search

NixOS / nixpkgs

Nix Packages collection & NixOS
MIT License
17.45k stars 13.65k forks source link

Build failure: petsc #307298

Closed TomaSajt closed 4 months ago

TomaSajt commented 4 months ago

Steps To Reproduce

Steps to reproduce the behavior:

  1. build petsc

Build log

These are the last few lines of the build logs.

mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -g3 -O0  -I/build/petsc-3.19.4/include -I/build/petsc-3.19.4/arch-linux-c-debug/include     -Wl,-export-dynamic ex19.c  -Wl,-rpath,/build/petsc-3.19.4/arch-linux-c-debug/lib -L/build/petsc-3.19.4/arch-linux-c-debug/lib -Wl,-rpath,/nix/store/vr8njqmvv9z1wkwrqk7jy56x6lb43l31-openmpi-4.1.6/lib -L/nix/store/vr8njqmvv9z1wkwrqk7jy56x6lb43l31-openmpi-4.1.6/lib -Wl,-rpath,/nix/store/kcyymk901cy4p2x2sqhml7nb9zhab5f8-libfabric-1.21.0-dev/lib -L/nix/store/kcyymk901cy4p2x2sqhml7nb9zhab5f8-libfabric-1.21.0-dev/lib -Wl,-rpath,/nix/store/cl9wrjrc75ir36331icq4i7r4998jiwr-pmix-5.0.1/lib -L/nix/store/cl9wrjrc75ir36331icq4i7r4998jiwr-pmix-5.0.1/lib -Wl,-rpath,/nix/store/vwrz2sj2xxb7jnq38mplqs7fq7dk6x66-libnl-3.8.0-dev/lib -L/nix/store/vwrz2sj2xxb7jnq38mplqs7fq7dk6x66-libnl-3.8.0-dev/lib -Wl,-rpath,/nix/store/hlk3hfg1j6j3rbmbsa8f0g3nnxzvbwvf-libpsm2-12.0.1/lib -L/nix/store/hlk3hfg1j6j3rbmbsa8f0g3nnxzvbwvf-libpsm2-12.0.1/lib -Wl,-rpath,/nix/store/cy6dh661j89s69mxlbi604z06arqb474-blas-3/lib -L/nix/store/cy6dh661j89s69mxlbi604z06arqb474-blas-3/lib -Wl,-rpath,/nix/store/ssjp1ryvwndqf4wa8530zfxpprrp2g5i-lapack-3/lib -L/nix/store/ssjp1ryvwndqf4wa8530zfxpprrp2g5i-lapack-3/lib -Wl,-rpath,/nix/store/35pq4hr29c3sl79lgfwgsvd9nwzyp4am-glibc-2.39-5/lib -L/nix/store/35pq4hr29c3sl79lgfwgsvd9nwzyp4am-glibc-2.39-5/lib -Wl,-rpath,/nix/store/nn152mgpdfcw92b3b03g9kmnlpd9jris-gcc-13.2.0/lib/gcc/x86_64-unknown-linux-gnu/13.2.0 -L/nix/store/nn152mgpdfcw92b3b03g9kmnlpd9jris-gcc-13.2.0/lib/gcc/x86_64-unknown-linux-gnu/13.2.0 -Wl,-rpath,/nix/store/f1ii69v7p27z1r5zybmlbld3bdzm6a5f-gcc-13.2.0-lib/lib -L/nix/store/f1ii69v7p27z1r5zybmlbld3bdzm6a5f-gcc-13.2.0-lib/lib -Wl,-rpath,/nix/store/k8njqq4rc3knarvp24waf7isbvxrpi7d-gfortran-13.2.0-lib/lib -L/nix/store/k8njqq4rc3knarvp24waf7isbvxrpi7d-gfortran-13.2.0-lib/lib -Wl,-rpath,/nix/store/s8i61f6l2xr63kc1wfba5065wwdkayxa-gfortran-wrapper-13.2.0/bin -L/nix/store/s8i61f6l2xr63kc1wfba5065wwdkayxa-gfortran-wrapper-13.2.0/bin -Wl,-rpath,/nix/store/bkhd01jbwzxqjn2qgi95vxhncfrivgga-gfortran-13.2.0/lib/gcc/x86_64-unknown-linux-gnu/13.2.0 -L/nix/store/bkhd01jbwzxqjn2qgi95vxhncfrivgga-gfortran-13.2.0/lib/gcc/x86_64-unknown-linux-gnu/13.2.0 -Wl,-rpath,/nix/store/bkhd01jbwzxqjn2qgi95vxhncfrivgga-gfortran-13.2.0/lib64 -L/nix/store/bkhd01jbwzxqjn2qgi95vxhncfrivgga-gfortran-13.2.0/lib64 -Wl,-rpath,/nix/store/bkhd01jbwzxqjn2qgi95vxhncfrivgga-gfortran-13.2.0/lib -L/nix/store/bkhd01jbwzxqjn2qgi95vxhncfrivgga-gfortran-13.2.0/lib -Wl,-rpath,/nix/store/xyghgs8nf62l24z78qn3273yv82gm0si-petsc-3.19.4/lib -lpetsc -llapack -lblas -lm -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath -o ex19
In file included from /nix/store/ij144ma6vs8acil8r9hgr8xkb1dp9azg-glibc-2.39-5-dev/include/bits/libc-header-start.h:33,
