Closed MarcoVando closed 2 weeks ago
Process: python3.10 [77047] Path: /Users/USER/*/GSAS-II.app/Contents/MacOS/GSAS-II Identifier: python3.10 Version: ??? Code Type: ARM-64 (Native) Parent Process: zsh [77026] Responsible: Terminal [76989] User ID: 501
Date/Time: 2024-07-17 10:22:23.0895 +0200 OS Version: macOS 14.2.1 (23C71) Report Version: 12 Anonymous UUID: 33538B53-E95C-E28D-F034-B3CFC202AC76
Sleep/Wake UUID: A1AB8E64-EED8-4FD9-83B1-2C5A965A4427
Time Awake Since Boot: 170000 seconds Time Since Wake: 1014 seconds
System Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x000058050ce06880 Exception Codes: 0x0000000000000001, 0x000058050ce06880
Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [77047]
VM Region Info: 0x58050ce06880 is not in any region. Bytes after previous region: 96297677777025 Bytes before following region: 8774402152320 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL commpage (reserved) 1000000000-7000000000 [384.0G] ---/--- SM=NUL ...(unallocated) ---> GAP OF 0x5f9000000000 BYTES MALLOC_NANO 600000000000-600020000000 [512.0M] rw-/rwx SM=PRV
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_platform.dylib 0x1808d16e0 _platform_memmove + 144
1 libc++.1.dylib 0x1807d2d90 std::1::basic_string<wchar_t, std::1::char_traits
Thread 1: 0 libsystem_pthread.dylib 0x18089ce28 start_wqthread + 0
Thread 2: 0 libsystem_pthread.dylib 0x18089ce28 start_wqthread + 0
Thread 3:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x180861874 mach_msg2_trap + 8 1 libsystem_kernel.dylib 0x180873cf0 mach_msg2_internal + 80 2 libsystem_kernel.dylib 0x18086a4b0 mach_msg_overwrite + 476 3 libsystem_kernel.dylib 0x180861bf8 mach_msg + 24 4 CoreFoundation 0x18097fbf4 CFRunLoopServiceMachPort + 160 5 CoreFoundation 0x18097e4bc CFRunLoopRun + 1208 6 CoreFoundation 0x18097d9ac CFRunLoopRunSpecific + 608 7 AppKit 0x184284510 _NSEventThread + 144 8 libsystem_pthread.dylib 0x1808a2034 _pthread_start + 136 9 libsystem_pthread.dylib 0x18089ce3c thread_start + 8
Thread 4: 0 libsystem_pthread.dylib 0x18089ce28 start_wqthread + 0
Thread 5: 0 libsystem_pthread.dylib 0x18089ce28 start_wqthread + 0
Thread 0 crashed with ARM Thread State (64-bit): x0: 0x000000015e315da0 x1: 0x000058050ce06880 x2: 0x0000000000000148 x3: 0x000000015e315dc0 x4: 0x00005803aeaf0ae0 x5: 0x0000000000003540 x6: 0x000000016ae85420 x7: 0x000000012857f213 x8: 0x0000000000000144 x9: 0x0000000000000103 x10: 0x0000000008000180 x11: 0x0000000000000100 x12: 0x0000000000000100 x13: 0x0000000008000180 x14: 0x000000007fffffff x15: 0x0000000000000100 x16: 0x00000001808d1650 x17: 0x00000001e00ef980 x18: 0x0000000000000000 x19: 0x0000600001eb7540 x20: 0x00000001597045d0 x21: 0x000000012868ee80 x22: 0x00000001285ec448 x23: 0x0000000000000000 x24: 0x0000000000000001 x25: 0x000000012971bbf8 x26: 0x00000001597045d0 x27: 0x0000000105022aec x28: 0x000000012971bbf0 fp: 0x000000016ae853f0 lr: 0x00000001807d2d90 sp: 0x000000016ae853e0 pc: 0x00000001808d16e0 cpsr: 0x80001000 far: 0x000058050ce06880 esr: 0x92000005 (Data Abort) byte read Translation fault
Binary Images:
0x15d544000 - 0x15d547fff com.apple.TextInputUIMac.axbundle (1.0)
External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0
