![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 2 years ago
#8827 closed defect (duplicate)
Out of memory after opening small mmCIF 7phr on Mac. Also ssl certificate error from Toolshed update.
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | high | Milestone: | 1.7 |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304070153 (2023-04-07 01:53:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700015f3b000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700014f38000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700013f35000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700012f32000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700011f2f000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700010f2c000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070000ff29000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000105bec600 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-04-13 09:06:28.00 -0700","app_version":"1.6.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.6.2 (21G320)","incident_id":"C74EAD72-2E30-44A3-8D53-189B719BB039","name":"ChimeraX"}
{
"uptime" : 50000,
"procLaunch" : "2023-04-12 19:56:43.4986 -0700",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro13,2",
"procStartAbsTime" : 49733444579496,
"coalitionID" : 8328,
"osVersion" : {
"train" : "macOS 12.6.2",
"build" : "21G320",
"releaseType" : "User"
},
"captureTime" : "2023-04-13 09:05:35.6960 -0700",
"incident" : "C74EAD72-2E30-44A3-8D53-189B719BB039",
"bug_type" : "309",
"pid" : 42506,
"procExitAbsTime" : 50983485177420,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E3FDEAD0-68FD-5845-B695-52894B332E63","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "41643F83-BC13-7B04-166A-C2D60850F66E",
"wakeTime" : 8,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "388C6557-F551-4875-8423-9DC7E114FFF9",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486536680\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe44000-7fffffe45000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486536680\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe44000-7fffffe45000 [ 4K] r-x\/r-x SM=ALI ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4335562752,
"size" : 8192,
"uuid" : "1eae6074-8612-3bc6-b16b-c173a995e90c",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so",
"name" : "_queue.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4317036544,
"size" : 20480,
"uuid" : "2f042ce6-bef0-3ad9-97f5-2da7655122a4",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so",
"name" : "select.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4481118208,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703543721984,
"size" : 19331678208,
"uuid" : "3172f8f5-c412-3210-95e0-1cfd89e01f8a"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=13.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=13.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 116K 15 \nColorSync 224K 26 \nCoreAnimation 232K 21 \nCoreGraphics 16K 3 \nCoreUI image data 2532K 29 \nFoundation 16K 1 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 12.7G 720 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 124K 31 \nStack 274.7M 32 \nStack Guard 56.0M 1 \nVM_ALLOCATE 83.7M 115 \n__CTF 756 1 \n__DATA 45.0M 671 \n__DATA_CONST 32.4M 337 \n__DATA_DIRTY 1641K 212 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 675.9M 149 \n__TEXT 822.2M 670 \n__UNICODE 592K 1 \ndyld private memory 1056K 3 \nmapped file 112.4M 42 \nshared memory 2984K 26 \n=========== ======= ======= \nTOTAL 15.0G 3139 \nTOTAL, minus reserved VM space 14.8G 3139 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
},
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
}
],
"experiments" : [
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000013
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)
UCSF ChimeraX version: 1.6rc202304070153 (2023-04-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
2023-04-12 19:57:29,702 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)'))':
/cxservices/api/v1/chimerax/updates?uuid=0babdd10-85e2-57fa-
ade8-4b691a471813&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.6rc202304070153
2023-04-12 19:57:29,760 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)'))':
/cxservices/api/v1/chimerax/updates?uuid=0babdd10-85e2-57fa-
ade8-4b691a471813&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.6rc202304070153
> open /Users/tholenj/Downloads/7phr.cif
Summary of feedback from opening /Users/tholenj/Downloads/7phr.cif
---
warning | Unable to fetch template for 'NAG': might have incorrect bonds
7phr.cif title:
Structure of a fully assembled T-cell receptor engaging a tumor-associated
peptide-MHC I [more info...]
Chain information for 7phr.cif #1
---
Chain | Description | UniProt
A | T-cell receptor alpha chain |
B | T-cell receptor beta chain |
C | T-cell surface glycoprotein CD3 gamma chain | CD3G_HUMAN 1-122
D | T-cell surface glycoprotein CD3 delta chain, green fluorescent protein |
CD3D_HUMAN 1-111, GFP_AEQVI 118-356
E e | T-cell surface glycoprotein CD3 epsilon chain | CD3E_HUMAN 1-136
H | HLA class I histocompatibility antigen, A alpha chain | HLAA_HUMAN 1-280
L | Beta-2-microglobulin | B2MG_HUMAN 0-99
P | Tumor-associated antigentic peptide gp100 | PMEL_HUMAN 1-9
Z z | T-cell surface glycoprotein CD3 zeta chain | CD3Z_HUMAN 1-36
Non-standard residues in 7phr.cif #1
---
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)
> hide atoms
> show cartoons
> sequence chain #1/D
Alignment identifier is 1/D
> select /D:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /D:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> select /C:3-116
872 atoms, 892 bonds, 114 residues, 1 model selected
> sequence chain #1/C
Alignment identifier is 1/C
> select /C:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C:3-6
22 atoms, 21 bonds, 4 residues, 1 model selected
> sequence chain #1/E#1/e
Alignment identifier is 1
> select /E,e:11-13
46 atoms, 46 bonds, 6 residues, 1 model selected
> sequence chain #1/L
Alignment identifier is 1/L
> select /L:1-99
829 atoms, 853 bonds, 99 residues, 1 model selected
> open P61769 fromDatabase uniprot
Cannot open 'P61769':
> sequence chain #1/Z#1/z
Alignment identifier is 2
> select /Z:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /Z:2-3
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /Z:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /Z,z
506 atoms, 517 bonds, 63 residues, 1 model selected
> select /Z:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /Z:2-3
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /Z:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /Z:2-3
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /Z:1-2
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /Z:1-2
15 atoms, 14 bonds, 2 residues, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:9-14
43 atoms, 43 bonds, 6 residues, 1 model selected
> sequence chain #1/B
Alignment identifier is 1/B
> select /B:2-7
37 atoms, 36 bonds, 6 residues, 1 model selected
> select /A:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:15-18
31 atoms, 30 bonds, 4 residues, 1 model selected
> select /A:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:9-12
29 atoms, 29 bonds, 4 residues, 1 model selected
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.6rc202304070153 (2023-04-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)
> open /Users/tholenj/Downloads/7phr.cif
Summary of feedback from opening /Users/tholenj/Downloads/7phr.cif
---
warning | Unable to fetch template for 'NAG': might have incorrect bonds
7phr.cif title:
Structure of a fully assembled T-cell receptor engaging a tumor-associated
peptide-MHC I [more info...]
