Improve the TriBITS Netcdf and MPI TPLs #11175

ibaned · 2022-10-21T04:17:17Z

@trilinos/tribits

Motivation

This is motivated by issues TriBITSPub/TriBITS#533 and TriBITSPub/TriBITS#534, which are respectively:

The desire for the Netcdf TriBITS TPL to load only the CMake config files installed by NetCDF and HDF5, using the most modern CMake approach to bringing in those packages (using the targets that those projects define)
The desire to be able to use a custom implementation of MPI (not a compile wrapper but actually an include dir and library) to supply the TriBITS MPI TPL

Stakeholder Feedback

As both the TriBITS contributor and also the ASC IC PI stakeholder, I would really like the capabilities listed in Motivation.

Testing

That's what this branch is for!

this is required to fix TriBITSPub/TriBITS#534

when this CMake cache variable is set to a true value, the TriBITS Netcdf TPL code will only look for externally installed CMake config files for CMake packages called netCDF and possibly hdf5. Such files are installed by the latest versions of NetCDF and HDF5. This effectively allows loading NetCDF and its HDF5 dependency using the most modern CMake approach. This is needed to resolve TriBITSPub/TriBITS#533

trilinos-autotester · 2022-10-21T13:26:26Z

Status Flag 'Pre-Test Inspection' - Auto Inspected - Inspection Is Not Necessary for this Pull Request.

trilinos-autotester · 2022-10-21T13:28:18Z

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Using Repos:

Repo: TRILINOS (ibaned/Trilinos)

Pull Request Author: ibaned

trilinos-autotester · 2022-10-21T16:13:24Z

Status Flag 'Pull Request AutoTester' - Jenkins Testing: 1 or more Jobs FAILED

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CDash Test Results for PR# 11175.

Wiki: How to Reproduce PR Testing Builds and Errors.

bartlettroscoe

I would like to see if we can accomplish this without mass duplication if what is implemented in TriBITS. Please see above comment.

bartlettroscoe · 2022-10-21T12:49:54Z

cmake/tribits/core/std_tpls/FindTPLMPI.cmake

-tribits_tpl_find_include_dirs_and_libraries(MPI)
+tribits_tpl_find_include_dirs_and_libraries(
+    MPI
+    REQUIRED_HEADERS mpi.h)


This is very reasonable.

But it breaks the configure of Trilinos, see here, for example showing:

Processing enabled external package/TPL: MPI (enabled explicitly, disable with -DTPL_ENABLE_MPI=OFF) -- MPI_LIBRARY_NAMES='' -- Searching for headers in MPI_INCLUDE_DIRS='' -- Searching for a header file in the set "mpi.h": -- Searching for header 'mpi.h' ... -- ERROR: Could not find a header file in the set "mpi.h" -- ERROR: Could not find the include directories for TPL 'MPI'! -- TIP: If the TPL 'MPI' is on your system then you can set: -DMPI_INCLUDE_DIRS='<dir0>;<dir1>;...' to point to directories where these header files may be found. Or, just set: -DTPL_MPI_INCLUDE_DIRS='<dir0>;<dir1>;...' to point to the include directories which will bypass any search for header files and these include directories will be used without question in the build. (But this will result in a build-time error obviously if the necessary header files are not found in these include directories.) -- ERROR: Failed finding all of the parts of TPL 'MPI' (see above), Aborting! -- NOTE: The find module file for this failed TPL 'MPI' is: /scratch/trilinos/jenkins/ascic115/workspace/Trilinos_PR_clang-10.0.0/Trilinos/cmake/tribits/core/std_tpls/FindTPLMPI.cmake which is pointed to in the file: /scratch/trilinos/jenkins/ascic115/workspace/Trilinos_PR_clang-10.0.0/Trilinos/TPLsList.cmake TIP: Even though the TPL 'MPI' was explicitly enabled in input, it can be disabled with: -DTPL_ENABLE_MPI=OFF which will disable it and will recursively disable all of the downstream packages that have required dependencies on it. When you reconfigure, just grep the cmake stdout for 'MPI' and then follow the disables that occur as a result to see what impact this TPL disable has on the configuration of Trilinos. CMake Error at cmake/tribits/core/package_arch/TribitsProcessEnabledTpl.cmake:148 (message): ERROR: TPL_MPI_NOT_FOUND=TRUE, aborting! Call Stack (most recent call first): cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:1445 (tribits_process_enabled_tpl) cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:197 (tribits_process_enabled_tpls) cmake/tribits/core/package_arch/TribitsProject.cmake:92 (tribits_project_impl) CMakeLists.txt:109 (TRIBITS_PROJECT) -- Configuring incomplete, errors occurred! See also "/scratch/trilinos/jenkins/ascic115/workspace/Trilinos_PR_clang-10.0.0/pull_request_test/CMakeFiles/CMakeOutput.log".

