Limit loop bounds to avoid division by zero by andrewdnolan · Pull Request #562 · E3SM-Project/Omega

andrewdnolan · 2026-09-17T20:18:38Z

Limit loop extents to avoid division by zero.

The issue was exposed using SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF, with the gnu compiler, on chrysalis. The _D modifier in the test name resulted in a debug build, which adds the -ffpe-trap=invalid,zero,overflow flags.

This has not been caught previously, because a standalone Debug build of Omega does not use the -ffpe-trap=invalid,zero,overflow flags.

Closes #556.

Checklist

andrewdnolan · 2026-09-17T20:41:53Z

Testing:

A single node, non-threaded, smoke test on chrysalis using debug build:

20260917_140012_rqz30d: 1 test
  SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu (Overall: PASS) details:
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu CREATE_NEWCASE
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu XML
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu SETUP
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu SHAREDLIB_BUILD time=276
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu MODEL_BUILD time=567
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu SUBMIT
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu RUN time=1024
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu MEMLEAK
    PASS SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu SHORT_TERM_ARCHIVER

Prior to this PR, that same test failed with:

29: 
29: Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
29: 
29: Backtrace for this error:
...
17: #0  0x155549b1a62f in ???
22: #0  0x155549b1a62f in ???
42: #0  0x155549b1a62f in ???
52: #0  0x155549b1a62f in ???
25: #0  0x155549b1a62f in ???
30: #0  0x155549b1a62f in ???
28: #0  0x155549b1a62f in ???
41: #0  0x155549b1a62f in ???
17: #1  0xa9e6c1 in _ZZNK5OMEGA16VorticityAuxVars19computeVarsOnVertexERKN6Kokkos4Impl20HostThreadTeamMemberINS1_6SerialEEEiRKNS1_4ViewIPPdJNS1_11LayoutRightENS1_9HostSpaceEEEESF_ENKUliE2_clEi
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/ocn/auxiliaryVars/VorticityAuxVars.h:70
17: #2  0xaa28c0 in _ZN6Kokkos12parallel_forIiZNK5OMEGA16VorticityAuxVars19computeVarsOnVertexERKNS_4Impl20HostThreadTeamMemberINS_6SerialEEEiRKNS_4ViewIPPdJNS_11LayoutRightENS_9HostSpaceEEEESG_EUliE2_S6_EEvRKNS3_31TeamThreadRangeBoundariesStructIT_T1_EERKT0_PPKNSt9enable_ifIXsrNS3_26is_host_thread_team_memberISK_EE5valueEvE4typeE
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/externals/ekat/extern/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp:788
17: #3  0xaa1352 in _ZN5OMEGA16parallelForInnerIZNKS_16VorticityAuxVars19computeVarsOnVertexERKN6Kokkos4Impl20HostThreadTeamMemberINS2_6SerialEEEiRKNS2_4ViewIPPdJNS2_11LayoutRightENS2_9HostSpaceEEEESG_EUliE2_EEvS8_NS_5RangeEOT_
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/infra/OmegaKokkosHiPar.h:253
17: #4  0xa9f188 in _ZNK5OMEGA16VorticityAuxVars19computeVarsOnVertexERKN6Kokkos4Impl20HostThreadTeamMemberINS1_6SerialEEEiRKNS1_4ViewIPPdJNS1_11LayoutRightENS1_9HostSpaceEEEESF_
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/ocn/auxiliaryVars/VorticityAuxVars.h:68
17: #5  0xa89712 in operator()
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/ocn/AuxiliaryState.cpp:217
17: #6  0xa8f121 in operator()<>
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/infra/OmegaKokkos.h:241
17: #7  0xa8f121 in operator()
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/infra/OmegaKokkosHiPar.h:142
17: #8  0xa971a7 in exec<void>
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/externals/ekat/extern/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Team.hpp:229
17: #9  0xa94870 in execute
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/externals/ekat/extern/kokkos/core/src/Serial/Kokkos_Serial_Parallel_Team.hpp:265
17: #10  0xa918af in parallel_for<Kokkos::TeamPolicy<Kokkos::Serial>, OMEGA::parallelForOuter<1, OMEGA::AuxiliaryState::computeMomAux(const OMEGA::OceanState*, const Array3DReal&, int, int, OMEGA::TimeInterval) const::<lambda(int, const TeamMember&)> >(const string&, const OMEGA::LaunchConfig<1>&, OMEGA::AuxiliaryState::computeMomAux(const OMEGA::OceanState*, const Array3DRea
l&, int, int, OMEGA::TimeInterval) const::<lambda(int, const TeamMember&)>&&)::<lambda(const TeamMember&)> >
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/externals/ekat/extern/kokkos/core/src/Kokkos_Parallel.hpp:146
17: #11  0xa8f307 in parallelForOuter<1, OMEGA::AuxiliaryState::computeMomAux(const OMEGA::OceanState*, const Array3DReal&, int, int, OMEGA::TimeInterval) const::<lambda(int, const TeamMember&)> >
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/infra/OmegaKokkosHiPar.h:139
17: #12  0xa89f3f in _ZNK5OMEGA14AuxiliaryState13computeMomAuxEPKNS_10OceanStateERKN6Kokkos4ViewIPPPdJNS4_11LayoutRightENS4_9HostSpaceEEEEiiNS_12TimeIntervalE
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/ocn/AuxiliaryState.cpp:212
17: #13  0xa8bd74 in _ZNK5OMEGA14AuxiliaryState10computeAllEPKNS_10OceanStateERKN6Kokkos4ViewIPPPdJNS4_11LayoutRightENS4_9HostSpaceEEEEiiNS_12TimeIntervalE
17:     at /gpfs/fs1/home/ac.anolan/repos/Omega/develop/components/omega/src/ocn/AuxiliaryState.cpp:382

