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PaNOSC-ViNYL / SimEx

Start-to-end photon experiment simulation platform
https://simex.readthedocs.io/
GNU General Public License v3.0
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Build error: undefined references to libgio-2.0 symbols #243

Open godot11 opened 2 years ago

godot11 commented 2 years ago

I'm compiling SimEx from the develop branch, but I'm hitting a wall. System is Ubuntu 18.04 LTS. I'm using Intel compliers (OpenAPI 4.4.20(1), ifort and icc version 2021.3.0).

After I set up the environment with ./install.sh conda-env and activating it, the build fails with a dozen of undefined refs in libgio-2.0. Specifically:

[ 42%] Building C object CMakeFiles/geoptimiser.dir/src/hdfsee-render.c.o
[ 43%] Linking C executable geoptimiser
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_fds'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_utf8_validate_len'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_source_set_dispose_function'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_dec'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_unix_get_passwd_entry'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_join'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_with_user'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_canonicalize_filename'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_pipes_and_fds'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_network'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_is_valid'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_file_set_contents_full'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ptr_array_steal'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_init'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_dec'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_init'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_inc'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_memdup2'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_inc'
collect2: error: ld returned 1 exit status
CMakeFiles/geoptimiser.dir/build.make:117: recipe for target 'geoptimiser' failed
make[5]: *** [geoptimiser] Error 1
CMakeFiles/Makefile2:257: recipe for target 'CMakeFiles/geoptimiser.dir/all' failed
make[4]: *** [CMakeFiles/geoptimiser.dir/all] Error 2
Makefile:145: recipe for target 'all' failed
make[3]: *** [all] Error 2
Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/build.make:85: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build' failed
make[2]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build] Error 2
CMakeFiles/Makefile2:333: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all' failed
make[1]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all] Error 2
Makefile:135: recipe for target 'all' failed
make: *** [all] Error 2

I attempted to both sudo apt-get install libglib2.0-dev (it was already installed), and conda install -c anaconda glib, but it didn't change anything. I do have a suspicious warning from ./install.sh conda:

CMake Warning at libcrystfel/CMakeLists.txt:132 (add_library):
  Cannot generate a safe runtime search path for target libcrystfel because
  files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
      /home/nagyg/anaconda3/envs/simex/lib

  Some of these libraries may not be found correctly.

But I'm not convinced it's relevant: I complied everything successfully on another system with Ubuntu 20.04 and GNU compliers following the same steps, and the same warning came up there as well.

I changed exactly two things in the install.sh:

Do you have any insight about what may be the cause?

Full outputs of ./install.sh conda-env, ./install.sh conda, conda list and dpkg -l | grep libglib are below. Please tell me if you need anything else.