The question is, why can't your MPI just supply the compiler wrappers and mpiexec? There should be no need to specifically look for mpi.h. The include dirs should be automatically handled by the MPI compiler wrappers.

Ah sorry, I didn't see the question at the end of this comment, didn't mean to ignore it. I guess philosophically I think that in a full-modern-CMake world compiler wrappers should not be necessary and so I'm trying as hard as possible to do the whole build without them, however I may soon have to give in and implement them.

@ibaned, you can use raw compilers with MPI. See "Configuring to build using raw compilers and flags/libraries:" at:

https://docs.trilinos.org/files/TrilinosBuildReference.html#configuring-with-mpi-support

This has been supported and used with Trilinos for at least 14 years.

bartlettroscoe · 2022-10-21T16:17:17Z

cmake/tribits/common_tpls/FindTPLNetcdf.cmake

+    # instead of using tribits_extpkg_create_imported_all_libs_target_and_config_file,
+    # we will do what it does ourselves because we need to bring in two
+    # inner find packages (netCDF and hdf5) because netCDF does not properly


This is a really unfortunate chuck of duplication and would be a terrible precedent to set. Might we consider having the TriBITS Netcdf TPL depend on the TriBITS HDF5 TPL and then have the Netcdf TPL depend on the HDF5 TPL as I tried to outline in TriBITSPub/TriBITS#533 (comment)? I think that would be very compact and you could essentially accomplish what this large amount of duplicated code is doing. Is that something you would be willing to consider? I can add a commit to this branch that attempts that (but I don't have a way to test it with Netcdf_ALLOW_MODERN=ON).

Yes, I'm fine with moving in that direction. If you'd be willing to add a commit to this branch that would be super helpful, and I could test the modern option on my end.

bartlettroscoe · 2022-10-21T16:31:59Z

@ibaned, for an easier way to run the Trilinos GenConfig PR builds locally, try out:

https://gitlab-ex.sandia.gov/rabartl/run_trilinos_pr_builds

That way, one can debug these issues without having to wait in the Trilinos PR testing system (and bog down builds for other PRs that are ready to merge).

…TriBITS#534) See TriBITSPub/TriBITS#534

…#534) This reverts commit e49070d. This causes configure failures.

…ITS#533) This makes Netcdf depend on HDF5 using modern CMake targets. ToDo: Finish this commit message.

bartlettroscoe · 2022-10-24T12:55:30Z

@ibaned, as of the commit 4f18ccc (#11175), this should be close to what you want (and with almost no duplication). There are some adjustments that may be needed or should be made but this should maintain backward compatibility.

I can't fully test this because I don't have the updated versions of HDF5 and Netcdf installed on any machine that I have access to. Please give this a test and let me know what happens (or give me access to a machine with the updated HDF5 and Netcdf installed so I can test this myself).

trilinos-autotester · 2022-10-24T13:06:50Z

Status Flag 'Pre-Test Inspection' - Auto Inspected - Inspection Is Not Necessary for this Pull Request.

trilinos-autotester · 2022-10-24T13:08:51Z

Status Flag 'Pull Request AutoTester' - Testing Jenkins Projects:

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Using Repos:

Repo: TRILINOS (ibaned/Trilinos)

Pull Request Author: ibaned

e10harvey · 2022-10-24T14:49:08Z

@bartlettroscoe : I cancelled the jobs running on the problematic nodes reported in #10999 (comment). Please try adding a RETEST label.

