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{2025.06-001}[2025a] SciPy-bundle 2025.06 #25

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@julianmorillo julianmorillo commented Jan 26, 2026

Dependency towards finally adding ESPResSo

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julianmorillo commented Jan 26, 2026

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

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riscv-eessi-io-bot bot commented Jan 26, 2026 •
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New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.01/pr_25/262698

date job status comment
Jan 26 12:09:44 UTC 2026 submitted job id 262698 awaits release by job manager
Jan 26 12:09:51 UTC 2026 released job awaits launch by Slurm scheduler
Jan 26 12:10:54 UTC 2026 running job 262698 is running
Jan 26 19:20:02 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-262698.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-riscv64-generic-riscv-1769453656.tar.gzsize: 326 MiB (342031346 bytes)
entries: 3679
modules under 2025.06-001/software/linux/riscv64/generic/modules/all
Catch2/2.13.10-GCCcore-14.2.0.lua
Cython/3.1.1-GCCcore-14.2.0.lua
Eigen/3.4.0-GCCcore-14.2.0.lua
ICU/76.1-GCCcore-14.2.0.lua
expat/2.6.4-GCCcore-14.2.0.lua
flit/3.10.1-GCCcore-14.2.0.lua
gfbf/2025a.lua
git/2.49.0-GCCcore-14.2.0.lua
hatchling/1.27.0-GCCcore-14.2.0.lua
patchelf/0.18.0-GCCcore-14.2.0.lua
scikit-build-core/0.11.1-GCCcore-14.2.0.lua
scikit-build/0.18.1-GCCcore-14.2.0.lua
setuptools-rust/1.11.0-GCCcore-14.2.0.lua
software under 2025.06-001/software/linux/riscv64/generic/software
Catch2/2.13.10-GCCcore-14.2.0
Cython/3.1.1-GCCcore-14.2.0
Eigen/3.4.0-GCCcore-14.2.0
ICU/76.1-GCCcore-14.2.0
expat/2.6.4-GCCcore-14.2.0
flit/3.10.1-GCCcore-14.2.0
gfbf/2025a
git/2.49.0-GCCcore-14.2.0
hatchling/1.27.0-GCCcore-14.2.0
patchelf/0.18.0-GCCcore-14.2.0
scikit-build-core/0.11.1-GCCcore-14.2.0
scikit-build/0.18.1-GCCcore-14.2.0
setuptools-rust/1.11.0-GCCcore-14.2.0
reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod
no reprod directories in tarball
other under 2025.06-001/software/linux/riscv64/generic
no other files in tarball
Jan 26 19:20:02 UTC 2026 test result
🤷 UNKNOWN (click triangle for detailed information)
  • Job test file _bot_job262698.test does not exist in job directory, or parsing it failed.

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bedroge commented Jan 27, 2026 •
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Two internal compiler errors when it was compiling Boost:

gcc.compile.c++ bin.v2/libs/log/build/gcc-14/release/riscv_64/threading-multi/visibility-hidden/setup/default_formatter_factory.o
In file included from ./boost/range/functions.hpp:18,
                 from ./boost/range/iterator_range_core.hpp:41,
                 from ./boost/algorithm/string/replace.hpp:16,
                 from ./boost/date_time/date_facet.hpp:17,
                 from ./boost/date_time/gregorian/gregorian_io.hpp:16,
                 from ./boost/date_time/gregorian/gregorian.hpp:31,
                 from ./boost/date_time/posix_time/time_formatters.hpp:12,
                 from ./boost/date_time/posix_time/posix_time.hpp:24,
                 from ./boost/date_time/local_time/local_date_time.hpp:18,
                 from ./boost/date_time/local_time/local_time_types.hpp:11,
                 from libs/log/src/setup/default_formatter_factory.cpp:29:
./boost/range/begin.hpp:46:5: internal compiler error: in ggc_set_mark, at ggc-page.cc:1554
   46 |     }
      |     ^
0x856c39 ggc_set_mark(void const*)
        ../../gcc/ggc-page.cc:1554
0x7bb673 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:107
0x7bbc6b gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:450
0x7bc3fb gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:441
0x7bc3cb gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:435
0x7bc381 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:418
0x7bbbeb gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:468
0x7bbc01 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:472
0x7bbc01 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:472
0x7bbc01 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:472
0x7bbc01 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:472
0x7bbc01 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:472
0xa20e4b gt_ggc_mx_tree_statement_list_node(void*)
        /tmp/eessibot/easybuild/build/GCCcore/14.2.0/system-system/gcc-14.2.0/stage3_obj/gcc/gtype-desc.cc:1882
0x7bba95 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:519
0x7bbc01 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:472
0x7bc243 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:352
0x7bb973 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:568
0x7bb973 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:568
0x7bc079 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:208
0x7bbc01 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:472
Please submit a full bug report, with preprocessed source (by using -freport-bug).
Please include the complete backtrace with any bug report.
See <https://gcc.gnu.org/bugs/> for instructions.

