{2025.06}[2024a] LAMMPS v22Jul2025 #1335

laraPPr · 2025-12-12T12:54:39Z

No description provided.

laraPPr · 2025-12-12T12:55:12Z

bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=aarch64/neoverse_n1

eessi-bot-aws · 2025-12-12T12:55:19Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: neoverse_n1
Building for: aarch64/neoverse_n1
Job dir: /project/def-users/SHARED/jobs/2025.12/pr_1335/112381

date	job status	comment
Dec 12 12:55:18 UTC 2025	submitted	job id `112381` awaits release by job manager
Dec 12 12:56:11 UTC 2025	released	job awaits launch by Slurm scheduler
Dec 12 13:06:14 UTC 2025	running	job `112381` is running
Dec 12 14:02:23 UTC 2025	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-112381.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_n1-17655480150.tar.zst` size: 44 MiB (46437129 bytes) entries: 1832 modules under 2025.06/software/linux/aarch64/neoverse_n1/modules/all `archspec/0.2.5-GCCcore-13.3.0.lua` `kim-api/2.4.1-GCC-13.3.0.lua` `MDI/1.4.26-gompi-2024a.lua` `mpi4py/4.0.1-gompi-2024a.lua` `PLUMED/2.9.3-foss-2024a.lua` `ScaFaCoS/1.0.4-foss-2024a.lua` `tbb/2021.13.0-GCCcore-13.3.0.lua` `Voro++/0.4.6-GCCcore-13.3.0.lua` `xxd/9.1.1275-GCCcore-13.3.0.lua` software under 2025.06/software/linux/aarch64/neoverse_n1/software `archspec/0.2.5-GCCcore-13.3.0` `kim-api/2.4.1-GCC-13.3.0` `MDI/1.4.26-gompi-2024a` `mpi4py/4.0.1-gompi-2024a` `PLUMED/2.9.3-foss-2024a` `ScaFaCoS/1.0.4-foss-2024a` `tbb/2021.13.0-GCCcore-13.3.0` `Voro++/0.4.6-GCCcore-13.3.0` `xxd/9.1.1275-GCCcore-13.3.0` reprod directories under 2025.06/software/linux/aarch64/neoverse_n1/reprod `archspec/0.2.5-GCCcore-13.3.0/20251212_130702UTC` `kim-api/2.4.1-GCC-13.3.0/20251212_130934UTC` `MDI/1.4.26-gompi-2024a/20251212_131023UTC` `mpi4py/4.0.1-gompi-2024a/20251212_132422UTC` `PLUMED/2.9.3-foss-2024a/20251212_131747UTC` `ScaFaCoS/1.0.4-foss-2024a/20251212_133954UTC` `tbb/2021.13.0-GCCcore-13.3.0/20251212_132813UTC` `Voro++/0.4.6-GCCcore-13.3.0/20251212_130719UTC` `xxd/9.1.1275-GCCcore-13.3.0/20251212_131032UTC` other under 2025.06/software/linux/aarch64/neoverse_n1 no other files in tarball
Dec 12 14:02:23 UTC 2025	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:aarch64_neoverse_n1+default P: latency: 1.93 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:aarch64_neoverse_n1+default P: latency: 5.64 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:aarch64_neoverse_n1+default P: latency: 0.29 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:aarch64_neoverse_n1+default P: bandwidth: 16029.27 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-112381.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

laraPPr · 2025-12-12T14:03:32Z

bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen4

eessi-bot-aws · 2025-12-12T14:03:39Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: amd-zen4
Building for: x86_64/amd/zen4
Job dir: /project/def-users/SHARED/jobs/2025.12/pr_1335/112382

