Update compiler flags #148

minghangli-uni · 2025-09-08T02:41:05Z

Same flags as in #82 (comment)

🚀 The latest prerelease access-om3/pr148-18 at 927e963 is here: #148 (comment) 🚀

github-actions · 2025-09-08T04:37:16Z

🚀 Attempted to deploy access-om3 Prerelease pr148-1 with commit 241b5bd

🖥️ `Gadi` Deployment ✔️

Usage Instructions

access-om3, defined in ./spack.yaml, will be deployed to Gadi as:

2025.08.001 as a Release (when merged).
pr148-1 as a Prerelease (during this PR).

This Prerelease is accessible on Gadi using:

module use /g/data/vk83/prerelease/modules
module load access-om3/pr148-1

When using the above modules, the binaries shall be on your $PATH.

For advanced users, this Prerelease is also accessible on Gadi via /g/data/vk83/prerelease/apps/spack/0.22/spack in the access-om3-pr148-1 environment.
Due to inode-saving measures, one will have to manually untar the environment metadata before environment activation with tar -xf .spack-env .spack-env.tar. It will require one to have write privileges.

Configuration Information

This Prerelease is deployed using:

access-nri/spack on branch 0.22
access-nri/spack-packages version 2025.08.003
access-nri/spack-config version 2025.08.000

If the above was not what was expected, commit changes to config/versions.json in this PR.

minghangli-uni · 2025-09-08T04:45:53Z

It takes ~2 hours to build the code... I don't think this is what we expect? Or there is something I'm missing?

anton-seaice · 2025-09-09T23:24:14Z

It’s possibly just a transient Gadi thing ? That is a bit long , I don’t think it’s going to be related to changing the compiler flags.

github-actions · 2025-09-25T07:14:26Z

🚀 Attempted to deploy access-om3 Prerelease pr148-2 with commit c8adb30

🖥️ `Gadi` Deployment ❌

minghangli-uni · 2025-09-25T07:18:04Z

!redeploy

minghangli-uni · 2025-09-25T08:00:34Z

I thought the long esmf build issue had already been resolved - is it still a problem, or is there a workaround to speed it up?

github-actions · 2025-09-25T09:12:33Z

🚀 Attempted to deploy access-om3 Prerelease pr148-3 with commit c8adb30

🖥️ `Gadi` Deployment ✔️

Usage Instructions

access-om3, defined in ./spack.yaml, will be deployed to Gadi as:

2025.08.001 as a Release (when merged).
pr148-3 as a Prerelease (during this PR).

This Prerelease is accessible on Gadi using:

module use /g/data/vk83/prerelease/modules
module load access-om3/pr148-3

When using the above modules, the binaries shall be on your $PATH.

For advanced users, this Prerelease is also accessible on Gadi via /g/data/vk83/prerelease/apps/spack/0.22/spack in the access-om3-pr148-3 environment.
Due to inode-saving measures, one will have to manually untar the environment metadata before environment activation with tar -xf .spack-env .spack-env.tar. It will require one to have write privileges.

Configuration Information

This Prerelease is deployed using:

access-nri/spack on branch 0.22
access-nri/spack-packages version 2025.08.003
access-nri/spack-config version 2025.08.000

If the above was not what was expected, commit changes to config/versions.json in this PR.

github-actions · 2025-09-25T10:11:01Z

🚀 Attempted to deploy access-om3 Prerelease pr148-4 with commit 2c12228

🖥️ `Gadi` Deployment ❌

minghangli-uni · 2025-09-26T00:55:52Z

!redeploy

github-actions · 2025-09-26T01:56:48Z

🚀 Attempted to deploy access-om3 Prerelease pr148-5 with commit 2c12228

🖥️ `Gadi` Deployment ❌

github-actions · 2025-09-26T04:16:39Z

🚀 Attempted to deploy access-om3 Prerelease pr148-6 with commit 07df87a

🖥️ `Gadi` Deployment ❌

minghangli-uni · 2025-09-28T22:48:42Z

!redeploy

github-actions · 2025-09-29T00:40:39Z

🚀 Attempted to deploy access-om3 Prerelease pr148-7 with commit 07df87a

🖥️ `Gadi` Deployment ✔️

Usage Instructions

access-om3, defined in ./spack.yaml, will be deployed to Gadi as:

2025.08.001 as a Release (when merged).
pr148-7 as a Prerelease (during this PR).

This Prerelease is accessible on Gadi using:

module use /g/data/vk83/prerelease/modules
module load access-om3/pr148-7

When using the above modules, the binaries shall be on your $PATH.