and

gcc.compile.c++ bin.v2/libs/log/build/gcc-14/release/riscv_64/link-static/threading-multi/visibility-hidden/setup/default_formatter_factory.o
In file included from ./boost/range/functions.hpp:18,
                 from ./boost/range/iterator_range_core.hpp:41,
                 from ./boost/algorithm/string/replace.hpp:16,
                 from ./boost/date_time/date_facet.hpp:17,
                 from ./boost/date_time/gregorian/gregorian_io.hpp:16,
                 from ./boost/date_time/gregorian/gregorian.hpp:31,
                 from ./boost/date_time/posix_time/time_formatters.hpp:12,
                 from ./boost/date_time/posix_time/posix_time.hpp:24,
                 from ./boost/date_time/local_time/local_date_time.hpp:18,
                 from ./boost/date_time/local_time/local_time_types.hpp:11,
                 from libs/log/src/setup/default_formatter_factory.cpp:29:
./boost/range/begin.hpp:46:5: internal compiler error: Segmentation fault
   46 |     }
      |     ^
0xc62307 crash_signal
        ../../gcc/toplev.cc:319
0x856bfc ggc_set_mark(void const*)
        ../../gcc/ggc-page.cc:1563
0x7bb673 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:107
0x7bbc1d gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:455
0x7bbc6b gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:450
0x7bb83d gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:613
0x7bb921 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:672
0x7bc733 gt_ggc_mx_lang_decl(void*)
        ./gt-cp-tree.h:56
0x7bc61b gt_ggc_mx_lang_decl(void*)
        ./gt-cp-tree.h:49
0x7bc61b gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:326
0x7bc3eb gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:439
0x7bbc61 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:449
0x7bbc3b gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:460
0x7bbc6b gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:450
0x7bb83d gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:613
0x7bb921 gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:672
0x7bc733 gt_ggc_mx_lang_decl(void*)
        ./gt-cp-tree.h:56
0x7bc61b gt_ggc_mx_lang_decl(void*)
        ./gt-cp-tree.h:49
0x7bc61b gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:326
0x7bc3eb gt_ggc_mx_lang_tree_node(void*)
        ./gt-cp-tree.h:439
Please submit a full bug report, with preprocessed source (by using -freport-bug).
Please include the complete backtrace with any bug report.
See <https://gcc.gnu.org/bugs/> for instructions.

@julianmorillo julianmorillo mentioned this pull request Jan 27, 2026
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julianmorillo commented Jan 27, 2026

Let's go step by step, then. Submitted #26 (first dependency of SciPy-bundle 2025.06)

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bedroge commented Jan 28, 2026

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

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riscv-eessi-io-bot bot commented Jan 28, 2026 •
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New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.01/pr_25/263059

date job status comment
Jan 28 22:44:07 UTC 2026 submitted job id 263059 awaits release by job manager
Jan 28 22:44:48 UTC 2026 released job awaits launch by Slurm scheduler
Jan 28 22:45:54 UTC 2026 running job 263059 is running
Jan 29 07:20:03 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-263059.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-riscv64-generic-riscv-1769670887.tar.zstsize: 67 MiB (71225859 bytes)
entries: 19836
modules under 2025.06-001/software/linux/riscv64/generic/modules/all
Boost/1.88.0-GCC-14.2.0.lua
Catch2/2.13.10-GCCcore-14.2.0.lua
Cython/3.1.1-GCCcore-14.2.0.lua
Eigen/3.4.0-GCCcore-14.2.0.lua
ICU/76.1-GCCcore-14.2.0.lua
gfbf/2025a.lua
meson-python/0.18.0-GCCcore-14.2.0.lua
pybind11/2.13.6-GCC-14.2.0.lua
spin/0.14-GCCcore-14.2.0.lua
software under 2025.06-001/software/linux/riscv64/generic/software
Boost/1.88.0-GCC-14.2.0
Catch2/2.13.10-GCCcore-14.2.0
Cython/3.1.1-GCCcore-14.2.0
Eigen/3.4.0-GCCcore-14.2.0
ICU/76.1-GCCcore-14.2.0
gfbf/2025a
meson-python/0.18.0-GCCcore-14.2.0
pybind11/2.13.6-GCC-14.2.0
spin/0.14-GCCcore-14.2.0
reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod
no reprod directories in tarball
other under 2025.06-001/software/linux/riscv64/generic
no other files in tarball
Jan 29 07:20:03 UTC 2026 test result
🤷 UNKNOWN (click triangle for detailed information)
  • Job test file _bot_job263059.test does not exist in job directory, or parsing it failed.

@julianmorillo julianmorillo mentioned this pull request Jan 29, 2026
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julianmorillo commented Jan 29, 2026

Failed again, submitted #28 with another dependency to go step by step

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bedroge commented Jan 29, 2026

It got pretty far this time. Boost installed without issues, and it even built the scipy extension, but a bunch of tests failed:

=========================== short test summary info ============================
FAILED scipy/_lib/tests/test_import_cycles.py::test_public_modules_importable
FAILED scipy/special/tests/test_nan_inputs.py::test_nan_inputs[sph_harm] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[1-7] - Ass...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[1-10] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[1-50] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[4-7] - Ass...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[4-10] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[4-50] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[5-7] - Ass...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[5-10] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[5-50] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[9-7] - Ass...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[9-10] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[9-50] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[14-7] - As...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[14-10] - A...
FAILED scipy/special/tests/test_sph_harm.py::TestSphHarm::test_all[14-50] - A...
= 17 failed, 78492 passed, 5163 skipped, 305 xfailed, 15 xpassed, 2748 warnings in 6123.71s (1:42:03) =

@julianmorillo julianmorillo mentioned this pull request Jan 29, 2026
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julianmorillo commented Jan 29, 2026

Submitted #29. Let's build dependencies to avoid wasting compute hours.

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@julianmorillo @bedroge @Neves-P