date	job status	comment
Dec 12 14:03:38 UTC 2025	submitted	job id `112382` awaits release by job manager
Dec 12 14:04:26 UTC 2025	released	job awaits launch by Slurm scheduler
Dec 12 14:10:29 UTC 2025	running	job `112382` is running
Dec 12 15:00:34 UTC 2025	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-112382.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-zen4-17655515380.tar.zst` size: 45 MiB (48205632 bytes) entries: 1832 modules under 2025.06/software/linux/x86_64/amd/zen4/modules/all `archspec/0.2.5-GCCcore-13.3.0.lua` `kim-api/2.4.1-GCC-13.3.0.lua` `MDI/1.4.26-gompi-2024a.lua` `mpi4py/4.0.1-gompi-2024a.lua` `PLUMED/2.9.3-foss-2024a.lua` `ScaFaCoS/1.0.4-foss-2024a.lua` `tbb/2021.13.0-GCCcore-13.3.0.lua` `Voro++/0.4.6-GCCcore-13.3.0.lua` `xxd/9.1.1275-GCCcore-13.3.0.lua` software under 2025.06/software/linux/x86_64/amd/zen4/software `archspec/0.2.5-GCCcore-13.3.0` `kim-api/2.4.1-GCC-13.3.0` `MDI/1.4.26-gompi-2024a` `mpi4py/4.0.1-gompi-2024a` `PLUMED/2.9.3-foss-2024a` `ScaFaCoS/1.0.4-foss-2024a` `tbb/2021.13.0-GCCcore-13.3.0` `Voro++/0.4.6-GCCcore-13.3.0` `xxd/9.1.1275-GCCcore-13.3.0` reprod directories under 2025.06/software/linux/x86_64/amd/zen4/reprod `archspec/0.2.5-GCCcore-13.3.0/20251212_141126UTC` `kim-api/2.4.1-GCC-13.3.0/20251212_141343UTC` `MDI/1.4.26-gompi-2024a/20251212_141434UTC` `mpi4py/4.0.1-gompi-2024a/20251212_142525UTC` `PLUMED/2.9.3-foss-2024a/20251212_142308UTC` `ScaFaCoS/1.0.4-foss-2024a/20251212_143815UTC` `tbb/2021.13.0-GCCcore-13.3.0/20251212_142831UTC` `Voro++/0.4.6-GCCcore-13.3.0/20251212_141139UTC` `xxd/9.1.1275-GCCcore-13.3.0/20251212_141439UTC` other under 2025.06/software/linux/x86_64/amd/zen4 no other files in tarball
Dec 12 15:00:34 UTC 2025	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_amd_zen4+default P: latency: 1.41 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_amd_zen4+default P: latency: 3.29 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_amd_zen4+default P: latency: 0.17 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_amd_zen4+default P: bandwidth: 14176.12 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-112382.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

laraPPr · 2025-12-12T15:05:45Z

@lorisercole We have tested this up and down but clearly not enough. It failed during the make step with

/cvmfs/software.eessi.io/versions/2025.06/compat/linux/aarch64/usr/bin/ld: /home/larappr/eessi/versions/2025.06/software/linux/aarch64/neoverse_n1/software/ScaFaCoS/1.0.4-foss-2024a/lib64/libfcs_fmm.so.0: undefined reference to `armci_die'

/cvmfs/software.eessi.io/versions/2025.06/compat/linux/aarch64/usr/bin/ld: /home/larappr/eessi/versions/2025.06/software/linux/aarch64/neoverse_n1/software/ScaFaCoS/1.0.4-foss-2024a/lib64/libfcs_fmm.so.0: undefined reference to `atomic_fetch_and_add'

collect2: error: ld returned 1 exit status

lorisercole · 2025-12-15T09:35:28Z

@laraPPr is this only a problem of scafacos on aarch64?

laraPPr · 2025-12-15T09:38:29Z

The error above is on aarch64. And it looks ARM specific. I'll have to check what happened with the zen4 build.

laraPPr · 2025-12-15T09:49:24Z

With zen4 the sanity checks failed

 l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/atm/in.atm"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/atm/in.atm"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/balance/in.balance"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/balance/in.balance"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/colloid/in.colloid"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/colloid/in.colloid"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/crack/in.crack"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/crack/in.crack"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/dipole/in.dipole"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/dipole/in.dipole"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/friction/in.friction"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/friction/in.friction"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/hugoniostat/in.hugoniostat"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/hugoniostat/in.hugoniostat"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/indent/in.indent"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/indent/in.indent"); l.finalize()'': FAILED

  >> running command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/melt/in.melt"); l.finalize()'' ...

