search

conda-forge / gmsh-feedstock

A conda-smithy repository for gmsh.
BSD 3-Clause "New" or "Revised" License
3 stars 13 forks source link

gmsh 4.11.1: symbol lookup error #73

Open inducer opened 1 year ago

inducer commented 1 year ago

Solution to issue cannot be found in the documentation.

Issue

After installing gmsh, I get

gmsh: symbol lookup error: /home/andreas/pack/mambaforge/envs/ceesd/bin/../lib/libgmsh.so.4.11: undefined symbol: _ZNK20XCAFDoc_MaterialTool11GetMaterialERK9TDF_LabelRN11opencascade6handleI24TCollection_HAsciiStringEES7_RdS7_S7_

Here's a CI log that shows the issue: https://gitlab.tiker.net/inducer/boxtree/-/jobs/540925#L849

Maybe gmsh -version could be run as a test to check the package?

Installed packages

gmsh                      4.11.1               h5c738d0_0    conda-forge

Full list:
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiohttp                   3.8.4           py311h2582759_0    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
aom                       3.5.0                h27087fc_0    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    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
cantera                   2.6.0           py311ha1fc806_5    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
curl                      7.88.1               hdc1c0ab_1    conda-forge
cython                    0.29.33         py311hcafe171_0    conda-forge
double-conversion         3.2.0                h27087fc_1    conda-forge
eigen                     3.4.0                h4bd325d_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
ffmpeg                    5.1.2           gpl_h8dda1f0_106    conda-forge
fltk                      1.3.8                h83e168f_0    conda-forge
fmt                       9.1.0                h924138e_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               he1b5a44_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
frozenlist                1.3.3           py311hd4cff14_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gl2ps                     1.4.2                h0708190_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmsh                      4.11.1               h5c738d0_0    conda-forge
gnutls                    3.7.8                hf3e180e_0    conda-forge
h5py                      3.8.0           nompi_py311h1db17ec_100    conda-forge
hdf4                      4.2.15               h9772cbc_5    conda-forge
hdf5                      1.12.2          nompi_h4df4325_101    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
intel-cmplr-lib-rt        2023.0.0         h3eb15da_25371    conda-forge
intel-cmplr-lic-rt        2023.0.0         ha770c72_25371    conda-forge
intel-opencl-rt           2023.0.0         h68971e6_25371    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
jsoncpp                   1.9.5                h4bd325d_1    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
ld_impl_linux-64          2.40                 h41732ed_0    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
libcantera                2.6.0                h587f4e0_5    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libclang-cpp12            12.0.1          default_ha53f305_4    conda-forge
libclang-cpp14            14.0.6          default_h2e3cab8_0    conda-forge
libcurl                   7.88.1               hdc1c0ab_1    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
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   12.2.0              h65d4601_19    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
libllvm12                 12.0.1               hf817b99_2    conda-forge
libllvm14                 14.0.6               he0ac6c6_1    conda-forge
libnetcdf                 4.9.1           nompi_h34a3ff0_101    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
libsqlite                 3.40.0               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    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
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libva                     2.18.0               h0b41bf4_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libvpx                    1.11.0               h9c3ff4c_3    conda-forge
libwebp-base              1.3.0                h0b41bf4_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.10.3               hfdac1af_6    conda-forge
libzip                    1.9.2                hc929e4a_1    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
loguru                    0.6.0           py311h38be061_2    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mpfr                      4.2.0                hb012696_0    conda-forge
multidict                 6.0.4           py311h2582759_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nettle                    3.8.1                hc379101_1    conda-forge
nlohmann_json             3.11.2               h27087fc_0    conda-forge
numpy                     1.24.2          py311h8e6699e_0    conda-forge
occt                      7.7.1                h6cf717c_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
openh264                  2.3.1                hcb278e6_2    conda-forge
openssl                   3.1.0                h0b41bf4_0    conda-forge
p11-kit                   0.24.1               hc5aa10d_0    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pocl                      3.1                  h311816e_0    conda-forge
proj                      9.1.1                h8ffa02c_2    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pugixml                   1.11.4               h9c3ff4c_0    conda-forge
python                    3.11.2          h2755cc3_0_cpython    conda-forge
python_abi                3.11                    3_cp311    conda-forge
rapidjson                 1.1.0             he1b5a44_1002    conda-forge
readline                  8.2                  h8228510_1    conda-forge
ruamel_yaml               0.15.80         py311hd4cff14_1008    conda-forge
setuptools                67.6.1             pyhd8ed1ab_0    conda-forge
sqlite                    3.40.0               h4ff8645_0    conda-forge
suitesparse               5.10.1               h9e50725_1    conda-forge
sundials                  5.7.0                h558c624_0    conda-forge
svt-av1                   1.4.1                hcb278e6_0    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
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
utfcpp                    3.2.3                ha770c72_0    conda-forge
vtk                       9.2.5           egl_py311h7054ab3_3    conda-forge
wheel                     0.40.0             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
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
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
yarl                      1.8.2           py311hd4cff14_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Environment info

active environment : ceesd
    active env location : /home/andreas/pack/mambaforge/envs/ceesd
            shell level : 2
       user config file : /home/andreas/.condarc
 populated config files : /home/andreas/pack/mambaforge/.condarc
                          /home/andreas/.condarc
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.9.13.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.36=0
                          __linux=6.1.0=0
                          __unix=0=0
       base environment : /home/andreas/pack/mambaforge  (writable)
      conda av data dir : /home/andreas/pack/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : 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
          package cache : /home/andreas/pack/mambaforge/pkgs
                          /home/andreas/.conda/pkgs
       envs directories : /home/andreas/pack/mambaforge/envs
                          /home/andreas/.conda/envs
               platform : linux-64
             user-agent : conda/23.3.1 requests/2.28.2 CPython/3.9.13 Linux/6.1.0-6-amd64 debian/12 glibc/2.36
                UID:GID : 1000:1000
             netrc file : None
           offline mode : Fals
isuruf commented 1 year ago

We need to do a few more things to fix this. See https://github.com/conda-forge/gmsh-feedstock/pull/72#issuecomment-1496384160

matthiasdiener commented 1 year ago

gmsh-4.11.1 * _1 just hit the mirrors and should provide a short-term fix for this issue (ie, by running conda update gmsh). I'll work on the other items mentioned in #72.

Maybe gmsh -version could be run as a test to check the package?

This is already done. The issue was that an occt update from 7.7.0 to 7.7.1 broke ABI compatibility, and the occt feedstock itself provides no ABI restrictions (see https://github.com/conda-forge/occt-feedstock/issues/97).