conda-forge / sundials-feedstock

A conda-smithy repository for sundials.
BSD 3-Clause "New" or "Revised" License
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Sundials package fails to install libsundials_sunlinsolsuperlumt.4.6.0.dylib as of v6.6.1 #98

Closed darothen closed 10 months ago

darothen commented 10 months ago

Solution to issue cannot be found in the documentation.

Issue

I'm the maintainer of http://github.com/darothen/pyrcel, and we rely on an integration w/ sundials via the Assimulo package to power our simulation. Recently, a user reached out because pyrcel was failing to run when using the standard setup; the model would fail with errors similar to:

Could not find dlopen(/Users/daniel/mambaforge/envs/pyrcel_grz/lib/python3.11/site-packages/assimulo/solvers/sundials.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libsundials_sunlinsolsuperlumt.4.6.0.dylib Referenced from: /Users/daniel/mambaforge/envs/pyrcel_grz/lib/python3.11/site-packages/assimulo/solvers/sundials.cpython-311-darwin.so Reason: tried: '/Users/daniel/mambaforge/envs/pyrcel_grz/lib/python3.11/site-packages/assimulo/solvers/../../../../libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/Users/daniel/mambaforge/envs/pyrcel_grz/lib/python3.11/site-packages/assimulo/solvers/../../../../libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/Users/daniel/mambaforge/envs/pyrcel_grz/bin/../lib/libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/Users/daniel/mambaforge/envs/pyrcel_grz/bin/../lib/libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS@rpath/libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/Users/daniel/mambaforge/envs/pyrcel_grz/lib/python3.11/site-packages/assimulo/solvers/../../../../libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/Users/daniel/mambaforge/envs/pyrcel_grz/lib/python3.11/site-packages/assimulo/solvers/../../../../libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/Users/daniel/mambaforge/envs/pyrcel_grz/bin/../lib/libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/Users/daniel/mambaforge/envs/pyrcel_grz/bin/../lib/libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/usr/local/lib/libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file), '/usr/lib/libsundials_sunlinsolsuperlumt.4.6.0.dylib' (no such file, not in dyld cache)

I was able to reproduce the error - both of us build from osx_arm64 (can check a Linux machine later today). Bumping sundials back down to v6.6.0 fixed things, so it seems like there's just an error in building this one dynamic library with the latest 6.6.1/6.6.2 release.

Installed packages

# packages in environment at /Users/daniel/mambaforge/envs/pyrcel_grz:
#
# Name                    Version                   Build  Channel
appnope                   0.1.3                    pypi_0    pypi
assimulo                  3.4.1           py311h221a87e_4    conda-forge
asttokens                 2.4.1                    pypi_0    pypi
bzip2                     1.0.8                h93a5062_5    conda-forge
ca-certificates           2023.7.22            hf0a4a13_0    conda-forge
decorator                 5.1.1                    pypi_0    pypi
executing                 2.0.1                    pypi_0    pypi
gmp                       6.3.0                h965bd2d_0    conda-forge
ipython                   8.17.2                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
libblas                   3.9.0           19_osxarm64_openblas    conda-forge
libcblas                  3.9.0           19_osxarm64_openblas    conda-forge
libcxx                    16.0.6               h4653b0c_0    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
liblapack                 3.9.0           19_osxarm64_openblas    conda-forge
libopenblas               0.3.24          openmp_hd76b1f2_0    conda-forge
libsqlite                 3.44.0               h091b4b1_0    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
llvm-openmp               17.0.4               hcd81f8e_0    conda-forge
llvmlite                  0.41.1                   pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
metis                     5.1.0             h13dd4ca_1007    conda-forge
mpfr                      4.2.1                h9546428_0    conda-forge
ncurses                   6.4                  h463b476_2    conda-forge
numba                     0.58.1                   pypi_0    pypi
numpy                     1.26.2                   pypi_0    pypi
openssl                   3.1.4                h0d3ecfb_0    conda-forge
packaging                 23.2                     pypi_0    pypi
pandas                    2.1.3                    pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
pexpect                   4.8.0                    pypi_0    pypi
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.40                   pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pygments                  2.16.1                   pypi_0    pypi
pyrcel                    1.3.2                    pypi_0    pypi
python                    3.11.6          h47c9636_0_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.11                    4_cp311    conda-forge
pytz                      2023.3.post1             pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
readline                  8.2                  h92ec313_1    conda-forge
scipy                     1.11.3          py311h93d07a4_1    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
setuptools-scm            8.0.4                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
suitesparse               5.10.1               h7cd81ec_1    conda-forge
sundials                  6.6.0                h81c0fc7_1    conda-forge
tbb                       2021.10.0            h1995070_2    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
traitlets                 5.13.0                   pypi_0    pypi
typing-extensions         4.8.0                    pypi_0    pypi
tzdata                    2023.3                   pypi_0    pypi
wcwidth                   0.2.9                    pypi_0    pypi
wheel                     0.41.3             pyhd8ed1ab_0    conda-forge
xarray                    2023.10.1                pypi_0    pypi
xz                        5.2.6                h57fd34a_0    conda-forge

Environment info

active environment : pyrcel_grz
    active env location : /Users/daniel/mambaforge/envs/pyrcel_grz
            shell level : 2
       user config file : /Users/daniel/.condarc
 populated config files : /Users/daniel/mambaforge/.condarc
                          /Users/daniel/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.15.final.0
       virtual packages : __osx=13.2.1=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/daniel/mambaforge  (writable)
      conda av data dir : /Users/daniel/mambaforge/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/daniel/mambaforge/pkgs
                          /Users/daniel/.conda/pkgs
       envs directories : /Users/daniel/mambaforge/envs
                          /Users/daniel/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.15 Darwin/22.3.0 OSX/13.2.1
                UID:GID : 501:20
             netrc file : /Users/daniel/.netrc
           offline mode : False
jschueller commented 10 months ago

you will probably need to rebuild after the new revision is published