Trilinos issueshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues2019-04-20T20:00:47Zhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/4915Panzer: Link problem when Tpetra_INST_INT_INT=OFF2019-04-20T20:00:47ZJames WillenbringPanzer: Link problem when Tpetra_INST_INT_INT=OFF*Created by: kddevin*
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@trilinos/panzer
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## Expectations
Panzer should build with Tpetra_INST_INT_INT=OFF
## Current Behavior
I get link errors due to use of Tpetra::MultiVector with global ordinals = int.
```
"virtual thunk to Tpetra::MultiVector<int, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> >::describe(Teuchos::basic_FancyOStream<char, std::__1::char_traits<char> >&, Teuchos::EVerbosityLevel) const", referenced from:
vtable for Tpetra::MultiVector<int, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> > in libpanzer-dof-mgr.a(Panzer_DOFManager.cpp.o)
construction vtable for Tpetra::MultiVector<int, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> >-in-Tpetra::Vector<int, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> > in libpanzer-dof-mgr.a(Panzer_Filtered_UniqueGlobalIndexer.cpp.o)
vtable for Tpetra::MultiVector<int, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> > in libpanzer-dof-mgr.a(Panzer_Filtered_UniqueGlobalIndexer.cpp.o)
"virtual thunk to Tpetra::Vector<int, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> >::describe(Teuchos::basic_FancyOStream<char, std::__1::char_traits<char> >&, Teuchos::EVerbosityLevel) const", referenced from:
vtable for Tpetra::Vector<int, int, int, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace> > in libpanzer-dof-mgr.a(Panzer_Filtered_UniqueGlobalIndexer.cpp.o)
```
## Motivation and Context
We'd like to build Trilinos with only one global ordinal type enabled.
## Definition of Done
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Panzer builds and runs with Tpetra_INST_INT_INT=OFF.
## Possible Solution
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Not obligatory, but suggest a fix for the bug or documentation, or suggest
ideas on how to implement the addition or change.
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I see Tpetra::MultiVector<int,int,int> in tUniqueGlobalIndexerUtilities.cpp; perhaps this is the source of the problem. One could disable this test when Tpetra_INST_INT_INT=OFF.
Or perhaps the problem is due to some Epetra vs Tpetra issue?
## Steps to Reproduce
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```
cmake \
-D Trilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON \
-D Tpetra_INST_INT_LONG_LONG:BOOL=ON \
-D Tpetra_INST_INT_INT:BOOL=OFF \
-D CMAKE_BUILD_TYPE:STRING="DEBUG" \
-D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
\
-D TPL_ENABLE_MPI:BOOL=ON \
-D MPI_EXEC_MAX_NUMPROCS:STRING=11 \
\
-D TPL_ENABLE_BinUtils:BOOL=OFF \
-D TPL_ENABLE_Pthread:BOOL=OFF \
\
-D CMAKE_C_FLAGS:STRING="-Wall -pedantic -Wno-unknown-pragmas -Wno-narrowing -Wno-inline -Wshadow -Wdeprecated-declarations -Wempty-body -Wignored-qualifiers -Wmissing-field-initializers -Wsign-compare -Wtype-limits -Wuninitialized -Winit-self -fstrict-aliasing -Wno-long-long" \
-D CMAKE_CXX_FLAGS:STRING="-Wall -pedantic -Wno-unknown-pragmas -Wno-narrowing -Wno-delete-non-virtual-dtor -Wno-inline -Wshadow -Wdeprecated-declarations -Wempty-body -Wignored-qualifiers -Wmissing-field-initializers -Wsign-compare -Wtype-limits -Wuninitialized -Winit-self -fstrict-aliasing" \
\
-D Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON \
-D Trilinos_ENABLE_TESTS:BOOL=ON \
-D Trilinos_ENABLE_EXAMPLES:BOOL=ON \
\
-D Trilinos_ENABLE_SHADOW_WARNINGS:BOOL=ON \
-D Trilinos_VERBOSE_CONFIGURE:BOOL=OFF \
-D Trilinos_ENABLE_Fortran:BOOL=OFF \
\
-D Tpetra_ENABLE_DEPRECATED_CODE:BOOL=OFF \
\
-D Trilinos_ENABLE_Stokhos:BOOL=ON \
-D Trilinos_ENABLE_Nox:BOOL=ON \
-D Trilinos_ENABLE_ROL:BOOL=ON \
