{2025.06}[foss/2025b] gnuplot 6.0.3 by boegel · Pull Request #1512 · EESSI/software-layer

boegel · 2026-06-01T12:46:23Z

3 out of 128 required modules missing:

* Lua/5.4.8-GCCcore-14.3.0 (Lua-5.4.8-GCCcore-14.3.0.eb)
* libcerf/3.0-GCCcore-14.3.0 (libcerf-3.0-GCCcore-14.3.0.eb)
* gnuplot/6.0.3-GCCcore-14.3.0 (gnuplot-6.0.3-GCCcore-14.3.0.eb)

boegel · 2026-06-01T12:51:01Z

bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=aarch64/neoverse_v1
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-jsc for:arch=aarch64/nvidia/grace
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-deucalion for:arch=aarch64/a64fx
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-aws-eu-south for:arch=x86_64/amd/zen5

eessi-bot-aws · 2026-06-01T12:51:09Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: neoverse_v1
Building for: aarch64/neoverse_v1
Job dir: /project/def-users/SHARED/jobs/2026.06/pr_1512/162285

date	job status	comment
Jun 01 12:51:07 UTC 2026	submitted	job id `162285` awaits release by job manager
Jun 01 12:51:19 UTC 2026	released	job awaits launch by Slurm scheduler
Jun 01 12:56:25 UTC 2026	running	job `162285` is running
Jun 01 13:13:08 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-162285.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.* created!` Artefacts `eessi-2025.06-software-linux-aarch64-neoverse_v1-17803194750.tar.zst` size: 0 MiB (433966 bytes) entries: 127 modules under 2025.06/software/linux/aarch64/neoverse_v1/modules/all `libcerf/3.0-GCCcore-14.3.0.lua` `Lua/5.4.8-GCCcore-14.3.0.lua` software under 2025.06/software/linux/aarch64/neoverse_v1/software `libcerf/3.0-GCCcore-14.3.0` `Lua/5.4.8-GCCcore-14.3.0` reprod directories under 2025.06/software/linux/aarch64/neoverse_v1/reprod `libcerf/3.0-GCCcore-14.3.0/20260601_130153UTC` `Lua/5.4.8-GCCcore-14.3.0/20260601_130205UTC` other under 2025.06/software/linux/aarch64/neoverse_v1 no other files in tarball
Jun 01 13:13:08 UTC 2026	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] (1/5) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/22Jul2025-foss-2024a-kokkos %scale=1_node /ade8cad7 @BotBuildTests:aarch64-neoverse_v1+default P: perf: 964.143 timesteps/s (r:0, l:None, u:None) [ OK ] (2/5) 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:aarch64-neoverse_v1+default P: latency: 1.63 us (r:0, l:None, u:None) [ OK ] (3/5) 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:aarch64-neoverse_v1+default P: latency: 5.41 us (r:0, l:None, u:None) [ OK ] (4/5) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /3255009a @BotBuildTests:aarch64-neoverse_v1+default P: latency: 0.25 us (r:0, l:None, u:None) [ OK ] (5/5) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /59f4b331 @BotBuildTests:aarch64-neoverse_v1+default P: bandwidth: 26968.61 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 5/5 test case(s) from 5 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-162285.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot-jsc · 2026-06-01T12:51:11Z

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/2026.06/pr_1512/14823425

date	job status	comment
Jun 01 12:51:10 UTC 2026	submitted	job id `14823425` awaits release by job manager
Jun 01 12:51:15 UTC 2026	released	job awaits launch by Slurm scheduler
Jun 01 12:52:19 UTC 2026	running	job `14823425` is running
Jun 01 13:29:40 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-14823425.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.* created!` Artefacts `eessi-2025.06-software-linux-aarch64-nvidia-grace-17803200670.tar.gz` size: 0 MiB (817217 bytes) entries: 127 modules under 2025.06/software/linux/aarch64/nvidia/grace/modules/all `libcerf/3.0-GCCcore-14.3.0.lua` `Lua/5.4.8-GCCcore-14.3.0.lua` software under 2025.06/software/linux/aarch64/nvidia/grace/software `libcerf/3.0-GCCcore-14.3.0` `Lua/5.4.8-GCCcore-14.3.0` reprod directories under 2025.06/software/linux/aarch64/nvidia/grace/reprod `libcerf/3.0-GCCcore-14.3.0/20260601_131151UTC` `Lua/5.4.8-GCCcore-14.3.0/20260601_131216UTC` other under 2025.06/software/linux/aarch64/nvidia/grace no other files in tarball
Jun 01 13:29:40 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite produced failures. ReFrame Summary [ FAILED ] Ran 17/29 test case(s) from 29 check(s) (4 failure(s), 12 skipped, 0 aborted) Details ✅ job output file `slurm-14823425.out` ❌ found message matching `ERROR:` ❌ found message matching `[\sFAILED\s].Ran . test case`

