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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 statusCMakeFiles/geoptimiser.dir/build.make:117: recipe for target 'geoptimiser' failedmake[5]: *** [geoptimiser] Error 1CMakeFiles/Makefile2:257: recipe for target 'CMakeFiles/geoptimiser.dir/all' failedmake[4]: *** [CMakeFiles/geoptimiser.dir/all] Error 2Makefile:145: recipe for target 'all' failedmake[3]: *** [all] Error 2Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/build.make:85: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build' failedmake[2]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build] Error 2CMakeFiles/Makefile2:333: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all' failedmake[1]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all] Error 2Makefile:135: recipe for target 'all' failedmake: *** [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:
line 113: uncomment export FC=ifort
line 144: use -j1 with 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-envCreate conda environment simexCollecting package metadata (repodata.json): ...working... doneSolving environment: ...working... doneDownloading and Extracting Packagespillow-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... doneVerifying transaction: ...working... doneExecuting transaction: ...working... doneInstalling 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.whlCollecting 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.whlRequirement 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.whlRequirement 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-geomSuccessfully installed cfelpyutils-1.0.1 extra-geom-1.5.0 future-0.18.2 openpmd-api-0.14.2 xraydb-4.4.7done
#
# To activate this environment, use
#
# $ conda activate simex
#
# To deactivate an active environment, use
#
# $ conda deactivateconda 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:
condamkdir: 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_DMCHECKING Analyzers/S2EReconstruction_EMCCHECKING Detectors/XCSITPhotonDetectorCHECKING Diffractors/CrystFELPhotonDiffractorCHECKING Diffractors/GAPDPhotonDiffractorCHECKING Diffractors/SingFELPhotonDiffractorCHECKING Others/s2eCHECKING Others/sdfCHECKING PhotonInteractors/FEFFPhotonInteractorCHECKING Propagators/WavePropagator/wpgCHECKING 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/includeHDF5_INCLUDE_DIR= /home/nagyg/anaconda3/envs/simex/includeHDF5_DEFINITIONS= -DBOOST_MATH_DISABLE_FLOAT128HDF5_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.soHDF5_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.soHDF5_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.soHDF5_FOUND= TRUEHDF5_VERSION= 1.10.3HDF5_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 doneCMake 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_extcythoning rotateIntens.pyx to rotateIntens.cbuilding 'rotateIntens' extensioncreating buildcreating build/temp.linux-x86_64-3.7gcc -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 -O2In 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 doneCMake 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 statusCMakeFiles/geoptimiser.dir/build.make:117: recipe for target 'geoptimiser' failedmake[5]: *** [geoptimiser] Error 1CMakeFiles/Makefile2:257: recipe for target 'CMakeFiles/geoptimiser.dir/all' failedmake[4]: *** [CMakeFiles/geoptimiser.dir/all] Error 2Makefile:145: recipe for target 'all' failedmake[3]: *** [all] Error 2Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/build.make:85: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build' failedmake[2]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build] Error 2CMakeFiles/Makefile2:333: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all' failedmake[1]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all] Error 2Makefile:135: recipe for target 'all' failedmake: *** [all] Error 2
Output of conda list in the fresh new environment:
and finally, the output of dpkg -l | grep libglib:
ii libglib-object-introspection-perl 0.044-2 amd64 Perl bindings for gobject-introspection librariesii libglib-perl 3:1.326-1build1 amd64 interface to the GLib and GObject librariesii libglib2.0-0:amd64 2.56.4-0ubuntu0.18.04.8 amd64 GLib library of C routinesii libglib2.0-bin 2.56.4-0ubuntu0.18.04.8 amd64 Programs for the GLib libraryii libglib2.0-cil 2.12.40-2 amd64 CLI binding for the GLib utility library 2.12ii libglib2.0-cil-dev 2.12.40-2 amd64 CLI binding for the GLib utility library 2.12ii libglib2.0-data 2.56.4-0ubuntu0.18.04.8 all Common files for GLib libraryii libglib2.0-dev:amd64 2.56.4-0ubuntu0.18.04.8 amd64 Development files for the GLib libraryii libglib2.0-dev-bin 2.56.4-0ubuntu0.18.04.8 amd64 Development utilities for the GLib libraryii libglib2.0-doc 2.56.4-0ubuntu0.18.04.8 all Documentation files for the GLib libraryii libglib2.0-tests 2.56.4-0ubuntu0.18.04.8 amd64 GLib library of C routines - installed testsii libglibmm-2.4-1v5:amd64 2.56.0-1 amd64 C++ wrapper for the GLib toolkit (shared libraries)
The text was updated successfully, but these errors were encountered:
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:I attempted to both
sudo apt-get install libglib2.0-dev
(it was already installed), andconda install -c anaconda glib
, but it didn't change anything. I do have a suspicious warning from./install.sh conda
: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
:export FC=ifort
-j1
with 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
anddpkg -l | grep libglib
are below. Please tell me if you need anything else.--> [spoiler, click] <--
Output of
./install.sh conda-env
- seems OK:Output of
./install conda
after changing into the new env:Output of
conda list
in the fresh new environment:and finally, the output of
dpkg -l | grep libglib
:The text was updated successfully, but these errors were encountered: