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4 out of 39 required modules missing:

  • MUSCLE/5.1.0-GCCcore-12.3.0 (MUSCLE-5.1.0-GCCcore-12.3.0.eb)
  • Gblocks/0.91b (Gblocks-0.91b.eb)
  • RAxML/8.2.13-gompi-2023a-avx2 (RAxML-8.2.13-gompi-2023a-avx2.eb)
  • bcgTree/1.2.1-foss-2023a (bcgTree-1.2.1-foss-2023a.eb)

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eessi-bot bot commented Apr 17, 2025

Instance eessi-bot-mc-aws is configured to build for:

  • architectures: x86_64/generic, x86_64/intel/haswell, x86_64/intel/sapphirerapids, x86_64/intel/skylake_avx512, x86_64/amd/zen2, x86_64/amd/zen3, aarch64/generic, aarch64/neoverse_n1, aarch64/neoverse_v1
  • repositories: eessi.io-2023.06-software, eessi.io-2023.06-compat

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Instance eessi-bot-mc-azure is configured to build for:

  • architectures: x86_64/amd/zen4
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Instance eessi-bot-vsc-ugent is configured to build for:

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Instance rt-Grace-jr is configured to build for:

  • architectures: aarch64/nvidia/grace
  • repositories: eessi.io-2023.06-software

@PetrKralCZ PetrKralCZ changed the title {bio}[2023a] bcgTree 1.2.1 {2023.06}[2023a] bcgTree 1.2.1 Apr 17, 2025
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bedroge commented Apr 17, 2025

bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws arch:aarch64/neoverse_v1

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Updates by the bot instance eessi-bot-mc-aws (click for details)
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    • expanded format: build repository:eessi.io-2023.06-software instance:eessi-bot-mc-aws architecture:aarch64/neoverse_v1
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  • received bot command build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws arch:aarch64/neoverse_v1 from bedroge

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Updates by the bot instance rt-Grace-jr (click for details)
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eessi-bot bot commented Apr 17, 2025

New job on instance eessi-bot-mc-aws for CPU micro-architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2025.04/pr_1032/57368

date job status comment
Apr 17 13:45:56 UTC 2025 submitted job id 57368 awaits release by job manager
Apr 17 13:46:55 UTC 2025 released job awaits launch by Slurm scheduler
Apr 17 13:51:58 UTC 2025 running job 57368 is running
Apr 17 14:00:07 UTC 2025 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-57368.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-aarch64-neoverse_v1-1744898001.tar.gzsize: 0 MiB (45 bytes)
entries: 0
modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all
no module files in tarball
software under 2023.06/software/linux/aarch64/neoverse_v1/software
no software packages in tarball
other under 2023.06/software/linux/aarch64/neoverse_v1
no other files in tarball
Apr 17 14:00:07 UTC 2025 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ OK ] ( 1/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos %scale=1_node /aeb2d9df @BotBuildTests:aarch64_neoverse_v1+default
P: perf: 951.384 timesteps/s (r:0, l:None, u:None)
[ OK ] ( 2/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:aarch64_neoverse_v1+default
P: perf: 982.064 timesteps/s (r:0, l:None, u:None)
[ OK ] ( 3/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /775175bf @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 3.23 us (r:0, l:None, u:None)
[ OK ] ( 4/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /52707c40 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 3.21 us (r:0, l:None, u:None)
[ OK ] ( 5/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /b1aacda9 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 4.35 us (r:0, l:None, u:None)
[ OK ] ( 6/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /c6bad193 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 4.38 us (r:0, l:None, u:None)
[ OK ] ( 7/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /15cad6c4 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 0.38 us (r:0, l:None, u:None)
[ OK ] ( 8/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /6672deda @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 0.41 us (r:0, l:None, u:None)
[ OK ] ( 9/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /2a9a47b1 @BotBuildTests:aarch64_neoverse_v1+default
P: bandwidth: 36763.74 MB/s (r:0, l:None, u:None)
[ OK ] (10/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /1b24ab8e @BotBuildTests:aarch64_neoverse_v1+default
P: bandwidth: 36708.85 MB/s (r:0, l:None, u:None)
[ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-57368.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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bedroge commented Apr 17, 2025

The sanity check of MUSCLE is failing:

== FAILED: Installation ended unsuccessfully: Sanity check failed: sanity check command muscle -h failed with exit code 1 (output: 


Elapsed time 00:00
Max memory 0.0b

---Fatal error---
myutils.cpp(122) assert failed: sizeof(void *) == 4

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laraPPr commented Apr 18, 2025

The release noted of MUSCLE suggest that they support Aarch64, See https://github.com/rcedgar/muscle/releases/tag/v5.1. But the failure suggests otherwise. I found this in their myustils.cpp file which suggest that for some reason its is picking the wrong bit size. (https://github.com/rcedgar/muscle/blob/cfc3eeedb98fa9cc9bd5b32c2edad95ae0416725/src/myutils.cpp#L105-L117)

#if	BITS==32
	asserta(sizeof(void *) == 4);
#ifdef _MSC_VER
	return "win32";
#elif defined(__APPLE__)
	return "osx32";
#elif defined(__GNUC__)
	return "linux32";
#else
#error "Unknown compiler"
#endif
#elif BITS==64
	asserta(sizeof(void *) == 8);

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laraPPr commented Apr 18, 2025

A LLM says I should try this and it does not seem crazy. (Asked him what is wrong with this line #if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) (https://github.com/rcedgar/muscle/blob/cfc3eeedb98fa9cc9bd5b32c2edad95ae0416725/src/myutils.h#L13)

LLM:

The line of code you provided is a preprocessor directive that checks for definitions of specific macros, which are typically used to identify the system architecture.

