SPARC Trilinos Integration builds shown over the last few days [here](http://compsim-dashboard.sandia.gov/cdash/index.php?project=SPARC&date=2019-03-30&filtercombine=and&filtercount=2&showfilters=1&filtercombine=and&field1=buildname&compare1=66&value1=-trildev&field2=buildstarttime&compare2=83&value2=5%20days%20ago).
## Steps to Reproduce
Instructions to reproduce builds are at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for the system 'cee-rhel6' are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#cee-rhel6-environment
The exact commands to reproduce this warning should (hopefully) be:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh \
Trilinos-atdm-cee-rhel6_clang-5.0.1_openmpi-1.10.2_serial_static_opt
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_Tpetra=ON \
$TRILINOS_DIR
$ make NP=16
```https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4532Provide correct and accurate Trilinos version info during development to help...2019-04-05T13:37:59ZJames WillenbringProvide correct and accurate Trilinos version info during development to help address changes in backward compatibility*Created by: bartlettroscoe*
CC: @trilinos/framework, @fryeguy52
## Description
The current setup of Trilinos is that it contains a static version-controlled `Version.cmake` file with static version information:
```
SET(Trili...*Created by: bartlettroscoe*
CC: @trilinos/framework, @fryeguy52
## Description
The current setup of Trilinos is that it contains a static version-controlled `Version.cmake` file with static version information:
```
SET(Trilinos_VERSION 12.13)
SET(Trilinos_MAJOR_VERSION 12)
SET(Trilinos_MAJOR_MINOR_VERSION 121300)
SET(Trilinos_VERSION_STRING "12.13 (Dev)")
SET(Trilinos_ENABLE_DEVELOPMENT_MODE_DEFAULT ON) # Change to 'OFF' for a release
```
This info is used to configure the `Trilinos_version.h` file in the build directory that is installed with the contents:
```
#define TRILINOS_MAJOR_VERSION 12
#define TRILINOS_MAJOR_MINOR_VERSION 121300
#define TRILINOS_VERSION_STRING "12.13 (Dev)"
```
The even/odd minor version number (13 currently) does tell the user if one is looking at an (odd-numbere) development version or an (even-numbered) release version but it does not give enough info for codes that use almost continuous integration with Trilinos (e.g. ASC Sierra, ATDM APPs, etc.). For example, Trilinos breaks backward compatibility from time to time which causes downstream customer codes to fail to build or pass all of the tests. In a staged integration processes for customer APPs like ATDM SPARC (see [TRIL-243](https://sems-atlassian-son.sandia.gov/jira/browse/TRIL-243) and [TRIL-256](https://sems-atlassian-son.sandia.gov/jira/browse/TRIL-256)), the SPARC 'master' code needs to be able to build and pass tests against both their older accepted version of Trilinos and a newer Trilinos version on the 'develop' (or 'master') branch. To accomplish this, when Trilinos 'develop' breaks backward compatibility, APP customer codes need to add ifdefs and other conditional logic to know what version of Trilinos they are pointing to. In particular, they need to know if they are pointing a version of Trilinos before or after a particular version that breaks backward compatibility. For example, they need to be able to write ifdefs like:
```
# if <current-trilinos-version> >= <known-version-that-breaks-x>
# This is a newer version of Trilinos and we need to adjust for that change
...
#else
# This is an older version of Trilinos were our current code works just fine
...
#endif
```
A Trilinos installation needs to be able to advertise its exact development version both at configure-time and at compile-time to enable logic like above.
Whatever solution is provided, it must be able to determine in simple C/C++ processor logic if a version of Trilinos is greater or less than some known version where a break in backward compatibility or a new feature is added. It must work from direct builds of Trilinos and installations of Trilinos as well as from builds and installations created from source tarballs of Trilinos.
NOTE: Comparing git SHA1s is not an option because one must have access to the git repo in order compare versions with < or > comparisons and an installation of Trilinos does not have a full git repo.
