Segfault or reading ABINIT file

General Discussion
1

The reproducible error is:

New Thread 0x40200940 (LWP 14602)]
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x1086190 not contained in stack
dev warning: Extension “GAMESS” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Orbitals” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Vibration” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
No matching basis set file found: "/home/rcohen/untitled.cml"
GLWidget initialisation…
GLWidget initialised…
createObjects()
[New Thread 0x40401940 (LWP 15450)]
[New Thread 0x40602940 (LWP 15451)]
[Thread 0x40401940 (LWP 15450) exited]
[Thread 0x40602940 (LWP 15451) exited]
[New Thread 0x40602940 (LWP 17304)]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x40602940 (LWP 17304)]
OpenBabel::ABINITFormat::ReadMolecule (this=,
pOb=, pConv=0x40601b50)
at /home/rcohen/SRC/openbabel/src/formats/abinitformat.cpp:188
188 atom->SetAtomicNum(atomicNumbers[type]);
The abinit output file is attached. Ron

2

Hi Ron,

Thanks for the report. Is this issue fixed by the patch you sent, or
is this a separate issue?

Dave

On Mon, Apr 29, 2013 at 2:12 PM, Cohen, Ron rcohen@carnegiescience.edu wrote:

The reproducible error is:

New Thread 0x40200940 (LWP 14602)]
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x1086190 not contained in stack
dev warning: Extension “GAMESS” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Orbitals” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Vibration” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
No matching basis set file found: “/home/rcohen/untitled.cml”
GLWidget initialisation…
GLWidget initialised…
createObjects()
[New Thread 0x40401940 (LWP 15450)]
[New Thread 0x40602940 (LWP 15451)]
[Thread 0x40401940 (LWP 15450) exited]
[Thread 0x40602940 (LWP 15451) exited]
[New Thread 0x40602940 (LWP 17304)]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x40602940 (LWP 17304)]
OpenBabel::ABINITFormat::ReadMolecule (this=,
pOb=, pConv=0x40601b50)
at /home/rcohen/SRC/openbabel/src/formats/abinitformat.cpp:188
188 atom->SetAtomicNum(atomicNumbers[type]);
The abinit output file is attached. Ron

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3

On Mon, Apr 29, 2013 at 2:12 PM, Cohen, Ron rcohen@carnegiescience.edu wrote:

The reproducible error is:

> > Program received signal SIGSEGV, Segmentation fault. > [Switching to Thread 0x40602940 (LWP 17304)] > OpenBabel::ABINITFormat::ReadMolecule (this=, > pOb=, pConv=0x40601b50) > at /home/rcohen/SRC/openbabel/src/formats/abinitformat.cpp:188 > 188 atom->SetAtomicNum(atomicNumbers[type]); > The abinit output file is attached. Ron > This looks like a bug in the Open Babel format, and would need to be fixed there.

Marcus

4

Yes, but I am having trouble with git–I just sent an email on it. Ron

On Tue, Apr 30, 2013 at 9:17 AM, David Lonie david.lonie@kitware.com wrote:

Hi Ron,

Thanks for the report. Is this issue fixed by the patch you sent, or
is this a separate issue?

Dave

On Mon, Apr 29, 2013 at 2:12 PM, Cohen, Ron rcohen@carnegiescience.edu wrote:

The reproducible error is:

New Thread 0x40200940 (LWP 14602)]
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x1086190 not contained in stack
dev warning: Extension “GAMESS” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Orbitals” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Vibration” is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
No matching basis set file found: “/home/rcohen/untitled.cml”
GLWidget initialisation…
GLWidget initialised…
createObjects()
[New Thread 0x40401940 (LWP 15450)]
[New Thread 0x40602940 (LWP 15451)]
[Thread 0x40401940 (LWP 15450) exited]
[Thread 0x40602940 (LWP 15451) exited]
[New Thread 0x40602940 (LWP 17304)]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x40602940 (LWP 17304)]
OpenBabel::ABINITFormat::ReadMolecule (this=,
pOb=, pConv=0x40601b50)
at /home/rcohen/SRC/openbabel/src/formats/abinitformat.cpp:188
188 atom->SetAtomicNum(atomicNumbers[type]);
The abinit output file is attached. Ron

Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap1

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Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap1

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options