Build error: undefined references to libgio-2.0 symbols #243
Description
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 2I 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:
- line 113: uncomment
export FC=ifort - line 144: use
-j1with cmake (for organized log)
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:
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 condaOutput of ./install conda after changing into the new env:
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 <PackageName>_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'
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-- 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'
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-- 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
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-- 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'
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-- 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
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/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 */,
^~~~~~~~~~~~~~~~~~~~
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[ 37%] Building C object CMakeFiles/hdfsee.dir/src/hdfsee.c.o
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//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:
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:
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)