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conda-forge / gmsh-feedstock

A conda-smithy repository for gmsh.
BSD 3-Clause "New" or "Revised" License
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Issue with imath #71

Closed sblauth closed 1 year ago

sblauth commented 1 year ago

Solution to issue cannot be found in the documentation.

Issue

Today, I started having issues with the conda installation of Gmsh, which is used in my CI runs. I believe that this issue is related to the release of imath 3.1.7, which also occurred today, whereas the old runs with imath 3.1.6 had no problems.

The error I get is the following one:

gmsh: error while loading shared libraries: libImath.so.29: cannot open shared object file: No such file or directory

For reference, here is a failing CI run: https://github.com/sblauth/cashocs/actions/runs/4351521455/jobs/7603265998 and here is a successful CI run: https://github.com/sblauth/cashocs/actions/runs/4348563734/jobs/7597243927

Note, that the conda list and conda info commands are taken from the CI output...

Installed packages

List of packages in environment: "/home/runner/micromamba-root/envs/test"

    Name                       Version       Build                    Channel    
  ─────────────────────────────────────────────────────────────────────────────────
    _libgcc_mutex              0.1           conda_forge              conda-forge
    _openmp_mutex              4.5           2_gnu                    conda-forge
    aiohttp                    3.8.4         py310h1fa729e_0          conda-forge
    aiosignal                  1.3.1         pyhd8ed1ab_0             conda-forge
    alsa-lib                   1.2.8         h166bdaf_0               conda-forge
    aom                        3.5.0         h27087fc_0               conda-forge
    async-timeout              4.0.2         pyhd8ed1ab_0             conda-forge
    attr                       2.5.1         h166bdaf_1               conda-forge
    attrs                      22.2.0        pyh71513ae_0             conda-forge
    binutils_impl_linux-64     2.39          he00db2b_1               conda-forge
    binutils_linux-64          2.39          h5fc0e48_11              conda-forge
    boost-cpp                  1.78.0        h75c5d50_1               conda-forge
    bzip2                      1.0.8         h7f98852_4               conda-forge
    c-ares                     1.18.1        h7f98852_0               conda-forge
    ca-certificates            2022.12.7     ha878542_0               conda-forge
    cached-property            1.5.2         hd8ed1ab_1               conda-forge
    cached_property            1.5.2         pyha770c72_1             conda-forge
    cairo                      1.16.0        ha61ee94_1014            conda-forge
    cftime                     1.6.2         py310hde88566_1          conda-forge
    charset-normalizer         2.1.1         pyhd8ed1ab_0             conda-forge
    cmake                      3.25.2        h077f3f9_0               conda-forge
    colorama                   0.4.6         pyhd8ed1ab_0             conda-forge
    curl                       7.88.1        hdc1c0ab_0               conda-forge
    dbus                       1.13.6        h5008d03_3               conda-forge
    double-conversion          3.2.0         h27087fc_1               conda-forge
    eigen                      3.4.0         h4bd325d_0               conda-forge
    exceptiongroup             1.1.0         pyhd8ed1ab_0             conda-forge
    expat                      2.5.0         h27087fc_0               conda-forge
    fenics                     2019.1.0      py310hff52083_34         conda-forge
    fenics-dijitso             2019.1.0      py310hff52083_34         conda-forge
    fenics-dolfin              2019.1.0      py310h17b16a0_34         conda-forge
    fenics-ffc                 2019.1.0      py310hff52083_34         conda-forge
    fenics-fiat                2019.1.0      py310hff52083_34         conda-forge
    fenics-libdolfin           2019.1.0      h0f808bc_34              conda-forge
    fenics-ufl                 2019.1.0      py310hff52083_34         conda-forge
    ffmpeg                     5.1.2         gpl_h8dda1f0_106         conda-forge
    fftw                       3.3.10        mpi_mpich_h3e343da_6     conda-forge
    fltk                       1.3.8         h83e168f_0               conda-forge
    font-ttf-dejavu-sans-mono  2.37          hab24e00_0               conda-forge
    font-ttf-inconsolata       3.000         h77eed37_0               conda-forge
    font-ttf-source-code-pro   2.038         h77eed37_0               conda-forge
    font-ttf-ubuntu            0.83          hab24e00_0               conda-forge