#define x86_64 is typically defined for 64-bit x86 systems.
#define _M_X64 is typically defined by Microsoft compilers for 64-bit x86 systems.
#define arm64 is typically defined for 64-bit ARM systems.

The issue is that the ARM Neoverse V1 system is a 64-bit ARM system, but the line of code only checks for arm64, which might not be defined for all 64-bit ARM systems.

Try adding || defined(__aarch64__) to the line to also check for the aarch64 macro, which is commonly defined for 64-bit ARM systems.

So, the modified line would look like this:
#if defined(x86_64) || defined(_M_X64) || defined(arm64) || defined(aarch64)

This should correctly identify the ARM Neoverse V1 system as a 64-bit ARM system.

If this still doesn't work, please provide more context or details about your build environment, compiler, and target system, and I'll be happy to help you further.

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laraPPr commented Apr 18, 2025

Tested this pr, easybuilders/easybuild-easyconfigs#22780, on the neoverse_v1 node and than it completed the build.

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Pick-up MUSLE with patch for Aarch64

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laraPPr commented Apr 18, 2025

bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws arch:aarch64/neoverse_v1

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    • expanded format: build repository:eessi.io-2023.06-software instance:eessi-bot-mc-aws architecture:aarch64/neoverse_v1
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  • received bot command build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws arch:aarch64/neoverse_v1 from laraPPr

    • expanded format: build repository:eessi.io-2023.06-software instance:eessi-bot-mc-aws architecture:aarch64/neoverse_v1
  • handling command build repository:eessi.io-2023.06-software instance:eessi-bot-mc-aws architecture:aarch64/neoverse_v1 resulted in:

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  • received bot command build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws arch:aarch64/neoverse_v1 from laraPPr

    • expanded format: build repository:eessi.io-2023.06-software instance:eessi-bot-mc-aws architecture:aarch64/neoverse_v1
  • handling command build repository:eessi.io-2023.06-software instance:eessi-bot-mc-aws architecture:aarch64/neoverse_v1 resulted in:

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New job on instance eessi-bot-mc-aws for CPU micro-architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2025.04/pr_1032/57576

date job status comment
Apr 18 14:11:47 UTC 2025 submitted job id 57576 awaits release by job manager
Apr 18 14:12:17 UTC 2025 released job awaits launch by Slurm scheduler
Apr 18 14:13:20 UTC 2025 running job 57576 is running
Apr 18 14:20:28 UTC 2025 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-57576.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-aarch64-neoverse_v1-1744985650.tar.gzsize: 0 MiB (511781 bytes)
entries: 44
modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all
Gblocks/0.91b.lua
MUSCLE/5.1.0-GCCcore-12.3.0.lua
software under 2023.06/software/linux/aarch64/neoverse_v1/software
Gblocks/0.91b
MUSCLE/5.1.0-GCCcore-12.3.0
other under 2023.06/software/linux/aarch64/neoverse_v1
no other files in tarball
Apr 18 14:20:28 UTC 2025 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ OK ] ( 1/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos %scale=1_node /aeb2d9df @BotBuildTests:aarch64_neoverse_v1+default
P: perf: 973.009 timesteps/s (r:0, l:None, u:None)
[ OK ] ( 2/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:aarch64_neoverse_v1+default
P: perf: 977.436 timesteps/s (r:0, l:None, u:None)
[ OK ] ( 3/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /775175bf @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 3.44 us (r:0, l:None, u:None)
[ OK ] ( 4/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /52707c40 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 3.12 us (r:0, l:None, u:None)
[ OK ] ( 5/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /b1aacda9 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 4.19 us (r:0, l:None, u:None)
[ OK ] ( 6/10) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /c6bad193 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 4.42 us (r:0, l:None, u:None)
[ OK ] ( 7/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /15cad6c4 @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 0.43 us (r:0, l:None, u:None)
[ OK ] ( 8/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /6672deda @BotBuildTests:aarch64_neoverse_v1+default
P: latency: 0.42 us (r:0, l:None, u:None)
[ OK ] ( 9/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /2a9a47b1 @BotBuildTests:aarch64_neoverse_v1+default
P: bandwidth: 35690.74 MB/s (r:0, l:None, u:None)
[ OK ] (10/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /1b24ab8e @BotBuildTests:aarch64_neoverse_v1+default
P: bandwidth: 35851.54 MB/s (r:0, l:None, u:None)
[ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-57576.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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laraPPr commented Apr 18, 2025

