Add hook to restore filtered deps for Graphviz by Crivella · Pull Request #148 · EESSI/software-layer-scripts

Crivella · 2026-01-15T08:52:32Z

Graphviz ECs use $EBROOTLIBTOOL and $EBROOTZLIB in their configopts

Addresses build failure in

{2023.06}[2023a] aiida-core v2.5.1 software-layer#1333

eb_hooks.py

Co-authored-by: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>

casparvl

I'm now getting:

--prefix=/home/casparl/eessi/versions/2023.06/software/linux/x86_64/amd/zen2/software/Graphviz/8.1.0-G
CCcore-12.3.0 --with-ltdl-lib=/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/lib64
--enable-ltdl --enable-ruby=no --with-javalibdir=$JAVA_HOME/lib --enable-ocaml=no
--with-javaincludedir=$JAVA_HOME/include --enable-r=no --enable-guile=no --without-included-ltdl
--with-zlibdir=/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/lib64
--with-javaincludedir=$JAVA_HOME/include/linux --with-zlibdir=$EBROOTZLIB/lib --disable-ltdl-install
--with-ltdl-include=$EBROOTLIBTOOL/include --enable-lua=no --enable-php=no
--with-expatlibdir=$EBROOTEXPAT/lib --with-expatincludedir=$EBROOTEXPAT/include --enable-python3=yes
--with-zincludedir=$EBROOTZLIB/include

Two questions:

The options --with-ltdl-lib and --with-zlibdir are now unconditionally added. Wouldn't it be better to only set those options if they were already set? I mean, we don't know what will change upstream in EasyBuild to the Graphviz installation. I guess setting the lib dirs is rather 'innocent', but why not use your item.startswith check to only replace that particular item _if it exists?
I also see --with-zincludedir=$EBROOTZLIB/include. It's not leading to issues (my build completes just fine), but I guess that should be replaced too with the equivalent include dir from the compat layer, right?

Crivella · 2026-01-27T15:54:27Z

It's weird that you are still seeing double --with-zlibdir after the previous fix you pointed out.

The options --with-ltdl-lib and --with-zlibdir are now unconditionally added. Wouldn't it be better to only set those options if they were already set? I mean, we don't know what will change upstream in EasyBuild to the Graphviz installation. I guess setting the lib dirs is rather 'innocent', but why not use your item.startswith check to only replace that particular item _if it exists?

Can adapt it i think i wanted to avoid to many nested loops for checks, and the flags are there up to the latest version

EDIT: Done in a394fd2
I think either this flags will always be there or automatically set by an EasyBlock if one is ever written, at which point we would need to patch the EBlock anyway

I also see --with-zincludedir=$EBROOTZLIB/include. It's not leading to issues (my build completes just fine), but I guess that should be replaced too with the equivalent include dir from the compat layer, right?

The way we set the $EBROOT... variables will point the include dir to the correct location, but we need to hard fix the lib locations since our libraries are in lib64 and not lib for the compat layer

casparvl · 2026-01-28T13:22:59Z

The way we set the $EBROOT... variables will point the include dir to the correct location, but we need to hard fix the lib locations since our libraries are in lib64 and not lib for the compat layer

Aaah, ok, that makes sense - sorry, I missed that crucial point.

EDIT: Done in a394fd2

Ok, retesting...

casparvl

Testing, I get:

        ./autogen.sh NOCONFIG &&  ./configure --prefix=/home/casparl/eessi/versions/2023.06/software/linux/x86_64/amd/zen2/software/Graphviz/8.1.0-GCCcore-12.3.0 --enable-ruby=no --enable-python3=yes --enable-guile=no --enable-ltdl --with-javaincludedir=$JAVA_HOME/include
--enable-php=no --with-ltdl-include=$EBROOTLIBTOOL/include --disable-ltdl-install --enable-r=no --enable-lua=no --with-expatlibdir=$EBROOTEXPAT/lib --with-javaincludedir=$JAVA_HOME/include/linux --with-zlibdir=/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/lib64
--with-ltdl-lib=/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/lib64 --with-zincludedir=$EBROOTZLIB/include --enable-ocaml=no --without-included-ltdl --with-expatincludedir=$EBROOTEXPAT/include --with-javalibdir=$JAVA_HOME/lib

So both option now occur only once, and have the correct value. (local) Build is successful. Approved!