  >> result for command 'cd /tmp/eb-_zihpb_x/eb-bxtvzvor/tmpgxc01u41 && mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/LAMMPS/22Jul2025-foss-2024a-kokkos/examples/melt/in.melt"); l.finalize()'': FAILED

laraPPr · 2025-12-15T09:51:03Z

[x86-64-amd-zen4-node1:192127:0:192127] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x10)

==== backtrace (tid: 192127) ====

 0  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/UCX/1.16.0-GCCcore-13.3.0/lib64/libucs.so.0(ucs_handle_error+0x2b4) [0x153af4a23ba4]

 1  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/UCX/1.16.0-GCCcore-13.3.0/lib64/libucs.so.0(+0x2bd79) [0x153af4a23d79]

 2  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/UCX/1.16.0-GCCcore-13.3.0/lib64/libucs.so.0(+0x2bf2a) [0x153af4a23f2a]

 3  /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libc.so.6(+0x3be10) [0x153b03ad2e10]

 4  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(Py_FinalizeEx+0x41) [0x153b03fe5551]

 5  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/libffi/3.4.5-GCCcore-13.3.0/lib64/libffi.so.8(+0x709a) [0x153b0341509a]

 6  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/libffi/3.4.5-GCCcore-13.3.0/lib64/libffi.so.8(+0x65f5) [0x153b034145f5]

 7  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/libffi/3.4.5-GCCcore-13.3.0/lib64/libffi.so.8(ffi_call+0xbd) [0x153b03414c7d]

 8  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/lib-dynload/_ctypes.cpython-312-x86_64-linux-gnu.so(+0x987d) [0x153b0342387d]

 9  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/lib-dynload/_ctypes.cpython-312-x86_64-linux-gnu.so(+0x9188) [0x153b03423188]

10  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(_PyObject_MakeTpCall+0x6b) [0x153b03f4593b]

11  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(+0x10e9f2) [0x153b03e6c9f2]

12  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(PyEval_EvalCode+0xa9) [0x153b03fc47a9]

13  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(+0x28a777) [0x153b03fe8777]

14  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(+0x2854ab) [0x153b03fe34ab]

15  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(PyRun_StringFlags+0x69) [0x153b03fd6479]

16  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(PyRun_SimpleStringFlags+0x3c) [0x153b03fd62dc]

17  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(Py_RunMain+0x444) [0x153b03ff3d74]

18  /cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen4/software/Python/3.12.3-GCCcore-13.3.0/lib/libpython3.12.so.1.0(Py_BytesMain+0x27) [0x153b03fadae7]

19  /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libc.so.6(+0x26c3a) [0x153b03abdc3a]

20  /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libc.so.6(__libc_start_main+0x85) [0x153b03abdcf5]

21  python(_start+0x21) [0x401061]

=================================

--------------------------------------------------------------------------

prterun noticed that process rank 0 with PID 192127 on node x86-64-amd-zen4-node1 exited on

signal 11 (Segmentation fault).

--------------------------------------------------------------------------

)

ocaisa · 2025-12-15T09:51:41Z

IIRC ScaFaCos fails to build on Arm, I thought at some point we made it a x86-only dependency. I tracked down #384 but can't see anything in the hooks any more.

lorisercole · 2025-12-15T09:55:27Z

IIRC ScaFaCos fails to build on Arm, I thought at some point we made it a x86-only dependency. I tracked down #384 but can't see anything in the hooks any more.

We've removed the x86-only condition in the latest PR, see this comment:
easybuilders/easybuild-easyconfigs#23719 (comment)
I could not test it myself though

lorisercole · 2025-12-15T09:58:06Z

@laraPPr for the zen4 builds, is that everything we can see from the log files? It's not clear to me if MPI managed to start LAMMPS and it fails at the end of the run, or if it crashes immediately (in which case it seems to be more an MPI-related issue)

laraPPr · 2025-12-15T09:59:48Z

For zen4 we can't see more but I'm building it interactively to check what goes wrong

laraPPr · 2025-12-15T12:24:12Z

It seems to run because it does not crash immedially when I run the sanity check so I think it is running.

laraPPr · 2025-12-15T16:33:38Z

@lorisercole I just build it by ignorig the sanity check and tested it. It seem to be a problem with the python binding. because running without python the tests run without any problems. when I ran lmp -in in.lj and mpirun -n lmp -in in.lj

When running mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("in.lj"); l.finalize()'. It finished the run and the resluts look ok but it still finishes with the segmentation fault.

lorisercole · 2025-12-15T16:46:48Z

When running mpirun -n 1 python -c 'from lammps import lammps; l=lammps(); l.file("in.lj"); l.finalize()'. It finished the run and the resluts look ok but it still finishes with the segmentation fault.

