ElmerGUI crash when loading a gmsh mesh

The graphical user interface of Elmer
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einatlev
Posts: 47
Joined: 13 Jan 2010, 06:54

ElmerGUI crash when loading a gmsh mesh

Post by einatlev »

Hello all
I am trying to load a mesh created in gmsh and converted to Elmer format using the command "ElmerGrid 14 2".
ElmerGUI simply crashes when I try to load the mesh.
Attached are the Elmer format mesh files.
I'm running on MacOS 10.6. I couldn't find the version numbers for ElmerGUI or ElmerGrid.
Thanks!!


This is the output in the error window:
Process: ElmerGUI [32761]
Path: /Applications/ElmerGUI.app/Contents/MacOS/ElmerGUI
Identifier: ElmerGUI
Version: ??? (???)
Code Type: X86 (Native)
Parent Process: launchd [90]

Date/Time: 2011-07-17 16:11:01.371 -0400
OS Version: Mac OS X 10.6.7 (10J869)
Report Version: 6

Interval Since Last Report: 318603 sec
Crashes Since Last Report: 9
Per-App Crashes Since Last Report: 7
Anonymous UUID: 180E367A-152B-4287-AE5D-5EB680A6FB03

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x000000009ed4f01f
Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 ElmerGUI 0x00056958 Meshutils::findSurfaceElementEdges(mesh_t*) + 530
1 ElmerGUI 0x0003fe42 MainWindow::loadElmerMesh(QString) + 5814
2 ElmerGUI 0x000432ef MainWindow::loadSlot() + 399
3 ElmerGUI 0x000bf84f MainWindow::qt_metacall(QMetaObject::Call, int, void**) + 477
4 ElmerGUI 0x00807103 QMetaObject::activate(QObject*, int, int, void**) + 1373
5 ElmerGUI 0x00807391 QMetaObject::activate(QObject*, QMetaObject const*, int, int, void**) + 171
6 ElmerGUI 0x001e0631 QAction::triggered(bool) + 83
7 ElmerGUI 0x001e0e17 QAction::activate(QAction::ActionEvent) + 261
8 ElmerGUI 0x00642c78 qt_mac_activate_action(OpaqueMenuRef*, unsigned int, QAction::ActionEvent, bool) + 508
9 ElmerGUI 0x006432af qt_mac_menu_event(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 951
10 com.apple.HIToolbox 0x93617c2f DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1567
11 com.apple.HIToolbox 0x93616ef6 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 411
12 com.apple.HIToolbox 0x936397f3 SendEventToEventTarget + 52
13 com.apple.HIToolbox 0x93665e87 SendHICommandEvent(unsigned long, HICommand const*, unsigned long, unsigned long, unsigned char, void const*, OpaqueEventTargetRef*, OpaqueEventTargetRef*, OpaqueEventRef**) + 448
14 com.apple.HIToolbox 0x9368ab90 SendMenuCommandWithContextAndModifiers + 66
15 com.apple.HIToolbox 0x9368ab47 SendMenuItemSelectedEvent + 121
16 com.apple.HIToolbox 0x9368aa5d FinishMenuSelection(SelectionData*, MenuResult*, MenuResult*) + 152
17 com.apple.HIToolbox 0x9365a160 MenuSelectCore(MenuData*, Point, double, unsigned long, OpaqueMenuRef**, unsigned short*) + 454
18 com.apple.HIToolbox 0x9380c936 MenuSelect + 190
19 ElmerGUI 0x00248cc9 QApplicationPrivate::globalEventProcessor(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 7965
20 com.apple.HIToolbox 0x93617c2f DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1567
21 com.apple.HIToolbox 0x93616ef6 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 411
22 com.apple.HIToolbox 0x936397f3 SendEventToEventTarget + 52
23 com.apple.HIToolbox 0x9364b3ef ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 1417
24 com.apple.HIToolbox 0x93618080 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 2672
25 com.apple.HIToolbox 0x93616ef6 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 411
26 com.apple.HIToolbox 0x936397f3 SendEventToEventTarget + 52
27 ElmerGUI 0x00241b32 qt_mac_send_event(QFlags<QEventLoop::ProcessEventsFlag>, OpaqueEventRef*, OpaqueWindowPtr*) + 216
28 ElmerGUI 0x00252321 QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 859
29 ElmerGUI 0x007f1a4a QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 98
30 ElmerGUI 0x007f1bba QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 220
31 ElmerGUI 0x007f6913 QCoreApplication::exec() + 277
32 ElmerGUI 0x001e64e2 QApplication::exec() + 24
33 ElmerGUI 0x00029cc1 main + 455
34 ElmerGUI 0x0000623a start + 54

Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x946a4922 kevent + 10
1 libSystem.B.dylib 0x946a503c _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x946a44f9 _dispatch_queue_invoke + 163
3 libSystem.B.dylib 0x946a429e _dispatch_worker_thread2 + 240
4 libSystem.B.dylib 0x946a3d21 _pthread_wqthread + 390
5 libSystem.B.dylib 0x946a3b66 start_wqthread + 30

Thread 2:
0 libSystem.B.dylib 0x946a39b2 __workq_kernreturn + 10
1 libSystem.B.dylib 0x946a3f48 _pthread_wqthread + 941
2 libSystem.B.dylib 0x946a3b66 start_wqthread + 30

Thread 3:
0 libSystem.B.dylib 0x9467e09a mach_msg_trap + 10
1 libSystem.B.dylib 0x9467e807 mach_msg + 68
2 com.apple.CoreFoundation 0x991f137f __CFRunLoopRun + 2079
3 com.apple.CoreFoundation 0x991f0464 CFRunLoopRunSpecific + 452
4 com.apple.CoreFoundation 0x991f63a4 CFRunLoopRun + 84
5 com.apple.DesktopServices 0x965ccc7d TSystemNotificationTask::SystemNotificationTaskProc(void*) + 643
6 ...ple.CoreServices.CarbonCore 0x9935f7ca PrivateMPEntryPoint + 68
7 libSystem.B.dylib 0x946ab7fd _pthread_start + 345
8 libSystem.B.dylib 0x946ab682 thread_start + 34

Thread 4:
0 libSystem.B.dylib 0x946a39b2 __workq_kernreturn + 10
1 libSystem.B.dylib 0x946a3f48 _pthread_wqthread + 941
2 libSystem.B.dylib 0x946a3b66 start_wqthread + 30

Thread 5:
0 libSystem.B.dylib 0x946a39b2 __workq_kernreturn + 10
1 libSystem.B.dylib 0x946a3f48 _pthread_wqthread + 941
2 libSystem.B.dylib 0x946a3b66 start_wqthread + 30

Thread 6:
0 libSystem.B.dylib 0x946a39b2 __workq_kernreturn + 10
1 libSystem.B.dylib 0x946a3f48 _pthread_wqthread + 941
2 libSystem.B.dylib 0x946a3b66 start_wqthread + 30

Thread 7:
0 libSystem.B.dylib 0x946a39b2 __workq_kernreturn + 10
1 libSystem.B.dylib 0x946a3f48 _pthread_wqthread + 941
2 libSystem.B.dylib 0x946a3b66 start_wqthread + 30

Thread 8: com.apple.CFSocket.private
0 libSystem.B.dylib 0x9469d066 select$DARWIN_EXTSN + 10
1 com.apple.CoreFoundation 0x99230c83 __CFSocketManager + 1091
2 libSystem.B.dylib 0x946ab7fd _pthread_start + 345
3 libSystem.B.dylib 0x946ab682 thread_start + 34

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x9ed4efff ebx: 0x00056757 ecx: 0x0000001c edx: 0x00c01f68
edi: 0x00000000 esi: 0x00000003 ebp: 0xbfffd848 esp: 0xbfffd700
ss: 0x0000001f efl: 0x00010282 eip: 0x00056958 cs: 0x00000017
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
cr2: 0x9ed4f01f

Binary Images:
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0x140e9000 - 0x14261fe7 GLEngine ??? (???) <0E1DF3E4-0EEE-9FD8-8F52-FFFCF0DF23A7> /System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/GLEngine
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0x900f6000 - 0x90178ffb SecurityFoundation ??? (???) <3670AE8B-06DA-C447-EB14-79423DB9C474> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
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0x90b43000 - 0x90c45fef com.apple.MeshKitIO 1.1 (49.2) <34322CDD-E67E-318A-F03A-A3DD05201046> /System/Library/PrivateFrameworks/MeshKit.framework/Versions/A/Frameworks/MeshKitIO.framework/Versions/A/MeshKitIO
0x90c9d000 - 0x90d56fe7 libsqlite3.dylib 9.6.0 (compatibility 9.0.0) <52438E77-55D1-C231-1936-76F1369518E4> /usr/lib/libsqlite3.dylib
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0x92b79000 - 0x92b79ff7 liblangid.dylib ??? (???) <B99607FC-5646-32C8-2C16-AFB5EA9097C2> /usr/lib/liblangid.dylib
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Model: MacBookPro5,3, BootROM MBP53.00AC.B03, 2 processors, Intel Core 2 Duo, 2.8 GHz, 8 GB, SMC 1.48f2
Graphics: NVIDIA GeForce 9600M GT, NVIDIA GeForce 9600M GT, PCIe, 512 MB
Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.131.36.9)
Bluetooth: Version 2.4.0f1, 2 service, 19 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en1
Serial ATA Device: ST9320423ASG, 298.09 GB
Serial ATA Device: MATSHITADVD-R UJ-868
USB Device: Internal Memory Card Reader, 0x05ac (Apple Inc.), 0x8403, 0x26500000
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x24400000
USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x06100000
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8217, 0x06110000
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0236, 0x04600000
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x04500000

