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Add hook to restore filtered deps for Graphviz #148

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@Crivella Crivella commented Jan 15, 2026

Graphviz ECs use $EBROOTLIBTOOL and $EBROOTZLIB in their configopts

Addresses build failure in

@Crivella Crivella mentioned this pull request Jan 15, 2026
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@Crivella Crivella mentioned this pull request Jan 15, 2026
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casparvl
casparvl reviewed Jan 27, 2026
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casparvl
casparvl reviewed Jan 27, 2026
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Crivella and others added 2 commits January 27, 2026 15:26
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Update eb_hooks.py
de30136 
Co-authored-by: Caspar van Leeuwen <[email protected]>
@Crivella @casparvl
Update eb_hooks.py
75ffb0c 
Co-authored-by: Caspar van Leeuwen <[email protected]>
casparvl
casparvl requested changes Jan 27, 2026
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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:

  1. 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?
  2. 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?

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Crivella commented Jan 27, 2026 •
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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

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casparvl commented Jan 28, 2026

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...

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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!

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casparvl commented Jan 28, 2026

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

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eessi-bot-aws bot commented Jan 28, 2026 •
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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.zstsize: 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 [\s*FAILED\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

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eessi-bot-aws bot commented Jan 28, 2026 •
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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.zstsize: 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 [\s*FAILED\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

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