CC: @DaveBeCoding

ibaned · 2022-10-24T17:15:30Z

Thanks @bartlettroscoe ! I confirmed that the MPI part works for me, let me check the improvements to HDF5 dependence and report back

ibaned · 2022-10-24T18:33:20Z

I've had to make a couple of changes for the HDF5 and Netcdf setup to work in modern mode, I'll commit these here when the build completes

1. set the minimum version to the one I'm testing with 2. use HDF5_EXPORT_LIBRARIES since the targets defined are hard to predict

1. don't expect HDF5 target to be set. in the general case, Netcdf may not use HDF5, but also HDF5 has no predictable catch-all target 2. TPL_Netcdf_NOT_FOUND still has to be manually set to FALSE

ibaned · 2022-10-24T18:44:08Z

Okay, with the latest changes in this branch this works in my use case with the MODERN option on and custom MPI!

trilinos-autotester · 2022-10-24T18:44:20Z

Status Flag 'Pull Request AutoTester' - Error: Jenkins Jobs - A user has commited a change to the PR before testing completed. The original testing SHA = 4f18ccc Does not match the current commit SHA = 1312a36. The Jenkins Jobs will be shutdown; Testing of this PR must occur again.

trilinos-autotester · 2022-10-24T18:44:28Z

Status Flag 'Pull Request AutoTester' - Jenkins Testing: 1 or more Jobs FAILED

Note: Testing will normally be attempted again in approx. 2 Hrs 30 Mins. If a change to the PR source branch occurs, the testing will be attempted again on next available autotester run.

Pull Request Auto Testing has FAILED (click to expand)

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CDash Test Results for PR# 11175.

Wiki: How to Reproduce PR Testing Builds and Errors.

ibaned · 2022-10-24T18:55:44Z

It looks like the PR build for this still thinks that MPI has REQUIRED_HEADERS even though you reverted that change? is there some mechanism for clearing the CMake cache of the PR build that we need to do?

e10harvey · 2022-10-24T19:02:33Z

It looks like the PR build for this still thinks that MPI has REQUIRED_HEADERS even though you reverted that change? is there some mechanism for clearing the CMake cache of the PR build that we need to do?

Hi @ibaned: Each PR build configures and builds from scratch. I see that this MPI build configured properly: https://trilinos-cdash.sandia.gov/build/545791/configure. Please try adding a RETEST...

e10harvey · 2022-10-24T19:04:16Z

It looks like the PR build for this still thinks that MPI has REQUIRED_HEADERS even though you reverted that change? is there some mechanism for clearing the CMake cache of the PR build that we need to do?

Hi @ibaned: Each PR build configures and builds from scratch. I see that this MPI build configured properly: https://trilinos-cdash.sandia.gov/build/545791/configure. Please try adding a RETEST...

@ibaned: Note that I sorted by start time in CDash Test Results for PR# 11175 to find the most recent CDash results.

bartlettroscoe · 2022-10-24T22:06:33Z

Please try adding a RETEST...

@ibaned and @e10harvey, I took off AT: RETEST, that is not going to work. See #10999 (comment).

@e10harvey, how do these bad nodes (or at least nodes where the SEMS modules are broken) keep getting into the pool of Jenkins PR build machines?

e10harvey · 2022-10-24T22:15:31Z

Please try adding a RETEST...

@ibaned and @e10harvey, I took off AT: RETEST, that is not going to work. See #10999 (comment).

@e10harvey, how do these bad nodes (or at least nodes where the SEMS modules are broken) keep getting into the pool of Jenkins PR build machines?

It should work now. I've added both of you to the related help desk ticket.

trilinos-autotester · 2022-10-26T01:47:43Z

Status Flag 'Pull Request AutoTester' - Testing Jenkins Projects:

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Using Repos:

Repo: TRILINOS (ibaned/Trilinos)

Pull Request Author: ibaned

trilinos-autotester · 2022-10-26T07:10:07Z

Status Flag 'Pull Request AutoTester' - Jenkins Testing: 1 or more Jobs FAILED

Note: Testing will normally be attempted again in approx. 2 Hrs 30 Mins. If a change to the PR source branch occurs, the testing will be attempted again on next available autotester run.

Pull Request Auto Testing has FAILED (click to expand)

Build Information

Test Name: Trilinos_PR_gcc-8.3.0

Build Num: 1323
Status: PASSED

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Build Num: 852
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CDash Test Results for PR# 11175.