The segfault is due to the l.finalize() function call.
It is something that I fixed in the latest LAMMPS easyblock PR:
https://github.com/easybuilders/easybuild-easyblocks/blob/bef765e964e70c6bdcad32f53b5ec24b4ebb28ee/easybuild/easyblocks/l/lammps.py#L769-L771

easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.2-2024a.yml

…24a.yml Co-authored-by: Loris Ercole <30901257+lorisercole@users.noreply.github.com>

laraPPr · 2025-12-16T11:22:17Z

@lorisercole Can you check if the last change is still in the easyblock or if the merge sync removed it. Because I took the last commit of the pr.

laraPPr · 2025-12-16T11:22:39Z

bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen4

eessi-bot-aws · 2025-12-16T11:22:46Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: amd-zen4
Building for: x86_64/amd/zen4
Job dir: /project/def-users/SHARED/jobs/2025.12/pr_1335/113483

date	job status	comment
Dec 16 11:22:44 UTC 2025	submitted	job id `113483` awaits release by job manager
Dec 16 11:23:30 UTC 2025	released	job awaits launch by Slurm scheduler
Dec 16 11:29:41 UTC 2025	running	job `113483` is running
Dec 16 11:32:49 UTC 2025	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-113483.out` ✅ no message matching `FATAL:` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no 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-zen4-17658846710.tar.zst` size: 0 MiB (22 bytes) entries: 0 modules under 2025.06/software/linux/x86_64/amd/zen4/modules/all no module files in tarball software under 2025.06/software/linux/x86_64/amd/zen4/software no software packages in tarball reprod directories under 2025.06/software/linux/x86_64/amd/zen4/reprod no reprod directories in tarball other under 2025.06/software/linux/x86_64/amd/zen4 no other files in tarball
Dec 16 11:32:49 UTC 2025	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_amd_zen4+default P: latency: 3.84 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_amd_zen4+default P: latency: 3.22 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_amd_zen4+default P: latency: 0.16 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_amd_zen4+default P: bandwidth: 14520.71 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-113483.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

laraPPr · 2025-12-16T11:36:04Z

easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.2-2024a.yml

+        # See https://github.com/easybuilders/easybuild-easyconfigs/pull/23719
+        from-commit: 379c0f01a29109a3c3db1e1807838f50074af143
+        # See https://github.com/easybuilders/easybuild-easyblocks/pull/3894
+        include-easyblocks-from-commit: 433d723ceb5492ab22bf45566e40296d01db87c2


Was to quick in applying this change. I also cannot find this commit in the pr https://github.com/easybuilders/easybuild-easyblocks/pull/3894/commits

It's the final merge commit
easybuilders/easybuild-easyblocks@433d723

laraPPr · 2025-12-16T12:12:02Z

bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen4

eessi-bot-aws · 2025-12-16T12:12:10Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: amd-zen4
Building for: x86_64/amd/zen4
Job dir: /project/def-users/SHARED/jobs/2025.12/pr_1335/113484

date	job status	comment
Dec 16 12:12:09 UTC 2025	submitted	job id `113484` awaits release by job manager
Dec 16 12:12:44 UTC 2025	released	job awaits launch by Slurm scheduler
Dec 16 12:13:50 UTC 2025	running	job `113484` is running
Dec 16 12:16:58 UTC 2025	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-113484.out` ✅ no message matching `FATAL:` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no 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-zen4-17658873190.tar.zst` size: 0 MiB (22 bytes) entries: 0 modules under 2025.06/software/linux/x86_64/amd/zen4/modules/all no module files in tarball software under 2025.06/software/linux/x86_64/amd/zen4/software no software packages in tarball reprod directories under 2025.06/software/linux/x86_64/amd/zen4/reprod no reprod directories in tarball other under 2025.06/software/linux/x86_64/amd/zen4 no other files in tarball
Dec 16 12:16:58 UTC 2025	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_amd_zen4+default P: latency: 1.42 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_amd_zen4+default P: latency: 3.19 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_amd_zen4+default P: latency: 0.15 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_amd_zen4+default P: bandwidth: 14511.6 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-113484.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

laraPPr · 2025-12-16T12:21:56Z

We'll have to wait for the next EasyBuild release

laraPPr · 2025-12-16T13:28:14Z

@laraPPr is this only a problem of scafacos on aarch64?