--> [spoiler, click] <-- Output of `./install.sh conda-env` - seems OK: ```console conda-env Create conda environment simex Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Downloading and Extracting Packages pillow-8.3.2 | 692 KB | | 0% pillow-8.3.2 | 692 KB | 2 | 2% pillow-8.3.2 | 692 KB | ########## | 100% pillow-8.3.2 | 692 KB | ########## | 100% qtpy-1.11.0 | 37 KB | | 0% qtpy-1.11.0 | 37 KB | ########## | 100% qtpy-1.11.0 | 37 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Installing pip dependencies: ...working... Ran pip subprocess with arguments: ['/home/nagyg/anaconda3/envs/simex/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt'] Pip subprocess output: Collecting xraydb Using cached xraydb-4.4.7-py3-none-any.whl Collecting cfelpyutils Using cached cfelpyutils-1.0.1-py3-none-any.whl (23 kB) Collecting openpmd-api Using cached openPMD_api-0.14.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (6.9 MB) Collecting extra_geom Using cached EXtra_geom-1.5.0-py3-none-any.whl Requirement already satisfied: scipy in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.7.1) Requirement already satisfied: numpy in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.21.2) Requirement already satisfied: sqlalchemy in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.4.23) Collecting future Using cached future-0.18.2-py3-none-any.whl Requirement already satisfied: matplotlib in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (3.4.3) Requirement already satisfied: h5py>=2.7.1 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (2.8.0) Requirement already satisfied: six in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from h5py>=2.7.1->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (1.16.0) Requirement already satisfied: pyparsing>=2.2.1 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (1.3.2) Requirement already satisfied: python-dateutil>=2.7 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (2.8.2) Requirement already satisfied: pillow>=6.2.0 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (8.3.2) Requirement already satisfied: cycler>=0.10 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (0.10.0) Requirement already satisfied: greenlet!=0.4.17 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.1.1) Requirement already satisfied: importlib-metadata in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (4.8.1) Requirement already satisfied: typing-extensions>=3.6.4 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from importlib-metadata->sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (3.10.0.0) Requirement already satisfied: zipp>=0.5 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from importlib-metadata->sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (3.5.0) Installing collected packages: future, cfelpyutils, xraydb, openpmd-api, extra-geom Successfully installed cfelpyutils-1.0.1 extra-geom-1.5.0 future-0.18.2 openpmd-api-0.14.2 xraydb-4.4.7 done # # To activate this environment, use # # $ conda activate simex # # To deactivate an active environment, use # # $ conda deactivate conda environment was deployed. Please run the following to install SIMEX Platform: conda activate simex ./install.sh conda ``` Output of `./install conda` after changing into the new env: ```console conda mkdir: created directory 'build' Changed dir to /home/nagyg/Software/SimEx/build. -- The C compiler identification is GNU 7.5.0 -- The CXX compiler identification is GNU 7.5.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PythonInterp: /home/nagyg/anaconda3/envs/simex/bin/python3 (found suitable version "3.7.10", minimum required is "3.5") PYPATH=lib/python3.7/site-packages -- ************************ checking python dependencies ***************************** -- Python module Bio is found -- Python module Cython is found -- Python module dill is found -- Python module h5py is found -- Python module matplotlib is found -- Python module mpi4py is found -- Python module openpmd_api is found -- Python module numpy is found -- Python module periodictable is found -- Python module pint is found -- Python module pyFAI is found -- Python module scipy is found -- Python module setuptools is found -- Python module xraydb is found -- **************** Including modules (default OFF) **************** CHECKING Analyzers/S2EReconstruction_DM CHECKING Analyzers/S2EReconstruction_EMC CHECKING Detectors/XCSITPhotonDetector CHECKING Diffractors/CrystFELPhotonDiffractor CHECKING Diffractors/GAPDPhotonDiffractor CHECKING Diffractors/SingFELPhotonDiffractor CHECKING Others/s2e CHECKING Others/sdf CHECKING PhotonInteractors/FEFFPhotonInteractor CHECKING Propagators/WavePropagator/wpg CHECKING Sources/GenesisPhotonSource -- ***** Including module S2EReconstruction_DM from: Analyzers/S2EReconstruction_DM **** -- Found MKL: /opt/intel/oneapi/mkl/2021.3.0 -- ********************************************************* -- ***** Including module S2EReconstruction_EMC from: Analyzers/S2EReconstruction_EMC **** -- Python module Cython.Distutils is found -- Python module numpy is found -- Python module h5py is found -- ********************************************************* -- ***** Including module CrystFELPhotonDiffractor from: Diffractors/CrystFELPhotonDiffractor **** CMake Warning (dev) at Modules/Diffractors/CrystFELPhotonDiffractor/CMakeLists.txt:6 (FIND_PACKAGE): Policy CMP0074 is not set: find_package uses _ROOT variables. Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Environment variable HDF5_ROOT is set to: /home/nagyg/anaconda3/envs/simex For compatibility, CMake is ignoring the variable. This warning is for project developers. Use -Wno-dev to suppress it. -- Found HDF5: /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5_cpp.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.3") found components: C CXX HDF5_INCLUDE_DIRS= /home/nagyg/anaconda3/envs/simex/include HDF5_INCLUDE_DIR= /home/nagyg/anaconda3/envs/simex/include HDF5_DEFINITIONS= -DBOOST_MATH_DISABLE_FLOAT128 HDF5_C_LIBRARIES= /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so HDF5_CXX_LIBRARIES= /home/nagyg/anaconda3/envs/simex/lib/libhdf5_cpp.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so HDF5_Fortran_LIBRARIES= HDF5_HL_LIBRARIES= HDF5_Fortran_HL_LIBRARIES= HDF5_LIBRARIES= /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5_cpp.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so HDF5_FOUND= TRUE HDF5_VERSION= 1.10.3 HDF5_LIBRARY_DIRS= -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Found GSL: /usr/include (found version "2.4") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- ********************************************************* -- ***** Including module SingFELPhotonDiffractor from: Diffractors/SingFELPhotonDiffractor **** -- Python module numba is found -- Python module numpy is found -- Python module scipy is found -- Python module mpi4py is found -- Python module h5py is found -- ********************************************************* -- ***** Including module s2e from: Others/s2e **** -- ********************************************************* -- ***** Including module sdf from: Others/sdf **** -- ********************************************************* -- ***** Including module wpg from: Propagators/WavePropagator/wpg **** -- ********************************************************* -- ***** Including module GenesisPhotonSource from: Sources/GenesisPhotonSource **** -- ********************************************************* -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BOOST_ROOT GEANT4_ROOT XCSIT_ROOT XERCESC_ROOT -- Build files have been written to: /home/nagyg/Software/SimEx/build [ 1%] Creating directories for 'recon_dm' [ 2%] Performing download step (download, verify and extract) for 'recon_dm' -- Downloading... dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_DM/recon_dm-prefix/src/master.zip' timeout='none' inactivity timeout='none' -- Using src='https://github.com/eucall-software/emc_and_dm/archive/master.zip' -- [download 100% complete] -- Downloading... done -- extracting... src='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_DM/recon_dm-prefix/src/master.zip' dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_DM/recon_dm-prefix/src/recon_dm' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 4%] No update step for 'recon_dm' [ 5%] Performing patch step for 'recon_dm' [ 6%] No configure step for 'recon_dm' [ 8%] Performing build step for 'recon_dm' object_recon.c: In function ‘setup’: object_recon.c:266:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d %d", &qmax, &num_supp) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ object_recon.c:281:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d", &supp[s][i]) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ object_recon.c:363:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%lf", &intens) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~ object_recon.c:412:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%lf", &x[i][j][k]) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 9%] No install step for 'recon_dm' [ 11%] Completed 'recon_dm' [ 11%] Built target recon_dm [ 12%] Creating directories for 'recon_emc' [ 13%] Performing download step (download, verify and extract) for 'recon_emc' -- Downloading... dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/master.zip' timeout='none' inactivity timeout='none' -- Using src='https://github.com/eucall-software/emc_and_dm/archive/master.zip' -- [download 100% complete] -- Downloading... done -- extracting... src='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/master.zip' dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/recon_emc' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 15%] No update step for 'recon_emc' [ 16%] No patch step for 'recon_emc' [ 18%] No configure step for 'recon_emc' [ 19%] Performing build step for 'recon_emc' running build_ext cythoning rotateIntens.pyx to