eessi-bot-deucalion · 2026-06-01T12:51:13Z

New job on instance eessi-bot-deucalion for repository eessi.io-2025.06-software
Building on: a64fx
Building for: aarch64/a64fx
Job dir: /home/eessibot/new-bot/jobs/2026.06/pr_1512/1383346

date	job status	comment
Jun 01 12:51:12 UTC 2026	submitted	job id `1383346` awaits release by job manager
Jun 01 12:52:11 UTC 2026	released	job awaits launch by Slurm scheduler
Jun 01 12:53:14 UTC 2026	running	job `1383346` is running
Jun 01 13:39:46 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-1383346.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.* created!` Artefacts `eessi-2025.06-software-linux-aarch64-a64fx-17803208140.tar.zst` size: 0 MiB (438622 bytes) entries: 127 modules under 2025.06/software/linux/aarch64/a64fx/modules/all `Lua/5.4.8-GCCcore-14.3.0.lua` `libcerf/3.0-GCCcore-14.3.0.lua` software under 2025.06/software/linux/aarch64/a64fx/software `Lua/5.4.8-GCCcore-14.3.0` `libcerf/3.0-GCCcore-14.3.0` reprod directories under 2025.06/software/linux/aarch64/a64fx/reprod `Lua/5.4.8-GCCcore-14.3.0/20260601_125850UTC` `libcerf/3.0-GCCcore-14.3.0/20260601_125821UTC` other under 2025.06/software/linux/aarch64/a64fx no other files in tarball
Jun 01 13:39:46 UTC 2026	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ SKIP ] (1/5) 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:a64fx+default [Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed] [ SKIP ] (2/5) 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:a64fx+default [Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed] [ OK ] (3/5) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /3255009a @BotBuildTests:a64fx+default P: latency: 0.86 us (r:0, l:None, u:None) [ OK ] (4/5) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /59f4b331 @BotBuildTests:a64fx+default P: bandwidth: 7796.61 MB/s (r:0, l:None, u:None) [ OK ] (5/5) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/22Jul2025-foss-2024a-kokkos %scale=1_node /ade8cad7 @BotBuildTests:a64fx+default P: perf: 544.808 timesteps/s (r:0, l:None, u:None) [ PASSED ] Ran 3/5 test case(s) from 5 check(s) (0 failure(s), 2 skipped, 0 aborted) Details ✅ job output file `slurm-1383346.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot-aws-eu-south · 2026-06-01T12:51:15Z

New job on instance eessi-bot-aws-eu-south for repository eessi.io-2025.06-software
Building on: amd-zen5
Building for: x86_64/amd/zen5
Job dir: /project/def-users/SHARED/jobs/2026.06/pr_1512/181