## Proposed Solution
One way to provide the desired version info is to add the macro define:
```
#define TRILINOS_VERSION_DATE YYYYMMDDhh
```
which gives a monotonically increasing 10-digit integer for the version of Trilinos in terms of the 4-digit year (`YYYY`), 2-digit month (`MM`), 2-digit day (`DD`) and 2-digit hour (`hh`) that is taken from the git commit date (in UTC).
This 10-digit integer would fit in a 32-bit integer with a max signed value of `2^32/2 - 1` = `2147483647`. Therefore, this could represent the Trilinos version every hour till the end of the year 2147 (or 128 years from now) with the last hour being `2147 12 31 23` = `2147123123`. (Surely 64-bit integers will be handled in all C++ compilers in the year 2148).
This macro could be defined in a **new** file `Trilinos_version_date.h` that would not be included by any Trilinos code or tests (so as to not trigger any rebuilding of any Trilinos libraries or exectuables). This file would only get included by client source files that needs to know the exact fine-grained Trilinos version.
This date would be generated automatically from the git commit date of first-parent commits on the Trilinos 'develop' branch which gives a monotonically increasing date/time stamp. For example, the commit:
```
commit 930294d48f4661013265448c1f254a667c66bf0f
Merge: 6354c01 87054d8
Author: trilinos-autotester <trilinos-autotester@trilinos.org>
Date: Fri Mar 1 19:34:15 2019 -0700
Merge Pull Request #4530 from rppawlo/Trilinos/nox-remove-deprecated-code
Automatically Merged using Trilinos Pull Request AutoTester
PR Title: NOX: remove deprecated code
PR Author: rppawlo
```
has the commit date in UTC:
```
$ env TZ=GMT git log --format="%cd" --date=iso-local -1 930294d
2019-03-02 02:34:15 +0000
```
This date returned from this git command `2019-03-02 02:34:15` could be read in and set the date/time integer:
```
#define TRILINOS_VERSION_DATE 201903020234
```
A 32-bit integer in the C/C++ processor will be able to handle date/time integers of this format and correctly do integer comparisons with them.
To accomplish this, one could configure the file `Version.cmake` into the build directory from the template `Trilinos/cmake/Version.cmake.in` and then put that `Version.cmake` file in the install directory, put it into the source tarball, and also install it into the installation directory from the source tarball. (This would be exactly how this is done for the `<Project>RepoVersion.txt` file, see [here](https://tribits.org/doc/TribitsBuildReference.html#generating-a-project-repo-version-file).) Then `Trilinos_version_date.h` would be generated from `TRILINOS_VERSION_DATE` in the generated `Version.cmake` file.
Improve productivity, stability, and quality of Trilinoshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/4812Setting kokkos-ndevices in the ctest. 2019-04-04T22:32:41ZJames WillenbringSetting kokkos-ndevices in the ctest. *Created by: kyungjoo-kim*
A question or a suggestion.
When we run ctest, we in general use 4 mpi ranks. In cuda test (assuming we use ride or white), it would be better if we use ``--kokkos-ndevices=4`` as it can reduce the testing ...*Created by: kyungjoo-kim*
A question or a suggestion.
When we run ctest, we in general use 4 mpi ranks. In cuda test (assuming we use ride or white), it would be better if we use ``--kokkos-ndevices=4`` as it can reduce the testing time on cuda. When I just run the ctest, it does not append the kokkos option. Is there anyway to append the option in nightly tests ? This can also reduce time over failures in PR testing.
@bartlettroscoe @trilinos/framework @crtrott
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4661Tpetra: FECrsMatrix Tests Flagged as Experimental2019-04-04T16:12:08ZJames WillenbringTpetra: FECrsMatrix Tests Flagged as Experimental*Created by: csiefer2*
This is to avoid causing failures on some CUDA platforms.
This issue is to serve as a reminder to remove the Experimental flag when the issue is addressed.*Created by: csiefer2*
This is to avoid causing failures on some CUDA platforms.