For advanced users, this Prerelease is also accessible on Gadi via /g/data/vk83/prerelease/apps/spack/0.22/spack in the access-om3-pr148-7 environment.
Due to inode-saving measures, one will have to manually untar the environment metadata before environment activation with tar -xf .spack-env .spack-env.tar. It will require one to have write privileges.

Configuration Information

This Prerelease is deployed using:

access-nri/spack on branch 0.22
access-nri/spack-packages version 2025.08.003
access-nri/spack-config version 2025.08.000

If the above was not what was expected, commit changes to config/versions.json in this PR.

minghangli-uni · 2025-10-08T00:48:57Z

With the help of https://github.com/ACCESS-NRI/esmf-trace, I was able to extract timestep-level performance data, rather than relying on coarse wall-clock runtime. This allows each test case to be much shorter (only 2 days of simulation for below tests), while still producing reliable performance statistics.

I tested three compiler configurations, each repeated five times (repeat in config.yaml).
Each 2-day run produces 192 timesteps -> 192 * 5 samples per setup.

compiler_flag_1 - existing
compiler_flag_2 - pr148-1
compiler_flag_3 - pr148-7

In each run, the first timestep appears very very fast (not shown in below plot). I’m not entirely certain of the cause, but likely reflects nuopc bookkeeping or something I am not sure (happy to take comments from others on this).

The second timestep is then the first timestep where the full dynamics is active and it is consistently the slowest “real” step. This is supported where fms timing in access-om3.out only reports 191 timesteps, so implying that the model does not treat the first timestep as part of the main timing window.

Similarly, the final timestep is noticeably slower due to I/O things.

So to avoid biasing the statistics with these startup/shutdown artifacts, I exclude steps 1–2 and the final timestep, leaving 189 consistent timesteps per run for the statistical comparison.

From the box plot, compiler_flag_2 consistently achieves the lowest mean and median timestep runtime while also showing a tighter variance and no strong outliers, in contrast to the other two compiler setups.

minghangli-uni · 2025-10-08T01:02:47Z

Below shows the setup for the three configurations using experiment-generator

model_type: access-om3
repository_url: [email protected]:ACCESS-NRI/access-om3-configs.git
start_point: "7851c1e" # Control commit hash for new branches
test_path: "." # All control and perturbation experiment repositories will be created here; can be relative, absolute or ~ (user-defined)
repository_directory: mom6-cice6-compiler_flags_25km_ryf # Local directory name for the central repository (user-defined)
control_branch_name: ctrl
Control_Experiment:

Perturbation_Experiment:
  Parameter_block_compiler_flags_2days_from_scratch:
    branches:
      - "compiler_flag_1" # default
      - "compiler_flag_2" # pr148-1
      - "compiler_flag_3" # pr148-7

    config.yaml:
      manifest:
        reproduce:
          exe: False

      modules:
        use:
          - - PRESERVE
          - - /g/data/vk83/prerelease/modules
            - /g/data/vk83/modules 
          - - /g/data/vk83/prerelease/modules
            - /g/data/vk83/modules
        load:
          - - PRESERVE
          - - access-om3/pr148-1 # not adding model-tools/mppnccombine-fast because the positional indexing
          - - access-om3/pr148-7 # not adding model-tools/mppnccombine-fast because the positional indexing

      env:
        ESMF_RUNTIME_PROFILE: "on"
        ESMF_RUNTIME_TRACE: "on"
        ESMF_RUNTIME_TRACE_PETLIST: "0 1 291-292 1975"
        ESMF_RUNTIME_PROFILE_OUTPUT: "SUMMARY"

      repeat: True

    nuopc.runconfig:
      CLOCK_attributes:
        restart_n: 2
        restart_option: ndays
        stop_n: 2
        stop_option: ndays

And this is the yaml plan for the experiment-runner

test_path: /g/data/tm70/ml0072/COMMON/git_repos/access-experiment-generator/performance_runnings_ncmas/om3 # All control and perturbation experiment repositories.
repository_directory: mom6-cice6-compiler_flags_25km_ryf # Local directory name for the central repository, where the running_branches are forked from.
keep_uuid: True

running_branches: # List of experiment branches to run.
  - compiler_flag_1 # default
  - compiler_flag_2 # pr148-1
  - compiler_flag_3 # pr148-7

nruns: # Number of runs for each branch; must match the order of running_branches.
  - 5
  - 5
  - 5

startfrom_restart:
  - cold
  - cold
  - cold

github-actions · 2025-10-08T01:26:19Z

🚀 Attempted to deploy access-om3 Prerelease pr148-8 with commit 97ae9f0

🖥️ `Gadi` Deployment ❌

minghangli-uni · 2025-10-08T01:30:51Z

!redeploy

github-actions · 2025-10-08T02:30:51Z

🚀 Attempted to deploy access-om3 Prerelease pr148-9 with commit 97ae9f0

🖥️ `Gadi` Deployment ❌

minghangli-uni · 2025-10-09T01:09:45Z

This test only tested historical repro, is there another for restart repro ?

repro: All available reproducibility tests (all repro_ test markers but repro_determinism_restart).

