ElmerGUI crashes with segmentation fault

The graphical user interface of Elmer
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

ElmerGUI crashes with segmentation fault

Post by Ewald »

Dear All,

When trying to generate a SIF file for a mesh, ElmerGUI is aborting first with an error message "SifGenerator: Body index out of bounds" and then with a segmentation fault.
The ElmerGUI version is the current svn version 4269.
The mesh has been created with Salome and contains 6 bodies and 2 surfaces.
The error already occurs if I read in the mesh and then try to generate a SIF file (independent whether the model parameters have been entered or not).
The entering of model parameters is possible without problems.

Unfortunately, I cannot upload the test case since it's size exceeds the 1MByte boarder (23MBytes).

Can you help, please?

Thanks and best regards,

Ewald
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

Re: ElmerGUI crashes with segmentation fault

Post by Ewald »

Hi all,

some additional information:

Debugging with gdb gives the following backtrace:

Loading elmer mesh files
Summary:
Nodes: 225636
Point elements: 0
Edge elements: 0
Surface elements: 249047
Volume elements: 1109759
Found 368097 edges on boundary
Bcs/materials on surface elements: 2
Bcs/materials on edge elements: 0
Bcs/materials on point elements: 0
Generating lists to display
Generated 6 lists
Ready
SifGenerator: Body index out of bounds
SifGenerator: Body index out of bounds
SifGenerator: Body index out of bounds
SifGenerator: Body index out of bounds
SifGenerator: Body index out of bounds
SifGenerator: Body index out of bounds

Program received signal SIGSEGV, Segmentation fault.
0x00000000004c7e9c in ?? ()
(gdb) backtrace
#0 0x00000000004c7e9c in ?? ()
#1 0x0000000000481810 in ?? ()
#2 0x000000000056f60d in ?? ()
#3 0x00007ffff2bafee2 in QMetaObject::activate(QObject*, int, int, void**) ()
from /usr/lib64/libQtCore.so.4
#4 0x00007ffff489aa37 in QAction::triggered(bool) ()
from /usr/lib64/libQtGui.so.4
#5 0x00007ffff489beb0 in QAction::activate(QAction::ActionEvent) ()
from /usr/lib64/libQtGui.so.4
#6 0x00007ffff4c84dfd in ?? () from /usr/lib64/libQtGui.so.4
#7 0x00007ffff4c8adfe in ?? () from /usr/lib64/libQtGui.so.4
#8 0x00007ffff48f1a3d in QWidget::event(QEvent*) ()
from /usr/lib64/libQtGui.so.4
#9 0x00007ffff4c8d64b in QMenu::event(QEvent*) ()
from /usr/lib64/libQtGui.so.4
#10 0x00007ffff48a0a4d in QApplicationPrivate::notify_helper(QObject*, QEvent*)
() from /usr/lib64/libQtGui.so.4
#11 0x00007ffff48a943a in QApplication::notify(QObject*, QEvent*) ()
from /usr/lib64/libQtGui.so.4
#12 0x00007ffff2b9b15c in QCoreApplication::notifyInternal(QObject*, QEvent*)
() from /usr/lib64/libQtCore.so.4
#13 0x00007ffff48a8688 in QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&) ()

Best regards,

Ewald
raback
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Re: ElmerGUI crashes with segmentation fault

Post by raback »

It seems that your mesh has at least inproper body indexes. In what format is the original mesh read in to ElmerGUI?

-Peter
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

Re: ElmerGUI crashes with segmentation fault

Post by Ewald »

Hi Peter,

The mesh has been exported in unv format by Salome 5.1.2.
-
Then the UNV file has been translated to an Elmer mesh by

Elmergrid 8 2 mesh_filename -scale 1e-6 1e-6 1e-6.

The second column of mesh.elements includes the numbers 1 to 6.

Thanks in advance.

