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Opened 13 months ago
Closed 13 months ago
#15982 closed defect (can't reproduce)
Crash disconnecting hdmi projector, Mac, Qt 6.7.2
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407250342 (2024-07-25 03:42:42 UTC)
Description
Last time you used ChimeraX it crashed.
I unplugged the hdmi connection to a projector while the laptop display was open and ChimeraX immediately crashed. Sadly this was in Qt 6.7.2 so apparently the problem is not fixed in latest Qt.
Fatal Python error: Segmentation fault
Thread 0x000000034fe6b000 (most recent call first):
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Users/goddard/Library/Application Support/ChimeraX/1.9/lib/python/site-packages/tqdm/_monitor.py", line 60 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001ec5c0f40 (most recent call first):
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1037 in init
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1200 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, 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, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write, PIL._imagingmath, scipy._lib._ccallback_c, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, 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.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, sklearn.__check_build._check_build, lz4._version, lz4.frame._frame, psutil._psutil_osx, psutil._psutil_posix, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.special.cython_special, scipy.stats._stats, scipy.stats.beta_ufunc, scipy.stats._boost.beta_ufunc, scipy.stats.binom_ufunc, scipy.stats._boost.binom_ufunc, scipy.stats.nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, scipy.stats.hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats.ncf_ufunc, scipy.stats._boost.ncf_ufunc, scipy.stats.ncx2_ufunc, scipy.stats._boost.ncx2_ufunc, scipy.stats.nct_ufunc, scipy.stats._boost.nct_ufunc, scipy.stats.skewnorm_ufunc, scipy.stats._boost.skewnorm_ufunc, scipy.stats.invgauss_ufunc, scipy.stats._boost.invgauss_ufunc, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, 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, 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, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, 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.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 220)
{"app_name":"ChimeraX","timestamp":"2024-09-19 12:34:26.00 -0700","app_version":"1.9.0","slice_uuid":"66f78bb3-8c6d-31bc-ae07-ab3280d0670b","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"983F4A4E-8279-426F-A7EE-2DBA5692C20D"}
{
"uptime" : 370000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 3913,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-09-19 12:34:24.2360 -0700",
"codeSigningMonitor" : 1,
"incident" : "983F4A4E-8279-426F-A7EE-2DBA5692C20D",
"pid" : 47327,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-19 11:22:13.8955 -0700",
"procStartAbsTime" : 8930330634544,
"procExitAbsTime" : 9034258867641,
"procName" : "ChimeraX",
"procPath" : "\/Users\/USER\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1A51D9CB-C6EE-5F17-BA0A-8EB12C252AE4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BA6E14FF-9FD1-806E-F23A-DBA948840378",
"codeSigningID" : "ChimeraX",
"codeSigningTeamID" : "",
"codeSigningFlags" : 570556929,
"codeSigningValidationCategory" : 10,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 5441,
"sleepWakeUUID" : "BA956299-E3AB-4E87-96FB-5050762702FD",
"sip" : "enabled",
"vmRegionInfo" : "0x11833f192948 is not in any region. Bytes after previous region: 18774360664393 Bytes before following region: 86297719264952\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000091833f192948","rawCodes":[1,159992885356872],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000091833f192948 -> 0x000011833f192948 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":47327},
"vmregioninfo" : "0x11833f192948 is not in any region. Bytes after previous region: 18774360664393 Bytes before following region: 86297719264952\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202407250342 (2024-07-25)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 8xps format mmcif fromDatabase pdb
8xps title:
Structure of Nipah virus Bangladesh string G protein ectodomain monomer bound
to single-domain antibody n425 at 3.22 Angstroms overall resolution [more
info...]
