apply workaround for renamed Gentoo's zlib macro to VSEARCH, FreeXL, libspatialite #94

TopRichard · 2025-09-29T08:51:51Z

No description provided.

eb_hooks.py

bedroge · 2025-09-29T10:56:09Z

bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2

eessi-bot-aws · 2025-09-29T10:56:15Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2023.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /project/def-users/SHARED/jobs/2025.09/pr_94/93293

date	job status	comment
Sep 29 10:56:14 UTC 2025	submitted	job id `93293` awaits release by job manager
Sep 29 10:57:16 UTC 2025	released	job awaits launch by Slurm scheduler
Sep 29 11:02:19 UTC 2025	running	job `93293` is running
Sep 29 11:06:23 UTC 2025	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-93293.out` ✅ no message matching `FATAL:` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen2-17591437890.tar.gz` size: 0 MiB (21313 bytes) entries: 1 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/amd/zen2/software no software packages in tarball reprod directories under 2023.06/software/linux/x86_64/amd/zen2/reprod no reprod directories in tarball other under 2023.06/software/linux/x86_64/amd/zen2 `2023.06/init/easybuild/eb_hooks.py`
Sep 29 11:06:23 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:x86_64_amd_zen2+default P: perf: 440.942 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:x86_64_amd_zen2+default P: perf: 447.864 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:x86_64_amd_zen2+default P: latency: 2.6 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:x86_64_amd_zen2+default P: latency: 1.87 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:x86_64_amd_zen2+default P: latency: 3.91 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:x86_64_amd_zen2+default P: latency: 4.19 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:x86_64_amd_zen2+default P: latency: 0.6 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:x86_64_amd_zen2+default P: latency: 0.56 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:x86_64_amd_zen2+default P: bandwidth: 7462.5 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:x86_64_amd_zen2+default P: bandwidth: 7379.31 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-93293.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2025-09-29T11:06:52Z

bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2

eessi-bot-aws · 2025-09-29T11:06:58Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2023.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /project/def-users/SHARED/jobs/2025.09/pr_94/93294

date	job status	comment
Sep 29 11:06:57 UTC 2025	submitted	job id `93294` awaits release by job manager
Sep 29 11:07:26 UTC 2025	released	job awaits launch by Slurm scheduler
Sep 29 11:08:28 UTC 2025	running	job `93294` is running
Sep 29 11:13:38 UTC 2025	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-93294.out` ✅ no message matching `FATAL:` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen2-17591441640.tar.gz` size: 0 MiB (385418 bytes) entries: 23 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `VSEARCH/2.30.0-GCC-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `VSEARCH/2.30.0-GCC-13.2.0` reprod directories under 2023.06/software/linux/x86_64/amd/zen2/reprod no reprod directories in tarball other under 2023.06/software/linux/x86_64/amd/zen2 `2023.06/init/easybuild/eb_hooks.py`
Sep 29 11:13:38 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:x86_64_amd_zen2+default P: perf: 440.532 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:x86_64_amd_zen2+default P: perf: 446.08 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:x86_64_amd_zen2+default P: latency: 1.8 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:x86_64_amd_zen2+default P: latency: 1.86 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:x86_64_amd_zen2+default P: latency: 3.84 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:x86_64_amd_zen2+default P: latency: 4.14 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:x86_64_amd_zen2+default P: latency: 0.6 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:x86_64_amd_zen2+default P: latency: 0.53 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:x86_64_amd_zen2+default P: bandwidth: 7256.18 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:x86_64_amd_zen2+default P: bandwidth: 7219.97 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-93294.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2025-09-29T11:09:55Z

Works fine for VSEARCH:

