NEURON 7.2 on MAC OS X 10.7.4

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pranit
Posts: 7
Joined: Mon Nov 22, 2010 4:23 pm

NEURON 7.2 on MAC OS X 10.7.4

Post by pranit »

Hi,

Im running NEURON 7.2 on MAC 10.7.4. The installation and .mod compilation were all OKAY.
But when i ran the nrngui or any .hoc file, it gave me errors as below.
XCODE were installed as version 4.3.2 (4E2002).

Thanks!
-Pranit
Process: a.out [25323]
Path: /Users/USER/Desktop/*/nrngui.app/Contents/MacOS/a.out
Identifier: edu.yale.neuron.nrngui
Version: ??? (???)
Code Type: X86 (Native)
Parent Process: launchd [122]

Date/Time: 2012-06-04 13:24:12.872 -0400
OS Version: Mac OS X 10.7.4 (11E53)
Report Version: 9

Interval Since Last Report: 106917 sec
Crashes Since Last Report: 32
Per-App Crashes Since Last Report: 30
Anonymous UUID: F88DF3E0-BA0E-43A7-8BEF-E544603F50F0

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000

VM Regions Near 0:
--> __PAGEZERO 0000000000000000-0000000000001000 [ 4K] ---/--- SM=NUL /Users/USER/Desktop/*/nrngui.app/Contents/MacOS/a.out
__TEXT 0000000000001000-0000000000003000 [ 8K] r-x/rwx SM=COW /Users/USER/Desktop/*/nrngui.app/Contents/MacOS/a.out

Application Specific Information:
objc_msgSend() selector name: absoluteURL
objc[25323]: garbage collection is OFF

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libobjc.A.dylib 0x96e85d4b objc_msgSend + 27
1 com.apple.CoreFoundation 0x99c5b399 CFURLCopyAbsoluteURL + 121
2 com.apple.CoreFoundation 0x99d6b63c _CFURLInit + 76
3 com.apple.CoreFoundation 0x99c65fda _CFURLInitWithString + 170
4 com.apple.CoreFoundation 0x99c65b4a CFURLCreateWithString + 234
5 com.apple.CoreFoundation 0x99c70d82 _CFBundleCopyResourcesDirectoryURLInDirectory + 66
6 com.apple.CoreFoundation 0x99c7031b _CFBundleAddPreferredLprojNamesInDirectory + 43
7 com.apple.CoreFoundation 0x99c71544 _CFBundleGetLanguageSearchList + 148
8 com.apple.CoreFoundation 0x99c85cd8 CFBundleCopyResourceURL + 40
9 com.apple.CoreFoundation 0x99ca91b7 CFBundleGetLocalInfoDictionary + 71
10 com.apple.CoreFoundation 0x99cd360b CFBundleGetValueForInfoDictionaryKey + 43
11 com.apple.CoreServices.CarbonCore 0x991cff29 GetBugsForOurBundleIDFromCoreservicesd + 331
12 com.apple.CoreServices.CarbonCore 0x991cfd87 _CSCheckFix + 26
13 com.apple.CoreGraphics 0x9a02351e _CGSDisplayInitialize + 288
14 com.apple.CoreGraphics 0x9a023146 cg_setup + 50
15 libsystem_c.dylib 0x92cb8487 pthread_once + 76
16 com.apple.CoreGraphics 0x9a02310f CGSInitialize + 36
17 com.apple.QD 0x90223bf0 GetCGSConnectionID + 28
18 com.apple.QD 0x90224a60 InitCursor + 20
19 edu.yale.neuron.nrngui 0x000027f9 mac_args + 41
20 edu.yale.neuron.nrngui 0x00002555 main + 213
21 edu.yale.neuron.nrngui 0x00002475 start + 53

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00126090 ebx: 0x99d6b602 ecx: 0x94b09b6c edx: 0xacf73900
edi: 0x00000000 esi: 0x00126090 ebp: 0xbfffed28 esp: 0xbfffece4
ss: 0x00000023 efl: 0x00010206 eip: 0x96e85d4b cs: 0x0000001b
ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
cr2: 0x00000000
Logical CPU: 0