rotateIntens.c building 'rotateIntens' extension creating build creating build/temp.linux-x86_64-3.7 gcc -pthread -B /home/nagyg/anaconda3/envs/simex/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include -I/home/nagyg/anaconda3/envs/simex/include/python3.7m -c rotateIntens.c -o build/temp.linux-x86_64-3.7/rotateIntens.o -O2 In file included from /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0, from /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from rotateIntens.c:620: /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -pthread -shared -B /home/nagyg/anaconda3/envs/simex/compiler_compat -L/home/nagyg/anaconda3/envs/simex/lib -Wl,-rpath=/home/nagyg/anaconda3/envs/simex/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/rotateIntens.o -o /home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/recon_emc/EMC_Src/supp_py_modules/rotateIntens.cpython-37m-x86_64-linux-gnu.so /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/recon_emc/EMC_Src/supp_py_modules/rotateIntens.pyx tree = Parsing.p_module(s, pxd, full_module_name) [ 20%] No install step for 'recon_emc' [ 22%] Completed 'recon_emc' [ 22%] Built target recon_emc [ 23%] Creating directories for 'crystfel' [ 25%] Performing download step (download, verify and extract) for 'crystfel' -- Downloading... dst='/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-0.9.1.tar.gz' timeout='none' inactivity timeout='none' -- Using src='http://www.desy.de/~twhite/crystfel/crystfel-0.9.1.tar.gz' -- [download 2% complete] -- [download 4% complete] -- [download 6% complete] -- [download 8% complete] -- [download 10% complete] -- [download 12% complete] -- [download 14% complete] -- [download 16% complete] -- [download 18% complete] -- [download 20% complete] -- [download 22% complete] -- [download 24% complete] -- [download 26% complete] -- [download 28% complete] -- [download 30% complete] -- [download 32% complete] -- [download 34% complete] -- [download 36% complete] -- [download 38% complete] -- [download 40% complete] -- [download 42% complete] -- [download 45% complete] -- [download 47% complete] -- [download 49% complete] -- [download 51% complete] -- [download 53% complete] -- [download 55% complete] -- [download 57% complete] -- [download 59% complete] -- [download 61% complete] -- [download 63% complete] -- [download 65% complete] -- [download 67% complete] -- [download 69% complete] -- [download 71% complete] -- [download 73% complete] -- [download 75% complete] -- [download 77% complete] -- [download 79% complete] -- [download 81% complete] -- [download 83% complete] -- [download 85% complete] -- [download 87% complete] -- [download 89% complete] -- [download 91% complete] -- [download 93% complete] -- [download 95% complete] -- [download 97% complete] -- [download 99% complete] -- [download 100% complete] -- Downloading... done -- extracting... src='/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-0.9.1.tar.gz' dst='/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 26%] No update step for 'crystfel' [ 27%] No patch step for 'crystfel' [ 29%] Performing configure step for 'crystfel' -- The C compiler identification is GNU 7.5.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Found HDF5: /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.3") found components: C -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Found GSL: /usr/include (found version "2.4") -- Found TIFF: /home/nagyg/anaconda3/envs/simex/lib/libtiff.so (found version "4.3.0") -- Looking for CL_VERSION_2_2 -- Looking for CL_VERSION_2_2 - found -- Found OpenCL: /usr/lib/x86_64-linux-gnu/libOpenCL.so (found version "2.2") -- Checking for module 'glib-2.0' -- Found glib-2.0, version 2.56.4 -- Checking for one of the modules 'msgpack' -- MessagePack not found. -- Checking for one of the modules 'libzmq' -- ZMQ not found. -- Checking for one of the modules 'gtk+-3.0' -- Checking for one of the modules 'gtk+-2.0' -- Using GTK 2 -- Checking for one of the modules 'gdk-2.0' -- Checking for one of the modules 'cairo' -- Checking for one of the modules 'gdk-pixbuf-2.0' -- Performing Test HAVE_DIAG_COLOR -- Performing Test HAVE_DIAG_COLOR - Success -- This is a packaged release version -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for CL/cl.h -- Looking for CL/cl.h - found -- Looking for clock_gettime -- Looking for clock_gettime - found -- Looking for argp_parse -- Looking for argp_parse - found -- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so -- Could NOT find XGANDALF (missing: XGANDALF_LIBRARIES XGANDALF_INCLUDES) -- Could NOT find PINKINDEXER (missing: PINKINDEXER_LIBRARIES PINKINDEXER_INCLUDES) -- Could NOT find FDIP (missing: FDIP_LIBRARIES) -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found BISON: /usr/bin/bison (found version "3.0.4") -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot -- Checking for one of the modules 'fftw3' -- Looking for gzbuffer -- Looking for gzbuffer - found -- Looking for forkpty -- Looking