== configuring...
== Running pre-configure hook...
  >> running shell command:
        ./autogen.sh && ./configure --prefix=/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2/software/VSEARCH/2.30.0-GCC-13.2.0 --disable-pdfman  CPPFLAGS="-DOF=_Z_OF ${CPPFLAGS}"

bedroge · 2025-09-29T11:12:53Z

bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2

eessi-bot-aws · 2025-09-29T11:12:59Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2023.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /project/def-users/SHARED/jobs/2025.09/pr_94/93295

date	job status	comment
Sep 29 11:12:58 UTC 2025	submitted	job id `93295` awaits release by job manager
Sep 29 11:13:37 UTC 2025	released	job awaits launch by Slurm scheduler
Sep 29 11:19:42 UTC 2025	running	job `93295` is running
Sep 29 11:23:47 UTC 2025	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-93295.out` ✅ no message matching `FATAL:` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen2-17591448220.tar.gz` size: 0 MiB (21311 bytes) entries: 1 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/amd/zen2/software no software packages in tarball reprod directories under 2023.06/software/linux/x86_64/amd/zen2/reprod no reprod directories in tarball other under 2023.06/software/linux/x86_64/amd/zen2 `2023.06/init/easybuild/eb_hooks.py`
Sep 29 11:23:47 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:x86_64_amd_zen2+default P: perf: 428.361 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:x86_64_amd_zen2+default P: perf: 439.339 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:x86_64_amd_zen2+default P: latency: 2.02 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:x86_64_amd_zen2+default P: latency: 1.93 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:x86_64_amd_zen2+default P: latency: 3.95 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:x86_64_amd_zen2+default P: latency: 4.05 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:x86_64_amd_zen2+default P: latency: 0.56 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:x86_64_amd_zen2+default P: latency: 0.54 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:x86_64_amd_zen2+default P: bandwidth: 7145.58 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:x86_64_amd_zen2+default P: bandwidth: 7194.36 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-93295.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Sep 29 11:24:34 UTC 2025	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen2-17591448220.tar.gz` to S3 bucket succeeded

eessi-bot-aws · 2025-09-29T11:13:03Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /project/def-users/SHARED/jobs/2025.09/pr_94/93296

date	job status	comment
Sep 29 11:13:02 UTC 2025	submitted	job id `93296` awaits release by job manager
Sep 29 11:13:34 UTC 2025	released	job awaits launch by Slurm scheduler
Sep 29 11:14:39 UTC 2025	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-93296.out` ✅ no message matching `FATAL:` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2025.06-software-linux-x86_64-amd-zen2-17591444230.tar.gz` size: 0 MiB (21312 bytes) entries: 1 modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all no module files in tarball software under 2025.06/software/linux/x86_64/amd/zen2/software no software packages in tarball reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod no reprod directories in tarball other under 2025.06/software/linux/x86_64/amd/zen2 `2025.06/init/easybuild/eb_hooks.py`
Sep 29 11:14:39 UTC 2025	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite was not run, test step itself failed to execute. Details ✅ job output file `slurm-93296.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Sep 29 11:24:42 UTC 2025	uploaded	transfer of `eessi-2025.06-software-linux-x86_64-amd-zen2-17591444230.tar.gz` to S3 bucket succeeded

changes required for PR 1208 in software-layer

c1cf9de

bedroge reviewed Sep 29, 2025

View reviewed changes

eb_hooks.py Outdated Show resolved Hide resolved

updated the hook to target several packages

e7e369b

TopRichard added the 2023.06-software.eessi.io 2023.06 version of software.eessi.io label Sep 29, 2025

test new hook

3ce5cf4

force rebuild

4c13e92

bedroge added 2 commits September 29, 2025 13:10

remove test easystack

b922e34

insert blank line

9c5a503

bedroge approved these changes Sep 29, 2025

View reviewed changes

bedroge changed the title ~~eb_hooks.py changes required for PR 1208 in software-layer~~ apply workaround for renamed Gentoo's zlib macro to VSEARCH, FreeXL, libspatialite Sep 29, 2025

bedroge added the bot:deploy label Sep 29, 2025

bedroge merged commit 93ed6c6 into EESSI:main Sep 29, 2025
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apply workaround for renamed Gentoo's zlib macro to VSEARCH, FreeXL, libspatialite #94

apply workaround for renamed Gentoo's zlib macro to VSEARCH, FreeXL, libspatialite #94

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apply workaround for renamed Gentoo's zlib macro to VSEARCH, FreeXL, libspatialite #94

apply workaround for renamed Gentoo's zlib macro to VSEARCH, FreeXL, libspatialite #94

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