Wiki: How to Reproduce PR Testing Builds and Errors.

ibaned · 2022-10-26T18:31:22Z

@e10harvey a vortex3 runner snuck in there and did this:

Error: error in ptssup_mkcltsock_afunix()
10-26-2022 00:23:23:819 121619 main: Error initializing RM connection. Exiting.
jsrun return value: 1

bartlettroscoe · 2022-10-26T18:34:50Z

@e10harvey a vortex3 runner snuck in there and did this:

Error: error in ptssup_mkcltsock_afunix()
10-26-2022 00:23:23:819 121619 main: Error initializing RM connection. Exiting.
jsrun return value: 1

@ibaned, this is a long known random error on this build. See:

Random mass test failures showing "Error initializing RM connection. Exiting" on 'vortex' #6861
Random tests failures on 'ats2' 'vortex' with no STDOUT/STDERR and return code 255 #7122
Framework: Please remove problematic Trilinos PR ats2 build using cuda-10.1.243 on 'vortex' with mass random test failures #11109

trilinos-autotester · 2022-10-26T18:57:43Z

Status Flag 'Pull Request AutoTester' - User Requested Retest - Label AT: RETEST will be reset after testing.

trilinos-autotester · 2022-10-26T18:59:42Z

Status Flag 'Pull Request AutoTester' - Testing Jenkins Projects:

Pull Request Auto Testing STARTING (click to expand)

Build Information

Test Name: Trilinos_PR_gcc-8.3.0

Build Num: 1328
Status: STARTED

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Using Repos:

Repo: TRILINOS (ibaned/Trilinos)

Pull Request Author: ibaned

bartlettroscoe

Thanks for those final improvements!

trilinos-autotester · 2022-10-26T19:07:19Z

Status Flag 'Pull Request AutoTester' - Error: Jenkins Jobs - A user has commited a change to the PR before testing completed. The original testing SHA = ccbc874 Does not match the current commit SHA = d82f1b6. The Jenkins Jobs will be shutdown; Testing of this PR must occur again.

trilinos-autotester · 2022-10-26T19:07:35Z

Status Flag 'Pull Request AutoTester' - Jenkins Testing: 1 or more Jobs FAILED

Note: Testing will normally be attempted again in approx. 2 Hrs 30 Mins. If a change to the PR source branch occurs, the testing will be attempted again on next available autotester run.

Pull Request Auto Testing has FAILED (click to expand)

Build Information

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Status: ERROR

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CDash Test Results for PR# 11175.

Wiki: How to Reproduce PR Testing Builds and Errors.

ibaned · 2022-10-26T19:07:59Z

@bartlettroscoe I've made the next round of improvements you pointed out. Once the CI on this PR gets figured out, should I open a PR on TriBITS with these changes?

bartlettroscoe · 2022-10-26T19:12:00Z

@bartlettroscoe I've made the next round of improvements you pointed out. Once the CI on this PR gets figured out, should I open a PR on TriBITS with these changes?

@ibaned, I can take care of that. (It is just careful usage of git format-patch and git am.)

And unless something new comes up, the next PR testing iteration is likely to pass and allow the merge.

trilinos-autotester · 2022-10-26T19:36:32Z

Status Flag 'Pre-Test Inspection' - Auto Inspected - Inspection Is Not Necessary for this Pull Request.

trilinos-autotester · 2022-10-26T19:38:27Z

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Using Repos:

Repo: TRILINOS (ibaned/Trilinos)

Pull Request Author: ibaned

cmake/tribits/common_tpls/FindTPLHDF5.cmake

cmake/tribits/common_tpls/FindTPLNetcdf.cmake

see TriBITSPub#533 and also trilinos/Trilinos#11175 (comment)

bartlettroscoe · 2022-10-26T21:58:57Z

FYI: The matching changes to the TriBITS repo are in:

Update MPI, HDF5, and Netcdf TriBITS find modules (#533, #534) TriBITSPub/TriBITS#535

I will merge that PR as soon as this PR merges (fingers crossed on PR testing).

trilinos-autotester · 2022-10-27T01:47:12Z

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CDash Test Results for PR# 11175.

trilinos-autotester · 2022-10-27T01:47:29Z

Status Flag 'Pre-Merge Inspection' - SUCCESS: The last commit to this Pull Request has been INSPECTED AND APPROVED by [ bartlettroscoe ]!

trilinos-autotester · 2022-10-27T01:47:36Z

Status Flag 'Pull Request AutoTester' - Pull Request will be Automerged

trilinos-autotester · 2022-10-27T01:47:38Z

Merge on Pull Request# 11175: IS A SUCCESS - Pull Request successfully merged

ibaned added 2 commits October 20, 2022 21:59

add REQUIRED_HEADERS for TriBITS MPI TPL

e49070d

this is required to fix TriBITSPub/TriBITS#534

ibaned mentioned this pull request Oct 21, 2022

Find NetCDF and HDF5 using only CMake config files TriBITSPub/TriBITS#533

Closed

bartlettroscoe reviewed Oct 21, 2022

View reviewed changes

ibaned mentioned this pull request Oct 21, 2022

Using a custom MPI library TriBITSPub/TriBITS#534

Closed

bartlettroscoe added 3 commits October 23, 2022 12:17

Don't wipe out TPL_<tplName>_INCLUDE_DIRS if set by user (TriBITSPub/…

b7f3209

…TriBITS#534) See TriBITSPub/TriBITS#534

Revert "add REQUIRED_HEADERS for TriBITS MPI TPL" (TriBITSPub/TriBITS…

dbc5f6b

…#534) This reverts commit e49070d. This causes configure failures.