This issue is to serve as a reminder to remove the Experimental flag when the issue is addressed.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4731Teuchos: VerboseObject fix filestreams2019-04-04T05:26:32ZJames WillenbringTeuchos: VerboseObject fix filestreams*Created by: jjellio*
Currently, VerboseObject provides an option to allow output to be redirected to a file. Unfortunately, this feature results in every MPI process opening/writing the file, which is not typically what an OStream is u...*Created by: jjellio*
Currently, VerboseObject provides an option to allow output to be redirected to a file. Unfortunately, this feature results in every MPI process opening/writing the file, which is not typically what an OStream is used to accomplish. For file output, this implementation leads to extreme performance degradation with large parallel jobs.
@trilinos/teuchos @bartlettroscoe @mhoemmen
## Expectations
VerboseObject should write to a single file (and be as performant at stdout.
## Current Behavior
Currently, we open multiple files and typically write exactly the same data to the same file. This gives the illusion of working as intended. Since the file will actually be correct at the end of the run. The issue is that every MPI process is writing the data, and this is not intended.
## Motivation and Context
ATDM apps would like to use this functionality. We uncovered/identified this issue by running with VerboseObject output to files with >64 nodes.
## Possible Solution
This fix is straightforward, and is addressed in PR#4629
(This is an issue to map to the PR... I should create the issues first in the future ... woops!)https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4630Tpetra::MultiVector not using cuBLAS for GEMM, making Belos slow2019-04-03T23:52:52ZJames WillenbringTpetra::MultiVector not using cuBLAS for GEMM, making Belos slow*Created by: mhoemmen*
@trilinos/tpetra @trilinos/belos @trilinos/kokkos-kernels @vbrunini
This is a Trilinos mirror of the following kokkos-kernels issue: https://github.com/kokkos/kokkos-kernels/issues/397 . Once we verify the pr...*Created by: mhoemmen*
@trilinos/tpetra @trilinos/belos @trilinos/kokkos-kernels @vbrunini
This is a Trilinos mirror of the following kokkos-kernels issue: https://github.com/kokkos/kokkos-kernels/issues/397 . Once we verify the proposed fix, be sure to patch Trilinos and submit a fix to kokkos-kernels.
## Related Issues
* Related to https://github.com/kokkos/kokkos-kernels/issues/397, https://github.com/kokkos/kokkos-kernels/issues/396, https://github.com/trilinos/Trilinos/issues/4626
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4738Intrepid2_unit-test_Projection_Serial_Test_InterpolationProjection_TET_MPI_1 ...2019-04-03T19:48:10ZJames WillenbringIntrepid2_unit-test_Projection_Serial_Test_InterpolationProjection_TET_MPI_1 failing ATDM mutrino build*Created by: fryeguy52*
CC: @trilinos/intrepid2, @mperego (Trilinos Discretizations Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
<status-and-or-first-action>
## Description
As shown in [this query](https...*Created by: fryeguy52*
CC: @trilinos/intrepid2, @mperego (Trilinos Discretizations Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
<status-and-or-first-action>
## Description
As shown in [this query](https://testing.sandia.gov/cdash/queryTests.php?project=Trilinos&filtercombine=and&filtercombine=&filtercombine=and&filtercount=5&showfilters=1&filtercombine=and&field1=buildname&compare1=61&value1=Trilinos-atdm-mutrino-intel-opt-openmp-HSW&field2=testname&compare2=61&value2=Intrepid2_unit-test_Projection_Serial_Test_InterpolationProjection_TET_MPI_1&field3=site&compare3=61&value3=mutrino&field4=buildstarttime&compare4=84&value4=2019-03-27T00%3A00%3A00&field5=buildstarttime&compare5=83&value5=2019-02-25T00%3A00%3A00) the test:
* `Intrepid2_unit-test_Projection_Serial_Test_InterpolationProjection_TET_MPI_1`
started failing in the build:
* `Trilinos-atdm-mutrino-intel-opt-openmp-HSW`
starting on 2019-03-26
test output can be found [here](https://testing.sandia.gov/cdash/testDetails.php?test=72286414&build=4781169)
new commits on the day it started failing can be found [here](https://testing.sandia.gov/cdash/viewNotes.php?buildid=4781164#!#note7)
## Current Status on CDash
current status can be found [here](https://testing.sandia.gov/cdash/queryTests.php?project=Trilinos&filtercombine=and&filtercombine=&filtercombine=and&filtercombine=and&filtercount=5&showfilters=1&filtercombine=and&field1=buildname&compare1=61&value1=Trilinos-atdm-mutrino-intel-opt-openmp-HSW&field2=testname&compare2=61&value2=Intrepid2_unit-test_Projection_Serial_Test_InterpolationProjection_TET_MPI_1&field3=site&compare3=61&value3=mutrino&field4=buildstarttime&compare4=84&value4=today&field5=buildstarttime&compare5=83&value5=yesterday)