-D Trilinos_ENABLE_MiniTensor:BOOL=OFF \
-D ROL_ENABLE_MiniTensor:BOOL=OFF \
-D Trilinos_ENABLE_Panzer:BOOL=ON \
-D Trilinos_ENABLE_PanzerAdaptersSTK:BOOL=OFF \
-D Trilinos_ENABLE_PanzerAdaptersIOSS:BOOL=OFF \
-D Trilinos_ENABLE_Thyra:BOOL=ON \
-D Trilinos_ENABLE_MueLu:BOOL=ON \
-D Trilinos_ENABLE_Anasazi:BOOL=ON \
-D Trilinos_ENABLE_Belos:BOOL=ON \
\
-D Teuchos_ENABLE_STACKTRACE:BOOL=OFF \
-D Teuchos_ENABLE_LONG_LONG_INT:BOOL=ON \
.. |& tee OUTPUT.CMAKE
make -j 8 |& tee OUTPUT.MAKE
```
## Your Environment
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- **Relevant repo SHA1s:**
- **Relevant configure flags or configure script:**
- **Operating system and version:**
- **Compiler and TPL versions:**
## Related Issues
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## Additional Information
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https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4807Percept: integrate as a new package into trilinos2019-04-04T16:56:32ZJames WillenbringPercept: integrate as a new package into trilinos*Created by: rppawlo*
Percept used to be a subpackage in STK during the "classic stk" era. When STK was refactored, percept was no longer ported over. Since percept is tied strongly to STK and the two must be in sync, it makes sense to ...*Created by: rppawlo*
Percept used to be a subpackage in STK during the "classic stk" era. When STK was refactored, percept was no longer ported over. Since percept is tied strongly to STK and the two must be in sync, it makes sense to start snapshotting percept into trilinos along with stk once again. This issue is to set up percept build as a tribits package.
Percept is developed in sierra and is thoroughly test with sierra. The tests will not be ported into trilinos - only a few small acceptance tests and some panzer tests will be in trilinos. This will prevent a large size increase in the Trilinos code base from binary mesh files.
1. [DONE] Set up snapshot tool. Port src directory only.
2. [DONE] Set up config file to mirror compile time defines.
3. Hide dependencies on cgns and open nurbs behind ifdefs so we can compile without those TPL requirements.
4. Setup test scripts for Brian and Byron to build against.
5. Coordinate with STK team on snapshots.
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/4141Intrepid2: improve performance of LagrangianInterpolation 2019-01-04T21:08:27ZJames WillenbringIntrepid2: improve performance of LagrangianInterpolation *Created by: rppawlo*
An application is using the function `Intrepid2::Experimental::LagrangianInterpolation<DeviceSpace>::getDofCoordsAndCoeffs`. The function is not optimized to use kokkos and is causing scaling issues for large probl...*Created by: rppawlo*
An application is using the function `Intrepid2::Experimental::LagrangianInterpolation<DeviceSpace>::getDofCoordsAndCoeffs`. The function is not optimized to use kokkos and is causing scaling issues for large problems.
@trilinos/intrepid2
@mperego
@bathmatt https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3939PanzerAdaptersSTK_[Mixed]CurlLaplacianExample tests failing in Trilinos-atdm-...2018-12-22T19:45:49ZJames WillenbringPanzerAdaptersSTK_[Mixed]CurlLaplacianExample tests failing in Trilinos-atdm-waterman-cuda-9.2-release-debug build*Created by: fryeguy52*
CC: @trilinos/panzer, @mperego (Trilinos Discretizations Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
With the merge of PR #4079 to 'develop' on 12/19/2018, these tests should now be dis...*Created by: fryeguy52*
CC: @trilinos/panzer, @mperego (Trilinos Discretizations Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
With the merge of PR #4079 to 'develop' on 12/19/2018, these tests should now be disabled in this build `Trilinos-atdm-waterman-cuda-9.2-release-debug`. All tests that should be disabled were disabled on 12/19/2018 and all of the Panzer tests in this build passed on 12/19/2018 and 12/20/2018.