BR

Ewald
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

Re: ElmerGUI crashes with segmentation fault

Post by Ewald »

Hi Peter,

When I read in the mesh in UNV format directly into ElmerGUI, I do not get a segmentation fault anymore.
Still the are the warnings "SifGenerator: Body index out of bounds", but a SIF file is generated:

Header
CHECK KEYWORDS Warn
Mesh DB "." "."
Include Path ""
Results Directory ""
End

Simulation
Max Output Level = 4
Coordinate System = Cartesian
Coordinate Mapping(3) = 1 2 3
Simulation Type = Steady state
Steady State Max Iterations = 1
Output Intervals = 1
Timestepping Method = BDF
BDF Order = 1
Solver Input File = case.sif
Post File = case.ep
End

Constants
Gravity(4) = 0 -1 0 9.82
Stefan Boltzmann = 5.67e-08
Permittivity of Vacuum = 8.8542e-12
Boltzmann Constant = 1.3807e-23
Unit Charge = 1.602e-19
End

How can I do a scaling of the UNV coordinates in this flow?

BR

Ewald
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

Re: ElmerGUI crashes with segmentation fault

Post by Ewald »

Hi Peter,

Another intersting thing I found just out:

1. Reading in UNV mesh file directly from ElmerGUI and then generating a SIF is working

2. Reading in UNV mesh file directly from ElmerGUI, then save the MESH. Exit ElmerGUI. Start ElmerGUI again. Read in Mesh, generate SIF, a voila: A segmentation fault.

Any idea?


BR

Ewald
raback
Site Admin
Posts: 4812
Joined: 22 Aug 2009, 11:57
Antispam: Yes
Location: Espoo, Finland
Contact:

Re: ElmerGUI crashes with segmentation fault

Post by raback »

Smells like a bug. Could you possibly reproduce these results with a smaller .unv file and sent it for debugging.

-Peter
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

Re: ElmerGUI crashes with segmentation fault

Post by Ewald »

Hi Peter

Please find attached two split files generated with 'split -b 1000000 Elmer_crashes.tgz'.
Please merge them at your side and then unpack the resulting tgz file as usual.

The reduced data base shows the same behaviour as the big one.

I will upload in a separet e-mail also the corresponding UNV mesh file.

Thanks in advance.

Best regards,

Ewald
Attachments
xab.tgz
second split file
(892.74 KiB) Downloaded 356 times
xaa.tgz
first split file
(976.56 KiB) Downloaded 376 times
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

Re: ElmerGUI crashes with segmentation fault

Post by Ewald »

Hi Peter,

here are the split files of the UNV mesh test case generated by 'split -b 1000000 test.unv.gz'.
Please merge them first before unzipping.

Thanks a lot in advance.

Best regards,

Ewald
Attachments
xac.gz
third split file
(86.85 KiB) Downloaded 354 times
xab.gz
second split file
(976.56 KiB) Downloaded 361 times
xaa.gz
first split file
(976.56 KiB) Downloaded 376 times
Ewald
Posts: 14
Joined: 26 Nov 2009, 09:19

Re: ElmerGUI crashes with segmentation fault

Post by Ewald »

Hi Peter,

Sorry for being not precise enough how to merge the three split files.

I've just verified again with the downloaded split files:

cat xaa.gz xab.gz xac.gz > test.unv.gz
gzip -d test.unv.gz

Then I opened 'tets.unv' with ElmerGUI from today's svn 4298.
Interestingly, the segmentation fault is gone. However, I did also a distribution upgrade of my OpenSUSE 11.1 LINUX OS in between.

Still I get the warning

SifGenerator: Body index out of bounds
SifGenerator: Body index out of bounds

An incomplete SIF file is generated. Both ElmergUIlogger output and the generated SIF file are attached.

Could you advise on the wrong body index, please?

Thanks and best regards

Ewald
Attachments
case.sif
(552 Bytes) Downloaded 377 times
ElmerGUIlogger.txt
(4.71 KiB) Downloaded 367 times
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