## Steps to Reproduce
One should be able to reproduce this failure on mutrino as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for mutrino are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#mutrino
The exact commands to reproduce this issue should be:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh Trilinos-atdm-mutrino-intel-opt-openmp-HSW
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_Intrepid2=ON \
$TRILINOS_DIR
$ make NP=16
$ salloc -N 1 -p standard -J $ATDM_CONFIG_JOB_NAME ctest -j16
```
Keep promoted "ATDM" builds of Trilinos cleanhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/3544STK tests failing in targeted CUDA PR builds Trilinos-atdm-white-ride-cuda-9....2019-04-03T18:34:25ZJames WillenbringSTK tests failing in targeted CUDA PR builds Trilinos-atdm-white-ride-cuda-9.2-release-debug-pt*Created by: bartlettroscoe*
CC: @trilinos/stk , @kddevin (Trilinos Data Services Product Area Lead)
## Next Action Status
## Description
The STK package has 3 failing tests in the build `Trilinos-atdm-white-ride-cuda-9.2-relea...*Created by: bartlettroscoe*
CC: @trilinos/stk , @kddevin (Trilinos Data Services Product Area Lead)
## Next Action Status
## Description
The STK package has 3 failing tests in the build `Trilinos-atdm-white-ride-cuda-9.2-release-debug-pt ` on 'white' and 'ride' as shown [here](https://testing.sandia.gov/cdash-dev-view/viewTest.php?onlyfailed&buildid=3998255) which shows the failing tests:
* STKUnit_tests_stk_mesh_unit_tests_MPI_4
* STKUnit_tests_stk_ngp_unit_tests_MPI_4
* STKUnit_tests_stk_tools_unit_tests_MPI_4
The test `STKUnit_tests_stk_mesh_unit_tests_MPI_4` has output shown [here](https://testing.sandia.gov/cdash-dev-view/testDetails.php?test=55725258&build=3998255) and shows the failures:
```
*** Starting test BulkData.testFieldComm from UnitTestBulkData.cpp:2177
[white27:4867] *** An error occurred in MPI_Neighbor_alltoallv
[white27:4867] *** reported by process [2079326209,2]
[white27:4867] *** on communicator MPI COMMUNICATOR 3 CREATE FROM 0
[white27:4867] *** MPI_ERR_ARG: invalid argument of some other kind
[white27:4867] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[white27:4867] *** and potentially your MPI job)
[white27:04859] 1 more process has sent help message help-mpi-errors.txt / mpi_errors_are_fatal
[white27:04859] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
```
The test output for the test `STKUnit_tests_stk_ngp_unit_tests_MPI_4` shown [here](https://testing.sandia.gov/cdash-dev-view/testDetails.php?test=55725259&build=3998255) shows:
```
*** Starting test NGP_Kokkos.bucket0 from KokkosBulkDataBucketCentroidCalculation.cpp:230
[ OK ] NGP_Kokkos.bucket0 (7002379918061956201 ms)
*** Starting test NGP_Kokkos.calculate_centroid_field_with_gather_on_device_bucket from KokkosBulkDataBucketCentroidCalculation.cpp:235
[white27:4914] *** An error occurred in MPI_Neighbor_alltoallv
[white27:4914] *** reported by process [2048983041,2]
[white27:4914] *** on communicator MPI COMMUNICATOR 3 CREATE FROM 0
[white27:4914] *** MPI_ERR_ARG: invalid argument of some other kind
[white27:4914] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[white27:4914] *** and potentially your MPI job)
[white27:04906] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal
[white27:04906] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
```
Finally, the output for the test `STKUnit_tests_stk_tools_unit_tests_MPI_4` shown [here](https://testing.sandia.gov/cdash-dev-view/testDetails.php?test=55725262&build=3998255) shows:
```
*** Starting test CloningMesh.cloningBulkDataNoAura_selector from UnitTestBulkDataClone.cpp:418
[ OK ] CloningMesh.cloningBulkDataNoAura_selector (0 ms)
*** Starting test CloningMesh.cloningBulkDataWithAura_selector from UnitTestBulkDataClone.cpp:427
[white27:5053] *** An error occurred in MPI_Neighbor_alltoallv
[white27:5053] *** reported by process [2059272193,2]
[white27:5053] *** on communicator MPI COMMUNICATOR 3 CREATE FROM 0
[white27:5053] *** MPI_ERR_ARG: invalid argument of some other kind
[white27:5053] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[white27:5053] *** and potentially your MPI job)
[white27:05045] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal
[white27:05045] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
```
Therefore, it seems all of these tests are failing due to errors in the function `MPI_Neighbor_alltoallv()`.