Here's a full log file, if you're interested:

/lcrc/group/e3sm/ac.anolan/scratch/chrys/SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF.chrysalis_gnu.20260917_112659_wzv07b/run/e3sm.log.1289521.260917-114035

andrewdnolan · 2026-09-17T21:49:32Z

Testing

CTest unit tests

Machine: chrysalis
Compiler: gnu
Build type: Debug
Result: All tests passed
- Log: /lcrc/group/e3sm/ac.anolan/Omega_PR562/build/feature/ctest_2026-09-17_16:08.log

Tried running the omega_pr suite, but hit a filesystem error because chrysalis has run out of inodes. I can run the polaris tests once that's resolved.

cbegeman · 2026-09-21T20:02:20Z

Under what conditions is PseudoThickVertex zero? Is this PR indicating a horizontal or vertical index bounds issue?

mwarusz · 2026-09-22T16:20:11Z

@cbegeman

Under what conditions is PseudoThickVertex zero? Is this PR indicating a horizontal or vertical index bounds issue?

I think this is harmless, but can happen when computing over all vertices in the halo region. An outermost halo vertex may have only one active cell that is on a different rank.

@andrewdnolan

I think a better fix for this issue may be to limit the horizontal bounds here

Omega/components/omega/src/ocn/AuxiliaryState.cpp

Lines 212 to 219 in 0c3353c

    
           parallelForOuter( 
        
               "vertexAuxState1", 
        
               LaunchConfig({Mesh->NVerticesAll}, 
        
                            TeamScratch<Real>(2 * VCoord->NVertLayers)), 
        
               KOKKOS_LAMBDA(int IVertex, const TeamMember &Team) { 
        
                  LocVorticityAux.computeVarsOnVertex(Team, IVertex, PseudoThickCell, 
        
                                                      NormalVelEdge); 
        
               });

to loop only over NVerticesHaloH(2). I think this should prevent division by zero and be BFB.

andrewdnolan · 2026-09-22T17:17:22Z

@mwarusz's diagnosis is consistent with my understanding. This only occurs in the halo region when not all cells on vertex are active, so I don't think it's really accurate to call it a vertical masking issue.

The issue was exposed by SMS_Vmct_D_P64x1.T62_oQU240.COMEGA-IAF on chrysalis. The _D modifier in the test name resulted in a debug build, which adds the -ffpe-trap=invalid,zero,overflow flags. It's specifically the compiler flags during a debug build that cause the PseudoThickVertex to be zero in the halo region.

@mwarusz I like that suggestion! Thanks for it. I'll switch to that approach and re-test.

cbegeman · 2026-10-13T13:42:44Z

@andrewdnolan do you need help with testing?

andrewdnolan · 2026-10-13T14:23:08Z

I will be in touch depending on how my standalone (polaris) testing goes. I should be OK to handle coupled and unit tests.

andrewdnolan · 2026-10-13T21:53:31Z

Rebased onto b42d508 to avoid coupled model issue currently on develop (e.g. #602). Added benefit that that commit matches the Omega submodule in polaris.

andrewdnolan · 2026-10-13T21:59:07Z

Testing, `chrysalis` with `gnu` compiler

SMS_Vmct_D.T62_oQU240.COMEGA-IAF now passes.

After the initial test completed, I re-ran with this user_nl_omega:

Omega:
  Decomp:
    HaloWidth: 4

to confirm the dynamic halo extent in src/ocn/AuxiliaryState.cpp works as expected.