Chain information for 8xps #1
---
Chain | Description
A | Nipah virus Bangladesh string G protein
B | single-domain antibody n425
Non-standard residues in 8xps #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> color bychain
> ui tool show "Similar Structures"
> foldseek /A
Found 194 similar structures to 8xps #1/A in pdb database using foldseek, name
fs1
> similarstructures traces
194 traces showing 39457 residues with 25376 far or short segment residues
hidden
> lighting soft
> similarstructures cluster /A:579,220,506,360,348 clusterDistance 1.5
Clustered 148 of 194 hits that have the specified 5 residues into 6 groups
> similarstructures cluster /A:579,220,506,360,348 clusterDistance 1.5
> ofStructures
> 1inh_A,6lxk_C,5nwe_C,8g3r_E,2ht5_A,8g3m_L,8g3o_H,4mc7_D,2cml_A,4b7j_A,2hu4_C,1iny_A,1nma_N,4k3y_C,2htv_A,2b8h_D,1l7g_A,4k3y_D,8g30_M,1nmb_N,5hug_A,7u4e_A,6lxi_B,7e6q_B,4mjv_A,4ks1_A,4mju_A,4d8s_A,6pzy_A,5hun_A,4wa3_A,4wa4_A,6q20_A,4gdj_A,4gdj_C,4gdj_B,4gdj_D,4gez_C,2aep_A,7s0i_A,6n6b_A,8dwb_AAA,5huk_D,6br5_A,4h52_A,4h53_D,4k1j_A,7u4g_A,6pzf_B,6pzd_A,4hzv_A,4hzy_A,6nn9_A,6g01_A,2bat_A,3cl2_E,3ckz_A,6v4n_I,6v4o_I,8g3z_C,1inf_A,4cpo_A,4cpl_A,1b9t_A,3k37_B,3k38_A,1a4g_A
Clustered 66 of 67 hits that have the specified 5 residues into 2 groups
> similarstructures ligands ofStructures
> 1inh_A,6lxk_C,5nwe_C,8g3r_E,2ht5_A,8g3m_L,8g3o_H,4mc7_D,2cml_A,4b7j_A,2hu4_C,1iny_A,1nma_N,4k3y_C,2htv_A,2b8h_D,1l7g_A,4k3y_D,8g30_M,1nmb_N,5hug_A,7u4e_A,6lxi_B,7e6q_B,4mjv_A,4ks1_A,4mju_A,4d8s_A,6pzy_A,5hun_A,4wa3_A,4wa4_A,6q20_A,4gdj_A,4gdj_C,4gdj_B,4gdj_D,4gez_C,2aep_A,7s0i_A,6n6b_A,8dwb_AAA,5huk_D,6br5_A,4h52_A,4h53_D,4k1j_A,7u4g_A,6pzf_B,6pzd_A,4hzv_A,4hzy_A,6nn9_A,6g01_A,2bat_A,3cl2_E,3ckz_A,6v4n_I,6v4o_I,8g3z_C,1inf_A,4cpo_A,4cpl_A,1b9t_A,3k37_B,3k38_A,1a4g_A
Found 4680 ligands in 57 hits: CA, EDO, EPE, GLC, GOL, HOH, NAG, SO4, YT3, ZMR
> hide #2 models
> show #2 models
> hide #2 models
> hide solvent
> hide #1 atoms
> hide #!3 models
> show #!3 models
> open 2cml
2cml title:
Structure of Neuraminidase from English Duck Subtype N6 Complexed with 30 MM
ZANAMIVIR, Crystal Soaked for 3 Hours at 291 K. [more info...]
Chain information for 2cml #4
---
Chain | Description | UniProt
A B C D | NEURAMINIDASE | Q6XV27_9INFA 88-476 1088-1476 2088-2476 3088-3476
Non-standard residues in 2cml #4
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
CA — calcium ion
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
ZMR — zanamivir (4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID;
4-guanidino-Neu5Ac2en; MODIFIED SIALIC ACID)
Deleted 3 extra chains, 15 C-terminal residues, 1 N-terminal residues.
Alignment of 2cml chain A to query has RMSD 1.33 using 71 of 329 paired
residues within cutoff distance 2.0
> ui tool show "Side View"
> sequence search #1/A
Found 158 similar structures to 8xps #1/A in pdb database using mmseqs2, name
mm1
> open /Users/goddard/Downloads/ChimeraX/Foldseek/8xps_foldseek_pdb_1.sms
> format sms
Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/Foldseek/8xps_foldseek_pdb_1.sms
---
note | Found 194 similar structures to 8xps #1/A in pdb database using foldseek, name fs1
Read 194 similar structures to 8xps #1/A in pdb database using foldseek, name
fs1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9.dev202407250342 (2024-07-25)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.0, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: MK1H3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 16 days, 19 hours, 3 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.14
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202407250342
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.3
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.7
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.5
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.1.18
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.1.5
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.13
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.3
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.40.1
ChimeraX-Ummbas-Anaglyph: 0.1
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.2
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.3
jedi: 0.19.1
Jinja2: 3.1.4
joblib: 1.4.2
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
llvmlite: 0.43.0
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.60.0
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.1.2
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt_toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.17.2
pynmrstar: 3.3.4
pynndescent: 0.5.13
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject_hooks: 1.1.0
PyQt6: 6.7.0
PyQt6-Qt6: 6.7.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.2
PyQt6-WebEngineSubwheel-Qt6: 6.7.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.2
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.32.3
scikit-learn: 1.5.1
scipy: 1.13.0
setuptools: 70.3.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
Sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.6
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.8
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia_utils: 1.5.1
threadpoolctl: 3.5.0
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
tqdm: 4.66.4
traitlets: 5.14.2
typing_extensions: 4.12.2
tzdata: 2024.1
umap-learn: 0.5.6
urllib3: 2.2.2
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Attachments (1)
Change History (8)
comment:1 by , 13 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash disconnecting hdmi projector, Mac, Qt 6.7.2 |
comment:2 by , 13 months ago
Was not able to reproduce this crash in about 10 tries with Mac laptop connected to work Philips desktop display.