VM Region Summary: ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%) Writable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG image 5184K 48 CG raster data 4944K 3 ColorSync 640K 32 CoreAnimation 7040K 205 CoreGraphics 64K 4 CoreGraphics (reserved) 32K 2 reserved VM address space (unallocated) CoreImage 32K 1 CoreUI image data 4800K 35 Foundation 16K 1 Kernel Alloc Once 32K 1 MALLOC 1.6G 68 MALLOC guard page 192K 12 STACK GUARD 96K 6 Stack 18.7M 6 VM_ALLOCATE 258.4M 83 VM_ALLOCATE (reserved) 288.0M 5 reserved VM address space (unallocated) AUTH 1794K 334 AUTH_CONST 26.4M 534 CTF 824 1 DATA 17.1M 735 DATA_CONST 30.6M 736 __DATA_DIRTY 1535K 174 FONT_DATA 4K 1 INFO_FILTER 8 1 LINKEDIT 921.0M 203 OBJC_RO 71.1M 1 OBJC_RW 2168K 1 __TEXT 685.9M 753 dyld private memory 544K 4 mapped file 276.4M 38 shared memory 1520K 24 =========== ======= ======= TOTAL 4.2G 4056 TOTAL, minus reserved VM space 3.9G 4056
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":77047},
"vmregioninfo" : "0x58050ce06880 is not in any region. Bytes after previous region: 96297677777025 Bytes before following region: 8774402152320\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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Model: MacBookPro18,3, BootROM 10151.61.4, proc 8:6:2 processors, 16 GB, SMC Graphics: Apple M1 Pro, Apple M1 Pro, Built-In Display: Color LCD, 3024 x 1964 Retina, Main, MirrorOff, Online Memory Module: LPDDR5, Hynix AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4387), wl0: Sep 1 2023 19:46:07 version 20.10.1073.3.8.7.165 FWID 01-b66346c5 AirPort: Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB31Bus USB Device: USB31Bus USB Device: USB31Bus Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc.
Hi Marco,
Thanks for reporting this. The usual reason why python crashes like this is that a delay is needed when updating the GUI. It only happens on the Mac (not usually Linux or Windows) and sometimes will happen on one Mac and not another. I do have an M1 laptop, so I have a good shot at trying to reproduce this. In theory the crash dump would allow me to figure out where the crash is occurring, but I'm not sure how to translate the binary info supplied into a Python code location.
Would you me able to share the .gpx file that causes the crash? If not too large, you can e-mail it to me. If too large for e-mail, use of dropbox, etc. might be a good choice. If you would rather not share it, is there a possibility to create a .gpx that shows the problem with files you can share? Alternately, I can try to debug on your computer with you over zoom -- not as easy, but this has worked.
Brian
Yep, I'll try to create a gpx file that can replicate the bug. Thank you so much
Anything new on this? Is it still happening for you? If so, perhaps I can debug it with you over Zoom.
I'll close this ticket for now, but feel free to reopen it.
I tried to reproduce the error with another dataset but I failed. I think there were some problems with the way I imported datafiles and set up GSAS for the fitting. Looks fine now
I do suspect there is a bug here, but may only surface when the computer running the code is particularly busy, or... If you do see it again, please let me know. Brian
Hi, I was trying to do a lebail fitting of multiple patterns at the same time without using the sequential refinement. As soon as the first LeBail cycle has been done and I click ok to run the other cycles GSAS crashes. To do that I've created the phase, linked the histograms (just 2) and turned on the lebail extraction. Prior to this I refined the first histogram with the same phase and everything worked well. just before starting the refinement, I've deleted the plot as if I start the procedure with the plot window displaying one of the two histograms, refinement got stucked (prob for some matplotlib related issues) Is it possible to do this procedure?