Attachments
slab.tar.gz
Mesh files
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raback
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Re: ElmerGUI crash when loading a gmsh mesh

Post by raback »

Hi, Does '-autoclean' flag in ElmerGrid help? -Peter
einatlev
Posts: 47
Joined: 13 Jan 2010, 06:54

Re: ElmerGUI crash when loading a gmsh mesh

Post by einatlev »

Yes! what is this flag? what happened?
Thanks!
studioa
Posts: 23
Joined: 23 Jul 2011, 23:39
Antispam: Yes

Re: ElmerGUI crash when loading a gmsh mesh

Post by studioa »

Sorry to piggyback on this tread, but I'm having the same issue running Elmer on a Windows 7 machine - whenever I try to load a mesh saved as .msh (from GMSH) and ElmerGUI is crashing - any suggestions appreciated - I'm trying to see if ELMER can give similar solutions to OpenFOAM in simulation of airflow in a building atrium - thanks for help!
raback
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Re: ElmerGUI crash when loading a gmsh mesh

Post by raback »

Hi

For the '-autoclean' flag look at ElmerGrid documentation, or the output that you get when calling ElmerGrid without arguments. Basically it renumbers some entities and removes obsolite ones.

-Peter
studioa
Posts: 23
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Re: ElmerGUI crash when loading a gmsh mesh

Post by studioa »

Thanks Peter -

when I run

C:\Elmer6.2\bin> ElmerGrid.exe

at the command prompt, I see:

-removeunused : remove nodes that are not used in any element
-bulkorder : renumber materials types from 1 so that every number is u
sed
-boundorder : renumber boundary types from 1 so that every number is us
ed
-autoclean : this performs the united action of the three above


I'll read the documentation.

I'm trying to explore the capabilities of Elmer for airflow circulations inside buildings. So this time I'm testing Elmer on a Win7 machine. Is it supposed that ElmerGrid to start as an independent application with its own GUI, or it is "embedded" into ElmerGUI (I'm referring to ElmerGUI 2D modeler) ? Thanks for your help!
raback
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Re: ElmerGUI crash when loading a gmsh mesh

Post by raback »

Hi

ElmerGrid is embeded in ElmerGUI but it merely handles the same files as the stand alone version. There is no modeler ralated to that. The experimental 2D modeler writes .in2d format that is treated by netgen to make Delaunay triangularizations. What preprocessors have you used previously in conjunction with OpenFOAM?

It would also be interesting to here what approach you have chosen for the problems: DNS, LES or RANS?

-Peter
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Re: ElmerGUI crash when loading a gmsh mesh

Post by studioa »

Peter - thanks for help!


1. mostly used discretizer, engrid, gmsh and a bit of salome. But the architectural models are done in other software packages like Revit, ArchiCAD and sometimes we use Blender.
2. LES
3. once I have a thorough/meaningful material for the simulation using Elmer I'll post the results, videos, etc. - create a tutorial so community can benefit from our experience with these packages.

raback wrote:Hi

ElmerGrid is embeded in ElmerGUI but it merely handles the same files as the stand alone version. There is no modeler ralated to that. The experimental 2D modeler writes .in2d format that is treated by netgen to make Delaunay triangularizations. What preprocessors have you used previously in conjunction with OpenFOAM?

It would also be interesting to here what approach you have chosen for the problems: DNS, LES or RANS?

-Peter
raback
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Re: ElmerGUI crash when loading a gmsh mesh

Post by raback »

Hi

Ok, it seems that Gmsh with .msh format and Salome with .unv format might provide common workflows.

In Elmer there is LES model based on VMS (variational multiscale) that might be evoked by setting the "stabilization method" to "vms" in the standard flow solver. Using this and the "FilterTimeSeries" solver might be your best shot at the problem.

When it comes to linear systems for transient problems it would be preferable if a rather cheap preconditioner "none" could be used in conjunction with the iterative Krylov methods (e.g. BiCGstab). This ensures also that exactly the same convergence behavior may be obtained in parallel runs.

-Peter
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