DO NOT MERGE MueLu: Cut drop refactor #13282

jhux2 · 2024-07-24T22:10:58Z

@trilinos/muelu

Motivation

This is part of Ian Halim's summer project. Converts an aggregation thresholding algorithm to use Kokkos to make it performance portable. A bonus is that the host-based implementation is now faster.

Related Issues

Related to MueLu: Prep for CoalesceDrop refactor #13278.

Stakeholder Feedback

N/A

Testing

Covered by existing unit tests.

cgcgcg · 2024-07-24T22:18:36Z

packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp

+						typename STS::magnitudeType x_aij    = static_cast<SC>(std::fabs(static_cast<double>(rowView.value(x) * rowView.value(x))));
+						typename STS::magnitudeType y_aij    = static_cast<SC>(std::fabs(static_cast<double>(rowView.value(y) * rowView.value(y))));
+						typename STS::magnitudeType x_aiiajj = static_cast<SC>(std::fabs(static_cast<double>(threshold * threshold * ghostedDiagValsView(rowView.colidx(x)) * ghostedDiagValsView(row))));
+						typename STS::magnitudeType y_aiiajj = static_cast<SC>(std::fabs(static_cast<double>(threshold * threshold * ghostedDiagValsView(rowView.colidx(y)) * ghostedDiagValsView(row))));


std::fabs might need to be replaced with Kokkos::ArithTraits<impl_scalar_type>::magnitude. We need to think through this a bit for complex scalar type. Same for the other spots where we cast things around.

Original code within ORIGINAL ifdef. New code within NEW ifdef. DropTol structure marked with KOKKOS_INLINE_FUNCTION and default values are hard coded. Default Algorithm and Cut Drop Algorithm split into separate for loops in NEW code. Cut Drop converted to use Kokkos nested parallel loops. Timers placed in new code and are commented out. Code passes current unit tests. Saw a speedup of about 1.5x with Cuda and 1.2x with Serial when running unit tests with 10,000,000 rows. Signed-off-by: Ian Halim <ihalim@ascicgpu031.sandia.gov>

DropTol structure in algorithm replaced with new, smaller DropTolKokkos structure. Computations are now done on the fly. Code passes current unit tests. No significant change in speed. Signed-off-by: Ian Halim <ihalim@ascicgpu031.sandia.gov>

Per Christian's request. DropTolKokkos structure removed and replaced with view indices and view of drop flags. ORIGINAL code removed. BuildKokkos removed. Removed commented out timers. Added comments. Signed-off-by: Ian Halim <ihalim@ascicgpu031.sandia.gov>

trilinos-autotester · 2024-07-25T02:23:28Z

Status Flag 'Pre-Test Inspection' - - This Pull Request Requires Inspection... The code must be inspected by a member of the Team before Testing/Merging
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trilinos-autotester · 2024-07-25T17:05:43Z

Status Flag 'Pre-Test Inspection' - SUCCESS: The last commit to this Pull Request has been INSPECTED by label AT: PRE-TEST INSPECTED! Autotester is Removing Label; this inspection will remain valid until a new commit to source branch is performed.

trilinos-autotester · 2024-07-25T17:12:37Z

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Using Repos:

Repo: TRILINOS (NyquilDreams/Trilinos)

Pull Request Author: jhux2

trilinos-autotester · 2024-07-25T18:48:13Z

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trilinos-autotester · 2024-07-25T23:38:30Z

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PULLREQUESTNUM	13282
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Build Num: 268
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TRILINOS_TARGET_SHA	`12afd07`

Using Repos:

Repo: TRILINOS (NyquilDreams/Trilinos)

Pull Request Author: jhux2

jhux2 · 2024-07-26T00:41:46Z

packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp

+						typename implATS::magnitudeType y_aij    = implATS::magnitude(rowView.value(y) * rowView.value(y));
+						typename implATS::magnitudeType x_aiiajj = implATS::magnitude(threshold * threshold * ghostedDiagValsView(rowView.colidx(x)) * ghostedDiagValsView(row));
+						typename implATS::magnitudeType y_aiiajj = implATS::magnitude(threshold * threshold * ghostedDiagValsView(rowView.colidx(y)) * ghostedDiagValsView(row));
+						return x_aij / x_aiiajj > y_aij / y_aiiajj;


Suggested change

return x_aij / x_aiiajj > y_aij / y_aiiajj;

return (x_aij / x_aiiajj) > (y_aij / y_aiiajj);

maybe?

trilinos-autotester · 2024-07-26T01:22:38Z

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: PR_gcc-openmpi-openmp

Build Num: 220
Status: FAILED

Jenkins Parameters

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Build Num: 268
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Build Num: 268
Status: FAILED

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TRILINOS_TARGET_BRANCH	develop
TRILINOS_TARGET_REPO	https://github.com/trilinos/Trilinos
TRILINOS_TARGET_SHA	`12afd07`

CDash Test Results for PR# 13282.

