Print Page - SEGMENTATION FAULT

QuantumATK => General Questions and Answers => Topic started by: Sarvesh Agarwal on October 25, 2012, 09:01

Title: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 25, 2012, 09:01

hiiii,
i had installed 12.2 in replacement of 11.8 but on running the simulations it is giving the below error

Title: Re: SEGMENTATION FAULT
Post by: Anders Blom on October 25, 2012, 09:23

That's an unusual one... Which Linux?

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 25, 2012, 14:54

thanks for the help
iam using RHEL 6.2

Title: Re: SEGMENTATION FAULT
Post by: Anders Blom on October 25, 2012, 15:02

Is it completely reproducible? It is extremely unusual to have such crashes and RHEL 6 is a common platform, so I don't have any clear idea, to be honest... Try saving the script and running "atkpython script.py" from the command line. Although, I don't expect that to work differently...

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 26, 2012, 08:20

yes everytime when i try to simulate any script it gives the same error!!!

Title: Re: SEGMENTATION FAULT
Post by: Anders Blom on October 26, 2012, 10:38

Ok... We will need your help in troubleshooting this. It could be related to ATK, or it could be localized to your machine, but to find this out, please follow the steps below.

Start by downloading the attached script atkpython_debug onto your Linux machine. You will probably need to give it executable permission:

Code

chmod +x atkpython_debug

Save a simple test script, like the Ag fcc calculation you indicated before, as a file, let's call it ag.py. Put it in the same directory as atkpython_debug.

Then open a terminal, and navigate to the directory where you saved the scripts. At the prompt, type

Code

./atkpython_debug ag.py

The script will automatically perform "run", "bt", and "quit" in gdb (the GNU Debugger). When it finishes you are left at the prompt again - send us the information it printed; this will allow us to learn more about this problem.

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 26, 2012, 14:30

thanks sir!
i had done the same thing as u told me and its giving the following information...

Title: Re: SEGMENTATION FAULT
Post by: Anders Blom on October 26, 2012, 16:44

I apologize for not studying the gdb command line options better. I have amended my post above to show a better way.

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 27, 2012, 08:05

done as u said and its again the segmentation error. i have attached the errorr_txt file.

Title: Re: SEGMENTATION FAULT
Post by: Nordland on October 27, 2012, 08:25

Can you post the script your are running?

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 27, 2012, 08:29

sure!! and this error is with every script

Title: Re: SEGMENTATION FAULT
Post by: Nordland on October 27, 2012, 20:10

With every script do that mean that you see this error every time you run this script or does it mean that any script no matter what gives this error?

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 28, 2012, 14:44

oh sorry !!! I mean to say ATK 12.2 is giving this error no matter what is the script...

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 30, 2012, 11:18

sir please help me with this!!!

Title: Re: SEGMENTATION FAULT
Post by: zh on October 30, 2012, 12:29

This following log is generated by running your script file.

Quote

+------------------------------------------------------------------------------+
| NanoLanguageScript execution started |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Atomistix ToolKit 12.2.2 [Build 144eba5] |
| |
+------------------------------------------------------------------------------+
+----------------------------------------------------------+
| Bulk Bravais lattice |
+----------------------------------------------------------+
Type:
FaceCenteredCubic

Lattice constants:
a = 4.085700 Ang
b = 4.085700 Ang
c = 4.085700 Ang

Lattice angles:
alpha = 90.000000 deg
beta = 90.000000 deg
gamma = 90.000000 deg

Primitive vectors:
u_1 = 0.000000 2.042850 2.042850 Ang
u_2 = 2.042850 0.000000 2.042850 Ang
u_3 = 2.042850 2.042850 0.000000 Ang