for forkpty - found -- Looking for forkpty -- Looking for forkpty - not found -- Found forkpty() in pty.h -- Configuring done CMake Warning at libcrystfel/CMakeLists.txt:132 (add_library): Cannot generate a safe runtime search path for target libcrystfel because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/nagyg/anaconda3/envs/simex/lib Some of these libraries may not be found correctly. -- Generating done -- Build files have been written to: /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-build [ 30%] Performing build step for 'crystfel' [ 1%] [BISON][symopp] Building parser with bison 3.0.4 [ 2%] [FLEX][symopl] Building scanner with flex 2.6.4 [ 3%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/reflist.c.o [ 4%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/utils.c.o [ 4%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/cell.c.o [ 5%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/detector.c.o [ 6%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/thread-pool.c.o [ 7%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/image.c.o [ 8%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/hdf5-file.c.o [ 8%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/geometry.c.o [ 9%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/peakfinder8.c.o [ 10%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/symmetry.c.o [ 11%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/stream.c.o [ 12%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/peaks.c.o [ 13%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/reflist-utils.c.o [ 13%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/filters.c.o [ 14%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/render.c.o [ 15%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/index.c.o [ 16%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/dirax.c.o [ 17%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/mosflm.c.o [ 18%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/cell-utils.c.o [ 18%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/integer_matrix.c.o [ 19%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/crystal.c.o [ 20%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/xds.c.o [ 21%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/integration.c.o [ 22%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/predict-refine.c.o [ 23%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/events.c.o [ 23%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/felix.c.o [ 24%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/taketwo.c.o [ 25%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/xgandalf.c.o [ 26%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/pinkindexer.c.o [ 27%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/rational.c.o [ 27%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/spectrum.c.o [ 28%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/symop-parse.c.o [ 29%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/symop-lex.c.o [ 30%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/asdf.c.o [ 31%] Linking C shared library libcrystfel.so [ 31%] Built target libcrystfel [ 32%] Building C object CMakeFiles/partial_sim.dir/src/partial_sim.c.o [ 32%] Linking C executable partial_sim [ 32%] Built target partial_sim [ 33%] Building C object CMakeFiles/pattern_sim.dir/src/pattern_sim.c.o [ 34%] Building C object CMakeFiles/pattern_sim.dir/src/diffraction.c.o [ 35%] Building C object CMakeFiles/pattern_sim.dir/src/cl-utils.c.o [ 36%] Building C object CMakeFiles/pattern_sim.dir/src/diffraction-gpu.c.o /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c: In function ‘check_sinc_lut’: /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:124:2: warning: ‘clCreateImage2D’ is deprecated [-Wdeprecated-declarations] gctx->sinc_luts[n-1] = clCreateImage2D(gctx->ctx, ^~~~ In file included from /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:42:0: /usr/include/CL/cl.h:1402:1: note: declared here clCreateImage2D(cl_context /* context */, ^~~~~~~~~~~~~~~ /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c: In function ‘setup_gpu’: /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:445:2: warning: ‘clCreateCommandQueue’ is deprecated [-Wdeprecated-declarations] gctx->cq = clCreateCommandQueue(gctx->ctx, dev, 0, &err); ^~~~ In file included from /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:42:0: /usr/include/CL/cl.h:1443:1: note: declared here clCreateCommandQueue(cl_context /* context */, ^~~~~~~~~~~~~~~~~~~~ [ 36%] Linking C executable pattern_sim [ 36%] Built target pattern_sim [ 37%] Building C object CMakeFiles/hdfsee.dir/src/hdfsee.c.o [ 38%] Building C object CMakeFiles/hdfsee.dir/src/dw-hdfsee.c.o [ 39%] Building C object CMakeFiles/hdfsee.dir/src/hdfsee-render.c.o [ 40%] Linking C executable hdfsee [ 40%] Built target hdfsee [ 41%] Building C object CMakeFiles/geoptimiser.dir/src/geoptimiser.c.o [ 42%] Building C object