Closed guyer closed 9 months ago
Environment created with previous release is OK
conda create --channel conda-forge --name scotch_lt_7 "scotch<7.0" petsc4py
# packages in environment at /Users/guyer/mambaforge-arm/envs/scotch_lt_7:
#
# Name Version Build Channel
bzip2 1.0.8 h93a5062_5 conda-forge
c-ares 1.23.0 h93a5062_0 conda-forge
ca-certificates 2023.11.17 hf0a4a13_0 conda-forge
fftw 3.3.10 mpi_openmpi_haef8dc3_8 conda-forge
gmp 6.3.0 h965bd2d_0 conda-forge
hdf5 1.14.3 mpi_openmpi_h20f603a_0 conda-forge
hypre 2.28.0 mpi_openmpi_haba3941_0 conda-forge
icu 73.2 hc8870d7_0 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
libaec 1.1.2 h13dd4ca_1 conda-forge
libblas 3.9.0 20_osxarm64_openblas conda-forge
libcblas 3.9.0 20_osxarm64_openblas conda-forge
libcurl 8.5.0 h2d989ff_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h93a5062_2 conda-forge
libexpat 2.5.0 hb7217d7_1 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_1 conda-forge
libgfortran5 13.2.0 hf226fd6_1 conda-forge
libhwloc 2.9.3 default_h4394839_1009 conda-forge
libiconv 1.17 he4db4b2_0 conda-forge
liblapack 3.9.0 20_osxarm64_openblas conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libopenblas 0.3.25 openmp_h6c19121_0 conda-forge
libsqlite 3.44.2 h091b4b1_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libxml2 2.11.6 h0d0cfa8_0 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
llvm-openmp 17.0.6 hcd81f8e_0 conda-forge
metis 5.1.0 h13dd4ca_1007 conda-forge
mpfr 4.2.1 h9546428_0 conda-forge
mpi 1.0 openmpi conda-forge
mumps-include 5.2.1 hce30654_11 conda-forge
mumps-mpi 5.2.1 h51c74a9_11 conda-forge
ncurses 6.4 h463b476_2 conda-forge
numpy 1.26.2 py312h5d55045_0 conda-forge
openmpi 4.1.6 h526c993_101 conda-forge
openssl 3.2.0 h0d3ecfb_1 conda-forge
parmetis 4.0.3 h6eb5794_1005 conda-forge
petsc 3.20.2 real_hcab63ac_100 conda-forge
petsc4py 3.20.1 real_h17b5e51_100 conda-forge
pip 23.3.1 pyhd8ed1ab_0 conda-forge
ptscotch 6.0.9 h1aec651_2 conda-forge
python 3.12.0 h47c9636_0_cpython conda-forge
python_abi 3.12 4_cp312 conda-forge
readline 8.2 h92ec313_1 conda-forge
scalapack 2.2.0 h515df86_1 conda-forge
scotch 6.0.9 h7537618_2 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
suitesparse 5.10.1 h7cd81ec_1 conda-forge
superlu 5.2.2 hc615359_0 conda-forge
superlu_dist 7.2.0 hfdb8677_0 conda-forge
tbb 2021.11.0 h6aa02a4_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
active environment : scotch_lt_7
active env location : /Users/guyer/mambaforge-arm/envs/scotch_lt_7
shell level : 2
user config file : /Users/guyer/.condarc
populated config files : /Users/guyer/mambaforge-arm/.condarc
/Users/guyer/.condarc
conda version : 23.7.4
conda-build version : not installed
python version : 3.10.10.final.0
virtual packages : __archspec=1=arm64
__osx=13.6.2=0
__unix=0=0
base environment : /Users/guyer/mambaforge-arm (writable)
conda av data dir : /Users/guyer/mambaforge-arm/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/osx-arm64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-arm64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /Users/guyer/mambaforge-arm/pkgs
/Users/guyer/.conda/pkgs
envs directories : /Users/guyer/mambaforge-arm/envs
/Users/guyer/.conda/envs
platform : osx-arm64
user-agent : conda/23.7.4 requests/2.31.0 CPython/3.10.10 Darwin/22.6.0 OSX/13.6.2 solver/libmamba conda-libmamba-solver/23.3.0 libmambapy/1.5.1
UID:GID : 17723:36677
netrc file : None
offline mode : False
Let see if conda-forge/petsc4py-feedstock#84 solves the issue.
Indeed, there seem to be issues with macOS, I can see the Symbol not found: _SCOTCH_errorPrint
in the build logs.
Unfortunately, I will not have time to figure out what's going on until end January. You will have to ask other petsc/petsc4py recipe maintainers for help.
For the time being, I'm fine with pinning the previous release. I just wanted to be sure you knew about it.
I believe this is an issue in scotch itself where libscotcherr wasn't linked from libscotch (possibly due to conda-forge -Wl,dead_strip_dylibs
combined with something weird in how libscotch splits its functionality), but it should be fixed by the 7.0.4 migration, which should start today https://github.com/conda-forge/conda-forge-pinning-feedstock/pull/4807
> otool -L ~/conda/envs/scotch702/lib/libscotch.dylib
/Users/minrk/conda/envs/scotch702/lib/libscotch.dylib:
@rpath/libscotch.7.0.2.dylib (compatibility version 0.0.0, current version 7.0.2)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.0.0)
@rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.13)
@rpath/libbz2.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/liblzma.5.dylib (compatibility version 8.0.0, current version 8.6.0)
> otool -L ~/conda/envs/scotch/lib/libscotch.dylib
/Users/minrk/conda/envs/scotch/lib/libscotch.dylib:
@rpath/libscotch.7.0.4.dylib (compatibility version 0.0.0, current version 7.0.4)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.0.0)
@rpath/libscotcherr.dylib (compatibility version 0.0.0, current version 0.0.0) <---- missing from 7.0.2
@rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.13)
@rpath/libbz2.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/liblzma.5.dylib (compatibility version 8.0.0, current version 8.6.0)
7.0.4 builds should fix this when they arrive
7.0.4 build works for me, thanks
Solution to issue cannot be found in the documentation.
Issue
Since merging #176, petsc4py raises a linkage error on macOS (both
osx-64
andosx-arm64
).linux-64
is fine.Environment created with
Installed packages
Environment info