I would expect all avail repro tests had been done using !test repro, but it seems not.

anton-seaice · 2025-10-09T01:15:12Z

Ah right - it runs the tests in the ci.json file - see https://github.com/ACCESS-NRI/access-om3-configs/blob/69b60c0c5719270d83a27a8d70b6d67b47e0f62b/config/ci.json#L26

That is some confusing re-use of terminology though !

minghangli-uni · 2025-10-09T01:16:56Z

so can i do !test repro_restart explicitly?

CodeGat · 2025-10-09T01:41:31Z

@minghangli-uni - @anton-seaice is right regarding not being able to apply flags in the spack.packages.all.require section. I don't think there is a syntactically neater way (at least, not in this version of spack)

dougiesquire · 2025-10-09T01:54:28Z

so can i do !test repro_restart explicitly?

Nope, unfortunately you can't choose which tests are run from within the PR

anton-seaice · 2025-10-09T02:00:12Z

In the most recent failed build, from /scratch/tm70/***/tmp/spack-stage/spack-stage-access3-2025.08.000-nii42jey5otzjpajtdcmbkcjqe3uyha4/spack-build-out.txt

It says:

[ 66%] Linking Fortran static library libOM3_cesm_driver_MOM6-CICE6.a
/apps/cmake/3.24.2/bin/cmake -P CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/cmake_clean_target.cmake
/apps/cmake/3.24.2/bin/cmake -E cmake_link_script CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/link.txt --verbose=1
/bin/ar qc libOM3_cesm_driver_MOM6-CICE6.a "CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/CMEPS/CMEPS/cesm/driver/esm.F90.o" "CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/CMEPS/CMEPS/cesm/driver/ensemble_driver.F90.o" "CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/CMEPS/CMEPS/cesm/driver/esm_time_mod.F90.o"
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
/bin/ranlib libOM3_cesm_driver_MOM6-CICE6.a
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
make[2]: Leaving directory '/scratch/tm70/tm70_ci/tmp/spack-stage/spack-stage-access3-2025.08.000-nii42jey5otzjpajtdcmbkcjqe3uyha4/spack-build-nii42je'

@manodeep says:

That means -flto was not applied. You likely need to use the -fuse-ld=lld flag at the link-line

Even though 'ldflags="-march=sapphirerapids -mtune=sapphirerapids -unroll -O3 -flto -fuse-ld=lld"' is in spack.yaml - maybe its not getting through to the linker ?

manodeep · 2025-10-09T02:04:09Z

In the most recent failed build, from /scratch/tm70/***/tmp/spack-stage/spack-stage-access3-2025.08.000-nii42jey5otzjpajtdcmbkcjqe3uyha4/spack-build-out.txt

It says:

[ 66%] Linking Fortran static library libOM3_cesm_driver_MOM6-CICE6.a
/apps/cmake/3.24.2/bin/cmake -P CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/cmake_clean_target.cmake
/apps/cmake/3.24.2/bin/cmake -E cmake_link_script CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/link.txt --verbose=1
/bin/ar qc libOM3_cesm_driver_MOM6-CICE6.a "CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/CMEPS/CMEPS/cesm/driver/esm.F90.o" "CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/CMEPS/CMEPS/cesm/driver/ensemble_driver.F90.o" "CMakeFiles/OM3_cesm_driver_MOM6-CICE6.dir/CMEPS/CMEPS/cesm/driver/esm_time_mod.F90.o"
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
/bin/ranlib libOM3_cesm_driver_MOM6-CICE6.a
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
bfd plugin: LLVM gold plugin has failed to create LTO module: Unknown attribute kind (102) (Producer: 'Intel.oneAPI.DPCPP.Compiler_2025.2.0' Reader: 'LLVM 19.1.7')
make[2]: Leaving directory '/scratch/tm70/tm70_ci/tmp/spack-stage/spack-stage-access3-2025.08.000-nii42jey5otzjpajtdcmbkcjqe3uyha4/spack-build-nii42je'

@manodeep says:

That means -flto was not applied. You likely need to use the -fuse-ld=lld flag at the link-line

Even though 'ldflags="-march=sapphirerapids -mtune=sapphirerapids -unroll -O3 -flto -fuse-ld=lld"' is in spack.yaml - maybe its not getting through to the linker ?