CMakeFiles/geoptimiser.dir/src/hdfsee-render.c.o [ 43%] Linking C executable geoptimiser //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_fds' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_utf8_validate_len' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_source_set_dispose_function' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_dec' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_unix_get_passwd_entry' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_join' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_with_user' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_canonicalize_filename' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_pipes_and_fds' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_network' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_is_valid' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_file_set_contents_full' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ptr_array_steal' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_init' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_dec' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_init' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_inc' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_memdup2' //home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_inc' collect2: error: ld returned 1 exit status CMakeFiles/geoptimiser.dir/build.make:117: recipe for target 'geoptimiser' failed make[5]: *** [geoptimiser] Error 1 CMakeFiles/Makefile2:257: recipe for target 'CMakeFiles/geoptimiser.dir/all' failed make[4]: *** [CMakeFiles/geoptimiser.dir/all] Error 2 Makefile:145: recipe for target 'all' failed make[3]: *** [all] Error 2 Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/build.make:85: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build' failed make[2]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build] Error 2 CMakeFiles/Makefile2:333: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all' failed make[1]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all] Error 2 Makefile:135: recipe for target 'all' failed make: *** [all] Error 2 ``` Output of `conda list` in the fresh new environment: ```console WARNING conda.core.prefix_data:_load_site_packages(293): Problem reading non-conda package record at lib/python3.7/site-packages/pyFAI-0.15.0-py3.7-linux-x86_64.egg-info/PKG-INFO. Please verify that you still need this, and if so, that this is still installed correctly. Reinstalling this package may help. # packages in environment at /home/nagyg/anaconda3/envs/simex: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge argcomplete 1.12.3 pyhd8ed1ab_2 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge biopython 1.79 py37h5e8e339_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.2 h7f98852_0 conda-forge ca-certificates 2020.10.14 0 anaconda certifi 2020.6.20 py37_0 anaconda cfelpyutils 1.0.1 pypi_0 pypi cmake 3.21.2 h8897547_0 conda-forge cycler 0.10.0 py_2 conda-forge cython 0.29.24 py37hcd2ae1e_0 conda-forge dbus 1.13.6 h48d8840_2 conda-forge debugpy 1.4.1 py37hcd2ae1e_0 conda-forge decorator 5.0.9 pyhd8ed1ab_0 conda-forge dill 0.3.4 pyhd8ed1ab_0 conda-forge entrypoints 0.3 pyhd8ed1ab_1003 conda-forge expat 2.4.1 h9c3ff4c_0 conda-forge extra-geom 1.5.0 pypi_0 pypi fabio 0.12.0 py37hb1e94ed_0 conda-forge fftw 3.3.9 nompi_h74d3f13_101 conda-forge fontconfig 2.13.1 hba837de_1005 conda-forge freetype 2.10.4 h0708190_1 conda-forge future 0.18.2 pypi_0 pypi gettext 0.19.8.1 h0b5b191_1005 conda-forge glib 2.68.4 h9c3ff4c_0 conda-forge glib-tools 2.68.4 h9c3ff4c_0 conda-forge glymur 0.9.4 pyhd8ed1ab_0 conda-forge greenlet 1.1.1 py37hcd2ae1e_0 conda-forge gst-plugins-base 1.18.4 hf529b03_2 conda-forge gstreamer 1.18.4 h76c114f_2 conda-forge h5py 2.8.0 py37hfb8609e_1004 conda-forge hdf5 1.10.3 hc401514_2 conda-forge icu 68.1 h58526e2_0 conda-forge importlib-metadata 4.8.1 py37h89c1867_0 conda-forge importlib_metadata 4.8.1 hd8ed1ab_0 conda-forge importlib_resources 5.2.2 pyhd8ed1ab_0 conda-forge ipykernel 6.3.1 py37h6531663_0 conda-forge ipython 7.27.0 py37h6531663_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jbig 2.1 h7f98852_2003 conda-forge jedi 0.18.0 py37h89c1867_2 conda-forge jpeg 9d h36c2ea0_0 conda-forge jupyter_client 7.0.2 pyhd8ed1ab_0 conda-forge jupyter_core 4.7.1 py37h89c1867_0 conda-forge kiwisolver 1.3.2 py37h2527ec5_0 conda-forge krb5 1.19.2 hcc1bbae_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge lerc 2.2.1 h9c3ff4c_0 conda-forge libblas 3.9.0 11_linux64_openblas conda-forge libcblas 3.9.0 11_linux64_openblas conda-forge libclang 11.1.0 default_ha53f305_1 conda-forge libcurl 7.78.0 h2574ce0_0 conda-forge libdeflate 1.7 h7f98852_5 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 hcdb4288_3 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 11.1.0 hc902ee8_8 conda-forge libgfortran 3.0.0 1 conda-forge libgfortran-ng 11.1.0 h69a702a_8 conda-forge libgfortran5 11.1.0 h6c583b3_8 conda-forge libglib 2.68.4 h3e27bee_0 