"Could not initialise GLX. Aborted (core dumped)" - Unable to install Cytoflow on Linux Mint 21.1 #377
Description
I was trying to install Cytoflow on my Linux Mint 22.1 machine. As per the instructions in here, I downloaded the .tar.bz2 file, extracted it, placed the cytoflow-1.2.1 folder in ~/.local/lib/ . I navigated to that directory and executed the binary with ./cytoflow, but I run into the error that essentially boils down to "Could not initialise GLX .. Aborted (core dumped)".
I reinstalled libgl1-mesa-dri as suggested in this Stack Overflow Post, but the problem persists.
Below is the complete error output I get after running the command ./cytoflow:
qt.glx: qglx_findConfig: Failed to finding matching FBConfig for QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile)
qt.glx: qglx_findConfig: Failed to finding matching FBConfig for QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile)
Could not initialize GLX
Fatal Python error: Aborted
Thread 0x0000738ea7c006c0 (most recent call first):
File "multiprocessing/popen_fork.py", line 27 in poll
File "multiprocessing/popen_fork.py", line 43 in wait
File "multiprocessing/process.py", line 149 in join
File "run.py", line 305 in monitor_remote_process
File "threading.py", line 982 in run
File "threading.py", line 1045 in _bootstrap_inner
File "threading.py", line 1002 in _bootstrap
Thread 0x0000738ea86006c0 (most recent call first):
File "multiprocessing/connection.py", line 395 in _recv
File "multiprocessing/connection.py", line 430 in _recv_bytes
File "multiprocessing/connection.py", line 216 in recv_bytes
File "multiprocessing/queues.py", line 103 in get
File "logging/handlers.py", line 1522 in dequeue
File "logging/handlers.py", line 1573 in _monitor
File "threading.py", line 982 in run
File "threading.py", line 1045 in _bootstrap_inner
File "threading.py", line 1002 in _bootstrap
Current thread 0x0000738f2b6a9080 (most recent call first):
File "pyface/ui/qt/init.py", line 36 in <module>
File "PyInstaller/loader/pyimod02_importers.py", line 450 in exec_module
File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
File "<frozen importlib._bootstrap>", line 1204 in _gcd_import
File "importlib/__init__.py", line 126 in import_module
File "importlib/metadata/__init__.py", line 202 in load
File "pyface/base_toolkit.py", line 219 in import_toolkit
File "pyface/base_toolkit.py", line 269 in find_toolkit
File "pyface/toolkit.py", line 23 in <module>
File "PyInstaller/loader/pyimod02_importers.py", line 450 in exec_module
File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
File "pyface/resource_manager.py", line 17 in <module>
File "PyInstaller/loader/pyimod02_importers.py", line 450 in exec_module
File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
File "run.py", line 131 in run_gui
File "run.py", line 402 in <module>
Extension modules: PyQt5.QtCore, PyQt5.QtGui, PyQt5.QtWidgets, PyQt5.QtPrintSupport, PyQt5.QtX11Extras, PyQt5.QtWebChannel, PyQt5.QtTextToSpeech, PyQt5.QtSvg, PyQt5.QtRemoteObjects, PyQt5.QtNetwork, PyQt5.QtPositioning, PyQt5.QtOpenGL, PyQt5.QtMultimedia, PyQt5.QtDBus, PyQt5.QtBluetooth, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, PIL._imaging, kiwisolver._cext, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._ansari_swilk_statistics, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.stats._unuran.unuran_wrapper, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, yaml._yaml, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, traits.ctraits, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, bottleneck.move, bottleneck.nonreduce, bottleneck.nonreduce_axis, bottleneck.reduce, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, _Logicle, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, sklearn.__check_build._check_build, psutil._psutil_linux, psutil._psutil_posix, sklearn.utils._isfinite, sklearn.utils.sparsefuncs_fast, sklearn.utils.murmurhash, sklearn.utils._openmp_helpers, sklearn.metrics.cluster._expected_mutual_info_fast, sklearn.preprocessing._csr_polynomial_expansion, sklearn.preprocessing._target_encoder_fast, sklearn.metrics._dist_metrics, sklearn.metrics._pairwise_distances_reduction._datasets_pair, sklearn.utils._cython_blas, sklearn.metrics._pairwise_distances_reduction._base, sklearn.metrics._pairwise_distances_reduction._middle_term_computer, sklearn.utils._heap, sklearn.utils._sorting, sklearn.metrics._pairwise_distances_reduction._argkmin, sklearn.metrics._pairwise_distances_reduction._argkmin_classmode, sklearn.utils._vector_sentinel, sklearn.metrics._pairwise_distances_reduction._radius_neighbors, sklearn.metrics._pairwise_distances_reduction._radius_neighbors_classmode, sklearn.metrics._pairwise_fast, sklearn.neighbors._partition_nodes, sklearn.neighbors._ball_tree, sklearn.neighbors._kd_tree, sklearn.utils.arrayfuncs, sklearn.utils._random, sklearn.utils._seq_dataset, sklearn.linear_model._cd_fast, _loss, sklearn._loss._loss, sklearn.svm._liblinear, sklearn.svm._libsvm, sklearn.svm._libsvm_sparse, sklearn.utils._weight_vector, sklearn.linear_model._sgd_fast, sklearn.linear_model._sag_fast, sklearn.decomposition._online_lda_fast, sklearn.decomposition._cdnmf_fast, sklearn.utils._fast_dict, sklearn.cluster._hierarchical_fast, sklearn.cluster._k_means_common, sklearn.cluster._k_means_elkan, sklearn.cluster._k_means_lloyd, sklearn.cluster._k_means_minibatch, sklearn.cluster._dbscan_inner, sklearn.cluster._hdbscan._tree, sklearn.cluster._hdbscan._linkage, sklearn.cluster._hdbscan._reachability, sklearn._isotonic, sklearn.tree._utils, sklearn.tree._tree, sklearn.tree._splitter, sklearn.tree._criterion, sklearn.neighbors._quad_tree, sklearn.manifold._barnes_hut_tsne, sklearn.manifold._utils, scipy.signal._sigtools, scipy.signal._max_len_seq_inner, scipy.signal._upfirdn_apply, scipy.signal._spline, scipy.signal._sosfilt, scipy.signal._spectral, scipy.signal._peak_finding_utils, PyQt5.QtWebEngineCore, PyQt5.QtWebEngine, PyQt5.QtWebEngineWidgets (total: 240)
Aborted (core dumped)
I'm not sure if this helps, but here are the relevant specs of my machine:
OS: Linux Mint 22.1 x86_64
Kernel: 6.8.0-55-generic
DE: Cinnamon 6.4.8
CPU: AMD Ryzen 5 PRO 5650U with Radeon Graphics (12) @ 4.289GHz
GPU: AMD ATI Radeon Vega Series / Radeon Vega Mobile Series