Looks like the line is calling the archiver. Instead of ar, you need to invoke the llvm-ar - the full path to which you can get by using ifx --print-prog-name=llvm-ar (or mpifort instead of ifx)

anton-seaice · 2025-10-09T02:23:38Z

Looks like the line is calling the archiver. Instead of ar, you need to invoke the llvm-ar - the full path to which you can get by using ifx --print-prog-name=llvm-ar (or mpifort instead of ifx)

Can you test @minghangli-uni ?

It looks like it should be

/apps/intel-tools/.packages/2025.2.0.575/compiler/2025.2/bin/compiler/llvm-ar ?

(and is maybe missing from https://github.com/ACCESS-NRI/spack-config/blob/main/common/gadi/linux/compilers.yaml ?)

But the best way to test it is not clear to me?

There is a CMAKE_AR variable, but i don't know how to set that from a spack.yaml file

github-actions · 2025-10-16T07:11:21Z

🚀 Attempted to deploy access-om3 Prerelease pr148-15 with commit df8640f

🖥️ `Gadi` Deployment ✔️

Usage Instructions

access-om3, defined in ./spack.yaml, will be deployed to Gadi as:

2025.08.002/x4lh6v3ng as a Release (when merged).
pr148-15 as a Prerelease (during this PR).

This Prerelease is accessible on Gadi using:

module use /g/data/vk83/prerelease/modules
module load access-om3/pr148-15

When using the above modules, the binaries shall be on your $PATH.

For advanced users, this Prerelease is also accessible on Gadi via /g/data/vk83/prerelease/apps/spack/0.22/spack in the access-om3-pr148-15 environment.
Due to inode-saving measures, one will have to manually untar the environment metadata before environment activation with tar -xf .spack-env .spack-env.tar. It will require one to have write privileges.

Configuration Information

This Prerelease is deployed using:

access-nri/spack on branch 0.22
access-nri/spack-packages version 2025.08.003
access-nri/spack-config version 2025.08.000

If the above was not what was expected, commit changes to config/versions.json in this PR.

github-actions · 2025-10-16T09:46:00Z

🚀 Attempted to deploy access-om3 Prerelease pr148-16 with commit 679c5dc

🖥️ `Gadi` Deployment ✔️

Usage Instructions

access-om3, defined in ./spack.yaml, will be deployed to Gadi as:

2025.08.002/x4lh6v3ng as a Release (when merged).
pr148-16 as a Prerelease (during this PR).

This Prerelease is accessible on Gadi using:

module use /g/data/vk83/prerelease/modules
module load access-om3/pr148-16

When using the above modules, the binaries shall be on your $PATH.

For advanced users, this Prerelease is also accessible on Gadi via /g/data/vk83/prerelease/apps/spack/0.22/spack in the access-om3-pr148-16 environment.
Due to inode-saving measures, one will have to manually untar the environment metadata before environment activation with tar -xf .spack-env .spack-env.tar. It will require one to have write privileges.

Configuration Information

This Prerelease is deployed using:

access-nri/spack on branch 0.22
access-nri/spack-packages version 2025.08.003
access-nri/spack-config version 2025.08.000

If the above was not what was expected, commit changes to config/versions.json in this PR.

minghangli-uni · 2025-10-16T20:15:10Z

Both pr148-15 and pr148-16 build successfully when using either the released version of access3 (default) or forcing llvm-ar (if my setting is correct)

It seems likely that the previous failure was caused still by filesystem rather than the build setup itself?

github-actions · 2025-10-17T00:04:42Z

🚀 Attempted to deploy access-om3 Prerelease pr148-17 with commit 2c87c1f

🖥️ `Gadi` Deployment ❌

github-actions · 2025-10-17T01:52:12Z

🚀 Attempted to deploy access-om3 Prerelease pr148-18 with commit 927e963

🖥️ `Gadi` Deployment ✔️

Usage Instructions

access-om3, defined in ./spack.yaml, will be deployed to Gadi as:

2025.08.002/x4lh6v3ng as a Release (when merged).
pr148-18 as a Prerelease (during this PR).