Binary Images:
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0x9774c000 - 0x97753ffd com.apple.NetFS (4.0 - 4.0) <D0D59145-D211-3E7C-9062-35A2833FA99B> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
0x9776f000 - 0x97775ffd com.apple.CommerceCore (1.0 - 17) <71641C17-1CA7-3AC9-974E-AAC9EB641035> /System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.framework/Versions/A/CommerceCore
0x97816000 - 0x9781dff9 libsystem_dnssd.dylib (??? - ???) <D3A766FC-C409-3A57-ADE4-94B7688E1C7E> /usr/lib/system/libsystem_dnssd.dylib
0x97954000 - 0x979a6ff7 libFontRegistry.dylib (??? - ???) <96E9602C-DFD3-3021-8090-60228CC80D26> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
0x979ad000 - 0x979fdff8 libTIFF.dylib (??? - ???) <4DC2025D-15E7-35CA-B7C5-9F73B26C8B53> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
0x97a5a000 - 0x97a62fff com.apple.DiskArbitration (2.4.1 - 2.4.1) <28D5D8B5-14E8-3DA1-9085-B9BC96835ACF> /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
0x97b21000 - 0x97b21fff com.apple.Carbon (153 - 153) <6FF98F0F-2CDE-3888-A304-4ED447D24CE3> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
0x97b22000 - 0x97b84ffb com.apple.datadetectorscore (3.0 - 179.4) <3A418498-C189-37A1-9B86-F0ECB33AD91C> /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
0x97b85000 - 0x97be3fff com.apple.coreui (1.2.2 - 165.10) <C6B099D6-7F02-3971-99B9-E415308959CF> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
0x97ffa000 - 0x9800bfff libbsm.0.dylib (??? - ???) <54ACF696-87C6-3652-808A-17BE7275C230> /usr/lib/libbsm.0.dylib
0x9800c000 - 0x98037fff com.apple.GSS (2.2 - 2.0) <2C468B23-FA87-30B5-B9A6-8C5D1373AA30> /System/Library/Frameworks/GSS.framework/Versions/A/GSS
0x9805c000 - 0x98085ffe com.apple.opencl (1.50.69 - 1.50.69) <2601993F-F3B3-3737-91AE-4A5795C52CD5> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x98097000 - 0x9809aff7 libmathCommon.A.dylib (2026.0.0 - compatibility 1.0.0) <69357047-7BE0-3360-A36D-000F55E39336> /usr/lib/system/libmathCommon.A.dylib
0x980eb000 - 0x980ffff7 com.apple.CFOpenDirectory (10.7 - 144) <665CDF77-F0C9-3AFF-8CF8-64257268B7DD> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
0x984bb000 - 0x984bfffa libcache.dylib (47.0.0 - compatibility 1.0.0) <98A82BC5-0DD9-3212-9CAE-35A77278EEB6> /usr/lib/system/libcache.dylib
0x9854f000 - 0x985a0ff9 com.apple.ScalableUserInterface (1.0 - 1) <C3FA7E40-0213-3ABC-A006-2CB00B6A7EAB> /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserInterface
0x985fb000 - 0x9874dfff com.apple.audio.toolbox.AudioToolbox (1.7.2 - 1.7.2) <E369AC9E-F548-3DF6-B320-9D09E486070E> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
0x9874e000 - 0x9874efff com.apple.Accelerate.vecLib (3.7 - vecLib 3.7) <22997C20-BEB7-301D-86C5-5BFB3B06D212> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x9874f000 - 0x98750ff7 libsystem_sandbox.dylib (??? - ???) <EBC6ED6B-7D94-32A9-A718-BB9EDA1732C9> /usr/lib/system/libsystem_sandbox.dylib
0x98751000 - 0x98780ff7 libsystem_info.dylib (??? - ???) <37640811-445B-3BB7-9934-A7C99848250D> /usr/lib/system/libsystem_info.dylib
0x98783000 - 0x987abff7 libxslt.1.dylib (3.24.0 - compatibility 3.0.0) <AB530FB2-8BD1-3328-95E8-CF449F0429CA> /usr/lib/libxslt.1.dylib
0x989cb000 - 0x98adafff com.apple.DesktopServices (1.6.3 - 1.6.3) <18CAAA9E-7065-3FF7-ACFE-CDB60E5426A2> /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
0x98adb000 - 0x98becff7 libJP2.dylib (??? - ???) <845C74F4-1074-3983-945F-EB669538CAA9> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
0x98bed000 - 0x99062ff7 FaceCoreLight (1.4.7 - compatibility 1.0.0) <3E2BF587-5168-3FC5-9D8D-183A9C7C1DED> /System/Library/PrivateFrameworks/FaceCoreLight.framework/Versions/A/FaceCoreLight
0x991ab000 - 0x991b6fff libkxld.dylib (??? - ???) <D8ED88D0-7153-3514-9927-AF15A12261A5> /usr/lib/system/libkxld.dylib
0x991b7000 - 0x994b9fff com.apple.CoreServices.CarbonCore (960.24 - 960.24) <9692D838-85A5-32C1-B7FB-7C141FFC2557> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
0x996d5000 - 0x996d6ff7 libquarantine.dylib (36.6.0 - compatibility 1.0.0) <600909D9-BD75-386E-8D3E-7CBD29079DF3> /usr/lib/system/libquarantine.dylib
0x99985000 - 0x99a48fff com.apple.CoreServices.OSServices (478.46 - 478.46) <F2063FC8-2BE1-3B97-98AF-8796B0D4BE58> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
0x99a49000 - 0x99b41ff7 libFontParser.dylib (??? - ???) <1A0DA421-62B2-3AA7-9F62-0E01C1887D09> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