This is an important build because we are targeting this build on 'white' and 'ride' as a Trilinos PR testing build (see #2464 ). Also, EMPIRE and SPARC uses STK. However, SPARC and EMPIRE do not enable the `STKUnit_tests` packages that has these tests. Therefore, from the ATDM perspective, we could disable these tests for ATDM. But since one would assume theses tests check the correct functioning of STK it would be good to get these fixed.
## Steps to reproduce
One should be able to reproduce these build errors on either 'white' or 'ride' by cloning the Trilinos git repo, checking out the 'develop' branch, creating a build directory, and then doing:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh cuda-9.2-release-debug
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnvAllPtPackages.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_STK=ON \
$TRILINOS_DIR
$ make NP=16
$ bsub -x -Is -q rhel7F -n 16 ctest -j16
```Initial cleanup of new ATDM builds of Trilinoshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/2013Create CODEOWNERS File2019-04-03T07:38:59ZJames WillenbringCreate CODEOWNERS File*Created by: jmgate*
@trilinos/framework
## Expectations
<!---
Tell us what you think should happen, how you think things should work, what
you would like to see in the documentation, etc.
-->
It'd be great for us to include a ...*Created by: jmgate*
@trilinos/framework
## Expectations
<!---
Tell us what you think should happen, how you think things should work, what
you would like to see in the documentation, etc.
-->
It'd be great for us to include a [CODEOWNERS](https://help.github.com/articles/about-codeowners/) file in the Trilinos repo root. Having such a file makes it such that we can assign default people or @trilinos/teams as reviewers when pull requests are created, depending on what files/packages/etc. are modified.
## Current Behavior
<!---
Tell us how the current behavior fails to meet your expectations in some way.
-->
Currently we rely on the one submitting the pull request to assign an appropriate reviewer if they know of one.
## Motivation and Context
<!---
How has this expectation failure affected you? What are you trying to
accomplish? Why do we need to address this? What does it have to do with
anything? Providing context helps us come up with a solution that is most
useful in the real world.
-->
This would provide some backup to ensure that the right people are reviewing the changes coming in.
## Related Issues
<!---
If applicable, let us know how this bug is related to any other open issues:
-->
* Related to #1583https://gitlab.osti.gov/jmwille/Trilinos/-/issues/1611Panzer: Tpetra Gathers2019-04-03T07:36:22ZJames WillenbringPanzer: Tpetra Gathers*Created by: jmgate*
In #615, all of Panzer's Epetra Gathers were switched over to the new way of doing things with `GlobalEvaluationData`s that have non-overlapping owned and ghosted vectors. The same needs to be done for Panzer's Tpe...*Created by: jmgate*
In #615, all of Panzer's Epetra Gathers were switched over to the new way of doing things with `GlobalEvaluationData`s that have non-overlapping owned and ghosted vectors. The same needs to be done for Panzer's Tpetra Gathers.
@trilinos/panzer