This Prerelease is accessible on Gadi using:

module use /g/data/vk83/prerelease/modules
module load access-om3/pr148-18

When using the above modules, the binaries shall be on your $PATH.

For advanced users, this Prerelease is also accessible on Gadi via /g/data/vk83/prerelease/apps/spack/0.22/spack in the access-om3-pr148-18 environment.
Due to inode-saving measures, one will have to manually untar the environment metadata before environment activation with tar -xf .spack-env .spack-env.tar. It will require one to have write privileges.

Configuration Information

This Prerelease is deployed using:

access-nri/spack on branch 0.22
access-nri/spack-packages version 2025.08.003
access-nri/spack-config version 2025.08.000

If the above was not what was expected, commit changes to config/versions.json in this PR.

Update compiler flags

241b5bd

minghangli-uni self-assigned this Sep 8, 2025

minghangli-uni temporarily deployed to Gadi Prerelease September 8, 2025 02:41 — with GitHub Actions Inactive

minghangli-uni mentioned this pull request Sep 22, 2025

What should the 100km mom config inherit from 25km / OM4-05? ACCESS-NRI/access-om3-configs#771

Open

5 tasks

Add -O3

c8adb30

minghangli-uni had a problem deploying to Gadi Prerelease September 25, 2025 07:05 — with GitHub Actions Failure

Add -qopt-prefetch

2c12228

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typo for sapphirerapids

07df87a

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compiler_flag_2

97ae9f0

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minghangli-uni mentioned this pull request Oct 9, 2025

repro tests for compiler flags updates ACCESS-NRI/access-om3-configs#822

Draft

Update access3 to force using llvm-ar

df8640f

minghangli-uni temporarily deployed to Gadi Prerelease October 16, 2025 05:58 — with GitHub Actions Inactive

revert access3 to release version

679c5dc

minghangli-uni temporarily deployed to Gadi Prerelease October 16, 2025 08:33 — with GitHub Actions Inactive

minghangli-uni added a commit that referenced this pull request Oct 16, 2025

Update compiler flags to be consistent with compiler_flag 2 in #148

57dd42b

set(CMAKE_AR "llvm-ar" CACHE FILEPATH "" FORCE)

2c87c1f

minghangli-uni had a problem deploying to Gadi Prerelease October 16, 2025 23:53 — with GitHub Actions Failure

Add CMAKE_RANLIB

927e963

minghangli-uni temporarily deployed to Gadi Prerelease October 17, 2025 00:25 — with GitHub Actions Inactive

minghangli-uni mentioned this pull request Oct 17, 2025

LTO IR plugin mismatch ACCESS-NRI/spack-packages#337

Open

anton-seaice added this to ACCESS-OM3 Mega Project board! Oct 27, 2025

anton-seaice moved this to Blocked in ACCESS-OM3 Mega Project board! Oct 27, 2025

anton-seaice added the MC_25km_jra_iaf label Oct 27, 2025

anton-seaice added this to the release-MC_25km_jra_iaf-1.0 milestone Oct 27, 2025

anton-seaice mentioned this pull request Oct 27, 2025

Coordinating changes for IAF release and new IAF-cycle test run ACCESS-NRI/access-om3-configs#847

Closed

minghangli-uni mentioned this pull request Oct 28, 2025

Update accessom3 scaling reports - switch timestep metrics from median to mean ACCESS-NRI/access-models-scaling#11

Merged

Update compiler flags #148

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Update compiler flags #148

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🖥️ Gadi Deployment ❌

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github-actions bot commented Oct 16, 2025

🖥️ Gadi Deployment ✔️

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github-actions bot commented Oct 16, 2025

🖥️ Gadi Deployment ✔️

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minghangli-uni commented Oct 16, 2025

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minghangli-uni commented Sep 8, 2025 •

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🖥️ `Gadi` Deployment ✔️

🖥️ `Gadi` Deployment ❌

🖥️ `Gadi` Deployment ✔️

🖥️ `Gadi` Deployment ❌

🖥️ `Gadi` Deployment ❌

🖥️ `Gadi` Deployment ❌

🖥️ `Gadi` Deployment ✔️

minghangli-uni commented Oct 8, 2025 •

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minghangli-uni commented Oct 8, 2025 •

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🖥️ `Gadi` Deployment ❌

🖥️ `Gadi` Deployment ❌

minghangli-uni commented Oct 9, 2025 •

edited

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🖥️ `Gadi` Deployment ✔️

🖥️ `Gadi` Deployment ✔️

🖥️ `Gadi` Deployment ❌

🖥️ `Gadi` Deployment ✔️