0x99b42000 - 0x99b43fff liblangid.dylib (??? - ???) <C8C204E9-1785-3785-BBD7-22D59493B98B> /usr/lib/liblangid.dylib
0x99b44000 - 0x99b44ff0 com.apple.ApplicationServices (41 - 41) <BED33E1D-C95C-3654-9A3A-0CB3607F9F10> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x99b45000 - 0x99c35ff1 libiconv.2.dylib (7.0.0 - compatibility 7.0.0) <9E5F86A3-8405-3774-9E0C-3A074273C96D> /usr/lib/libiconv.2.dylib
0x99c43000 - 0x99e1afe7 com.apple.CoreFoundation (6.7.2 - 635.21) <4D1D2BAF-1332-32DF-A81B-7E79D4F0A6CB> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x9a022000 - 0x9a94c59b com.apple.CoreGraphics (1.600.0 - ???) <62026E0C-E30F-3FF0-B0F6-6A2D270B20BF> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
0x9abcc000 - 0x9ac2dffb com.apple.audio.CoreAudio (4.0.2 - 4.0.2) <AA6EAFB8-1C27-3D42-B1CD-3A1258C198D9> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
0x9ac9d000 - 0x9acb7fff com.apple.Kerberos (1.0 - 1) <D7920A1C-FEC4-3460-8DD0-D02491578CBB> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
0x9acb8000 - 0x9acdaffe com.apple.framework.familycontrols (3.0 - 300) <5BCCDDC2-AFAC-3290-AEEF-23B2664CA11F> /System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyControls
0x9ad06000 - 0x9ad93fe7 libvMisc.dylib (325.4.0 - compatibility 1.0.0) <F2A8BBA3-6431-3CED-8CD3-0953410B6F96> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
0x9ada8000 - 0x9b01bffb com.apple.CoreImage (7.98 - 1.0.1) <EDC91BA1-673D-3B47-BFD5-BBF11C36EE6A> /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Versions/A/CoreImage
0x9b3d5000 - 0x9b3d5fff libdnsinfo.dylib (395.11.0 - compatibility 1.0.0) <7EFAD88C-AFBC-3D48-BE14-60B8EACC68D7> /usr/lib/system/libdnsinfo.dylib
0x9bb28000 - 0x9bc10fff libxml2.2.dylib (10.3.0 - compatibility 10.0.0) <1841196F-68B5-309F-8ED1-6714B1DFEC83> /usr/lib/libxml2.2.dylib
0x9bc11000 - 0x9bc13ffb libRadiance.dylib (??? - ???) <4721057E-5A1F-3083-911B-200ED1CE7678> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
0x9bcd2000 - 0x9bd5cffb com.apple.SearchKit (1.4.0 - 1.4.0) <CF074082-64AB-3A1F-831E-582DF1667827> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
0x9bd5d000 - 0x9bd61ff7 com.apple.OpenDirectory (10.7 - 146) <CFBA4CCF-65D4-3879-BC6A-8888C13E3345> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
0x9bd62000 - 0x9bdfefef com.apple.ink.framework (1.4 - 110) <1A3E2916-60C1-3AC1-86BF-202F6567B228> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
0x9bdff000 - 0x9be12ff8 com.apple.MultitouchSupport.framework (231.4 - 231.4) <083F7787-4C3B-31DA-B5BB-1993D9A9723D> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
0x9be35000 - 0x9be35ff2 com.apple.CoreServices (53 - 53) <7CB7AA95-D5A7-366A-BB8A-035AA9E582F8> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
0x9be36000 - 0x9be54ff7 libsystem_kernel.dylib (1699.26.8 - compatibility 1.0.0) <3705DE40-E00F-3E37-ADB0-D4AE5F9950F5> /usr/lib/system/libsystem_kernel.dylib
0x9c0db000 - 0x9c5b7ff6 libBLAS.dylib (??? - ???) <134ABFC6-F29E-3DC5-8E57-E13CB6EF7B41> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x9c7e5000 - 0x9c813ff7 com.apple.DictionaryServices (1.2.1 - 158.2) <DA16A8B2-F359-345A-BAF7-8E6A5A0741A1> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
0x9c860000 - 0x9c8d6fff com.apple.Metadata (10.7.0 - 627.32) <650EE880-1488-3DC6-963B-F3D6E043FFDC> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
0x9c8d7000 - 0x9c8dfff3 liblaunch.dylib (392.38.0 - compatibility 1.0.0) <D7F6E875-263A-37B5-B403-53F76710538C> /usr/lib/system/liblaunch.dylib
0x9c8e0000 - 0x9cc26ff3 com.apple.HIToolbox (1.9 - ???) <409E6397-0DCB-3431-9CCC-368317C62545> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
0x9cc79000 - 0x9cc7aff4 libremovefile.dylib (21.1.0 - compatibility 1.0.0) <6DE3FDC7-0BE0-3791-B6F5-C15422A8AFB8> /usr/lib/system/libremovefile.dylib
0x9ceb2000 - 0x9ceb4ff7 libdyld.dylib (195.5.0 - compatibility 1.0.0) <637660EA-8D12-3B79-B644-041FEADC9C33> /usr/lib/system/libdyld.dylib
0x9ceb5000 - 0x9cefdff7 com.apple.SystemConfiguration (1.11.3 - 1.11) <68B92FEA-F754-3E7E-B5E6-D512E26144E7> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 1
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: 8783
thread_create: 1
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=115.1M resident=73.8M(64%) swapped_out_or_unallocated=41.3M(36%)
Writable regions: Total=17.3M written=120K(1%) resident=244K(1%) swapped_out=0K(0%) unallocated=17.0M(99%)