date	job status	comment
Jun 01 12:51:13 UTC 2026	submitted	job id `181` awaits release by job manager
Jun 01 12:51:31 UTC 2026	released	job awaits launch by Slurm scheduler
Jun 01 12:57:35 UTC 2026	running	job `181` is running
Jun 01 13:11:05 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-181.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.* created!` Artefacts `eessi-2025.06-software-linux-x86_64-amd-zen5-17803193270.tar.zst` size: 0 MiB (442983 bytes) entries: 127 modules under 2025.06/software/linux/x86_64/amd/zen5/modules/all `libcerf/3.0-GCCcore-14.3.0.lua` `Lua/5.4.8-GCCcore-14.3.0.lua` software under 2025.06/software/linux/x86_64/amd/zen5/software `libcerf/3.0-GCCcore-14.3.0` `Lua/5.4.8-GCCcore-14.3.0` reprod directories under 2025.06/software/linux/x86_64/amd/zen5/reprod `libcerf/3.0-GCCcore-14.3.0/20260601_130215UTC` `Lua/5.4.8-GCCcore-14.3.0/20260601_130224UTC` other under 2025.06/software/linux/x86_64/amd/zen5 no other files in tarball
Jun 01 13:11:05 UTC 2026	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] (1/5) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/22Jul2025-foss-2024a-kokkos %scale=1_node /ade8cad7 @BotBuildTests:x86-64-zen5+default P: perf: 1557.993 timesteps/s (r:0, l:None, u:None) [ OK ] (2/5) 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-zen5+default P: latency: 1.33 us (r:0, l:None, u:None) [ OK ] (3/5) 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-zen5+default P: latency: 2.89 us (r:0, l:None, u:None) [ OK ] (4/5) 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-zen5+default P: latency: 0.14 us (r:0, l:None, u:None) [ OK ] (5/5) 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-zen5+default P: bandwidth: 46350.13 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 5/5 test case(s) from 5 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-181.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

boegel · 2026-06-01T13:30:05Z

build fails with:

/cvmfs/software.eessi.io/versions/2025.06/compat/linux/aarch64/usr/bin/ld: /cvmfs/software.eessi.io/versions/2025.06/software/linux/aarch64/neoverse_v1/software/Pango/1.57.0-GCCcore-14.3.0/lib/../lib64/libpangocairo-1.0.so: undefined reference to `FcConfigSetDefaultSubstitute'
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:912: gnuplot_x11] Error 1

edit: see also https://gitlab.gnome.org/GNOME/gnome-desktop/-/work_items/254

boegel · 2026-06-01T15:24:50Z

build fails with:

/cvmfs/software.eessi.io/versions/2025.06/compat/linux/aarch64/usr/bin/ld: /cvmfs/software.eessi.io/versions/2025.06/software/linux/aarch64/neoverse_v1/software/Pango/1.57.0-GCCcore-14.3.0/lib/../lib64/libpangocairo-1.0.so: undefined reference to `FcConfigSetDefaultSubstitute'
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:912: gnuplot_x11] Error 1

edit: see also https://gitlab.gnome.org/GNOME/gnome-desktop/-/work_items/254

The problem seems to be that libfontconfig.so is being picked up from the compat layer, rather than the (indirect) dependency of gnuplot.
It seems like adding this to the easyconfig file helps to avoid that, but then I run into other issues:

prebuildopts = "sed -i 's@-lfontconfig@-L${EBROOTFONTCONFIG}/lib -lfontconfig@g' src/Makefile && "

boegel · 2026-06-04T11:44:16Z

This looks relevant, but doesn't help (Pango/1.57.0-GCCcore-14.3.0 installation in EESSI already includes this patch):

ocaisa · 2026-06-09T11:30:12Z

I could get gnuplot to build but I am unclear why this approach is necessary. I added

prebuildopts = "sed -i 's@-lfontconfig@-liconv -L${EBROOTFONTCONFIG}/lib -lfontconfig@g' src/Makefile && "
prebuildopts += "sed -i 's@-lfontconfig@-liconv -L${EBROOTFONTCONFIG}/lib -lfontconfig@g' docs/Makefile && "

and I also added fontconfig and libiconv as dependencies....but I suspect I could have got away without doing that as they are already indirect dependencies.

boegel · 2026-06-09T18:30:57Z

Somehow gnuplot/6.0.3-GCCcore-14.2.0 doesn't suffer from the problems we observe here, it's getting built just fine as a dependency in:

{2025.06}[foss/2025a] OpenFOAM 13 #1515

boegel · 2026-06-10T19:14:02Z

Somehow gnuplot/6.0.3-GCCcore-14.2.0 doesn't suffer from the problems we observe here, it's getting built just fine as a dependency in:
* [{2025.06}[foss/2025a] OpenFOAM 13 #1515](https://github.com/EESSI/software-layer/pull/1515)

The problem doesn't pop up with an older toolchain because there we're using an older Pango (1.56.3 vs 1.57.0).