Ok got through 2 out of the 4 builds with the patch to MUSCLE

Gblocks/0.91b.lua
MUSCLE/5.1.0-GCCcore-12.3.0.lua

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laraPPr commented Apr 18, 2025

RAxML failed

gcc: error: unrecognized command-line option ‘-msse3’

make: *** [<builtin>: bipartitionList.o] Error 1



== 2025-04-18 14:13:12,191 run.py:603 WARNING Shell command FAILED (exit code 2, see output above): make  -j 16 -f Makefile.AVX2.gcc CC="$CC" && rm *.o && make -j 16 -f Makefile.AVX2.PTHREADS.gcc CC="$CC" && rm *.o && make -j 16 -f Makefile.AVX2.HYBRID.gcc CC="$CC"

@laraPPr laraPPr added ready-to-deploy Mark a PR as ready to deploy ready-to-review labels Apr 23, 2025
Co-authored-by: Bob Dröge <[email protected]>
@bedroge bedroge added bot:deploy Ask bot to deploy missing software installations to EESSI and removed ready-to-deploy Mark a PR as ready to deploy ready-to-review labels Apr 24, 2025
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@TopRichard TopRichard added the bot:deploy Ask bot to deploy missing software installations to EESSI label Apr 24, 2025
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bedroge commented Apr 24, 2025

Hmm, the missing installation CI is failing for the Arm targets because RAxML/8.2.13-gompi-2023a-avx2 is missing. How did we fix that before for similar apps with optional dependencies, with a hook?

edit: I guess we need to do something similar as we do for LAMMPS (https://github.com/EESSI/software-layer/blob/2023.06-software.eessi.io/eb_hooks.py#L376) and CP2K (https://github.com/EESSI/software-layer/blob/2023.06-software.eessi.io/eb_hooks.py#L394), because the checks are running on x86_64? Or maybe we could use a native Arm runner for the Arm targets, but I'm not sure how easy it is to split the CI.

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boegel commented Apr 24, 2025

Hmm, the missing installation CI is failing for the Arm targets because RAxML/8.2.13-gompi-2023a-avx2 is missing. How did we fix that before for similar apps with optional dependencies, with a hook?

edit: I guess we need to do something similar as we do for LAMMPS (https://github.com/EESSI/software-layer/blob/2023.06-software.eessi.io/eb_hooks.py#L376) and CP2K (https://github.com/EESSI/software-layer/blob/2023.06-software.eessi.io/eb_hooks.py#L394), because the checks are running on x86_64? Or maybe we could use a native Arm runner for the Arm targets, but I'm not sure how easy it is to split the CI.

Seems like it boils down to using a different runs-on value, see https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions#standard-github-hosted-runners-for-public-repositories

That doesn't seem very difficult to do, see https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions#example-using-a-multi-dimension-matrix

I'll take a quick stab at it, this PR is a good excuse to look into that (and it's a good test case).

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boegel commented Apr 24, 2025

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boegel commented Apr 24, 2025

synced with updated 2023.06-software.eessi.io branch after merge of #1046, let's see if CI is indeed happy now that missing installations for aarch64/* targets are checked on Arm GitHub Actions runners...

@bedroge bedroge merged commit 50a79dc into EESSI:2023.06-software.eessi.io Apr 24, 2025
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eessi-bot bot commented Apr 24, 2025

PR merged! Moved ['/project/def-users/SHARED/jobs/2025.04/pr_1032/57368', '/project/def-users/SHARED/jobs/2025.04/pr_1032/57576', '/project/def-users/SHARED/jobs/2025.04/pr_1032/57578', '/project/def-users/SHARED/jobs/2025.04/pr_1032/57579', '/project/def-users/SHARED/jobs/2025.04/pr_1032/57580', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58618', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58619', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58620', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58621', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58622', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58623', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58624', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58625', '/project/def-users/SHARED/jobs/2025.04/pr_1032/58626'] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.04.24

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PR merged! Moved ['/home/eessibot/new-bot/jobs/2025.04/pr_1032/406838'] to /home/eessibot/new-bot/trash-bin/EESSI/software-layer/2025.04.24

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eessi-bot bot commented Apr 24, 2025

PR merged! Moved ['/project/def-users/SHARED/jobs/2025.04/pr_1032/2425'] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.04.24

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gpu-bot-ugent bot commented Apr 24, 2025

PR merged! Moved [] to /scratch/gent/vo/002/gvo00211/SHARED/trash_bin/EESSI/software-layer/2025.04.24

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PR merged! Moved ['/projects/eessibot/eessi-bot-surf/jobs/2025.04/pr_1032/11334139'] to /projects/eessibot/eessi-bot-surf/trash_bin/EESSI/software-layer/2025.04.24

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PR merged! Moved ['/p/project1/ceasybuilders/bot-rt/jobs/2025.04/pr_1032/13621084', '/p/project1/ceasybuilders/bot-rt/jobs/2025.04/pr_1032/13627123'] to /p/project1/ceasybuilders/bot-rt/trash_bin/EESSI/software-layer/2025.04.24

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