SMS_Vmct_D.T62_oQU240.COMEGA-IAF also passes, with the user_nl_omega above.

andrewdnolan · 2026-10-13T22:00:53Z

Testing, `chrysalis` with `gnu` compiler

Polaris `omega_pr` suite

Baseline workdir: /lcrc/group/e3sm/ac.anolan/Omega_PR562/baseline
Baseline build: /lcrc/group/e3sm/ac.anolan/Omega_PR562/build/develop
PR build: /lcrc/group/e3sm/ac.anolan/Omega_PR562/build/feature
PR workdir: /lcrc/group/e3sm/ac.anolan/Omega_PR562/feature
Machine: chrysalis
Partition: debug
Compiler: gnu
Build type: Release
Log: /lcrc/group/e3sm/ac.anolan/Omega_PR562/feature/polaris_omega_pr.o1307686
Result: All tests passed

andrewdnolan · 2026-10-13T22:01:37Z

@mwarusz could you take another look at this? Sorry about letting it slip through the cracks.

mwarusz

I have one minor suggestion.

andrewdnolan · 2026-10-14T15:02:30Z

I rebuilt and re-ran my SMS_Vmct_D.T62_oQU240.COMEGA-IAF test following the most recent changes, just to be safe:

PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu CREATE_NEWCASE
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu XML
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu SETUP
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu SHAREDLIB_BUILD time=0
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu MODEL_BUILD time=183
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu SUBMIT
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu RUN time=59
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu MEMLEAK
PASS SMS_Vmct_D.T62_oQU240.COMEGA-IAF.chrysalis_gnu SHORT_TERM_ARCHIVER

Co-authored-by: Maciej Waruszewski <mwarusz@igf.fuw.edu.pl>

xylar · 2026-10-15T16:24:58Z

I'm running the full omega_pr testing matrix. Posts should come in in the next few hours.

xylar · 2026-10-15T18:12:56Z

Testing on frontier

Tested the merge of #562 (4801da101d) into develop (cdb935bb5a) as 5aa6097ab5, against Polaris' Omega submodule (cdb935bb5a).

Row	CTests	`omega_pr`	New build warnings
frontier, craygnu, mpich	59 of 59 passed	32 of 32 passed	0
frontier, craygnu-mphipcc, mpich	59 of 59 passed	32 of 32 passed	0

frontier, craygnu, mpich

Polaris `omega_pr` suite

Baseline workdir: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/baselines/frontier_craygnu_polaris-db75895_omega-cdb935b/omega_pr
Baseline build: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/baselines/frontier_craygnu_polaris-db75895_omega-cdb935b/build
PR build: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu/build
PR workdir: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu/omega_pr
Polaris: db758959debacf1e6066741182cab2d6dfd80f9b (1.1.0-108-gdb758959d)
Baseline Omega: cdb935bb5a8d995b0878616e001a2701a2627519 (bp_maint3.2-3428-gcdb935bb5a)
PR Omega: 5aa6097ab5982410e27aa73e3afa250ef914e6aa (bp_maint3.2-3433-g5aa6097ab5)
Machine: frontier
Partition: batch
Compiler: craygnu
Build type: Release
Log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu/omega_pr/polaris_omega_pr.o5684656
Result: All tests passed

Recent commits

Polaris:

db758959d Merge add-omega-testing-workflow locally for Omega PR testing
9dfb48ee5 Merge pull request #853 from xylar/add-co-drafted-signature
d6bf2af30 Merge pull request #849 from xylar/add-framework-for-pr-testing
9d6c837f9 Merge pull request #835 from xylar/update-to-mache-5.0.0
68998a2fe Merge pull request #840 from xylar/switch-mpaso-mfct-sln-back-to-rk4

Baseline Omega:

cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop
9aba4a8032 Merge pull request #597 from xylar/omega/fix-real-literal-nvcc

PR Omega:

5aa6097ab5 Test merge of E3SM-Project/Omega#562 (4801da101d) into develop (cdb935bb5a)
cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop

CTest unit tests:

Machine: frontier
Compiler: craygnu
Build type: Release
Build: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu/build
Omega: 5aa6097ab5982410e27aa73e3afa250ef914e6aa (bp_maint3.2-3433-g5aa6097ab5)
Result: All tests passed
Log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu/build/ctests.log

Build warnings

No new warnings (3 in the PR build, 3 in the baseline build).

