QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: Sarvesh Agarwal on February 5, 2013, 11:49

Title: Segmentation fault
Post by: Sarvesh Agarwal on February 5, 2013, 11:49

hello
      I installed the ATK12.8 version but when Iam running any simulation its giving segmentation fault.. i attached the log file also ...

Title: Re: Segmentation fault
Post by: Anders Blom on February 5, 2013, 14:08

On which Linux are you running?

Title: Re: Segmentation fault
Post by: Sarvesh Agarwal on February 5, 2013, 19:09

its RHEL 6.2

Title: Re: Segmentation fault
Post by: Anders Blom on February 5, 2013, 22:41

This is uncommon...

Can you try to check the dependencies of the ATK binaries. That is, "cd" into the ATK installation directory (type "ls" to make sure you have atkpython and vnl subdirectories here) and type

Code

LD_LIBRARY_PATH=atkpython/lib ldd atkpython/bin/atk_exec | grep "not found"
LD_LIBRARY_PATH=atkpython/lib ldd atkpython/lib/python2.7/_NLEngine.so | grep "not found"

Also, perhaps, just maybe, this will help: http://quantumwise.com/support/faq/164.

Title: Re: Segmentation fault
Post by: Sarvesh Agarwal on February 8, 2013, 13:11

attached are the steps i followed... plz. check

Title: Re: Segmentation fault
Post by: Anders Blom on February 8, 2013, 14:21

Was ATK installed by root? Check permissions on all files. The last message is strange.

EDIT: Ok, turns out that's actually how it's supposed to be. So we're back to trying if LD_PRELOAD helps, can you check that?

Title: Re: Segmentation fault
Post by: Sarvesh Agarwal on February 9, 2013, 11:38

OK!!! here are the commands I followed

Title: Re: Segmentation fault
Post by: Anders Blom on February 9, 2013, 22:20

Please see link above. The LD_PRELOAD command needs to be defined when you run the calculation which segfaulted. So, do

export LD_PRELOAD="libGLU.so libstdc++.so.6"

This is wild guess to be honest, but it's worth trying since it solves a segfault on another Linux.

Title: Re: Segmentation fault
Post by: Sarvesh Agarwal on February 11, 2013, 06:14

thanku sir !!! it actually worked and now simulations are running