That's very relevant, because Pango 1.57.0 includes changes related to adopting a newer fontconfig, which involves using FcConfigSetDefaultSubstitute (known from the undefined reference above) instead of FcDefaultSubstitute, see GNOME/pango@9d13588

So, while there is no immediate problem with gnuplot/6.0.3-GCCcore-14.2.0, it may just be a lucky shot, since there accidentally linking to the fontconfig from the compat layer happens to work out fine. That doesn't work anymore when Pango 1.57.0 is involved though, since that requires fontconfig 2.17.0+ which provides FcConfigSetDefaultSubstitute (see fontconfig/fontconfig@90a84c4)...

So, long story short: we should make sure that we're linking to the correct fontconfig library (and potentially do a rebuild of some gnuplot modules)

edit: ldd shows that correct fontconfig library is picked up at runtime for gnuplot_x11 in gnuplot/6.0.3-GCCcore-14.2.0:

$ ldd $(find $EBROOTGNUPLOT -name gnuplot_x11) | grep fontconfig
        libfontconfig.so.1 => /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen2/software/fontconfig/2.16.2-GCCcore-14.2.0/lib64/libfontconfig.so.1 (0x000014fce0686000)

boegel · 2026-06-10T19:36:32Z

Hmm, the trick may be to set $PKG_CONFIG_ALLOW_SYSTEM_LIBS (which is equivalent to running pkgconf with --keep-system-libs), so that -L options do not get removed:

eb-shell> PKG_CONFIG_ALLOW_SYSTEM_LIBS=1 pkgconf --libs fontconfig
-L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/fontconfig/2.17.0-GCCcore-14.3.0/lib -lfontconfig -L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/freetype/2.13.3-GCCcore-14.3.0/lib -lfreetype

eb-shell> PKG_CONFIG_ALLOW_SYSTEM_LIBS=1 pkgconf --libs pangocairo
-L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Pango/1.57.0-GCCcore-14.3.0/lib -lpangocairo-1.0 -lpango-1.0 -L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/cairo/1.18.4-GCCcore-14.3.0/lib -lcairo -L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/fontconfig/2.17.0-GCCcore-14.3.0/lib -lfontconfig -L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/HarfBuzz/11.4.1-GCCcore-14.3.0/lib -lharfbuzz -L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/freetype/2.13.3-GCCcore-14.3.0/lib -lfreetype -L/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/GLib/2.85.3-GCCcore-14.3.0/lib -lgobject-2.0 -lglib-2.0

boegel · 2026-06-10T20:04:35Z

Setting $PKG_CONFIG_ALLOW_SYSTEM_LIBS (in the environment in which eb is run) does the trick, but then I run into another problem:

/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: term.o: in function `gd_iconv':
term.c:(.text+0x11dd6): undefined reference to `libiconv_open'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: term.c:(.text+0x11df9): undefined reference to `libiconv'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: term.c:(.text+0x11e11): undefined reference to `libiconv_close'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: term.o: in function `EMF_put_text':
term.c:(.text+0x3a328): undefined reference to `libiconv_open'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: term.c:(.text+0x3a352): undefined reference to `libiconv'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: term.c:(.text+0x3a368): undefined reference to `libiconv_close'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: encoding.o: in function `init_special_chars':
encoding.c:(.text+0x22c): undefined reference to `libiconv_open'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: encoding.c:(.text+0x255): undefined reference to `libiconv'
/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: encoding.c:(.text+0x267): undefined reference to `libiconv_close'

This boils down to a missing -liconv, but why does this only occur when building on top of EESSI?
libiconv is an indirect dependency, it's loaded as a module in the build environment...

I guess it's related to how configure checks what provides iconv_open:

checking for library containing iconv_open... none required

There's a related part of the gnuplot easyconfig that looks related, but isn't helping here:

# fix undefined reference to symbol 'libiconv_open'
preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && '

{2025.06}[foss/2025b] gnuplot 6.0.3

5f70d53

boegel added the 2025.06-software.eessi.io 2025.06 version of software.eessi.io label Jun 1, 2026

boegel mentioned this pull request Jun 1, 2026

update QuantumESPRESSO demo for EESSI 2025.06 EESSI/eessi-demo#57

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eessi-bot-deucalion Bot commented Jun 1, 2026 •

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eessi-bot-aws-eu-south Bot commented Jun 1, 2026 •

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boegel commented Jun 1, 2026 •

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boegel commented Jun 4, 2026 •

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boegel commented Jun 10, 2026 •

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