## Description
As shown in [this query](https://testing.sandia.gov/cdash/queryTests.php?project=Trilinos&filtercombine=and&filtercombine=&filtercombine=and&filtercombine=and&filtercombine=and&filtercount=5&showfilters=1&filtercombine=and&field1=buildname&compare1=61&value1=Trilinos-atdm-waterman-cuda-9.2-release-debug&field2=testname&compare2=65&value2=PanzerAdaptersSTK_&field3=site&compare3=61&value3=waterman&field4=buildstarttime&compare4=84&value4=2018-11-27T00%3A00%3A00&field5=buildstarttime&compare5=83&value5=2018-11-26T00%3A00%3A00) the tests:
* [PanzerAdaptersSTK_MixedCurlLaplacianExample](https://testing.sandia.gov/cdash/testDetails.php?test=60054478&build=4214970)
* [PanzerAdaptersSTK_MixedCurlLaplacianExample-ConvTest-Tri-Order-1](https://testing.sandia.gov/cdash/testDetails.php?test=60054486&build=4214970)
* [PanzerAdaptersSTK_MixedCurlLaplacianExample-ConvTest-Tri-Order-2](https://testing.sandia.gov/cdash/testDetails.php?test=60054484&build=4214970)
* [PanzerAdaptersSTK_MixedCurlLaplacianExample-ConvTest-Quad-Order-2](https://testing.sandia.gov/cdash/testDetails.php?test=61601464&build=4301598)
* [PanzerAdaptersSTK_MixedCurlLaplacianExample-ConvTest-Quad-Order-3](https://testing.sandia.gov/cdash/testDetails.php?test=60054481&build=4214970)
* [PanzerAdaptersSTK_MixedCurlLaplacianMultiblockExample-ConvTest-Quad-Order-1](https://testing.sandia.gov/cdash/testDetails.php?test=61601467&build=4301598)
* [PanzerAdaptersSTK_CurlLaplacianExample-ConvTest-Quad-Order-2](https://testing.sandia.gov/cdash/testDetails.php?test=60054475&build=4214970)
* [PanzerAdaptersSTK_CurlLaplacianExample-ConvTest-Quad-Order-4](https://testing.sandia.gov/cdash/testDetails.php?test=61601465&build=4301598)
* [PanzerAdaptersSTK_CurlLaplacianMultiblockExample-ConvTest-Quad-Order-1](https://testing.sandia.gov/cdash/testDetails.php?test=61601462&build=4301598)
are failing in the build:
* Trilinos-atdm-waterman-cuda-9.2-release-debug
Test names above link to the test output
## Current Status on CDash
The current status of these tests/builds for the current testing day can be found [here](https://testing.sandia.gov/cdash/queryTests.php?project=Trilinos&filtercombine=and&filtercount=3&showfilters=1&filtercombine=and&field1=buildname&compare1=61&value1=Trilinos-atdm-waterman-cuda-9.2-release-debug&field2=testname&compare2=65&value2=PanzerAdaptersSTK_&field3=site&compare3=61&value3=waterman)
## Steps to Reproduce
One should be able to reproduce this failure on waterman as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for waterman are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#waterman
The exact commands to reproduce this issue should be:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh Trilinos-atdm-waterman-cuda-9.2-release-debug
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_Panzer=ON \
$TRILINOS_DIR
$ make NP=16
$ bsub -x -Is -n 20 ctest -j20
```Keep promoted "ATDM" builds of Trilinos cleanhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/2751Address timing out (or failing) test PanzerAdaptersSTK_MixedPoissonExample-Co...2018-11-30T11:16:53ZJames WillenbringAddress timing out (or failing) test PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3 test in the Trilinos-atdm-toss3-intel-debug-openmp-panzer build*Created by: bartlettroscoe*
Summary:
**CC:** @trilinos/panzer, @fryeguy52
## Next Action Status
After the commit 652a011 was merged on 5/16/2018, the test `PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3` disappeare...*Created by: bartlettroscoe*
Summary:
**CC:** @trilinos/panzer, @fryeguy52
## Next Action Status
After the commit 652a011 was merged on 5/16/2018, the test `PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3` disappeared from the build `Trilinos-atdm-toss3-intel-debug-openmp-panzer` starting 5/17/2018. PR #3559 merged on 10/8/2018 disables this test on 'waterman' `cuda-9.2` builds and the test was seen removed on CDash on 10/9/2018. Next: Fix this?
## Description
As can be seen in the queries
* https://testing-vm.sandia.gov/cdash/queryTests.php?project=Trilinos&filtercombine=and&filtercombine=and&filtercombine=and&filtercount=3&showfilters=1&filtercombine=and&field1=buildname&compare1=61&value1=Trilinos-atdm-toss3-intel-debug-openmp-panzer&field2=testname&compare2=65&value2=PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3&field3=buildstarttime&compare3=84&value3=now
*
The test `PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3` is the only failing test in the panzer-only test build `Trilinos-atdm-toss3-intel-debug-openmp-panzer` over the last few days, except when there are system issues that cause many of the tests to fail (see #2699).
In all but one of the builds were this test was the only Panzer test that failed, it timed out a 10 minutes. The one exception was on 2018-05-10 where it failed as shown at:
* https://testing-vm.sandia.gov/cdash/testDetails.php?test=46467457&build=3498830
which showed the failure.
```
--------------------------------------------------------------------------
ORTE has lost communication with its daemon located on node:
hostname: ser285
This is usually due to either a failure of the TCP network
connection to the node, or possibly an internal failure of
the daemon itself. We cannot recover from this failure, and
therefore will terminate the job.