REGION TYPE VIRTUAL
=========== =======
MALLOC 9316K
MALLOC guard page 16K
Stack 64.0M
__CI_BITMAP 80K
__DATA 6580K
__DATA/__OBJC 60K
__IMPORT 4K
__LINKEDIT 41.9M
__OBJC 512K
__PAGEZERO 4K
__TEXT 73.2M
__UNICODE 544K
mapped file 135.2M
shared memory 12K
shared pmap 11.8M
=========== =======
TOTAL 342.8M

Model: MacBookPro8,1, BootROM MBP81.0047.B0E, 2 processors, Intel Core i7, 2.7 GHz, 8 GB, SMC 1.68f96
Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In, 512 MB
Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1333 MHz, 0x80AD, 0x484D54333531533642465238432D48392020
Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1333 MHz, 0x80AD, 0x484D54333531533642465238432D48392020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xD6), Broadcom BCM43xx 1.0 (5.106.198.4.20)
Bluetooth: Version 4.0.5f11, 2 service, 18 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en1
Serial ATA Device: TOSHIBA MK7559GSXF, 750.16 GB
Serial ATA Device: MATSHITADVD-R UJ-8A8
USB Device: FaceTime HD Camera (Built-in), apple_vendor_id, 0x8509, 0xfa200000 / 3
USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfa100000 / 2
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0xfa110000 / 5
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821a, 0xfa113000 / 8
USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x0252, 0xfa120000 / 4
USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfd100000 / 2
USB Device: IR Receiver, apple_vendor_id, 0x8242, 0xfd110000 / 3
hines
Site Admin
Posts: 1600
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON 7.2 on MAC OS X 10.7.4

Post by hines »

So it crashed even before it got to the NEURON banner.
I don't have a 10.7 machine but I may need one to reproduce that problem and fix it.
It may be that my convoluted launch process is at fault. Please start a termina window
and see if you can launch nrniv directly. If you installed in /Applications the the command would be
/Applications/NEURON-7.2/nrn/i386/bin/nrniv
(I'm not sure about the 'i386' part, check if it should be i686 or umac.)
As a long shot, can you tell me if you get the same problem with
http://www.neuron.yale.edu/ftp/neuron/v ... 10.8.0.dmg
hines
Site Admin
Posts: 1600
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON 7.2 on MAC OS X 10.7.4

Post by hines »

I meant 'terminal', not 'termina'
pranit
Posts: 7
Joined: Mon Nov 22, 2010 4:23 pm

Re: NEURON 7.2 on MAC OS X 10.7.4

Post by pranit »

Yes it crashed before the banner.

I had installed on Desktop and got the following error msg :
dyld: Library not Loaded: /Applications/NEURON-7.2/nrn/i386/lib/library.dyld
Then i found out that neuron was not installed in application folder. So i moved it to applications folder and it worked.....

Thanks......
hines
Site Admin
Posts: 1600
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON 7.2 on MAC OS X 10.7.4

Post by hines »

Ok. It is my intention that NEURON be able to run from any install location.
I'll have to figure out why that is not the case. Til then, it is useful to know that you can get
the error you mentioned when NEURON-7.x is not located in /Applications
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