    fontconfig                 2.14.2        h14ed4e7_0               conda-forge
    fonts-conda-ecosystem      1             0                        conda-forge
    fonts-conda-forge          1             0                        conda-forge
    freeimage                  3.18.0        hca5c823_12              conda-forge
    freetype                   2.12.1        hca18f0e_1               conda-forge
    frozenlist                 1.3.3         py310h5764c6d_0          conda-forge
    gcc_impl_linux-64          10.4.0        h5231bdf_19              conda-forge
    gcc_linux-64               10.4.0        h9215b83_11              conda-forge
    gettext                    0.21.1        h27087fc_0               conda-forge
    gl2ps                      1.4.2         h0708190_0               conda-forge
    glew                       2.1.0         h9c3ff4c_2               conda-forge
    glib                       2.74.1        h6239696_1               conda-forge
    glib-tools                 2.74.1        h6239696_1               conda-forge
    gmp                        6.2.1         h58526e2_0               conda-forge
    gmpy2                      2.1.2         py310h3ec546c_1          conda-forge
    gmsh                       4.11.0        h5c738d0_1               conda-forge
    gnutls                     3.7.8         hf3e180e_0               conda-forge
    graphite2                  1.3.13        h58526e2_1001            conda-forge
    gst-plugins-base           1.22.0        h4243ec0_2               conda-forge
    gstreamer                  1.22.0        h25f0c4b_2               conda-forge
    gstreamer-orc              0.4.33        h166bdaf_0               conda-forge
    gxx_impl_linux-64          10.4.0        h5231bdf_19              conda-forge
    gxx_linux-64               10.4.0        h6e491c6_11              conda-forge
    h5py                       3.8.0         nompi_py310h0311031_100  conda-forge
    harfbuzz                   6.0.0         h8e241bc_0               conda-forge
    hdf4                       4.2.15        h9772cbc_5               conda-forge
    hdf5                       1.12.2        mpi_mpich_h5d83325_1     conda-forge
    hypre                      2.25.0        mpi_mpich_hed3a557_0     conda-forge
    icu                        70.1          h27087fc_0               conda-forge
    idna                       3.4           pyhd8ed1ab_0             conda-forge
    imath                      3.1.7         h3eb15da_0               conda-forge
    importlib-metadata         6.0.0         pyha770c72_0             conda-forge
    importlib_metadata         6.0.0         hd8ed1ab_0               conda-forge
    iniconfig                  2.0.0         pyhd8ed1ab_0             conda-forge
    jack                       1.9.22        h11f4161_0               conda-forge
    jpeg                       9e            h0b41bf4_3               conda-forge
    jsoncpp                    1.9.5         h4bd325d_1               conda-forge
    jxrlib                     1.1           h7f98852_2               conda-forge
    kernel-headers_linux-64    2.6.32        he073ed8_15              conda-forge
    keyutils                   1.6.1         h166bdaf_0               conda-forge
    krb5                       1.20.1        h81ceb04_0               conda-forge
    lame                       3.100         h166bdaf_1003            conda-forge
    lcms2                      2.14          hfd0df8a_1               conda-forge
    ld_impl_linux-64           2.39          hcc3a1bd_1               conda-forge
    lerc                       4.0.0         h27087fc_0               conda-forge
    libaec                     1.0.6         hcb278e6_1               conda-forge
    libblas                    3.9.0         16_linux64_openblas      conda-forge
    libcap                     2.66          ha37c62d_0               conda-forge
    libcblas                   3.9.0         16_linux64_openblas      conda-forge
    libclang                   15.0.7        default_had23c3d_1       conda-forge
    libclang13                 15.0.7        default_h3e3d535_1       conda-forge
    libcups                    2.3.3         h36d4200_3               conda-forge
    libcurl                    7.88.1        hdc1c0ab_0               conda-forge
    libdb                      6.2.32        h9c3ff4c_0               conda-forge
    libdeflate                 1.17          h0b41bf4_0               conda-forge
    libdrm                     2.4.114       h166bdaf_0               conda-forge
    libedit                    3.1.20191231  he28a2e2_2               conda-forge
    libev                      4.33          h516909a_1               conda-forge