Baseline build log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/baselines/frontier_craygnu_polaris-db75895_omega-cdb935b/build/build_omega.log
PR build log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu/build/build_omega.log

frontier, craygnu-mphipcc, mpich

Polaris `omega_pr` suite

Baseline workdir: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/baselines/frontier_craygnu-mphipcc_polaris-db75895_omega-cdb935b/omega_pr
Baseline build: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/baselines/frontier_craygnu-mphipcc_polaris-db75895_omega-cdb935b/build
PR build: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu-mphipcc/build
PR workdir: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu-mphipcc/omega_pr
Polaris: db758959debacf1e6066741182cab2d6dfd80f9b (1.1.0-108-gdb758959d)
Baseline Omega: cdb935bb5a8d995b0878616e001a2701a2627519 (bp_maint3.2-3428-gcdb935bb5a)
PR Omega: 5aa6097ab5982410e27aa73e3afa250ef914e6aa (bp_maint3.2-3433-g5aa6097ab5)
Machine: frontier
Partition: batch
Compiler: craygnu-mphipcc
Build type: Release
Log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu-mphipcc/omega_pr/polaris_omega_pr.o5684683
Result: All tests passed

Recent commits

Polaris:

db758959d Merge add-omega-testing-workflow locally for Omega PR testing
9dfb48ee5 Merge pull request #853 from xylar/add-co-drafted-signature
d6bf2af30 Merge pull request #849 from xylar/add-framework-for-pr-testing
9d6c837f9 Merge pull request #835 from xylar/update-to-mache-5.0.0
68998a2fe Merge pull request #840 from xylar/switch-mpaso-mfct-sln-back-to-rk4

Baseline Omega:

cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop
9aba4a8032 Merge pull request #597 from xylar/omega/fix-real-literal-nvcc

PR Omega:

5aa6097ab5 Test merge of E3SM-Project/Omega#562 (4801da101d) into develop (cdb935bb5a)
cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop

CTest unit tests:

Machine: frontier
Compiler: craygnu-mphipcc
Build type: Release
Build: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu-mphipcc/build
Omega: 5aa6097ab5982410e27aa73e3afa250ef914e6aa (bp_maint3.2-3433-g5aa6097ab5)
Result: All tests passed
Log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu-mphipcc/build/ctests.log

Build warnings

No new warnings (6 in the PR build, 6 in the baseline build).

Baseline build log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/baselines/frontier_craygnu-mphipcc_polaris-db75895_omega-cdb935b/build/build_omega.log
PR build log: /lustre/orion/cli115/scratch/xylar/polaris_1.1/frontier/omega_pr_test/pr562-4801da1/frontier_craygnu-mphipcc/build/build_omega.log

Posted by Claude Code on @xylar's behalf. The testing, analysis and wording above are AI-authored; please check them accordingly.

andrewdnolan added the bug Something isn't working label Sep 17, 2026

andrewdnolan requested a review from mwarusz September 17, 2026 20:26

andrewdnolan force-pushed the omega/guard-division-by-zero branch from 4df0539 to a328748 Compare September 23, 2026 22:13

mwarusz mentioned this pull request Sep 28, 2026

Floating-point exceptions #579

Open

8 of 22 tasks

andrewdnolan force-pushed the omega/guard-division-by-zero branch from a328748 to 6ff830b Compare October 12, 2026 22:32

andrewdnolan force-pushed the omega/guard-division-by-zero branch from b8e36e0 to 73ad77e Compare October 13, 2026 21:07

andrewdnolan changed the title ~~Guard against division by zero in VorticityAuxVars.h~~ Limit loop bounds to avoid division by zero Oct 13, 2026

mwarusz reviewed Oct 13, 2026

View reviewed changes

Comment thread components/omega/src/ocn/AuxiliaryState.cpp Outdated

mwarusz approved these changes Oct 14, 2026

View reviewed changes

andrewdnolan assigned sbrus89 Oct 14, 2026

andrewdnolan mentioned this pull request Oct 14, 2026

Update the e3sm_omega_developer suite #604

Open

andrewdnolan and others added 4 commits October 15, 2026 09:12

Limit horizontal bounds of VorticityAux loop

e53f7d3

Use host mirror, not device array

a7f8ac5

Restrict loop bounds for FCTPorvisLayerThickness

c0c4c71

Clarify calculation of the number of halo layers

4801da1

Co-authored-by: Maciej Waruszewski <mwarusz@igf.fuw.edu.pl>

andrewdnolan force-pushed the omega/guard-division-by-zero branch from 010ec52 to 4801da1 Compare October 15, 2026 14:18

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Testing, chrysalis with gnu compiler

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Testing, chrysalis with gnu compiler

Polaris omega_pr suite

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Testing on frontier

Polaris omega_pr suite

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Polaris omega_pr suite

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andrewdnolan commented Sep 17, 2026 •

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Testing, `chrysalis` with `gnu` compiler

Testing, `chrysalis` with `gnu` compiler

Polaris `omega_pr` suite

Polaris `omega_pr` suite

Polaris `omega_pr` suite