add pre-configure hook for PETSc to ensure that zlib is found in compat layer by boegel · Pull Request #274 · EESSI/software-layer-scripts

boegel · 2026-07-30T08:16:47Z

Without this, PETSc configure step for PETSc-3.24.0-foss-2025b.eb fails with:

  Package netcdf requested but dependency zlib not requested.
  Perhaps you want --download-zlib or --with-zlib-dir=directory or
  --with-zlib-lib=libraries and --with-zlib-include=directory

This happens because zlib is filtered out as dependency, and hence the PETSc easyblock won't automatically add --with-zlib-dir to the configure options

With this hook in place this is fixed, and PETSc configure step outputs:

zlib:
  Version:    1.3.1
  Includes:   -I/cvmfs/software.eessi.io/versions/2025.06/compat/linux/aarch64/usr/include
  Libraries:  -Wl,-rpath,/cvmfs/software.eessi.io/versions/2025.06/compat/linux/aarch64/usr/lib -L/cvmfs/software.eessi.io/versions/2025.06/compat/linux/aarch64/usr/lib -lz

I'm not sure why this is only required with PETSc 3.24.0+, this problem did not pop up for older PETSc versions (like 3.23.5)

…at layer

boegel · 2026-07-30T08:17:27Z

bot: build repo:eessi.io-2023.06-software instance:eessi-bot-jsc for:arch=aarch64/nvidia/grace
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-jsc for:arch=aarch64/nvidia/grace

eessi-bot-jsc · 2026-07-30T08:17:35Z

New job on instance eessi-bot-jsc for repository eessi.io-2023.06-software
Building on: nvidia-grace
Building for: aarch64/nvidia/grace
Job dir: /p/project1/ceasybuilders/eessibot/jobs/2026.07/pr_274/15480142

date	job status	comment
Jul 30 08:17:33 UTC 2026	submitted	job id `15480142` awaits release by job manager
Jul 30 08:17:55 UTC 2026	released	job awaits launch by Slurm scheduler
Jul 30 08:18:58 UTC 2026	running	job `15480142` is running
Jul 30 08:38:17 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15480142.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.* created!` Artefacts `eessi-2023.06-software-linux-aarch64-nvidia-grace-17853995870.tar.gz` size: 0 MiB (29394 bytes) entries: 1 modules under 2023.06/software/linux/aarch64/nvidia/grace/modules/all no module files in tarball software under 2023.06/software/linux/aarch64/nvidia/grace/software no software packages in tarball reprod directories under 2023.06/software/linux/aarch64/nvidia/grace/reprod no reprod directories in tarball other under 2023.06/software/linux/aarch64/nvidia/grace no other files in tarball
Jul 30 08:38:17 UTC 2026	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ SKIP ] ( 1/28) Skipping GPU test : only 1 GPU available for this test case [ SKIP ] ( 2/28) Skipping GPU test : only 1 GPU available for this test case [ SKIP ] ( 3/28) Skipping GPU test : only 1 GPU available for this test case [ SKIP ] ( 4/28) Skipping GPU test : only 1 GPU available for this test case [ SKIP ] ( 5/28) Skipping GPU test : only 1 GPU available for this test case [ SKIP ] ( 6/28) Skipping GPU test : only 1 GPU available for this test case [ SKIP ] ( 7/28) Skipping GPU test : only 1 GPU available for this test case [ SKIP ] ( 8/28) Skipping GPU test : only 1 GPU available for this test case [ OK ] ( 9/28) EESSI_LAMMPS_lj %device_type=gpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1 %scale=1_node /1f2ca7c1 @BotBuildTests:aarch64-nvidia-grace+default P: perf: 7046.56 timesteps/s (r:0, l:None, u:None) [ OK ] (10/28) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos %scale=1_node /aeb2d9df @BotBuildTests:aarch64-nvidia-grace+default P: perf: 1522.937 timesteps/s (r:0, l:None, u:None) [ OK ] (11/28) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:aarch64-nvidia-grace+default P: perf: 1522.493 timesteps/s (r:0, l:None, u:None) [ OK ] (12/28) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1 %scale=1_node /b22a48f5 @BotBuildTests:aarch64-nvidia-grace+default P: perf: 1469.088 timesteps/s (r:0, l:None, u:None) [ OK ] (13/28) 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-nvidia-grace+default P: latency: 4.79 us (r:0, l:None, u:None) [ OK ] (14/28) 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-nvidia-grace+default P: latency: 5.03 us (r:0, l:None, u:None) [ OK ] (15/28) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.5-gompi-2023b-CUDA-12.4.0 %scale=1_node %device_type=cpu /95ac9526 @BotBuildTests:aarch64-nvidia-grace+default P: latency: 5.62 us (r:0, l:None, u:None) [ OK ] (16/28) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023a-CUDA-12.1.1 %scale=1_node %device_type=cpu /1cff5d41 @BotBuildTests:aarch64-nvidia-grace+default P: latency: 5.77 us (r:0, l:None, u:None) [ OK ] (17/28) 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-nvidia-grace+default P: latency: 7.29 us (r:0, l:None, u:None) [ OK ] (18/28) 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-nvidia-grace+default P: latency: 6.96 us (r:0, l:None, u:None) [ OK ] (19/28) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.5-gompi-2023b-CUDA-12.4.0 %scale=1_node %device_type=cpu /0edb8a95 @BotBuildTests:aarch64-nvidia-grace+default P: latency: 10.69 us (r:0, l:None, u:None) [ OK ] (20/28) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023a-CUDA-12.1.1 %scale=1_node %device_type=cpu /b2ab2213 @BotBuildTests:aarch64-nvidia-grace+default P: latency: 10.86 us (r:0, l:None, u:None) [ OK ] (21/28) 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-nvidia-grace+default P: latency: 0.49 us (r:0, l:None, u:None) [ OK ] (22/28) 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-nvidia-grace+default P: latency: 0.5 us (r:0, l:None, u:None) [ OK ] (23/28) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.5-gompi-2023b-CUDA-12.4.0 %scale=1_node /8ec94746 @BotBuildTests:aarch64-nvidia-grace+default P: latency: 0.57 us (r:0, l:None, u:None) [ OK ] (24/28) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023a-CUDA-12.1.1 %scale=1_node /1a3a497b @BotBuildTests:aarch64-nvidia-grace+default P: latency: 0.55 us (r:0, l:None, u:None) [ OK ] (25/28) 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-nvidia-grace+default P: bandwidth: 42669.31 MB/s (r:0, l:None, u:None) [ OK ] (26/28) 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-nvidia-grace+default P: bandwidth: 41706.3 MB/s (r:0, l:None, u:None) [ OK ] (27/28) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.5-gompi-2023b-CUDA-12.4.0 %scale=1_node /c9ca6dc1 @BotBuildTests:aarch64-nvidia-grace+default P: bandwidth: 40657.27 MB/s (r:0, l:None, u:None) [ OK ] (28/28) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023a-CUDA-12.1.1 %scale=1_node /17289b2f @BotBuildTests:aarch64-nvidia-grace+default P: bandwidth: 41145.7 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 20/28 test case(s) from 28 check(s) (0 failure(s), 8 skipped, 0 aborted) Details ✅ job output file `slurm-15480142.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 30 09:58:01 UTC 2026	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-nvidia-grace-17853995870.tar.gz` to S3 bucket succeeded