+----------------------------------------------------------+
| Bulk: Cartesian (Angstrom) / fractional |
+----------------------------------------------------------+
1
Bulk
Ag 0.000000e+00 0.000000e+00 0.000000e+00 0.00000 0.00000 0.00000
+------------------------------------------------------------------------------+
| |
| DFT Calculation [Started Tue Oct 30 19:28:37 2012] |
| |
+------------------------------------------------------------------------------+
| Checkpoint Handler |
| Filename : c:\users\hou\appdata\local\temp\checkpoint75469840.nc |
| Interval : 0.5 h |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 -0.00000 |
+------------------------------------------------------------------------------+
| 0 E = -2.48369 dE = 1.000000e+00 dH = 1.048859e+00 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 -0.00000 |
+------------------------------------------------------------------------------+
| 1 E = -3.54806 dE = 1.064376e+00 dH = 8.864662e-01 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 0.00000 |
+------------------------------------------------------------------------------+
| 2 E = -3.71972 dE = 1.716576e-01 dH = 5.845031e-02 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 0.00000 |
+------------------------------------------------------------------------------+
| 3 E = -3.62943 dE = 9.028979e-02 dH = 5.714401e-02 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 0.00000 |
+------------------------------------------------------------------------------+
| 4 E = -3.62926 dE = 1.740746e-04 dH = 6.621888e-04 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 0.00000 |
+------------------------------------------------------------------------------+
| 5 E = -3.62818 dE = 1.070974e-03 dH = 3.679416e-04 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 0.00000 |
+------------------------------------------------------------------------------+
| 6 E = -3.62848 dE = 2.999333e-04 dH = 3.296760e-04 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 0.00000 |
+------------------------------------------------------------------------------+
| 7 E = -3.62864 dE = 1.591899e-04 dH = 1.112389e-04 |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report DM DD |
+------------------------------------------------------------------------------+
| 0 Ag [ 0.000 , 0.000 , 0.000 ] 11.00000 0.00000 |
+------------------------------------------------------------------------------+
| 8 E = -3.62865 dE = 1.709359e-06 dH = 2.481482e-06 |
+------------------------------------------------------------------------------+
| Calculation Converged in 8 steps |
| |
| Fermi Level = -8.080460 eV |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| DFT Calculation [Finished Tue Oct 30 19:28:41 2012] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Bandstructure Analysis |
| |
+------------------------------------------------------------------------------+

|--------------------------------------------------|
Calculating Bandstructure : ==================================================

Timing: Total Per Step %

--------------------------------------------------------------------------------

Valence Density : 0.89 s 0.09 s 10.63% |=============|
Real Space Integral : 0.84 s 0.08 s 10.10% |============|
Constant Terms : 0.83 s 0.83 s 9.91% |============|
Basis Set Generation : 0.72 s 0.72 s 8.59% |==========|
Difference Density : 0.22 s 0.02 s 2.62% |==|
Core Density : 0.14 s 0.01 s 1.69% |=|
Real Space Basis : 0.05 s 0.05 s 0.56% ||
Diagonalization : 0.03 s 0.00 s 0.38% ||
Neutral Atom Potential : 0.03 s 0.03 s 0.37% |
Exchange-Correlation : 0.03 s 0.00 s 0.37% |
Hartree Potential : 0.02 s 0.00 s 0.19% |
File IO, nlsave : 0.02 s 0.01 s 0.19% |
Mixing : 0.00 s 0.00 s 0.00% |
Setting Density Matrix : 0.00 s 0.00 s 0.00% |
Hubbard Term : 0.00 s 0.00 s 0.00% |
--------------------------------------------------------------------------------
Total : 8.35 s
+------------------------------------------------------------------------------+
| NanoLanguageScript execution finished |
+------------------------------------------------------------------------------+

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 30, 2012, 14:39

yeah iam able to run the script with 11.8 but when iam using ATK12.2 its giving the Segmentation error as mentioned above

Title: Re: SEGMENTATION FAULT
Post by: Anders Blom on October 30, 2012, 22:40

We can't help unless you provide the output of the atkpython_debug script I posted above (http://quantumwise.com/forum/index.php?topic=1917.msg9399#msg9399).

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 31, 2012, 06:59

the output of the debug is attached below!!!

Title: Re: SEGMENTATION FAULT
Post by: Anders Blom on October 31, 2012, 10:02

I apologize, you had sent it before already, I missed that. We are looking into it, but I can't promise a fast solution, these things are usually hard to troubleshoot.

The crucial line seems to be
#1 0x00007ffff049bcd5 in swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator<RadialFunction*, std::vector<RadialFunction, std::allocator<RadialFunction> > >, RadialFunction, swig::from_oper<RadialFunction> >::value() const () from /home/vlsi/QuantumWise/atk-12.2.2/atkpython/lib/python2.7/_NLEngine.so

My recommendation is to install 11.8, which worked for you, side-by-side with the new version, and use 12.2 for generating the scripts (perhaps on a Windows machine) and 11.8 for the calculations, for now. Unless you need special new functionality in 12.2, I think 11.8 should work rather well.

You can also try to download 12.8.b2, the preview version, and see if that gives similar problems. Download from http://quantumwise.com/publications/news-archive/188.

Title: Re: SEGMENTATION FAULT
Post by: Sarvesh Agarwal on October 31, 2012, 13:28

thanks sir for the help!!!
i will do that

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QuantumATK => General Questions and Answers => Topic started by: Sarvesh Agarwal on October 25, 2012, 09:01