--------------------------------------------------------------------------
```
## Steps to Reproduce
As described at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#chamaserrano
Clone the Trilinos git repo on 'serrano' and then do:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh intel-debug-openmp
$ cmake \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_Panzer=ON \
$TRILINOS_DIR
$ make -j16
$ salloc -N1 --time=0:20:00 --account=<YOUR_WCID> ctest -VV -R PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3
```
## Related Issues
* Related to: #2699
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2446Address expensive Panzer tests that timeout at 10 minutes in ATDM builds2018-11-30T11:16:52ZJames WillenbringAddress expensive Panzer tests that timeout at 10 minutes in ATDM builds*Created by: bartlettroscoe*
**CC:** @trilinos/panzer, @bathmatt, @fryeguy52
## Next Action Status
Pushed the commits 245e01d and d852fa3 to 'develop' to address timeouts and it removed the timing out tests on 3/25/2108. Addressi...*Created by: bartlettroscoe*
**CC:** @trilinos/panzer, @bathmatt, @fryeguy52
## Next Action Status
Pushed the commits 245e01d and d852fa3 to 'develop' to address timeouts and it removed the timing out tests on 3/25/2108. Addressing memory issues and re-enabling these tests will be done in other follow-on issues.
## Description
This story is to analyze and then to address some expensive Panzer tests that are timing out routinely in the ATDM Trilinos builds as shown, for example, in the following query that lists all of the timing out tests over the last week as shown in the query:
* https://testing-vm.sandia.gov/cdash/queryTests.php?project=Trilinos&date=2018-03-21&filtercombine=and&filtercombine=and&filtercombine=and&filtercount=7&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-&field2=testname&compare2=65&value2=Panzer&field3=status&compare3=62&value3=passed&field4=status&compare4=62&value4=notrun&field5=buildstarttime&compare5=84&value5=2018-03-23&field6=buildstarttime&compare6=83&value6=2018-03-16&field7=details&compare7=63&value7=timeout
This query shows the following 6 timing out tests:
* `PanzerAdaptersSTK_CurlLaplacianExample-ConvTest-Quad-Order-4`
* `PanzerAdaptersSTK_main_driver_energy-ss-loca-eigenvalue`
* `PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-2`
* `PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3`
* `PanzerAdaptersSTK_PoissonInterfaceExample_2d_diffsideids_MPI_1`
* `PanzerAdaptersSTK_PoissonInterfaceExample_2d_MPI_4`
which include the builds:
* `Trilinos-atdm-hansen-shiller-cuda-debug`
* `Trilinos-atdm-hansen-shiller-cuda-opt`
* `Trilinos-atdm-hansen-shiller-intel-debug-serial`
* `Trilinos-atdm-white-ride-cuda-debug`
* `Trilinos-atdm-white-ride-cuda-opt`
* `Trilinos-atdm-white-ride-gnu-debug-openmp`
As was discovered in https://github.com/trilinos/Trilinos/issues/2318#issuecomment-375494367, many of these tests will actually complete if you increase the timeouts . In particular, for the CUDA builds on hansen/shiller the following set of 5 tests all passed once the timeouts were increased to over 40 minutes for those CUDA builds:
* `PanzerAdaptersSTK_CurlLaplacianExample-ConvTest-Quad-Order-4`
* `PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-2`
* `PanzerAdaptersSTK_MixedPoissonExample-ConvTest-Hex-Order-3`
* `PanzerAdaptersSTK_PoissonInterfaceExample_2d_diffsideids_MPI_1`
* `PanzerAdaptersSTK_PoissonInterfaceExample_2d_MPI_4`
The only test missing from the above list for CUDA builds on hansen/shiller was `PanzerAdaptersSTK_main_driver_energy-ss-loca-eigenvalue` and that test only timed out on the `Trilinos-atdm-white-ride-cuda-opt` build.
This Issue will be to investigate these tests some more and then decide how to address them.
## Tasks:
0. Inspect the timing out tests in the last week on all builds of Trilinos ... All can be addressed with increasing timesouts and one disable (see [below](https://github.com/trilinos/Trilinos/issues/2446#issuecomment-375730569)) **[DONE]**
1. Increase timeouts on all of the timing out Panzer tests in the last week to 45 minutes and set `CATEGORIES NIGHTLY` ...
2. See if these tests pass with longer timeouts in automated builds and see what their runtimes are when they are displayed on CDash ...
3. Decrease the timeouts for some of the tests that are not taking 45 minutes to complete ...
5. ???
## Related Issues
* Related to #2318
Initial cleanup of new ATDM builds of Trilinos