conda-forge libgomp 11.1.0 hc902ee8_8 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 11_linux64_openblas conda-forge libllvm10 10.0.1 he513fc3_3 conda-forge libllvm11 11.1.0 hf817b99_2 conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.17 pthreads_h8fe5266_1 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libpq 13.3 hd57d9b9_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libssh2 1.10.0 ha56f1ee_0 conda-forge libstdcxx-ng 11.1.0 h56837e0_8 conda-forge libtiff 4.3.0 hf544144_1 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libuv 1.42.0 h7f98852_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.2.1 h7f98852_0 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.12 h72842e0_0 conda-forge libxslt 1.1.33 h15afd5d_2 conda-forge llvmlite 0.36.0 py37h9d7f4d0_0 conda-forge lxml 4.6.3 py37h77fd288_0 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge mako 1.1.5 pyhd8ed1ab_0 conda-forge markupsafe 2.0.1 py37h5e8e339_0 conda-forge matplotlib 3.4.3 py37h89c1867_0 conda-forge matplotlib-base 3.4.3 py37h1058ff1_0 conda-forge matplotlib-inline 0.1.2 pyhd8ed1ab_2 conda-forge mpi 1.0 mpich conda-forge mpi4py 3.1.1 py37h1e5cb63_0 conda-forge mpich 3.4.2 h846660c_100 conda-forge mysql-common 8.0.25 ha770c72_2 conda-forge mysql-libs 8.0.25 hfa10184_2 conda-forge ncurses 6.2 h58526e2_4 conda-forge nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge nspr 4.30 h9c3ff4c_0 conda-forge nss 3.69 hb5efdd6_0 conda-forge numba 0.53.1 py37hb11d6e1_1 conda-forge numexpr 2.7.3 py37he8f5f7f_0 conda-forge numpy 1.21.2 py37h31617e3_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openpmd-api 0.14.2 pypi_0 pypi openssl 1.1.1l h7f98852_0 conda-forge packaging 21.0 pyhd8ed1ab_0 conda-forge parso 0.8.2 pyhd8ed1ab_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge periodictable 1.5.2 py_0 conda-forge pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.3.2 py37h0f21c89_0 conda-forge pint 0.17 pyhd8ed1ab_1 conda-forge pip 21.2.4 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.20 pyha770c72_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge py3nvml 0.2.5 py37hc8dfbb8_2 conda-forge pyfai 0.15.0 py37h3010b51_1002 conda-forge pyfftw 0.12.0 py37h433d886_2 conda-forge pygments 2.10.0 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py37h89c1867_7 conda-forge pyqt-impl 5.12.3 py37he336c9b_7 conda-forge pyqt5-sip 4.19.18 py37hcd2ae1e_7 conda-forge pyqtchart 5.12 py37he336c9b_7 conda-forge pyqtwebengine 5.12.1 py37he336c9b_7 conda-forge python 3.7.10 hffdb5ce_100_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.7 2_cp37m conda-forge pyzmq 22.2.1 py37h336d617_0 conda-forge qt 5.12.9 hda022c4_4 conda-forge qtconsole 5.1.1 pyhd8ed1ab_0 conda-forge qtpy 1.11.0 pyhd8ed1ab_0 conda-forge readline 8.1 h46c0cb4_0 conda-forge rhash 1.4.1 h7f98852_0 conda-forge scipy 1.7.1 py37hf2a6cf1_0 conda-forge setuptools 57.4.0 py37h89c1867_0 conda-forge silx 0.15.2 hd8ed1ab_0 conda-forge silx-base 0.15.2 py37h219a48f_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlalchemy 1.4.23 py37h5e8e339_0 conda-forge sqlite 3.36.0 h9cd32fc_0 conda-forge tk 8.6.11 h27826a3_1 conda-forge tornado 6.1 py37h5e8e339_1 conda-forge traitlets 5.1.0 pyhd8ed1ab_0 conda-forge typing_extensions 3.10.0.0 pyha770c72_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge wheel 0.37.0 pyhd8ed1ab_1 conda-forge xmltodict 0.12.0 py_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xraydb 4.4.7 pypi_0 pypi xz 5.2.5 h516909a_1 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zipp 3.5.0 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.5.0 ha95c52a_0 conda-forge ``` and finally, the output of `dpkg -l | grep libglib`: ```console ii libglib-object-introspection-perl 0.044-2 amd64 Perl bindings for gobject-introspection libraries ii libglib-perl 3:1.326-1build1 amd64 interface to the GLib and GObject libraries ii libglib2.0-0:amd64 2.56.4-0ubuntu0.18.04.8 amd64 GLib library of C routines ii libglib2.0-bin 2.56.4-0ubuntu0.18.04.8 amd64 Programs for the GLib library ii libglib2.0-cil 2.12.40-2 amd64 CLI binding for the GLib utility library 2.12 ii libglib2.0-cil-dev 2.12.40-2 amd64 CLI binding for the GLib utility library 2.12 ii libglib2.0-data 2.56.4-0ubuntu0.18.04.8 all Common files for GLib library ii libglib2.0-dev:amd64 2.56.4-0ubuntu0.18.04.8 amd64 Development files for the GLib library ii libglib2.0-dev-bin 2.56.4-0ubuntu0.18.04.8 amd64 Development utilities for the GLib library ii libglib2.0-doc 2.56.4-0ubuntu0.18.04.8 all Documentation files for the GLib library ii libglib2.0-tests 2.56.4-0ubuntu0.18.04.8 amd64 GLib library of C routines - installed tests ii libglibmm-2.4-1v5:amd64 2.56.0-1 amd64 C++ wrapper for the GLib toolkit (shared libraries) ```
godot11 commented 2 years ago

As a workaround, getting rid of the conflicting module in anaconda as 

mv ~/anaconda3/envs/simex/lib/libgio-2.0.so.0 ~/anaconda3/envs/simex/lib/libgio-2.0.so.0.backup

solved it for now, but I'm not sure if this hack doesn't break anything else...