Wiki: How to Reproduce PR Testing Builds and Errors.

trilinos-autotester · 2024-08-28T02:49:10Z

All Jobs Finished; status = PASSED, However Inspection must be performed before merge can occur...

jhux2 · 2024-08-28T17:15:01Z

This doesn't look good:

119. Ifpack2Smoother_double_int_longlong_Tpetra_KokkosCompat_KokkosSerialWrapperNode_BlockCrsMatrix_Relaxation_ViaPoint_UnitTest ... [Passed] (0.0187 sec)
120. Ifpack2Smoother_double_int_longlong_Tpetra_KokkosCompat_KokkosSerialWrapperNode_BlockCrsMatrix_Relaxation_AsBlock_UnitTest ... [Passed] (0.0091 sec)
121. IndexManager_double_int_longlong_Tpetra_KokkosCompat_KokkosSerialWrapperNode_CreateGlobalLexicographicIndexManager_UnitTest ... [Passed] (0.00294 sec)
122. IndexManager_double_int_longlong_Tpetra_KokkosCompat_KokkosSerialWrapperNode_CreateLocalLexicographicIndexManager_UnitTest ... [Passed] (0.000992 sec)
123. IndexManager_double_int_longlong_Tpetra_KokkosCompat_KokkosSerialWrapperNode_CreateUncoupledIndexManager_UnitTest ... [Passed] (0.000798 sec)
124. IndexManager_double_int_longlong_Tpetra_KokkosCompat_KokkosSerialWrapperNode_UncoupledIndexManagerSingleCoarsePoint_UnitTest ... [Passed] (0.000704 sec)
125. LWGraph_double_int_longlong_Tpetra_KokkosCompat_KokkosSerialWrapperNode_CreateLWGraph_UnitTest ... [Passed] (0.00678 sec)
[ascic166:802005] 3 more processes have sent help message help-mpi-common-cuda.txt / dlopen failed
[ascic166:802005] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

See https://trilinos-cdash.sandia.gov/test/62758761.

@trilinos/framework Does this indicate an error that slipped through?

achauphan · 2024-08-28T18:49:17Z

@jhux2 I am not familiar enough to say for certain if this should have caused a failure for the test, but I did run a brief query on this test and I did not find any similar runs with that produced that same message

https://trilinos-cdash.sandia.gov/queryTests.php?project=Trilinos&begin=2024-08-21&end=2024-08-28&filtercount=2&showfilters=1&filtercombine=and&field1=testname&compare1=63&value1=MueLu_UnitTestsTpetra_MPI_4&field2=groupname&compare2=63&value2=Pull%20Request

jhux2 · 2024-08-28T19:11:06Z

I should have done a little googling first. The message indicates that MPI isn't CUDA aware. In fact, that's printed at the top of the output in the link I posted:

The library attempted to open the following supporting CUDA libraries,
but each of them failed.  CUDA-aware support is disabled.
libcuda.so.1: cannot open shared object file: No such file or directory
libcuda.dylib: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.so.1: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.dylib: cannot open shared object file: No such file or directory
If you are not interested in CUDA-aware support, then run with
--mca opal_warn_on_missing_libcuda 0 to suppress this message.  If you are interested
in CUDA-aware support, then try setting LD_LIBRARY_PATH to the location
of libcuda.so.1 to get passed this issue.

But since the build isn't enabling CUDA, it's weird that a library is looking for CUDA.

trilinos-autotester · 2024-08-29T03:21:47Z

All Jobs Finished; status = PASSED, However Inspection must be performed before merge can occur...

trilinos-autotester · 2024-08-30T03:21:58Z

All Jobs Finished; status = PASSED, However Inspection must be performed before merge can occur...

trilinos-autotester · 2024-08-31T13:22:47Z

All Jobs Finished; status = PASSED, However Inspection must be performed before merge can occur...

trilinos-autotester · 2024-09-01T13:22:49Z

All Jobs Finished; status = PASSED, However Inspection must be performed before merge can occur...

trilinos-autotester · 2024-09-01T23:42:46Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-03T03:05:42Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-04T04:21:49Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

cgcgcg · 2024-09-04T22:43:43Z

packages/muelu/test/unit_tests/CoalesceDropFactory.cpp

+    else {
+      A_t->insertGlobalValues(gblRow, Teuchos::tuple<GO>(gblRow - 1, gblRow, gblRow + 1), Teuchos::tuple<SC>(negOne, two, negOne));


Row 1 has diagonal entry 2 and two off-diagonal -1 entries.

cgcgcg · 2024-09-04T22:44:26Z

packages/muelu/test/unit_tests/CoalesceDropFactory.cpp

+    else {
+      rowID += 2;


Why do we drop one of the off-diagonal entries in row 1?

cgcgcg

@NyquilDreams I'm confused about the test, would you mind having a look?

trilinos-autotester · 2024-09-05T04:21:54Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

sebrowne · 2024-09-05T14:53:17Z

But since the build isn't enabling CUDA, it's weird that a library is looking for CUDA.