Had a little convo with an AI friend and he suggest trying to build with -DLAMMPS_EXTRA_LIBS="-latomic -larmci". I don't think it is a ScaFaCos problem since it build and passed the sanity check. I think I'll test this in dev.eessi.io.

laraPPr · 2025-12-17T09:20:59Z

Ah there is an open issue on this scafacos/scafacos#42

laraPPr · 2025-12-17T09:26:21Z

So two options:

We resolve this problem with ScaFaCos
Go back to removing ScaFaCos as a dependency (Than LAMMPS builds its own ScaFaCos)

laraPPr · 2025-12-17T09:54:12Z

Ah no. the internal ScaFaCos is not build on ARM
ARM:

{EESSI 2023.06} [larappr@aarch64-neoverse-n1-node1 2Aug2023_update2-foss-2023a-kokkos]$ mpirun -n 1 lmp -h | grep SCAFACOS

cascaselake:

{EESSI 2023.06} [vsc00000@nod4004 ]$ mpirun -n 1 lmp -h | grep SCAFACOS
RIGID SCAFACOS SHOCK SMTBQ SPH SPIN SRD TALLY UEF VORONOI VTK YAFF

laraPPr · 2025-12-17T09:58:48Z

Maybe we should add a sanity check that parses general_packages and check lmp -h if all of them are included?

lorisercole · 2025-12-17T12:57:41Z

Ah no. the internal ScaFaCos is not build on ARM ARM:

{EESSI 2023.06} [larappr@aarch64-neoverse-n1-node1 2Aug2023_update2-foss-2023a-kokkos]$ mpirun -n 1 lmp -h | grep SCAFACOS

cascaselake:

{EESSI 2023.06} [vsc00000@nod4004 ]$ mpirun -n 1 lmp -h | grep SCAFACOS
RIGID SCAFACOS SHOCK SMTBQ SPH SPIN SRD TALLY UEF VORONOI VTK YAFF

Of course it's not build on ARM, that old easyconfig (2Aug2023_update2-foss-2023a-kokkos) still had the if ARCH == 'x86_64' conditional:
https://github.com/easybuilders/easybuild-easyconfigs/blob/9d5add8ea92501ba9562cd5b298ed82ea8a1cec7/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb#L67-L72

You should check the easyconfigs that were modified by the #23719 PR:
https://github.com/easybuilders/easybuild-easyconfigs/pull/23719/changes

LAMMPS-29Aug2024-foss-2023b-kokkos.eb
LAMMPS-29Aug2024_update2-foss-2023a-kokkos.eb
LAMMPS-29Aug2024_update2-foss-2023b-kokkos-CUDA-12.4.0.eb
LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb
LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb
LAMMPS-22Jul2025-foss-2024a-kokkos.eb
LAMMPS-22Jul2025-foss-2024a-kokkos-CUDA-12.6.0.eb

Maybe we should add a sanity check that parses general_packages and check lmp -h if all of them are included?

I think that LAMMPS' own tests already check for all the desired packages to be there.

{2025.06}[2024a] LAMMPS v22Jul2025

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laraPPr added the 2025.06-software.eessi.io 2025.06 version of software.eessi.io label Dec 12, 2025

lorisercole suggested changes Dec 16, 2025

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…24a.yml Co-authored-by: Loris Ercole <30901257+lorisercole@users.noreply.github.com>

laraPPr commented Dec 16, 2025

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{2025.06}[2024a] LAMMPS v22Jul2025 #1335

Are you sure you want to change the base?

{2025.06}[2024a] LAMMPS v22Jul2025 #1335

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