                 from /nix/store/ij144ma6vs8acil8r9hgr8xkb1dp9azg-glibc-2.39-5-dev/include/limits.h:26,
                 from /nix/store/nn152mgpdfcw92b3b03g9kmnlpd9jris-gcc-13.2.0/lib/gcc/x86_64-unknown-linux-gnu/13.2.0/include/limits.h:205,
                 from /nix/store/nn152mgpdfcw92b3b03g9kmnlpd9jris-gcc-13.2.0/lib/gcc/x86_64-unknown-linux-gnu/13.2.0/include/syslimits.h:7,
                 from /nix/store/nn152mgpdfcw92b3b03g9kmnlpd9jris-gcc-13.2.0/lib/gcc/x86_64-unknown-linux-gnu/13.2.0/include/limits.h:34,
                 from /build/petsc-3.19.4/include/petscsystypes.h:16,
                 from /build/petsc-3.19.4/include/petscsys.h:44,
                 from /build/petsc-3.19.4/include/petscvec.h:9,
                 from /build/petsc-3.19.4/include/petscmat.h:7,
                 from /build/petsc-3.19.4/include/petscpc.h:7,
                 from /build/petsc-3.19.4/include/petscksp.h:7,
                 from /build/petsc-3.19.4/include/petscsnes.h:7,
                 from ex19.c:68:
/nix/store/ij144ma6vs8acil8r9hgr8xkb1dp9azg-glibc-2.39-5-dev/include/features.h:414:4: warning: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  414 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
See https://petsc.org/release/faq/
[1714248497.209873] [localhost:12150:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
[1714248497.212895] [localhost:12150:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
Number of SNES iterations = 2
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
See https://petsc.org/release/faq/
[1714248498.625277] [localhost:12179:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
[1714248498.625969] [localhost:12180:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
[1714248498.628325] [localhost:12180:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
[1714248498.628301] [localhost:12179:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
Number of SNES iterations = 2
Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process
See https://petsc.org/release/faq/
[1714248502.674702] [localhost:12286:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
[1714248502.676990] [localhost:12286:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
Number of SNES iterations =     3
Completed test examples
Error while running make check
make[1]: *** [makefile:123: check] Error 1
make: *** [GNUmakefile:17: check] Error 2

Additional context

Bisecting shows that the build started to fail after an update to ucx (https://github.com/NixOS/nixpkgs/pull/306020)

Looks like something related to tcp_iface.c

Notify maintainers

@cburstedde (listed in meta.maintainers) @twesterhout (last update to the package)

Metadata

Please run nix-shell -p nix-info --run "nix-info -m" and paste the result.

 - system: `"x86_64-linux"`
 - host os: `Linux 6.6.26, NixOS, 24.05 (Uakari), 24.05.20240412.cfd6b5f`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.18.2`
 - channels(root): `""`
 - nixpkgs: `/nix/store/yy5l09gfsagkv8rswblknmsjc2gyr20d-source`

Add a :+1: reaction to issues you find important.

TomaSajt commented 4 months ago

Looks like I managed to solve it myself, sorry for the pings.