eessi-bot-jsc · 2026-07-30T08:17:40Z

New job on instance eessi-bot-jsc for repository eessi.io-2025.06-software
Building on: nvidia-grace
Building for: aarch64/nvidia/grace
Job dir: /p/project1/ceasybuilders/eessibot/jobs/2026.07/pr_274/15480143

date	job status	comment
Jul 30 08:17:38 UTC 2026	submitted	job id `15480143` awaits release by job manager
Jul 30 08:17:51 UTC 2026	released	job awaits launch by Slurm scheduler
Jul 30 08:19:02 UTC 2026	running	job `15480143` is running
Jul 30 08:36:11 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15480143.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.* created!` Artefacts `eessi-2025.06-software-linux-aarch64-nvidia-grace-17853995760.tar.gz` size: 0 MiB (29396 bytes) entries: 1 modules under 2025.06/software/linux/aarch64/nvidia/grace/modules/all no module files in tarball software under 2025.06/software/linux/aarch64/nvidia/grace/software no software packages in tarball reprod directories under 2025.06/software/linux/aarch64/nvidia/grace/reprod no reprod directories in tarball other under 2025.06/software/linux/aarch64/nvidia/grace no other files in tarball
Jul 30 08:36:11 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite produced failures. ReFrame Summary [ FAILED ] Ran 18/30 test case(s) from 30 check(s) (4 failure(s), 12 skipped, 0 aborted) Details ✅ job output file `slurm-15480143.out` ❌ found message matching `ERROR:` ❌ found message matching `[\sFAILED\s].Ran . test case`
Jul 30 09:57:51 UTC 2026	uploaded	transfer of `eessi-2025.06-software-linux-aarch64-nvidia-grace-17853995760.tar.gz` to S3 bucket succeeded

bedroge · 2026-07-30T11:38:26Z

EESSI-extend CI is failing because it cannot download a make source tarball. That's not in any way related to this PR (which does not even touch EESSI-extend), so I'm going to ignore it.

add pre-configure hook for PETSc to ensure that zlib is found in comp…

1217d40

…at layer

bedroge approved these changes Jul 30, 2026

View reviewed changes

bedroge added the bot:deploy label Jul 30, 2026

boegel mentioned this pull request Jul 30, 2026

extend configure options for SymEngine to make sure that binutils is found + GMP/MPC/MPFR dependencies are correctly picked up #275

Merged

bedroge merged commit 9860a1f into EESSI:main Jul 30, 2026
97 of 104 checks passed

boegel deleted the PETSc_zlib branch July 30, 2026 12:52

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add pre-configure hook for PETSc to ensure that zlib is found in compat layer - #274

add pre-configure hook for PETSc to ensure that zlib is found in compat layer#274
bedroge merged 1 commit into
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boegel:PETSc_zlib

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