Chain information for 7phr.cif #1
---
Chain | Description | UniProt
A | T-cell receptor alpha chain |
B | T-cell receptor beta chain |
C | T-cell surface glycoprotein CD3 gamma chain | CD3G_HUMAN 1-122
D | T-cell surface glycoprotein CD3 delta chain, green fluorescent protein |
CD3D_HUMAN 1-111, GFP_AEQVI 118-356
E e | T-cell surface glycoprotein CD3 epsilon chain | CD3E_HUMAN 1-136
H | HLA class I histocompatibility antigen, A alpha chain | HLAA_HUMAN 1-280
L | Beta-2-microglobulin | B2MG_HUMAN 0-99
P | Tumor-associated antigentic peptide gp100 | PMEL_HUMAN 1-9
Z z | T-cell surface glycoprotein CD3 zeta chain | CD3Z_HUMAN 1-36
Non-standard residues in 7phr.cif #1
---
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)
OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro13,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 499.40.2.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.37f25
Software:
System Software Overview:
System Version: macOS 12.6.2 (21G320)
Kernel Version: Darwin 21.6.0
Time since boot: 2 days 21:52
Graphics/Displays:
Intel Iris Graphics 550:
Chipset Model: Intel Iris Graphics 550
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1927
Revision ID: 0x000a
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
DELL U3421WE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 727X653
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: ff.c1
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202304070153
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.1.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (7)
comment:1 by , 3 years ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Window Toolkit → Input/Output |
| Milestone: | → 1.6 |
| Owner: | changed from to |
| Priority: | normal → high |
| Summary: | QPainter::begin: Paint device returned engine == 0 → Out of memory after opening small mmCIF 7phr on Mac. Also ssl certificate error from Toolshed update. |
This problem appears to be ChimeraX running out of memory after opening PDB 7phr (only 11500 atoms) in mmCIF file. That is the only file opened and the Mac crash says
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Compressor failed a blocking pager_get\n",
and it says ChimeraX was using 15 GB with 12.7 GB allocated by malloc(). I suspect the crash was from a small allocation that failed and was unchecked and caused a segfault. I guess this is the same out-of-memory error we have seen multiple times on Windows. I think this has to be fixed for the 1.6 release.
Also in the Log for this bug report we see both in the crash log and after at the next startup the Toolshed update failed with an SSL certificate error.
Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129)
comment:3 by , 3 years ago
I don't think this one is that memory error. The user successfully opened 7phr (no MemoryError thrown) and then reported the previous crash, whose log ended with "QPainter::begin: Paint device returned engine == 0, type: 3" and whose stack trace ended in painting various Qt widgets. The certificate thing is certainly a problem though.
follow-up: 4 comment:4 by , 3 years ago
It did not get an out of memory error in the mmCIF reader in this crash report. But the log shows only opening 7phr, doing some selection commands and sequence and hide atoms resulting in 15 GB of memory use which is not the usual loading shared libraries, it is in malloc. So I am guessing the crash in Qt was simply Qt failed in a memory allocation. But the guess (only a guess) is that the high memory use was from opening the mmCIF file since we have seen that several times in the last month on Windows on machines with 4 - 16 GB of memory. I'm not at all sure if it is related to the mmCIF out-of-memory reports, but I mentioned it because if it is then the mmCIF problem on Windows is not specific to Windows.
comment:5 by , 3 years ago
The "[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129)" error is probably due to anti-virus or VPN software. ChimeraX depends on the root certificates in the certifi package, not the Apple keychain. So root certificates that are installed by such software to do man-in-the-middle decryption/attacks of encrypted web traffic will not work.
comment:7 by , 2 years ago
| Description: | modified (diff) |
|---|---|
| Resolution: | → duplicate |
| Status: | assigned → closed |
The out of memory bug is a duplicate of #8815 and is fixed in the daily build. The SSL certificate bug appears to be gone.
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Seems similar to #7739