Make Netcdf depend on HDF5, fix TriBITS find modules (TriBITSPub/TriB…

4f18ccc

…ITS#533) This makes Netcdf depend on HDF5 using modern CMake targets. ToDo: Finish this commit message.

ibaned added 2 commits October 24, 2022 12:39

fix modern HDF5 import (TriBITSPub/TriBITS#533)

2665240

1. set the minimum version to the one I'm testing with 2. use HDF5_EXPORT_LIBRARIES since the targets defined are hard to predict

fix modern Netcdf import (TriBITSPub/TriBITS#533)

1312a36

1. don't expect HDF5 target to be set. in the general case, Netcdf may not use HDF5, but also HDF5 has no predictable catch-all target 2. TPL_Netcdf_NOT_FOUND still has to be manually set to FALSE

ibaned added the AT: RETEST Causes the PR autotester to run a new round of PR tests on the next iteration label Oct 24, 2022

bartlettroscoe removed the AT: RETEST Causes the PR autotester to run a new round of PR tests on the next iteration label Oct 24, 2022

bartlettroscoe added the AT: RETEST Causes the PR autotester to run a new round of PR tests on the next iteration label Oct 26, 2022

small improvements (TriBITSPub/TriBITS#533)

d82f1b6

ibaned dismissed bartlettroscoe’s stale review via d82f1b6 October 26, 2022 19:05

bartlettroscoe approved these changes Oct 26, 2022

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trilinos-autotester removed the AT: RETEST Causes the PR autotester to run a new round of PR tests on the next iteration label Oct 26, 2022

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bartlettroscoe mentioned this pull request Oct 26, 2022

Framework: Please remove problematic Trilinos PR ats2 build using cuda-10.1.243 on 'vortex' with mass random test failures #11109

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bartlettroscoe pushed a commit to bartlettroscoe/TriBITS that referenced this pull request Oct 26, 2022

Netcdf modern is only used if HDF5 is modern

b960317

see TriBITSPub#533 and also trilinos/Trilinos#11175 (comment)

bartlettroscoe mentioned this pull request Oct 26, 2022

Update MPI, HDF5, and Netcdf TriBITS find modules (#533, #534) TriBITSPub/TriBITS#535

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trilinos-autotester merged commit aa2e582 into trilinos:develop Oct 27, 2022

trilinos-autotester removed the AT: AUTOMERGE Causes the PR autotester to automatically merge the PR branch once approvals are completed label Oct 27, 2022

Improve the TriBITS Netcdf and MPI TPLs #11175

Improve the TriBITS Netcdf and MPI TPLs #11175

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ibaned commented Oct 21, 2022

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trilinos-autotester commented Oct 21, 2022

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Test Name: Trilinos_PR_gcc-8.3.0

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Test Name: Trilinos_PR_gcc-7.2.0-serial

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Test Name: Trilinos_PR_gcc-7.2.0-debug

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Test Name: Trilinos_PR_intel-17.0.1

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Test Name: Trilinos_PR_clang-10.0.0

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Test Name: Trilinos_PR_cuda-10.1.243

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Test Name: Trilinos_PR_python3

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Test Name: Trilinos_PR_cuda-11.4.2-uvm-off

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trilinos-autotester commented Oct 21, 2022

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Test Name: Trilinos_PR_gcc-8.3.0

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Test Name: Trilinos_PR_gcc-7.2.0-serial

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Test Name: Trilinos_PR_gcc-7.2.0-debug

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Test Name: Trilinos_PR_intel-17.0.1

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Test Name: Trilinos_PR_clang-10.0.0

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Test Name: Trilinos_PR_cuda-10.1.243

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Test Name: Trilinos_PR_python3

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Test Name: Trilinos_PR_cuda-11.4.2-uvm-off

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Test Name: Trilinos_PR_gcc-8.3.0

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