casparvl · 2026-01-28T15:53:03Z

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 · 2026-01-28T15:53:14Z

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/2026.01/pr_148/125693

date	job status	comment
Jan 28 15:53:13 UTC 2026	submitted	job id `125693` awaits release by job manager
Jan 28 15:53:30 UTC 2026	released	job awaits launch by Slurm scheduler
Jan 28 16:02:50 UTC 2026	running	job `125693` is running
Jan 28 16:07:16 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-125693.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-x86_64-amd-zen2-17696161720.tar.zst` size: 0 MiB (25770 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`
Jan 28 16:07:16 UTC 2026	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-zen2+default P: perf: 291.177 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-zen2+default P: perf: 455.092 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-zen2+default P: latency: 3.0 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-zen2+default P: latency: 2.63 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-zen2+default P: latency: 6.02 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-zen2+default P: latency: 5.69 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-zen2+default P: latency: 0.88 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-zen2+default P: latency: 0.85 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-zen2+default P: bandwidth: 6384.06 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-zen2+default P: bandwidth: 6319.45 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-125693.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jan 28 16:12:45 UTC 2026	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen2-17696161720.tar.zst` to S3 bucket succeeded

eessi-bot-aws · 2026-01-28T15:53:19Z

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/2026.01/pr_148/125694

date	job status	comment
Jan 28 15:53:18 UTC 2026	submitted	job id `125694` awaits release by job manager
Jan 28 15:53:28 UTC 2026	released	job awaits launch by Slurm scheduler
Jan 28 15:54:33 UTC 2026	running	job `125694` is running
Jan 28 15:55:43 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-125694.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-x86_64-amd-zen2-17696156340.tar.zst` size: 0 MiB (25774 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`
Jan 28 15:55:43 UTC 2026	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] (1/4) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node %device_type=cpu /e4bf9965 @BotBuildTests:x86-64-zen2+default P: latency: 1.31 us (r:0, l:None, u:None) [ OK ] (2/4) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node %device_type=cpu /3da4890b @BotBuildTests:x86-64-zen2+default P: latency: 2.07 us (r:0, l:None, u:None) [ OK ] (3/4) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /3255009a @BotBuildTests:x86-64-zen2+default P: latency: 0.18 us (r:0, l:None, u:None) [ OK ] (4/4) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /59f4b331 @BotBuildTests:x86-64-zen2+default P: bandwidth: 8013.86 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 4/4 test case(s) from 4 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-125694.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jan 28 16:12:54 UTC 2026	uploaded	transfer of `eessi-2025.06-software-linux-x86_64-amd-zen2-17696156340.tar.zst` to S3 bucket succeeded

Add hook to restore filtered deps for Graphviz

b076dd1

Crivella mentioned this pull request Jan 15, 2026

{2023.06}[2023a] aiida-core v2.5.1 EESSI/software-layer#1333

Closed

Crivella added 2 commits January 15, 2026 14:16

Fix wrong line

88f5b6d

Fix also hardcoded /lib to /lib64 in the configopts

062d6c6

Crivella mentioned this pull request Jan 15, 2026

{2023.06}[2023a] aiida-core v2.7.2 + aiida-shell v0.8.2 EESSI/software-layer#1334

Merged

casparvl reviewed Jan 27, 2026

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casparvl reviewed Jan 27, 2026

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Crivella and others added 2 commits January 27, 2026 15:26

Update eb_hooks.py

de30136

Co-authored-by: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>

Update eb_hooks.py

75ffb0c

Co-authored-by: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>

casparvl requested changes Jan 27, 2026

View reviewed changes

Fix to only add libdirs if they are in the easyconfig

a394fd2

casparvl approved these changes Jan 28, 2026

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Merge branch 'main' into feature-GraphvizHook

ae17648

casparvl added the bot:deploy label Jan 28, 2026

Merge branch 'main' into feature-GraphvizHook

d61aebf

casparvl merged commit 6e27876 into EESSI:main Jan 29, 2026
68 of 70 checks passed

Crivella deleted the feature-GraphvizHook branch January 29, 2026 15:34

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Add hook to restore filtered deps for Graphviz#148

Add hook to restore filtered deps for Graphviz#148
casparvl merged 8 commits intoEESSI:mainfrom
Crivella:feature-GraphvizHook

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