I've seen this a couple of times, we'll let a RETEST stand here but I'll keep it in mind if we start seeing it again.

cgcgcg

The DistanceLaplacianCutSym test claims to be set up specifically to drop one of the entries. But when we look at what it actually checks we see that nothing is being dropped. So either the test is bad, or there is a bug in CutDrop.

trilinos-autotester · 2024-09-06T09:51:13Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-07T13:30:02Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-08T13:42:46Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-09T13:43:04Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-10T14:03:07Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-11T14:22:45Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-12T14:22:59Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-13T14:42:38Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-14T15:02:49Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-15T15:22:29Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-16T15:22:30Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

trilinos-autotester · 2024-09-17T17:55:42Z

All Jobs Finished; status = PASSED, However PR is now STALE, and must be retested. Set the AT: RETEST Label to force retest....

jhux2 requested a review from a team as a code owner July 24, 2024 22:10

cgcgcg reviewed Jul 24, 2024

View reviewed changes

cgcgcg changed the title ~~DO NOT MERGE: Cut drop refactor~~ DO NOT MERGE MueLu: Cut drop refactor Jul 24, 2024

cgcgcg added the pkg: MueLu label Jul 24, 2024

NyquilDreams force-pushed the cutDropRefactor branch from ea7bad3 to 3a60359 Compare July 24, 2024 22:59

Ian Halim added 3 commits July 24, 2024 18:35

MueLu: Cut Drop Memory Optimization

105e33e

DropTol structure in algorithm replaced with new, smaller DropTolKokkos structure. Computations are now done on the fly. Code passes current unit tests. No significant change in speed. Signed-off-by: Ian Halim <ihalim@ascicgpu031.sandia.gov>

NyquilDreams force-pushed the cutDropRefactor branch from 22d2e36 to bdc6d3d Compare July 25, 2024 00:35

jhux2 added pkg: MueLu AT: PRE-TEST INSPECTED Required to test outside contributions. This label alone will not allow a PR to merge. and removed pkg: MueLu labels Jul 25, 2024

trilinos-autotester removed the AT: PRE-TEST INSPECTED Required to test outside contributions. This label alone will not allow a PR to merge. label Jul 25, 2024

NyquilDreams force-pushed the cutDropRefactor branch 2 times, most recently from 1520bc5 to 64e64b8 Compare July 25, 2024 20:41

cgcgcg added the AT: WIP Causes the PR autotester to not test the PR. (Remove to allow testing to occur.) label Jul 25, 2024

jhux2 added AT: PRE-TEST INSPECTED Required to test outside contributions. This label alone will not allow a PR to merge. and removed AT: WIP Causes the PR autotester to not test the PR. (Remove to allow testing to occur.) labels Jul 25, 2024

trilinos-autotester removed the AT: PRE-TEST INSPECTED Required to test outside contributions. This label alone will not allow a PR to merge. label Jul 25, 2024

jhux2 commented Jul 26, 2024

View reviewed changes

NyquilDreams force-pushed the cutDropRefactor branch from 64e64b8 to e2fcfd1 Compare July 26, 2024 23:35

jhux2 added the AT: PRE-TEST INSPECTED Required to test outside contributions. This label alone will not allow a PR to merge. label Jul 26, 2024

NyquilDreams force-pushed the cutDropRefactor branch from e2fcfd1 to 8eb75e6 Compare July 27, 2024 01:07

trilinos-autotester added the AT: STALE Added by the PR autotester if too much time has elapsed since the last successful PR test iteration label Sep 1, 2024

cgcgcg reviewed Sep 4, 2024

View reviewed changes

cgcgcg reviewed Sep 5, 2024

View reviewed changes

	return x_aij / x_aiiajj > y_aij / y_aiiajj;
	return (x_aij / x_aiiajj) > (y_aij / y_aiiajj);

		else {
		A_t->insertGlobalValues(gblRow, Teuchos::tuple<GO>(gblRow - 1, gblRow, gblRow + 1), Teuchos::tuple<SC>(negOne, two, negOne));

DO NOT MERGE MueLu: Cut drop refactor #13282

Are you sure you want to change the base?

DO NOT MERGE MueLu: Cut drop refactor #13282

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jhux2 commented Jul 24, 2024 • edited Loading

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trilinos-autotester commented Jul 25, 2024

trilinos-autotester commented Jul 25, 2024

trilinos-autotester commented Jul 25, 2024

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Test Name: PR_gcc-openmpi-openmp

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Test Name: PR_gcc-openmpi_debug

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Test Name: PR_clang

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Test Name: Trilinos_PR_python3

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Test Name: PR_cuda

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Test Name: PR_intel

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Test Name: PR_cuda-uvm

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Using Repos:

trilinos-autotester commented Jul 25, 2024

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Test Name: PR_gcc-openmpi-openmp

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Test Name: PR_gcc

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Test Name: PR_gcc-openmpi_debug

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Test Name: PR_clang

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Test Name: Trilinos_PR_python3

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Test Name: PR_cuda

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Test Name: PR_intel

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Test Name: PR_cuda-uvm

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trilinos-autotester commented Jul 25, 2024

trilinos-autotester commented Jul 25, 2024

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Test Name: PR_gcc-openmpi-openmp

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Test Name: PR_gcc

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Test Name: PR_gcc-openmpi_debug

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Test Name: PR_clang

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Test Name: Trilinos_PR_python3

jhux2 commented Jul 24, 2024 •

edited

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