    libevent                   2.1.10        h28343ad_4               conda-forge
    libffi                     3.4.2         h7f98852_5               conda-forge
    libflac                    1.4.2         h27087fc_0               conda-forge
    libgcc-devel_linux-64      10.4.0        hd38fd1e_19              conda-forge
    libgcc-ng                  12.2.0        h65d4601_19              conda-forge
    libgcrypt                  1.10.1        h166bdaf_0               conda-forge
    libgfortran-ng             12.2.0        h69a702a_19              conda-forge
    libgfortran5               12.2.0        h337968e_19              conda-forge
    libglib                    2.74.1        h606061b_1               conda-forge
    libglu                     9.0.0         he1b5a44_1001            conda-forge
    libgomp                    12.2.0        h65d4601_19              conda-forge
    libgpg-error               1.46          h620e276_0               conda-forge
    libhwloc                   2.9.0         hd6dc26d_0               conda-forge
    libiconv                   1.17          h166bdaf_0               conda-forge
    libidn2                    2.3.4         h166bdaf_0               conda-forge
    liblapack                  3.9.0         16_linux64_openblas      conda-forge
    libllvm15                  15.0.7        hadd5161_0               conda-forge
    libnetcdf                  4.9.1         mpi_mpich_hf10a581_1     conda-forge
    libnghttp2                 1.52.0        h61bc06f_0               conda-forge
    libnsl                     2.0.0         h7f98852_0               conda-forge
    libogg                     1.3.4         h7f98852_1               conda-forge
    libopenblas                0.3.21        pthreads_h78a6416_3      conda-forge
    libopus                    1.3.1         h7f98852_1               conda-forge
    libpciaccess               0.17          h166bdaf_0               conda-forge
    libpng                     1.6.39        h753d276_0               conda-forge
    libpq                      15.2          hb675445_0               conda-forge
    libraw                     0.21.1        h89bc310_0               conda-forge
    libsanitizer               10.4.0        h5246dfb_19              conda-forge
    libsndfile                 1.2.0         hb75c966_0               conda-forge
    libsqlite                  3.40.0        h753d276_0               conda-forge
    libssh2                    1.10.0        hf14f497_3               conda-forge
    libstdcxx-devel_linux-64   10.4.0        hd38fd1e_19              conda-forge
    libstdcxx-ng               12.2.0        h46fd767_19              conda-forge
    libsystemd0                252           h2a991cd_0               conda-forge
    libtasn1                   4.19.0        h166bdaf_0               conda-forge
    libtheora                  1.1.1         h7f98852_1005            conda-forge
    libtiff                    4.5.0         h6adf6a1_2               conda-forge
    libtool                    2.4.7         h27087fc_0               conda-forge
    libudev1                   253           h0b41bf4_0               conda-forge
    libunistring               0.9.10        h7f98852_0               conda-forge
    libuuid                    2.32.1        h7f98852_1000            conda-forge
    libuv                      1.44.2        h166bdaf_0               conda-forge
    libva                      2.17.0        h0b41bf4_0               conda-forge
    libvorbis                  1.3.7         h9c3ff4c_0               conda-forge
    libvpx                     1.11.0        h9c3ff4c_3               conda-forge
    libwebp-base               1.2.4         h166bdaf_0               conda-forge
    libxcb                     1.13          h7f98852_1004            conda-forge
    libxkbcommon               1.5.0         h79f4944_0               conda-forge
    libxml2                    2.10.3        h7463322_0               conda-forge
    libzip                     1.9.2         hc929e4a_1               conda-forge
    libzlib                    1.2.13        h166bdaf_4               conda-forge
    loguru                     0.6.0         py310hff52083_2          conda-forge
    lz4-c                      1.9.4         hcb278e6_0               conda-forge
    markdown-it-py             2.2.0         pyhd8ed1ab_0             conda-forge
    mdurl                      0.1.0         pyhd8ed1ab_0             conda-forge
    meshio                     5.3.4         pyhd8ed1ab_0             conda-forge
    metis                      5.1.0         h58526e2_1006            conda-forge
    mpc                        1.3.1         hfe3b2da_0               conda-forge
    mpfr                       4.1.0         h9202a9a_1               conda-forge