Tried to reproduced the crash using same projector in room N436. Tried 4 times disconnecting the display. Never crashed.
comment:3 by , 13 months ago
Maybe this Qt ticket reported September 2024 is related, involves fullscreen app on Mac then disconnecting display
by , 13 months ago
| Attachment: | ChimeraX-2024-09-19-123426.ips added |
|---|
Crash log for this crash taken from Mac laptop. May be easier to read than version in Trac description.
comment:4 by , 13 months ago
The crash report lists
"procRole" : "Background",
Most Mac crash reports say Foreground. So maybe the crash needs the ChimeraX to be Background whatever that means. Maybe it means it is not the focused app or maybe it means it is sleeping.
Apple docs don't say much about procRole but I bet that is key to reproducing the crash
https://developer.apple.com/documentation/xcode/interpreting-the-json-format-of-a-crash-report
https://developer.apple.com/documentation/kernel/task_role_t
I should try giving the focus to another app (e.g. Safari) and then send abort signal to ChimeraX and see if its procRole is background. If so I should test connecting/disconnecting displays and waking from sleep when ChimeraX is background. If I can reproduce the crash I can test Qt 6.7.3 or 6.8.0 and also try work-arounds to avoid the crash.
Testing shows if I start ChimeraX and kill it with "kill -s ABRT <pid>" from a Terminal window that has the focus then the procRole of ChimeraX is "background". I run kill within about 30 seconds of starting ChimeraX. So it appears procRole just indicates whether ChimeraX has the input focus. And all the crashes show it is background. So my tests should have another app in the foreground.
comment:5 by , 13 months ago
I tried unplugging display as was done in this crash a dozen times with 3 different displays (UHD with usb3 to display port cable, HD display with hdmi cable, 4K TV display with hdmi cable) and different cables with mirroring and without, with ChimeraX 1.8 and daily build. It never crashed. I always put gave either a terminal or Safari the focus. Sometimes I waited a minute, sometimes I set the display to sleep after 1 minute then unplugged after it slept. Tried with laptop plugged into power (was not plugged in when crash in this report happened). Never crashed ChimeraX.
comment:6 by , 13 months ago
Ticket #15277 is this same problem where I describe work-arounds I put in for the ChimeraX 1.8 release. One of those was to avoid calling Qt OpenGL doneCurrent(). I only did that for the main graphics window. The status line also has an OpenGL context and may be involved in the crashes. But it does not call done_current() and instead restores the previous context with a make_current() call.
Other tools that call done_current() are Side View, Segmentations, GLTF save, Looking Glass. It could be that Side View is up when the crashes happen. I think I used Side View in the group meeting presentation where it crashed to clip to give a clear picture of the zanamivir ligand and near by protein backbone. Yes it is shown in the log.
My work-around blocks done_current() for the main graphics only after a screen is added. Maybe if I block done_current() in all cases on Mac (including for Side View) then this crash could be avoided. I suspect the crash reported in this ticket was related to Side View's done_current() call. Actually I probably plugged in the projector before starting ChimeraX, so it would not have blocked done_current() even for the main graphics.
When trying to reproduce the crash I should disable my previous work-arounds to make it more likely to get a reproducible case.
comment:7 by , 13 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Further attempts to reproduce this crash in ticket #16083 failed. The analysis in that ticket suggests that this crash is extremely rare, in the current ChimeraX daily builds, this being the only report using Qt 6.7. While the similar crash in 1.8 constituted 20% of all bug reports, in the daily builds this is the only report among 51 bug reports using Qt 6.7 (2% incidence). My suspicion described in #16083 is that a code change not in 1.8, made just after the release branch on May 21, 2024 assured that the ChimeraX graphics QOpenGLContext did not have its screen set to None, and that is probably what fixed this vulnerability in Qt 6.6.
Note:
See TracTickets
for help on using tickets.
Had not seen this frequently reported crash with Qt 6.7, only with Qt 6.6. So to avert the large number of crash reports we get from this bug I should look into more work arounds if I can reproduced the crash. I was giving group meeting for 90 minutes in a long ChimeraX session showing similar structures of Nipah virus and at the end of the meeting unplugged the HDMI cable to the projector with ChimeraX shown on the laptop screen and projector (mirrored) when it crashed. I think the aspect ratio of the two screen was different so my laptop screen had crop bars on top and bottom. That could be relevant to reproducing the crash. The project is the one in Genentech Hall N436, and the laptop was my work MacBook Pro M1 laptop.