    mpg123                     1.31.2        hcb278e6_0               conda-forge
    mpi                        1.0           mpich                    conda-forge
    mpi4py                     3.1.4         py310h37cc914_0          conda-forge
    mpich                      4.0.3         h846660c_100             conda-forge
    mpmath                     1.2.1         pyhd8ed1ab_0             conda-forge
    multidict                  6.0.4         py310h1fa729e_0          conda-forge
    mumps-include              5.2.1         ha770c72_11              conda-forge
    mumps-mpi                  5.2.1         h7ee95aa_11              conda-forge
    mysql-common               8.0.32        ha901b37_0               conda-forge
    mysql-libs                 8.0.32        hd7da12d_0               conda-forge
    ncurses                    6.3           h27087fc_1               conda-forge
    netcdf4                    1.6.3         nompi_py310h0feb132_100  conda-forge
    nettle                     3.8.1         hc379101_1               conda-forge
    nlohmann_json              3.11.2        h27087fc_0               conda-forge
    nspr                       4.35          h27087fc_0               conda-forge
    nss                        3.88          he45b914_0               conda-forge
    numpy                      1.24.2        py310h8deb116_0          conda-forge
    occt                       7.7.0         h6cf717c_2               conda-forge
    openexr                    3.1.5         he0ac6c6_1               conda-forge
    openh264                   2.3.1         hcb278e6_2               conda-forge
    openjpeg                   2.5.0         hfec8fc6_2               conda-forge
    openssl                    3.0.8         h0b41bf4_0               conda-forge
    p11-kit                    0.24.1        hc5aa10d_0               conda-forge
    packaging                  23.0          pyhd8ed1ab_0             conda-forge
    parmetis                   4.0.3         h2a9763c_1005            conda-forge
    pcre2                      10.40         hc3806b6_0               conda-forge
    petsc                      3.17.4        real_h15390b8_101        conda-forge
    petsc4py                   3.17.4        real_hce8fbc3_101        conda-forge
    pip                        23.0.1        pyhd8ed1ab_0             conda-forge
    pixman                     0.40.0        h36c2ea0_0               conda-forge
    pkg-config                 0.29.2        h36c2ea0_1008            conda-forge
    pkgconfig                  1.5.5         pyhd8ed1ab_4             conda-forge
    pluggy                     1.0.0         pyhd8ed1ab_5             conda-forge
    proj                       9.1.1         h8ffa02c_2               conda-forge
    pthread-stubs              0.4           h36c2ea0_1001            conda-forge
    ptscotch                   6.0.9         hb499603_2               conda-forge
    pugixml                    1.11.4        h9c3ff4c_0               conda-forge
    pulseaudio                 16.1          ha8d29e2_1               conda-forge
    pybind11                   2.10.1        py310hbf28c38_0          conda-forge
    pybind11-global            2.10.1        py310hbf28c38_0          conda-forge
    pygments                   2.14.0        pyhd8ed1ab_0             conda-forge
    pytest                     7.2.2         pyhd8ed1ab_0             conda-forge
    python                     3.10.9        he550d4f_0_cpython       conda-forge
    python_abi                 3.10          3_cp310                  conda-forge
    qt-main                    5.15.8        h5d23da1_6               conda-forge
    rapidjson                  1.1.0         he1b5a44_1002            conda-forge
    readline                   8.1.2         h0f457ee_0               conda-forge
    rhash                      1.4.3         h166bdaf_0               conda-forge
    rich                       13.3.2        pyhd8ed1ab_0             conda-forge
    scalapack                  2.2.0         hd931219_1               conda-forge
    scotch                     6.0.9         hb2e6521_2               conda-forge
    setuptools                 67.5.1        pyhd8ed1ab_0             conda-forge
    six                        1.16.0        pyh6c4a22f_0             conda-forge
    slepc                      3.17.2        real_hb19a63e_100        conda-forge
    slepc4py                   3.17.2        real_h45d0737_101        conda-forge
    sqlite                     3.40.0        h4ff8645_0               conda-forge
    suitesparse                5.10.1        h9e50725_1               conda-forge
    superlu                    5.2.2         h00795ac_0               conda-forge
    superlu_dist               7.2.0         h25dcc4a_0               conda-forge
    svt-av1                    1.4.1         hcb278e6_0               conda-forge
    sympy                      1.11.1        py310hff52083_2          conda-forge
    sysroot_linux-64           2.12          he073ed8_15              conda-forge
    tbb                        2021.8.0      hf52228f_0               conda-forge
    tbb-devel                  2021.8.0      hf52228f_0               conda-forge
    tk                         8.6.12        h27826a3_0               conda-forge
    tomli                      2.0.1         pyhd8ed1ab_0             conda-forge
    typing-extensions          4.4.0         hd8ed1ab_0               conda-forge
    typing_extensions          4.4.0         pyha770c72_0             conda-forge
    tzdata                     2022g         h191b570_0               conda-forge
    utfcpp                     3.2.3         ha770c72_0               conda-forge
    vtk                        9.2.5         qt_py310h8908f42_203     conda-forge
    wheel                      0.38.4        pyhd8ed1ab_0             conda-forge
    wslink                     1.10.1        pyhd8ed1ab_0             conda-forge
    x264                       1!164.3095    h166bdaf_2               conda-forge
    x265                       3.5           h924138e_3               conda-forge
    xcb-util                   0.4.0         h516909a_0               conda-forge
    xcb-util-image             0.4.0         h166bdaf_0               conda-forge
    xcb-util-keysyms           0.4.0         h516909a_0               conda-forge
    xcb-util-renderutil        0.3.9         h166bdaf_0               conda-forge
    xcb-util-wm                0.4.1         h516909a_0               conda-forge
    xorg-fixesproto            5.0           h7f98852_1002            conda-forge
    xorg-kbproto               1.0.7         h7f98852_1002            conda-forge
    xorg-libice                1.0.10        h7f98852_0               conda-forge
    xorg-libsm                 1.2.3         hd9c2040_1000            conda-forge
    xorg-libx11                1.8.4         h0b41bf4_0               conda-forge
    xorg-libxau                1.0.9         h7f98852_0               conda-forge
    xorg-libxdmcp              1.1.3         h7f98852_0               conda-forge
    xorg-libxext               1.3.4         h0b41bf4_2               conda-forge
    xorg-libxfixes             5.0.3         h7f98852_1004            conda-forge
    xorg-libxmu                1.1.3         h7f98852_0               conda-forge
    xorg-libxrender            0.9.10        h7f98852_1003            conda-forge
    xorg-libxt                 1.2.1         h7f98852_2               conda-forge
    xorg-renderproto           0.11.1        h7f98852_1002            conda-forge
    xorg-xextproto             7.3.0         h0b41bf4_1003            conda-forge
    xorg-xproto                7.0.31        h7f98852_1007            conda-forge
    xz                         5.2.6         h166bdaf_0               conda-forge
    yaml                       0.2.5         h7f98852_2               conda-forge
    yarl                       1.8.2         py310h5764c6d_0          conda-forge
    zipp                       3.15.0        pyhd8ed1ab_0             conda-forge
    zlib                       1.2.13        h166bdaf_4               conda-forge
    zstd                       1.5.2         h3eb15da_6               conda-forge

Environment info

environment : test (active)
             env location : /home/runner/micromamba-root/envs/test
        user config files : /home/runner/.mambarc
   populated config files : /home/runner/.condarc
         libmamba version : 1.3.1
       micromamba version : 1.3.1
             curl version : libcurl/7.87.0 OpenSSL/3.0.8 zlib/1.2.13 libssh2/1.10.0 nghttp2/1.47.0
       libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
         virtual packages : __unix=0=0
                            __linux=5.15.0=0
                            __glibc=2.35=0
                            __archspec=1=x86_64
                 channels : https://conda.anaconda.org/conda-forge/linux-64
                            https://conda.anaconda.org/conda-forge/noarch
                            https://repo.anaconda.com/pkgs/main/linux-64
                            https://repo.anaconda.com/pkgs/main/noarch
                            https://repo.anaconda.com/pkgs/r/linux-64
                            https://repo.anaconda.com/pkgs/r/noarch
         base environment : /home/runner/micromamba-root
                 platform : linux-64
sblauth commented 1 year ago

The behavior seems to be fixed (see the above references to this issue)